[Debian-med-packaging] Bug#1069359: python-cooler: FTBFS on arm64: FileNotFoundError: [Errno 2] No such file or directory: '/tmp/tmpi8kk3ih0/tmp_sf3nv42.multi.cool'
Lucas Nussbaum
lucas at debian.org
Sat Apr 20 13:16:49 BST 2024
Source: python-cooler
Version: 0.9.3-1
Severity: serious
Justification: FTBFS
Tags: trixie sid ftbfs
User: lucas at debian.org
Usertags: ftbfs-20240420 ftbfs-trixie ftbfs-t64-arm64
Hi,
During a rebuild of all packages in sid, your package failed to build
on arm64.
Relevant part (hopefully):
> debian/rules binary
> dh binary --with python3 --buildsystem=pybuild
> dh_update_autotools_config -O--buildsystem=pybuild
> dh_autoreconf -O--buildsystem=pybuild
> dh_auto_configure -O--buildsystem=pybuild
> dh_auto_build -O--buildsystem=pybuild
> I: pybuild plugin_pyproject:129: Building wheel for python3.12 with "build" module
> I: pybuild base:311: python3.12 -m build --skip-dependency-check --no-isolation --wheel --outdir /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler
> * Building wheel...
> Successfully built cooler-0.9.3-py3-none-any.whl
> I: pybuild plugin_pyproject:144: Unpacking wheel built for python3.12 with "installer" module
> I: pybuild plugin_pyproject:129: Building wheel for python3.11 with "build" module
> I: pybuild base:311: python3.11 -m build --skip-dependency-check --no-isolation --wheel --outdir /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler
> * Building wheel...
> Successfully built cooler-0.9.3-py3-none-any.whl
> I: pybuild plugin_pyproject:144: Unpacking wheel built for python3.11 with "installer" module
> dh_auto_test -O--buildsystem=pybuild
> I: pybuild base:311: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build; python3.12 -m pytest tests
> ============================= test session starts ==============================
> platform linux -- Python 3.12.3, pytest-8.1.1, pluggy-1.4.0
> rootdir: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build
> configfile: pyproject.toml
> collected 136 items
>
> tests/test_api.py .......... [ 7%]
> tests/test_balance.py .... [ 10%]
> tests/test_cli.py .s..s..... [ 17%]
> tests/test_cli_export.py .Fs [ 19%]
> tests/test_cli_fileops.py .... [ 22%]
> tests/test_cli_ingest.py FFFFFFFFFFF [ 30%]
> tests/test_cli_ops.py FFF. [ 33%]
> tests/test_core.py ........... [ 41%]
> tests/test_create.py Fs.F..FFF [ 48%]
> tests/test_create_ingest.py FFFFFFFFFFF.FFF [ 59%]
> tests/test_create_sanitize.py ........ [ 65%]
> tests/test_fileops.py ........s.. [ 73%]
> tests/test_parallel.py ... [ 75%]
> tests/test_reduce.py FFFFFFFFFF [ 83%]
> tests/test_util.py .........s............. [100%]
>
> =================================== FAILURES ===================================
> __________________________________ test_dump ___________________________________
>
> def test_dump():
> runner = CliRunner()
> with runner.isolated_filesystem():
> f_in = op.join(datadir, "toy.symm.upper.2.cool")
> result = runner.invoke(dump, [f_in])
> assert result.exit_code == 0
> result = runner.invoke(dump, [f_in, "-t", "chroms", "--columns", "length"])
> assert result.exit_code == 0
> result = runner.invoke(dump, [f_in, "-t", "bins", "--columns", "chrom,start"])
> assert result.exit_code == 0
> result = runner.invoke(dump, [f_in, "-r", "chr1"])
> assert result.exit_code == 0
> result = runner.invoke(dump, [f_in, "-r", "chr1:0-16", "-r2", "chr1:10-25"])
> assert result.exit_code == 0
> result = runner.invoke(dump, [f_in, "-r", "chr1:10-25", "-r2", "chr1:0-5"])
> assert result.exit_code == 0
> result = runner.invoke(dump, [f_in, "--join"])
> assert result.exit_code == 0
> result = runner.invoke(dump, [f_in, "--join", "--one-based-ids"])
> assert result.exit_code == 0
> result = runner.invoke(dump, [f_in, "--join", "--one-based-starts"])
> assert result.exit_code == 0
> result = runner.invoke(dump, [f_in, "--annotate", "chrom", "--one-based-starts"])
> assert result.exit_code == 0
>
> # unbalanced file
> result = runner.invoke(dump, [f_in, "-b"])
> assert result.exit_code == 1
>
> # roundtrip symm-upper data
> result = runner.invoke(dump, [f_in, "-H", "-t", "bins"])
> bins = pd.read_csv(StringIO(result.output), sep="\t")
> result = runner.invoke(dump, [f_in, "-H"])
> pixels = pd.read_csv(StringIO(result.output), sep="\t")
> > cooler.create_cooler("out.cool", bins, pixels, symmetric_upper=True)
>
> tests/test_cli_export.py:74:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> cooler/create/_create.py:1024: in create_cooler
> create(
> cooler/create/_create.py:514: in create
> from dask.dataframe import DataFrame as dask_df
> /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:81: in <module>
> from dask.dataframe import backends, dispatch, rolling
> /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in <module>
> from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame
> /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in <module>
> from dask.dataframe import methods
> /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in <module>
> from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like
> /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in <module>
> from dask.dataframe import ( # noqa: F401 register pandas extension types
> /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in <module>
> from dask.dataframe.extensions import make_array_nonempty, make_scalar
> /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in <module>
> from dask.dataframe.accessor import (
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in <module>
> class DatetimeAccessor(Accessor):
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__
> _bind_property(cls, pd_cls, attr, min_version)
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property
> setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func)))
> /usr/lib/python3/dist-packages/dask/utils.py:858: in wrapper
> method.__doc__ = _derived_from(
> /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from
> method_args = get_named_args(method)
> /usr/lib/python3/dist-packages/dask/utils.py:572: in get_named_args
> s = inspect.signature(func)
> /usr/lib/python3.12/inspect.py:3310: in signature
> return Signature.from_callable(obj, follow_wrapped=follow_wrapped,
> /usr/lib/python3.12/inspect.py:3054: in from_callable
> return _signature_from_callable(obj, sigcls=cls,
> /usr/lib/python3.12/inspect.py:2642: in _signature_from_callable
> call = _descriptor_get(call, obj)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> descriptor = <slot wrapper '__call__' of 'type' objects>
> obj = <property object at 0xffffa8eeed90>
>
> def _descriptor_get(descriptor, obj):
> if isclass(descriptor):
> return descriptor
> get = getattr(type(descriptor), '__get__', _sentinel)
> if get is _sentinel:
> return descriptor
> > return get(descriptor, obj, type(obj))
> E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
>
> /usr/lib/python3.12/inspect.py:2467: TypeError
> ________________ test_cload_symm_asymm[symm.upper-extra_args0] _________________
>
> ref = 'symm.upper', extra_args = []
>
> @pytest.mark.parametrize(
> "ref,extra_args",
> [
> ("symm.upper", []), # reflect triu pairs
> ("symm.upper", ["--input-copy-status", "unique"]), # reflect triu pairs
> ("asymm", ["--no-symmetric-upper"]),
> ],
> )
> def test_cload_symm_asymm(ref, extra_args):
> runner = CliRunner()
> with runner.isolated_filesystem():
> result = _run_cload_pairs(runner, 2, extra_args)
> > assert result.exit_code == 0
> E assert 1 == 0
> E + where 1 = <Result TypeError("descriptor '__call__' for 'type' objects doesn't apply to a 'property' object")>.exit_code
>
> tests/test_cli_ingest.py:72: AssertionError
> ________________ test_cload_symm_asymm[symm.upper-extra_args1] _________________
>
> ref = 'symm.upper', extra_args = ['--input-copy-status', 'unique']
>
> @pytest.mark.parametrize(
> "ref,extra_args",
> [
> ("symm.upper", []), # reflect triu pairs
> ("symm.upper", ["--input-copy-status", "unique"]), # reflect triu pairs
> ("asymm", ["--no-symmetric-upper"]),
> ],
> )
> def test_cload_symm_asymm(ref, extra_args):
> runner = CliRunner()
> with runner.isolated_filesystem():
> result = _run_cload_pairs(runner, 2, extra_args)
> > assert result.exit_code == 0
> E assert 1 == 0
> E + where 1 = <Result TypeError("descriptor '__call__' for 'type' objects doesn't apply to a 'property' object")>.exit_code
>
> tests/test_cli_ingest.py:72: AssertionError
> ___________________ test_cload_symm_asymm[asymm-extra_args2] ___________________
>
> ref = 'asymm', extra_args = ['--no-symmetric-upper']
>
> @pytest.mark.parametrize(
> "ref,extra_args",
> [
> ("symm.upper", []), # reflect triu pairs
> ("symm.upper", ["--input-copy-status", "unique"]), # reflect triu pairs
> ("asymm", ["--no-symmetric-upper"]),
> ],
> )
> def test_cload_symm_asymm(ref, extra_args):
> runner = CliRunner()
> with runner.isolated_filesystem():
> result = _run_cload_pairs(runner, 2, extra_args)
> > assert result.exit_code == 0
> E assert 1 == 0
> E + where 1 = <Result TypeError("descriptor '__call__' for 'type' objects doesn't apply to a 'property' object")>.exit_code
>
> tests/test_cli_ingest.py:72: AssertionError
> _________________ test_cload_mergepass[symm.upper-extra_args0] _________________
>
> ref = 'symm.upper', extra_args = ['--temp-dir', '.', '--no-delete-temp']
>
> @pytest.mark.parametrize(
> "ref,extra_args", [("symm.upper", ["--temp-dir", ".", "--no-delete-temp"])]
> )
> def test_cload_mergepass(ref, extra_args):
> runner = CliRunner()
> with runner.isolated_filesystem():
> result = _run_cload_pairs(runner, 2, extra_args)
> > assert result.exit_code == 0
> E assert 1 == 0
> E + where 1 = <Result TypeError("descriptor '__call__' for 'type' objects doesn't apply to a 'property' object")>.exit_code
>
> tests/test_cli_ingest.py:86: AssertionError
> _______________________________ test_cload_field _______________________________
>
> def test_cload_field():
> runner = CliRunner()
> with runner.isolated_filesystem():
> extra_args = ["--field", "score=8"]
> result = _run_cload_pairs(runner, 2, extra_args)
> > assert result.exit_code == 0
> E assert 1 == 0
> E + where 1 = <Result TypeError("descriptor '__call__' for 'type' objects doesn't apply to a 'property' object")>.exit_code
>
> tests/test_cli_ingest.py:98: AssertionError
> ___________________________ test_cload_other_options ___________________________
>
> def test_cload_other_options():
> runner = CliRunner()
> with runner.isolated_filesystem():
> meta = {"foo": "bar", "number": 42}
> with open("meta.json", "w") as f:
> json.dump(meta, f)
> extra_args = [
> "--metadata",
> "meta.json",
> "--zero-based",
> "--storage-options",
> "shuffle=True,fletcher32=True,compression=lzf",
> ]
> result = _run_cload_pairs(runner, 2, extra_args)
> > assert result.exit_code == 0
> E assert 1 == 0
> E + where 1 = <Result TypeError("descriptor '__call__' for 'type' objects doesn't apply to a 'property' object")>.exit_code
>
> tests/test_cli_ingest.py:161: AssertionError
> _________________ test_load_symm_asymm[symm.upper-extra_args0] _________________
>
> ref = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.symm.upper.2.bg2'
> extra_args = []
>
> @pytest.mark.parametrize(
> "ref,extra_args",
> [
> ("symm.upper", []), # reflect tril pairs
> ("symm.upper", ["--one-based", "--input-copy-status", "unique"]), # reflect tril pairs
> ("asymm", ["--one-based", "--no-symmetric-upper"]),
> ],
> )
> def test_load_symm_asymm(ref, extra_args):
> runner = CliRunner()
> with runner.isolated_filesystem():
> ref = op.join(datadir, f"toy.{ref}.2.bg2")
> result = _run_load(runner, ref, "bg2", 2, extra_args)
> > assert result.exit_code == 0
> E assert 1 == 0
> E + where 1 = <Result TypeError("descriptor '__call__' for 'type' objects doesn't apply to a 'property' object")>.exit_code
>
> tests/test_cli_ingest.py:201: AssertionError
> _________________ test_load_symm_asymm[symm.upper-extra_args1] _________________
>
> ref = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.symm.upper.2.bg2'
> extra_args = ['--one-based', '--input-copy-status', 'unique']
>
> @pytest.mark.parametrize(
> "ref,extra_args",
> [
> ("symm.upper", []), # reflect tril pairs
> ("symm.upper", ["--one-based", "--input-copy-status", "unique"]), # reflect tril pairs
> ("asymm", ["--one-based", "--no-symmetric-upper"]),
> ],
> )
> def test_load_symm_asymm(ref, extra_args):
> runner = CliRunner()
> with runner.isolated_filesystem():
> ref = op.join(datadir, f"toy.{ref}.2.bg2")
> result = _run_load(runner, ref, "bg2", 2, extra_args)
> > assert result.exit_code == 0
> E assert 1 == 0
> E + where 1 = <Result TypeError("descriptor '__call__' for 'type' objects doesn't apply to a 'property' object")>.exit_code
>
> tests/test_cli_ingest.py:201: AssertionError
> ___________________ test_load_symm_asymm[asymm-extra_args2] ____________________
>
> ref = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.asymm.2.bg2'
> extra_args = ['--one-based', '--no-symmetric-upper']
>
> @pytest.mark.parametrize(
> "ref,extra_args",
> [
> ("symm.upper", []), # reflect tril pairs
> ("symm.upper", ["--one-based", "--input-copy-status", "unique"]), # reflect tril pairs
> ("asymm", ["--one-based", "--no-symmetric-upper"]),
> ],
> )
> def test_load_symm_asymm(ref, extra_args):
> runner = CliRunner()
> with runner.isolated_filesystem():
> ref = op.join(datadir, f"toy.{ref}.2.bg2")
> result = _run_load(runner, ref, "bg2", 2, extra_args)
> > assert result.exit_code == 0
> E assert 1 == 0
> E + where 1 = <Result TypeError("descriptor '__call__' for 'type' objects doesn't apply to a 'property' object")>.exit_code
>
> tests/test_cli_ingest.py:201: AssertionError
> _______________________________ test_load_field ________________________________
>
> def test_load_field():
> runner = CliRunner()
> with runner.isolated_filesystem():
> extra_args = ["--field", "count=7:dtype=float"]
> result = _run_load(runner, "toy.symm.upper.2.bg2", "bg2", 2, extra_args)
> > assert result.exit_code == 0
> E assert 1 == 0
> E + where 1 = <Result TypeError("descriptor '__call__' for 'type' objects doesn't apply to a 'property' object")>.exit_code
>
> tests/test_cli_ingest.py:211: AssertionError
> _______________________________ test_load_field2 _______________________________
>
> def test_load_field2():
> runner = CliRunner()
> with runner.isolated_filesystem():
> extra_args = ["--count-as-float"]
> result = _run_load(runner, "toy.symm.upper.2.bg2", "bg2", 2, extra_args)
> > assert result.exit_code == 0
> E assert 1 == 0
> E + where 1 = <Result TypeError("descriptor '__call__' for 'type' objects doesn't apply to a 'property' object")>.exit_code
>
> tests/test_cli_ingest.py:225: AssertionError
> __________________________________ test_merge __________________________________
>
> def test_merge():
> runner = CliRunner()
> with runner.isolated_filesystem():
> f_in = op.join(datadir, "toy.symm.upper.2.cool")
> result = runner.invoke(
> merge, ["toy.2.double.cool", f_in, f_in, "--field", "count:dtype=int"]
> )
> > assert result.exit_code == 0
> E assert 1 == 0
> E + where 1 = <Result TypeError("descriptor '__call__' for 'type' objects doesn't apply to a 'property' object")>.exit_code
>
> tests/test_cli_ops.py:31: AssertionError
> _________________________________ test_coarsen _________________________________
>
> def test_coarsen():
> runner = CliRunner()
> with runner.isolated_filesystem():
> f_in = op.join(datadir, "toy.symm.upper.2.cool")
> f_ref = op.join(datadir, "toy.symm.upper.4.cool")
> result = runner.invoke(
> coarsen, [
> f_in,
> "--factor", "2",
> "--nproc", "2",
> "-o", "toy.2.coarsen_2.cool"
> ],
> )
> > assert result.exit_code == 0
> E assert 1 == 0
> E + where 1 = <Result TypeError("descriptor '__call__' for 'type' objects doesn't apply to a 'property' object")>.exit_code
>
> tests/test_cli_ops.py:50: AssertionError
> _________________________________ test_zoomify _________________________________
>
> def test_zoomify():
> runner = CliRunner()
>
> with runner.isolated_filesystem():
> f_in = op.join(datadir, "toy.symm.upper.2.cool")
> result = runner.invoke(
> zoomify, [f_in, "--balance", "--legacy", "-o", "toy.2.mcool"]
> )
> assert result.exit_code == 0
>
> f_in = op.join(datadir, "toy.symm.upper.2.cool")
> result = runner.invoke(
> zoomify, [
> f_in,
> "--balance",
> "--nproc", "2",
> "-o", "toy.2.mcool"
> ]
> )
> assert result.exit_code == 0
>
> f_in = op.join(datadir, "toy.symm.upper.2.cool")
> result = runner.invoke(
> zoomify, [
> f_in,
> "--balance",
> "--resolutions", "2,4,8",
> "-o", "toy.2.mcool"
> ]
> )
> > assert result.exit_code == 0
> E assert 1 == 0
> E + where 1 = <Result TypeError("descriptor '__call__' for 'type' objects doesn't apply to a 'property' object")>.exit_code
>
> tests/test_cli_ops.py:98: AssertionError
> _ test_create_append[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool] _
>
> fp = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool'
>
> @pytest.mark.parametrize(
> "fp", [op.join(datadir, "hg19.GM12878-MboI.matrix.2000kb.cool")]
> )
> def test_create_append(fp):
> > import dask.dataframe as dd
>
> tests/test_create.py:24:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:81: in <module>
> from dask.dataframe import backends, dispatch, rolling
> /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in <module>
> from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame
> /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in <module>
> from dask.dataframe import methods
> /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in <module>
> from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like
> /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in <module>
> from dask.dataframe import ( # noqa: F401 register pandas extension types
> /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in <module>
> from dask.dataframe.extensions import make_array_nonempty, make_scalar
> /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in <module>
> from dask.dataframe.accessor import (
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in <module>
> class DatetimeAccessor(Accessor):
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__
> _bind_property(cls, pd_cls, attr, min_version)
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property
> setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func)))
> /usr/lib/python3/dist-packages/dask/utils.py:858: in wrapper
> method.__doc__ = _derived_from(
> /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from
> method_args = get_named_args(method)
> /usr/lib/python3/dist-packages/dask/utils.py:572: in get_named_args
> s = inspect.signature(func)
> /usr/lib/python3.12/inspect.py:3310: in signature
> return Signature.from_callable(obj, follow_wrapped=follow_wrapped,
> /usr/lib/python3.12/inspect.py:3054: in from_callable
> return _signature_from_callable(obj, sigcls=cls,
> /usr/lib/python3.12/inspect.py:2642: in _signature_from_callable
> call = _descriptor_get(call, obj)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> descriptor = <slot wrapper '__call__' of 'type' objects>
> obj = <property object at 0xffffa8eeed90>
>
> def _descriptor_get(descriptor, obj):
> if isclass(descriptor):
> return descriptor
> get = getattr(type(descriptor), '__get__', _sentinel)
> if get is _sentinel:
> return descriptor
> > return get(descriptor, obj, type(obj))
> E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
>
> /usr/lib/python3.12/inspect.py:2467: TypeError
> ___________________________ test_create_custom_cols ____________________________
>
> def test_create_custom_cols():
>
> with isolated_filesystem():
> df = pd.DataFrame(
> {
> "bin1_id": [0, 1, 1, 1, 2, 2, 3, 4, 5],
> "bin2_id": [1, 1, 3, 4, 5, 6, 7, 8, 9],
> "foo": [1, 1, 1, 1, 1, 2, 2, 2, 2],
> "bar": [0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9],
> },
> columns=["bin1_id", "bin2_id", "foo", "bar"],
> )
> bins = pd.DataFrame(
> {
> "chrom": ["chr1"] * 5 + ["chr2"] * 5,
> "start": list(range(5)) * 2,
> "end": list(range(1, 6)) * 2,
> }
> )
> # works in unordered mode
> > cooler.create_cooler("test.cool", bins, df, columns=["foo", "bar"])
>
> tests/test_create.py:159:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> cooler/create/_create.py:1024: in create_cooler
> create(
> cooler/create/_create.py:514: in create
> from dask.dataframe import DataFrame as dask_df
> /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:81: in <module>
> from dask.dataframe import backends, dispatch, rolling
> /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in <module>
> from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame
> /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in <module>
> from dask.dataframe import methods
> /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in <module>
> from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like
> /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in <module>
> from dask.dataframe import ( # noqa: F401 register pandas extension types
> /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in <module>
> from dask.dataframe.extensions import make_array_nonempty, make_scalar
> /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in <module>
> from dask.dataframe.accessor import (
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in <module>
> class DatetimeAccessor(Accessor):
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__
> _bind_property(cls, pd_cls, attr, min_version)
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property
> setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func)))
> /usr/lib/python3/dist-packages/dask/utils.py:858: in wrapper
> method.__doc__ = _derived_from(
> /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from
> method_args = get_named_args(method)
> /usr/lib/python3/dist-packages/dask/utils.py:572: in get_named_args
> s = inspect.signature(func)
> /usr/lib/python3.12/inspect.py:3310: in signature
> return Signature.from_callable(obj, follow_wrapped=follow_wrapped,
> /usr/lib/python3.12/inspect.py:3054: in from_callable
> return _signature_from_callable(obj, sigcls=cls,
> /usr/lib/python3.12/inspect.py:2642: in _signature_from_callable
> call = _descriptor_get(call, obj)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> descriptor = <slot wrapper '__call__' of 'type' objects>
> obj = <property object at 0xffffa8eeed90>
>
> def _descriptor_get(descriptor, obj):
> if isclass(descriptor):
> return descriptor
> get = getattr(type(descriptor), '__get__', _sentinel)
> if get is _sentinel:
> return descriptor
> > return get(descriptor, obj, type(obj))
> E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
>
> /usr/lib/python3.12/inspect.py:2467: TypeError
> ______________________________ test_create_cooler ______________________________
>
> def test_create_cooler():
> chromsizes = cooler.util.read_chromsizes(
> op.join(datadir, "toy.chrom.sizes")
> )
> bins = cooler.util.binnify(chromsizes, 1)
> pixels = pd.read_csv(
> op.join(datadir, "toy.symm.upper.1.zb.coo"),
> sep='\t',
> names=['bin1_id', 'bin2_id', 'count']
> )
> pixels['foo'] = 42.0
>
> with isolated_filesystem():
> > cooler.create.create_cooler(
> "test.cool",
> bins,
> pixels,
> assembly='toy',
> metadata={'hello': 'world', 'list': [1, 2, 3]},
> )
>
> tests/test_create.py:304:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> cooler/create/_create.py:1024: in create_cooler
> create(
> cooler/create/_create.py:514: in create
> from dask.dataframe import DataFrame as dask_df
> /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:81: in <module>
> from dask.dataframe import backends, dispatch, rolling
> /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in <module>
> from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame
> /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in <module>
> from dask.dataframe import methods
> /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in <module>
> from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like
> /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in <module>
> from dask.dataframe import ( # noqa: F401 register pandas extension types
> /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in <module>
> from dask.dataframe.extensions import make_array_nonempty, make_scalar
> /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in <module>
> from dask.dataframe.accessor import (
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in <module>
> class DatetimeAccessor(Accessor):
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__
> _bind_property(cls, pd_cls, attr, min_version)
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property
> setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func)))
> /usr/lib/python3/dist-packages/dask/utils.py:858: in wrapper
> method.__doc__ = _derived_from(
> /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from
> method_args = get_named_args(method)
> /usr/lib/python3/dist-packages/dask/utils.py:572: in get_named_args
> s = inspect.signature(func)
> /usr/lib/python3.12/inspect.py:3310: in signature
> return Signature.from_callable(obj, follow_wrapped=follow_wrapped,
> /usr/lib/python3.12/inspect.py:3054: in from_callable
> return _signature_from_callable(obj, sigcls=cls,
> /usr/lib/python3.12/inspect.py:2642: in _signature_from_callable
> call = _descriptor_get(call, obj)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> descriptor = <slot wrapper '__call__' of 'type' objects>
> obj = <property object at 0xffffa8eeed90>
>
> def _descriptor_get(descriptor, obj):
> if isclass(descriptor):
> return descriptor
> get = getattr(type(descriptor), '__get__', _sentinel)
> if get is _sentinel:
> return descriptor
> > return get(descriptor, obj, type(obj))
> E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
>
> /usr/lib/python3.12/inspect.py:2467: TypeError
> _________________________ test_create_cooler_from_dask _________________________
>
> def test_create_cooler_from_dask():
> > dd = pytest.importorskip("dask.dataframe")
>
> tests/test_create.py:405:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:81: in <module>
> from dask.dataframe import backends, dispatch, rolling
> /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in <module>
> from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame
> /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in <module>
> from dask.dataframe import methods
> /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in <module>
> from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like
> /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in <module>
> from dask.dataframe import ( # noqa: F401 register pandas extension types
> /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in <module>
> from dask.dataframe.extensions import make_array_nonempty, make_scalar
> /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in <module>
> from dask.dataframe.accessor import (
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in <module>
> class DatetimeAccessor(Accessor):
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__
> _bind_property(cls, pd_cls, attr, min_version)
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property
> setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func)))
> /usr/lib/python3/dist-packages/dask/utils.py:858: in wrapper
> method.__doc__ = _derived_from(
> /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from
> method_args = get_named_args(method)
> /usr/lib/python3/dist-packages/dask/utils.py:572: in get_named_args
> s = inspect.signature(func)
> /usr/lib/python3.12/inspect.py:3310: in signature
> return Signature.from_callable(obj, follow_wrapped=follow_wrapped,
> /usr/lib/python3.12/inspect.py:3054: in from_callable
> return _signature_from_callable(obj, sigcls=cls,
> /usr/lib/python3.12/inspect.py:2642: in _signature_from_callable
> call = _descriptor_get(call, obj)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> descriptor = <slot wrapper '__call__' of 'type' objects>
> obj = <property object at 0xffffa8eeed90>
>
> def _descriptor_get(descriptor, obj):
> if isclass(descriptor):
> return descriptor
> get = getattr(type(descriptor), '__get__', _sentinel)
> if get is _sentinel:
> return descriptor
> > return get(descriptor, obj, type(obj))
> E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
>
> /usr/lib/python3.12/inspect.py:2467: TypeError
> _ test_create_scool[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool] _
>
> fp = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool'
>
> @pytest.mark.parametrize(
> "fp", [op.join(datadir, "hg19.GM12878-MboI.matrix.2000kb.cool")]
> )
> def test_create_scool(fp):
> c = cooler.Cooler(fp)
> # chromsizes = c.chromsizes
> bins = c.bins()[:]
> pixels = c.pixels()[:]
>
> # random and different content to prove only chrom, start, end is linked and the rest is independent for each cell
> from copy import deepcopy
> bins_cell1 = deepcopy(bins)
> bins_cell2 = deepcopy(bins)
> bins_cell3 = deepcopy(bins)
> bins_cell1['weight'] = np.array([0] * len(bins_cell1["start"]))
> bins_cell2['weight'] = np.array([1] * len(bins_cell1["start"]))
> bins_cell3['weight'] = np.array([2] * len(bins_cell1["start"]))
>
> bins_cell1['KR'] = np.array([3] * len(bins_cell1["start"]))
> bins_cell2['KR'] = np.array([4] * len(bins_cell1["start"]))
> bins_cell3['KR'] = np.array([5] * len(bins_cell1["start"]))
>
> name_pixel_dict = {'cell1': pixels, 'cell2': pixels, 'cell3': pixels}
> name_bins_dict = {'cell1': bins_cell1, 'cell2': bins_cell2, 'cell3': bins_cell3}
>
> with isolated_filesystem():
> > cooler.create_scool('outfile_test.scool', name_bins_dict, name_pixel_dict)
>
> tests/test_create.py:461:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> cooler/create/_create.py:1237: in create_scool
> create(
> cooler/create/_create.py:514: in create
> from dask.dataframe import DataFrame as dask_df
> /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:81: in <module>
> from dask.dataframe import backends, dispatch, rolling
> /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in <module>
> from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame
> /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in <module>
> from dask.dataframe import methods
> /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in <module>
> from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like
> /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in <module>
> from dask.dataframe import ( # noqa: F401 register pandas extension types
> /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in <module>
> from dask.dataframe.extensions import make_array_nonempty, make_scalar
> /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in <module>
> from dask.dataframe.accessor import (
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in <module>
> class DatetimeAccessor(Accessor):
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__
> _bind_property(cls, pd_cls, attr, min_version)
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property
> setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func)))
> /usr/lib/python3/dist-packages/dask/utils.py:858: in wrapper
> method.__doc__ = _derived_from(
> /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from
> method_args = get_named_args(method)
> /usr/lib/python3/dist-packages/dask/utils.py:572: in get_named_args
> s = inspect.signature(func)
> /usr/lib/python3.12/inspect.py:3310: in signature
> return Signature.from_callable(obj, follow_wrapped=follow_wrapped,
> /usr/lib/python3.12/inspect.py:3054: in from_callable
> return _signature_from_callable(obj, sigcls=cls,
> /usr/lib/python3.12/inspect.py:2642: in _signature_from_callable
> call = _descriptor_get(call, obj)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> descriptor = <slot wrapper '__call__' of 'type' objects>
> obj = <property object at 0xffffa8eeed90>
>
> def _descriptor_get(descriptor, obj):
> if isclass(descriptor):
> return descriptor
> get = getattr(type(descriptor), '__get__', _sentinel)
> if get is _sentinel:
> return descriptor
> > return get(descriptor, obj, type(obj))
> E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
>
> /usr/lib/python3.12/inspect.py:2467: TypeError
> _____________________________ test_from_hdf5_pairs _____________________________
>
> def test_from_hdf5_pairs():
> def should_not_depend_on_chunksize(chromsizes, bintable, mock_pairs):
> # try different chunk sizes
> binner = cooler.create.HDF5Aggregator(
> mock_pairs, chromsizes, bintable, chunksize=66
> )
> cooler.create.create(testcool_path, bintable, binner)
> with h5py.File(testcool_path, "r") as h5:
> oc1 = h5["indexes"]["chrom_offset"][:]
> ob1 = h5["indexes"]["bin1_offset"][:]
> p1 = cooler.api.pixels(h5, join=False)
>
> binner = cooler.create.HDF5Aggregator(
> mock_pairs, chromsizes, bintable, chunksize=666
> )
> cooler.create.create(testcool_path, bintable, binner)
> with h5py.File(testcool_path, "r") as h5:
> oc2 = h5["indexes"]["chrom_offset"][:]
> ob2 = h5["indexes"]["bin1_offset"][:]
> p2 = cooler.api.pixels(h5, join=False)
>
> assert np.all(oc1 == oc2)
> assert np.all(ob1 == ob2)
> assert np.all(p1.values == p2.values)
>
> def should_raise_if_input_not_sorted(chromsizes, bintable, mock_pairs):
> # not sorted by chrm1
> # with h5py.File(testcool_path, 'w') as h5:
> bad_reads = {
> "chrms1": mock_pairs["chrms2"],
> "cuts1": mock_pairs["cuts2"],
> "chrms2": mock_pairs["chrms1"],
> "cuts2": mock_pairs["cuts1"],
> }
> with pytest.raises(ValueError):
> cooler.create.HDF5Aggregator(bad_reads, chromsizes, bintable, chunksize=66)
>
> # not triu
> bad_reads = {
> "chrms1": mock_pairs["chrms1"].copy(),
> "cuts1": mock_pairs["cuts1"].copy(),
> "chrms2": mock_pairs["chrms2"].copy(),
> "cuts2": mock_pairs["cuts2"].copy(),
> }
> bad_reads["chrms1"][0] = 0
> bad_reads["chrms2"][0] = 0
> bad_reads["cuts1"][0] = 10
> bad_reads["cuts2"][0] = 9
> binner = cooler.create.HDF5Aggregator(
> bad_reads, chromsizes, bintable, chunksize=66
> )
> with pytest.raises(ValueError):
> cooler.create.create(testcool_path, bintable, binner)
>
> def should_work_with_int32_cols(chromsizes, bintable, mock_pairs):
> # int64
> binner = cooler.create.HDF5Aggregator(
> mock_pairs, chromsizes, bintable, chunksize=66
> )
> cooler.create.create(testcool_path, bintable, binner)
> with h5py.File(testcool_path, "r") as h5:
> oc1 = h5["indexes"]["chrom_offset"][:]
> ob1 = h5["indexes"]["bin1_offset"][:]
> p1 = cooler.api.pixels(h5, join=False)
>
> # int32
> mock_pairs32 = {
> "chrms1": mock_pairs["chrms1"].astype(np.int32),
> "cuts1": mock_pairs["cuts1"].astype(np.int32),
> "chrms2": mock_pairs["chrms2"].astype(np.int32),
> "cuts2": mock_pairs["cuts2"].astype(np.int32),
> }
> binner = cooler.create.HDF5Aggregator(
> mock_pairs32, chromsizes, bintable, chunksize=66
> )
> cooler.create.create(testcool_path, bintable, binner)
> with h5py.File(testcool_path, "r") as h5:
> oc2 = h5["indexes"]["chrom_offset"][:]
> ob2 = h5["indexes"]["bin1_offset"][:]
> p2 = cooler.api.pixels(h5, join=False)
>
> assert np.all(oc1 == oc2)
> assert np.all(ob1 == ob2)
> assert np.all(p1.values == p2.values)
>
> def _mock_hdf5_pairs():
> np.random.seed(1)
> chrms = np.random.randint(0, n_chroms, n_records * 2)
> cuts = np.random.randint(0, clen, n_records * 2)
> abs_cuts = np.array([clen * chrm + cut for chrm, cut in zip(chrms, cuts)])
> abs_cuts1, abs_cuts2 = abs_cuts[:n_records], abs_cuts[n_records:]
> mock_pairs = {
> "chrms1": chrms[:n_records],
> "cuts1": cuts[:n_records],
> "chrms2": chrms[n_records:],
> "cuts2": cuts[n_records:],
> }
> # Triu-sort
> mask = abs_cuts1 > abs_cuts2
> mock_pairs["chrms1"][mask], mock_pairs["chrms2"][mask] = (
> mock_pairs["chrms2"][mask],
> mock_pairs["chrms1"][mask],
> )
> mock_pairs["cuts1"][mask], mock_pairs["cuts2"][mask] = (
> mock_pairs["cuts2"][mask],
> mock_pairs["cuts1"][mask],
> )
> abs_cuts1[mask], abs_cuts2[mask] = abs_cuts2[mask], abs_cuts1[mask]
> idx = np.lexsort([abs_cuts2, abs_cuts1])
> for key in mock_pairs:
> mock_pairs[key] = mock_pairs[key][idx]
> return mock_pairs
>
> n_chroms = 2
> clen = 2000
> n_records = 3000
> chromsizes = pd.Series(index=["chr1", "chr2"], data=[clen, clen])
> mock_pairs = _mock_hdf5_pairs()
>
> # uniform bins
> bintable = cooler.binnify(chromsizes, 100)
> > should_not_depend_on_chunksize(chromsizes, bintable, mock_pairs)
>
> tests/test_create_ingest.py:167:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> tests/test_create_ingest.py:52: in should_not_depend_on_chunksize
> cooler.create.create(testcool_path, bintable, binner)
> cooler/create/_create.py:514: in create
> from dask.dataframe import DataFrame as dask_df
> /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:81: in <module>
> from dask.dataframe import backends, dispatch, rolling
> /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in <module>
> from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame
> /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in <module>
> from dask.dataframe import methods
> /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in <module>
> from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like
> /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in <module>
> from dask.dataframe import ( # noqa: F401 register pandas extension types
> /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in <module>
> from dask.dataframe.extensions import make_array_nonempty, make_scalar
> /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in <module>
> from dask.dataframe.accessor import (
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in <module>
> class DatetimeAccessor(Accessor):
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__
> _bind_property(cls, pd_cls, attr, min_version)
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property
> setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func)))
> /usr/lib/python3/dist-packages/dask/utils.py:858: in wrapper
> method.__doc__ = _derived_from(
> /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from
> method_args = get_named_args(method)
> /usr/lib/python3/dist-packages/dask/utils.py:572: in get_named_args
> s = inspect.signature(func)
> /usr/lib/python3.12/inspect.py:3310: in signature
> return Signature.from_callable(obj, follow_wrapped=follow_wrapped,
> /usr/lib/python3.12/inspect.py:3054: in from_callable
> return _signature_from_callable(obj, sigcls=cls,
> /usr/lib/python3.12/inspect.py:2642: in _signature_from_callable
> call = _descriptor_get(call, obj)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> descriptor = <slot wrapper '__call__' of 'type' objects>
> obj = <property object at 0xffffa8eeed90>
>
> def _descriptor_get(descriptor, obj):
> if isclass(descriptor):
> return descriptor
> get = getattr(type(descriptor), '__get__', _sentinel)
> if get is _sentinel:
> return descriptor
> > return get(descriptor, obj, type(obj))
> E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
>
> /usr/lib/python3.12/inspect.py:2467: TypeError
> _ test_cload_tabix[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/hg19.bins.2000kb.bed.gz-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/hg19.GM12878-MboI.pairs.subsample.sorted.txt.gz-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool] _
>
> bins_path = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/hg19.bins.2000kb.bed.gz'
> pairs_path = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/hg19.GM12878-MboI.pairs.subsample.sorted.txt.gz'
> ref_path = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool'
>
> @pytest.mark.filterwarnings("ignore")
> @pytest.mark.parametrize(
> "bins_path,pairs_path,ref_path",
> [
> (
> op.join(testdir, "data", "hg19.bins.2000kb.bed.gz"),
> op.join(testdir, "data", "hg19.GM12878-MboI.pairs.subsample.sorted.txt.gz"),
> op.join(testdir, "data", "hg19.GM12878-MboI.matrix.2000kb.cool"),
> )
> ],
> )
> def test_cload_tabix(bins_path, pairs_path, ref_path):
> > cload_tabix.callback(
> bins_path,
> pairs_path,
> testcool_path,
> metadata=None,
> assembly="hg19",
> nproc=8,
> zero_based=False,
> max_split=2,
> )
>
> tests/test_create_ingest.py:190:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> cooler/cli/cload.py:240: in tabix
> create_cooler(
> cooler/create/_create.py:1024: in create_cooler
> create(
> cooler/create/_create.py:514: in create
> from dask.dataframe import DataFrame as dask_df
> /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:81: in <module>
> from dask.dataframe import backends, dispatch, rolling
> /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in <module>
> from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame
> /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in <module>
> from dask.dataframe import methods
> /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in <module>
> from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like
> /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in <module>
> from dask.dataframe import ( # noqa: F401 register pandas extension types
> /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in <module>
> from dask.dataframe.extensions import make_array_nonempty, make_scalar
> /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in <module>
> from dask.dataframe.accessor import (
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in <module>
> class DatetimeAccessor(Accessor):
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__
> _bind_property(cls, pd_cls, attr, min_version)
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property
> setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func)))
> /usr/lib/python3/dist-packages/dask/utils.py:858: in wrapper
> method.__doc__ = _derived_from(
> /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from
> method_args = get_named_args(method)
> /usr/lib/python3/dist-packages/dask/utils.py:572: in get_named_args
> s = inspect.signature(func)
> /usr/lib/python3.12/inspect.py:3310: in signature
> return Signature.from_callable(obj, follow_wrapped=follow_wrapped,
> /usr/lib/python3.12/inspect.py:3054: in from_callable
> return _signature_from_callable(obj, sigcls=cls,
> /usr/lib/python3.12/inspect.py:2642: in _signature_from_callable
> call = _descriptor_get(call, obj)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> descriptor = <slot wrapper '__call__' of 'type' objects>
> obj = <property object at 0xffffa8eeed90>
>
> def _descriptor_get(descriptor, obj):
> if isclass(descriptor):
> return descriptor
> get = getattr(type(descriptor), '__get__', _sentinel)
> if get is _sentinel:
> return descriptor
> > return get(descriptor, obj, type(obj))
> E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
>
> /usr/lib/python3.12/inspect.py:2467: TypeError
> _ test_cload_pairix[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/hg19.bins.2000kb.bed.gz-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/hg19.GM12878-MboI.pairs.subsample.blksrt.txt.gz-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool] _
>
> bins_path = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/hg19.bins.2000kb.bed.gz'
> pairs_path = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/hg19.GM12878-MboI.pairs.subsample.blksrt.txt.gz'
> ref_path = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool'
>
> @pytest.mark.parametrize(
> "bins_path,pairs_path,ref_path",
> [
> (
> op.join(testdir, "data", "hg19.bins.2000kb.bed.gz"),
> op.join(testdir, "data", "hg19.GM12878-MboI.pairs.subsample.blksrt.txt.gz"),
> op.join(testdir, "data", "hg19.GM12878-MboI.matrix.2000kb.cool"),
> )
> ],
> )
> def test_cload_pairix(bins_path, pairs_path, ref_path):
> > cload_pairix.callback(
> bins_path,
> pairs_path,
> testcool_path,
> metadata=None,
> assembly="hg19",
> nproc=8,
> zero_based=False,
> max_split=2,
> )
>
> tests/test_create_ingest.py:221:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> cooler/cli/cload.py:308: in pairix
> create_cooler(
> cooler/create/_create.py:1024: in create_cooler
> create(
> cooler/create/_create.py:514: in create
> from dask.dataframe import DataFrame as dask_df
> /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:81: in <module>
> from dask.dataframe import backends, dispatch, rolling
> /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in <module>
> from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame
> /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in <module>
> from dask.dataframe import methods
> /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in <module>
> from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like
> /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in <module>
> from dask.dataframe import ( # noqa: F401 register pandas extension types
> /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in <module>
> from dask.dataframe.extensions import make_array_nonempty, make_scalar
> /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in <module>
> from dask.dataframe.accessor import (
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in <module>
> class DatetimeAccessor(Accessor):
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__
> _bind_property(cls, pd_cls, attr, min_version)
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property
> setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func)))
> /usr/lib/python3/dist-packages/dask/utils.py:858: in wrapper
> method.__doc__ = _derived_from(
> /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from
> method_args = get_named_args(method)
> /usr/lib/python3/dist-packages/dask/utils.py:572: in get_named_args
> s = inspect.signature(func)
> /usr/lib/python3.12/inspect.py:3310: in signature
> return Signature.from_callable(obj, follow_wrapped=follow_wrapped,
> /usr/lib/python3.12/inspect.py:3054: in from_callable
> return _signature_from_callable(obj, sigcls=cls,
> /usr/lib/python3.12/inspect.py:2642: in _signature_from_callable
> call = _descriptor_get(call, obj)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> descriptor = <slot wrapper '__call__' of 'type' objects>
> obj = <property object at 0xffffa8eeed90>
>
> def _descriptor_get(descriptor, obj):
> if isclass(descriptor):
> return descriptor
> get = getattr(type(descriptor), '__get__', _sentinel)
> if get is _sentinel:
> return descriptor
> > return get(descriptor, obj, type(obj))
> E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
>
> /usr/lib/python3.12/inspect.py:2467: TypeError
> _ test_cload_pairs[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.bins.var.bed-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.pairs-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.symm.upper.var.cool] _
>
> bins_path = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.bins.var.bed'
> pairs_path = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.pairs'
> ref_path = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.symm.upper.var.cool'
>
> @pytest.mark.skipif(
> _pandas_major_version < 1,
> reason="hash fix only works with pandas >= 1.0"
> )
> @pytest.mark.parametrize(
> "bins_path,pairs_path,ref_path",
> [
> (
> op.join(testdir, "data", "toy.bins.var.bed"),
> op.join(testdir, "data", "toy.pairs"),
> op.join(testdir, "data", "toy.symm.upper.var.cool"),
> ),
> (
> op.join(testdir, "data", "toy.bins.var.bed"),
> op.join(testdir, "data", "toy_hash.pairs"),
> op.join(testdir, "data", "toy.symm.upper.var.cool"),
> ),
> (
> op.join(testdir, "data", "toy.bins.var.bed"),
> op.join(testdir, "data", "toy_hash.pairs.gz"),
> op.join(testdir, "data", "toy.symm.upper.var.cool"),
> )
> ],
> )
> def test_cload_pairs(bins_path, pairs_path, ref_path):
> kwargs = dict(
> metadata=None,
> assembly="hg19",
> chunksize=int(15e6),
> zero_based=False,
> comment_char="#",
> input_copy_status="unique",
> no_symmetric_upper=False,
> field=(),
> temp_dir=None,
> no_delete_temp=False,
> storage_options=None,
> no_count=False,
> max_merge=200,
> chrom1=2,
> pos1=3,
> chrom2=4,
> pos2=5,
> append=False,
> )
> > cload_pairs.callback(bins_path, pairs_path, testcool_path, **kwargs)
>
> tests/test_create_ingest.py:286:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> cooler/cli/cload.py:584: in pairs
> create_cooler(
> cooler/create/_create.py:1042: in create_cooler
> create_from_unordered(
> cooler/create/_create.py:723: in create_from_unordered
> create(uri, bins, chunk, columns=columns, dtypes=dtypes, mode="a", **kwargs)
> cooler/create/_create.py:514: in create
> from dask.dataframe import DataFrame as dask_df
> /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:81: in <module>
> from dask.dataframe import backends, dispatch, rolling
> /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in <module>
> from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame
> /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in <module>
> from dask.dataframe import methods
> /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in <module>
> from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like
> /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in <module>
> from dask.dataframe import ( # noqa: F401 register pandas extension types
> /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in <module>
> from dask.dataframe.extensions import make_array_nonempty, make_scalar
> /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in <module>
> from dask.dataframe.accessor import (
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in <module>
> class DatetimeAccessor(Accessor):
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__
> _bind_property(cls, pd_cls, attr, min_version)
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property
> setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func)))
> /usr/lib/python3/dist-packages/dask/utils.py:858: in wrapper
> method.__doc__ = _derived_from(
> /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from
> method_args = get_named_args(method)
> /usr/lib/python3/dist-packages/dask/utils.py:572: in get_named_args
> s = inspect.signature(func)
> /usr/lib/python3.12/inspect.py:3310: in signature
> return Signature.from_callable(obj, follow_wrapped=follow_wrapped,
> /usr/lib/python3.12/inspect.py:3054: in from_callable
> return _signature_from_callable(obj, sigcls=cls,
> /usr/lib/python3.12/inspect.py:2642: in _signature_from_callable
> call = _descriptor_get(call, obj)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> descriptor = <slot wrapper '__call__' of 'type' objects>
> obj = <property object at 0xffffa8eeed90>
>
> def _descriptor_get(descriptor, obj):
> if isclass(descriptor):
> return descriptor
> get = getattr(type(descriptor), '__get__', _sentinel)
> if get is _sentinel:
> return descriptor
> > return get(descriptor, obj, type(obj))
> E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
>
> /usr/lib/python3.12/inspect.py:2467: TypeError
> _ test_cload_pairs[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.bins.var.bed-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy_hash.pairs-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.symm.upper.var.cool] _
>
> bins_path = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.bins.var.bed'
> pairs_path = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy_hash.pairs'
> ref_path = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.symm.upper.var.cool'
>
> @pytest.mark.skipif(
> _pandas_major_version < 1,
> reason="hash fix only works with pandas >= 1.0"
> )
> @pytest.mark.parametrize(
> "bins_path,pairs_path,ref_path",
> [
> (
> op.join(testdir, "data", "toy.bins.var.bed"),
> op.join(testdir, "data", "toy.pairs"),
> op.join(testdir, "data", "toy.symm.upper.var.cool"),
> ),
> (
> op.join(testdir, "data", "toy.bins.var.bed"),
> op.join(testdir, "data", "toy_hash.pairs"),
> op.join(testdir, "data", "toy.symm.upper.var.cool"),
> ),
> (
> op.join(testdir, "data", "toy.bins.var.bed"),
> op.join(testdir, "data", "toy_hash.pairs.gz"),
> op.join(testdir, "data", "toy.symm.upper.var.cool"),
> )
> ],
> )
> def test_cload_pairs(bins_path, pairs_path, ref_path):
> kwargs = dict(
> metadata=None,
> assembly="hg19",
> chunksize=int(15e6),
> zero_based=False,
> comment_char="#",
> input_copy_status="unique",
> no_symmetric_upper=False,
> field=(),
> temp_dir=None,
> no_delete_temp=False,
> storage_options=None,
> no_count=False,
> max_merge=200,
> chrom1=2,
> pos1=3,
> chrom2=4,
> pos2=5,
> append=False,
> )
> > cload_pairs.callback(bins_path, pairs_path, testcool_path, **kwargs)
>
> tests/test_create_ingest.py:286:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> cooler/cli/cload.py:584: in pairs
> create_cooler(
> cooler/create/_create.py:1042: in create_cooler
> create_from_unordered(
> cooler/create/_create.py:723: in create_from_unordered
> create(uri, bins, chunk, columns=columns, dtypes=dtypes, mode="a", **kwargs)
> cooler/create/_create.py:514: in create
> from dask.dataframe import DataFrame as dask_df
> /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:81: in <module>
> from dask.dataframe import backends, dispatch, rolling
> /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in <module>
> from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame
> /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in <module>
> from dask.dataframe import methods
> /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in <module>
> from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like
> /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in <module>
> from dask.dataframe import ( # noqa: F401 register pandas extension types
> /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in <module>
> from dask.dataframe.extensions import make_array_nonempty, make_scalar
> /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in <module>
> from dask.dataframe.accessor import (
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in <module>
> class DatetimeAccessor(Accessor):
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__
> _bind_property(cls, pd_cls, attr, min_version)
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property
> setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func)))
> /usr/lib/python3/dist-packages/dask/utils.py:858: in wrapper
> method.__doc__ = _derived_from(
> /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from
> method_args = get_named_args(method)
> /usr/lib/python3/dist-packages/dask/utils.py:572: in get_named_args
> s = inspect.signature(func)
> /usr/lib/python3.12/inspect.py:3310: in signature
> return Signature.from_callable(obj, follow_wrapped=follow_wrapped,
> /usr/lib/python3.12/inspect.py:3054: in from_callable
> return _signature_from_callable(obj, sigcls=cls,
> /usr/lib/python3.12/inspect.py:2642: in _signature_from_callable
> call = _descriptor_get(call, obj)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> descriptor = <slot wrapper '__call__' of 'type' objects>
> obj = <property object at 0xffffa8eeed90>
>
> def _descriptor_get(descriptor, obj):
> if isclass(descriptor):
> return descriptor
> get = getattr(type(descriptor), '__get__', _sentinel)
> if get is _sentinel:
> return descriptor
> > return get(descriptor, obj, type(obj))
> E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
>
> /usr/lib/python3.12/inspect.py:2467: TypeError
> _ test_cload_pairs[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.bins.var.bed-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy_hash.pairs.gz-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.symm.upper.var.cool] _
>
> bins_path = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.bins.var.bed'
> pairs_path = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy_hash.pairs.gz'
> ref_path = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.symm.upper.var.cool'
>
> @pytest.mark.skipif(
> _pandas_major_version < 1,
> reason="hash fix only works with pandas >= 1.0"
> )
> @pytest.mark.parametrize(
> "bins_path,pairs_path,ref_path",
> [
> (
> op.join(testdir, "data", "toy.bins.var.bed"),
> op.join(testdir, "data", "toy.pairs"),
> op.join(testdir, "data", "toy.symm.upper.var.cool"),
> ),
> (
> op.join(testdir, "data", "toy.bins.var.bed"),
> op.join(testdir, "data", "toy_hash.pairs"),
> op.join(testdir, "data", "toy.symm.upper.var.cool"),
> ),
> (
> op.join(testdir, "data", "toy.bins.var.bed"),
> op.join(testdir, "data", "toy_hash.pairs.gz"),
> op.join(testdir, "data", "toy.symm.upper.var.cool"),
> )
> ],
> )
> def test_cload_pairs(bins_path, pairs_path, ref_path):
> kwargs = dict(
> metadata=None,
> assembly="hg19",
> chunksize=int(15e6),
> zero_based=False,
> comment_char="#",
> input_copy_status="unique",
> no_symmetric_upper=False,
> field=(),
> temp_dir=None,
> no_delete_temp=False,
> storage_options=None,
> no_count=False,
> max_merge=200,
> chrom1=2,
> pos1=3,
> chrom2=4,
> pos2=5,
> append=False,
> )
> > cload_pairs.callback(bins_path, pairs_path, testcool_path, **kwargs)
>
> tests/test_create_ingest.py:286:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> cooler/cli/cload.py:584: in pairs
> create_cooler(
> cooler/create/_create.py:1042: in create_cooler
> create_from_unordered(
> cooler/create/_create.py:723: in create_from_unordered
> create(uri, bins, chunk, columns=columns, dtypes=dtypes, mode="a", **kwargs)
> cooler/create/_create.py:514: in create
> from dask.dataframe import DataFrame as dask_df
> /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:81: in <module>
> from dask.dataframe import backends, dispatch, rolling
> /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in <module>
> from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame
> /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in <module>
> from dask.dataframe import methods
> /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in <module>
> from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like
> /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in <module>
> from dask.dataframe import ( # noqa: F401 register pandas extension types
> /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in <module>
> from dask.dataframe.extensions import make_array_nonempty, make_scalar
> /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in <module>
> from dask.dataframe.accessor import (
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in <module>
> class DatetimeAccessor(Accessor):
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__
> _bind_property(cls, pd_cls, attr, min_version)
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property
> setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func)))
> /usr/lib/python3/dist-packages/dask/utils.py:858: in wrapper
> method.__doc__ = _derived_from(
> /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from
> method_args = get_named_args(method)
> /usr/lib/python3/dist-packages/dask/utils.py:572: in get_named_args
> s = inspect.signature(func)
> /usr/lib/python3.12/inspect.py:3310: in signature
> return Signature.from_callable(obj, follow_wrapped=follow_wrapped,
> /usr/lib/python3.12/inspect.py:3054: in from_callable
> return _signature_from_callable(obj, sigcls=cls,
> /usr/lib/python3.12/inspect.py:2642: in _signature_from_callable
> call = _descriptor_get(call, obj)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> descriptor = <slot wrapper '__call__' of 'type' objects>
> obj = <property object at 0xffffa8eeed90>
>
> def _descriptor_get(descriptor, obj):
> if isclass(descriptor):
> return descriptor
> get = getattr(type(descriptor), '__get__', _sentinel)
> if get is _sentinel:
> return descriptor
> > return get(descriptor, obj, type(obj))
> E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
>
> /usr/lib/python3.12/inspect.py:2467: TypeError
> _ test_cload_field[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.chrom.sizes:2-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.pairs] _
>
> bins_path = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.chrom.sizes:2'
> pairs_path = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.pairs'
>
> @pytest.mark.parametrize(
> "bins_path,pairs_path",
> [
> (
> op.join(testdir, "data", "toy.chrom.sizes") + ":2",
> op.join(testdir, "data", "toy.pairs"),
> )
> ],
> )
> def test_cload_field(bins_path, pairs_path):
> kwargs = dict(
> metadata=None,
> assembly="toy",
> chunksize=10,
> zero_based=False,
> comment_char="#",
> input_copy_status="unique",
> no_symmetric_upper=False,
> temp_dir=None,
> no_delete_temp=False,
> storage_options=None,
> no_count=True,
> max_merge=200,
> chrom1=2,
> pos1=3,
> chrom2=4,
> pos2=5,
> append=False,
> )
> > cload_pairs.callback(
> bins_path, pairs_path, testcool_path, field=("score=8:dtype=float",), **kwargs
> )
>
> tests/test_create_ingest.py:326:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> cooler/cli/cload.py:584: in pairs
> create_cooler(
> cooler/create/_create.py:1042: in create_cooler
> create_from_unordered(
> cooler/create/_create.py:723: in create_from_unordered
> create(uri, bins, chunk, columns=columns, dtypes=dtypes, mode="a", **kwargs)
> cooler/create/_create.py:514: in create
> from dask.dataframe import DataFrame as dask_df
> /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:81: in <module>
> from dask.dataframe import backends, dispatch, rolling
> /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in <module>
> from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame
> /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in <module>
> from dask.dataframe import methods
> /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in <module>
> from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like
> /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in <module>
> from dask.dataframe import ( # noqa: F401 register pandas extension types
> /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in <module>
> from dask.dataframe.extensions import make_array_nonempty, make_scalar
> /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in <module>
> from dask.dataframe.accessor import (
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in <module>
> class DatetimeAccessor(Accessor):
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__
> _bind_property(cls, pd_cls, attr, min_version)
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property
> setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func)))
> /usr/lib/python3/dist-packages/dask/utils.py:858: in wrapper
> method.__doc__ = _derived_from(
> /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from
> method_args = get_named_args(method)
> /usr/lib/python3/dist-packages/dask/utils.py:572: in get_named_args
> s = inspect.signature(func)
> /usr/lib/python3.12/inspect.py:3310: in signature
> return Signature.from_callable(obj, follow_wrapped=follow_wrapped,
> /usr/lib/python3.12/inspect.py:3054: in from_callable
> return _signature_from_callable(obj, sigcls=cls,
> /usr/lib/python3.12/inspect.py:2642: in _signature_from_callable
> call = _descriptor_get(call, obj)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> descriptor = <slot wrapper '__call__' of 'type' objects>
> obj = <property object at 0xffffa8eeed90>
>
> def _descriptor_get(descriptor, obj):
> if isclass(descriptor):
> return descriptor
> get = getattr(type(descriptor), '__get__', _sentinel)
> if get is _sentinel:
> return descriptor
> > return get(descriptor, obj, type(obj))
> E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
>
> /usr/lib/python3.12/inspect.py:2467: TypeError
> _ test_cload_custom_tempdir[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.chrom.sizes:2-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.pairs] _
>
> bins_path = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.chrom.sizes:2'
> pairs_path = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.pairs'
>
> @pytest.mark.parametrize(
> "bins_path,pairs_path",
> [
> (
> op.join(testdir, "data", "toy.chrom.sizes") + ":2",
> op.join(testdir, "data", "toy.pairs"),
> )
> ],
> )
> def test_cload_custom_tempdir(bins_path, pairs_path):
> for temp_dir in [op.join(testdir, "data"), "-"]:
> > cload_pairs.callback(
> bins_path,
> pairs_path,
> testcool_path,
> metadata=None,
> assembly="toy",
> chunksize=10,
> zero_based=False,
> comment_char="#",
> input_copy_status="unique",
> no_symmetric_upper=False,
> field=(),
> temp_dir=temp_dir,
> no_delete_temp=False,
> storage_options=None,
> no_count=True,
> max_merge=200,
> chrom1=2,
> pos1=3,
> chrom2=4,
> pos2=5,
> append=False,
> )
>
> tests/test_create_ingest.py:345:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> cooler/cli/cload.py:584: in pairs
> create_cooler(
> cooler/create/_create.py:1042: in create_cooler
> create_from_unordered(
> cooler/create/_create.py:723: in create_from_unordered
> create(uri, bins, chunk, columns=columns, dtypes=dtypes, mode="a", **kwargs)
> cooler/create/_create.py:514: in create
> from dask.dataframe import DataFrame as dask_df
> /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:81: in <module>
> from dask.dataframe import backends, dispatch, rolling
> /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in <module>
> from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame
> /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in <module>
> from dask.dataframe import methods
> /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in <module>
> from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like
> /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in <module>
> from dask.dataframe import ( # noqa: F401 register pandas extension types
> /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in <module>
> from dask.dataframe.extensions import make_array_nonempty, make_scalar
> /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in <module>
> from dask.dataframe.accessor import (
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in <module>
> class DatetimeAccessor(Accessor):
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__
> _bind_property(cls, pd_cls, attr, min_version)
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property
> setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func)))
> /usr/lib/python3/dist-packages/dask/utils.py:858: in wrapper
> method.__doc__ = _derived_from(
> /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from
> method_args = get_named_args(method)
> /usr/lib/python3/dist-packages/dask/utils.py:572: in get_named_args
> s = inspect.signature(func)
> /usr/lib/python3.12/inspect.py:3310: in signature
> return Signature.from_callable(obj, follow_wrapped=follow_wrapped,
> /usr/lib/python3.12/inspect.py:3054: in from_callable
> return _signature_from_callable(obj, sigcls=cls,
> /usr/lib/python3.12/inspect.py:2642: in _signature_from_callable
> call = _descriptor_get(call, obj)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> descriptor = <slot wrapper '__call__' of 'type' objects>
> obj = <property object at 0xffffa8eeed90>
>
> def _descriptor_get(descriptor, obj):
> if isclass(descriptor):
> return descriptor
> get = getattr(type(descriptor), '__get__', _sentinel)
> if get is _sentinel:
> return descriptor
> > return get(descriptor, obj, type(obj))
> E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
>
> /usr/lib/python3.12/inspect.py:2467: TypeError
> _____________________________ test_load_bg2_vs_coo _____________________________
>
> def test_load_bg2_vs_coo():
> kwargs = dict(
> metadata=None,
> assembly="hg19",
> chunksize=int(20e6),
> field=(),
> count_as_float=False,
> one_based=False,
> comment_char="#",
> input_copy_status="unique",
> no_symmetric_upper=False,
> temp_dir=None,
> no_delete_temp=False,
> storage_options=None,
> append=False,
> )
>
> out_path1 = op.join(tmp, "test1.cool")
> out_path2 = op.join(tmp, "test2.cool")
>
> > load.callback(
> op.join(testdir, "data", "hg19.bins.2000kb.bed.gz"),
> op.join(testdir, "data", "hg19.GM12878-MboI.matrix.2000kb.bg2.gz"),
> out_path1,
> format="bg2",
> **kwargs
> )
>
> tests/test_create_ingest.py:394:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> cooler/cli/load.py:339: in load
> create_from_unordered(
> cooler/create/_create.py:723: in create_from_unordered
> create(uri, bins, chunk, columns=columns, dtypes=dtypes, mode="a", **kwargs)
> cooler/create/_create.py:514: in create
> from dask.dataframe import DataFrame as dask_df
> /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:81: in <module>
> from dask.dataframe import backends, dispatch, rolling
> /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in <module>
> from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame
> /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in <module>
> from dask.dataframe import methods
> /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in <module>
> from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like
> /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in <module>
> from dask.dataframe import ( # noqa: F401 register pandas extension types
> /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in <module>
> from dask.dataframe.extensions import make_array_nonempty, make_scalar
> /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in <module>
> from dask.dataframe.accessor import (
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in <module>
> class DatetimeAccessor(Accessor):
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__
> _bind_property(cls, pd_cls, attr, min_version)
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property
> setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func)))
> /usr/lib/python3/dist-packages/dask/utils.py:858: in wrapper
> method.__doc__ = _derived_from(
> /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from
> method_args = get_named_args(method)
> /usr/lib/python3/dist-packages/dask/utils.py:572: in get_named_args
> s = inspect.signature(func)
> /usr/lib/python3.12/inspect.py:3310: in signature
> return Signature.from_callable(obj, follow_wrapped=follow_wrapped,
> /usr/lib/python3.12/inspect.py:3054: in from_callable
> return _signature_from_callable(obj, sigcls=cls,
> /usr/lib/python3.12/inspect.py:2642: in _signature_from_callable
> call = _descriptor_get(call, obj)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> descriptor = <slot wrapper '__call__' of 'type' objects>
> obj = <property object at 0xffffa8eeed90>
>
> def _descriptor_get(descriptor, obj):
> if isclass(descriptor):
> return descriptor
> get = getattr(type(descriptor), '__get__', _sentinel)
> if get is _sentinel:
> return descriptor
> > return get(descriptor, obj, type(obj))
> E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
>
> /usr/lib/python3.12/inspect.py:2467: TypeError
> _________________________ test_load_zero_one_based_bg2 _________________________
>
> def test_load_zero_one_based_bg2():
> kwargs = dict(
> format="bg2",
> metadata=None,
> assembly="toy",
> chunksize=10,
> field=(),
> count_as_float=False,
> comment_char="#",
> input_copy_status="unique",
> no_symmetric_upper=False,
> temp_dir=None,
> no_delete_temp=False,
> storage_options=None,
> append=False,
> )
> # 1-based-start BG2 input
> ref = "toy.symm.upper.1.ob.bg2"
> bins_path = op.join(testdir, "data", "toy.chrom.sizes") + ":1"
> pixels_path = op.join(testdir, "data", ref)
> > load.callback(bins_path, pixels_path, testcool_path, one_based=True, **kwargs)
>
> tests/test_create_ingest.py:441:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> cooler/cli/load.py:339: in load
> create_from_unordered(
> cooler/create/_create.py:723: in create_from_unordered
> create(uri, bins, chunk, columns=columns, dtypes=dtypes, mode="a", **kwargs)
> cooler/create/_create.py:514: in create
> from dask.dataframe import DataFrame as dask_df
> /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:81: in <module>
> from dask.dataframe import backends, dispatch, rolling
> /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in <module>
> from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame
> /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in <module>
> from dask.dataframe import methods
> /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in <module>
> from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like
> /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in <module>
> from dask.dataframe import ( # noqa: F401 register pandas extension types
> /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in <module>
> from dask.dataframe.extensions import make_array_nonempty, make_scalar
> /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in <module>
> from dask.dataframe.accessor import (
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in <module>
> class DatetimeAccessor(Accessor):
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__
> _bind_property(cls, pd_cls, attr, min_version)
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property
> setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func)))
> /usr/lib/python3/dist-packages/dask/utils.py:858: in wrapper
> method.__doc__ = _derived_from(
> /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from
> method_args = get_named_args(method)
> /usr/lib/python3/dist-packages/dask/utils.py:572: in get_named_args
> s = inspect.signature(func)
> /usr/lib/python3.12/inspect.py:3310: in signature
> return Signature.from_callable(obj, follow_wrapped=follow_wrapped,
> /usr/lib/python3.12/inspect.py:3054: in from_callable
> return _signature_from_callable(obj, sigcls=cls,
> /usr/lib/python3.12/inspect.py:2642: in _signature_from_callable
> call = _descriptor_get(call, obj)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> descriptor = <slot wrapper '__call__' of 'type' objects>
> obj = <property object at 0xffffa8eeed90>
>
> def _descriptor_get(descriptor, obj):
> if isclass(descriptor):
> return descriptor
> get = getattr(type(descriptor), '__get__', _sentinel)
> if get is _sentinel:
> return descriptor
> > return get(descriptor, obj, type(obj))
> E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
>
> /usr/lib/python3.12/inspect.py:2467: TypeError
> _________________________ test_load_zero_one_based_coo _________________________
>
> def test_load_zero_one_based_coo():
> kwargs = dict(
> format="coo",
> metadata=None,
> assembly="toy",
> chunksize=10,
> field=(),
> count_as_float=False,
> comment_char="#",
> input_copy_status="unique",
> no_symmetric_upper=False,
> temp_dir=None,
> no_delete_temp=False,
> storage_options=None,
> append=False,
> )
> # 1-based-start COO input
> ref = "toy.symm.upper.1.ob.coo"
> bins_path = op.join(testdir, "data", "toy.chrom.sizes") + ":1"
> pixels_path = op.join(testdir, "data", ref)
> > load.callback(bins_path, pixels_path, testcool_path, one_based=True, **kwargs)
>
> tests/test_create_ingest.py:490:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> cooler/cli/load.py:339: in load
> create_from_unordered(
> cooler/create/_create.py:723: in create_from_unordered
> create(uri, bins, chunk, columns=columns, dtypes=dtypes, mode="a", **kwargs)
> cooler/create/_create.py:514: in create
> from dask.dataframe import DataFrame as dask_df
> /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:81: in <module>
> from dask.dataframe import backends, dispatch, rolling
> /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in <module>
> from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame
> /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in <module>
> from dask.dataframe import methods
> /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in <module>
> from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like
> /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in <module>
> from dask.dataframe import ( # noqa: F401 register pandas extension types
> /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in <module>
> from dask.dataframe.extensions import make_array_nonempty, make_scalar
> /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in <module>
> from dask.dataframe.accessor import (
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in <module>
> class DatetimeAccessor(Accessor):
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__
> _bind_property(cls, pd_cls, attr, min_version)
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property
> setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func)))
> /usr/lib/python3/dist-packages/dask/utils.py:858: in wrapper
> method.__doc__ = _derived_from(
> /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from
> method_args = get_named_args(method)
> /usr/lib/python3/dist-packages/dask/utils.py:572: in get_named_args
> s = inspect.signature(func)
> /usr/lib/python3.12/inspect.py:3310: in signature
> return Signature.from_callable(obj, follow_wrapped=follow_wrapped,
> /usr/lib/python3.12/inspect.py:3054: in from_callable
> return _signature_from_callable(obj, sigcls=cls,
> /usr/lib/python3.12/inspect.py:2642: in _signature_from_callable
> call = _descriptor_get(call, obj)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> descriptor = <slot wrapper '__call__' of 'type' objects>
> obj = <property object at 0xffffa8eeed90>
>
> def _descriptor_get(descriptor, obj):
> if isclass(descriptor):
> return descriptor
> get = getattr(type(descriptor), '__get__', _sentinel)
> if get is _sentinel:
> return descriptor
> > return get(descriptor, obj, type(obj))
> E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
>
> /usr/lib/python3.12/inspect.py:2467: TypeError
> ____________________________ test_cload_append_mode ____________________________
>
> def test_cload_append_mode():
> for append in (True, False):
> out_path = op.join(tmp, "test.cool")
> with h5py.File(out_path, "w") as f:
> f.attrs["xxxx"] = True
> kwargs = dict(
> metadata=None,
> assembly="hg19",
> chunksize=int(15e6),
> zero_based=False,
> comment_char="#",
> input_copy_status="unique",
> no_symmetric_upper=False,
> field=(),
> temp_dir=None,
> no_delete_temp=False,
> storage_options=None,
> no_count=False,
> max_merge=200,
> chrom1=2,
> pos1=3,
> chrom2=4,
> pos2=5,
> append=append,
> )
> > cload_pairs.callback(
> op.join(testdir, "data", "toy.bins.var.bed"),
> op.join(testdir, "data", "toy.pairs"),
> out_path,
> **kwargs
> )
>
> tests/test_create_ingest.py:551:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> cooler/cli/cload.py:584: in pairs
> create_cooler(
> cooler/create/_create.py:1042: in create_cooler
> create_from_unordered(
> cooler/create/_create.py:723: in create_from_unordered
> create(uri, bins, chunk, columns=columns, dtypes=dtypes, mode="a", **kwargs)
> cooler/create/_create.py:514: in create
> from dask.dataframe import DataFrame as dask_df
> /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:81: in <module>
> from dask.dataframe import backends, dispatch, rolling
> /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in <module>
> from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame
> /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in <module>
> from dask.dataframe import methods
> /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in <module>
> from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like
> /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in <module>
> from dask.dataframe import ( # noqa: F401 register pandas extension types
> /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in <module>
> from dask.dataframe.extensions import make_array_nonempty, make_scalar
> /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in <module>
> from dask.dataframe.accessor import (
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in <module>
> class DatetimeAccessor(Accessor):
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__
> _bind_property(cls, pd_cls, attr, min_version)
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property
> setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func)))
> /usr/lib/python3/dist-packages/dask/utils.py:858: in wrapper
> method.__doc__ = _derived_from(
> /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from
> method_args = get_named_args(method)
> /usr/lib/python3/dist-packages/dask/utils.py:572: in get_named_args
> s = inspect.signature(func)
> /usr/lib/python3.12/inspect.py:3310: in signature
> return Signature.from_callable(obj, follow_wrapped=follow_wrapped,
> /usr/lib/python3.12/inspect.py:3054: in from_callable
> return _signature_from_callable(obj, sigcls=cls,
> /usr/lib/python3.12/inspect.py:2642: in _signature_from_callable
> call = _descriptor_get(call, obj)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> descriptor = <slot wrapper '__call__' of 'type' objects>
> obj = <property object at 0xffffa8eeed90>
>
> def _descriptor_get(descriptor, obj):
> if isclass(descriptor):
> return descriptor
> get = getattr(type(descriptor), '__get__', _sentinel)
> if get is _sentinel:
> return descriptor
> > return get(descriptor, obj, type(obj))
> E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
>
> /usr/lib/python3.12/inspect.py:2467: TypeError
> ____________________________ test_load_append_mode _____________________________
>
> def test_load_append_mode():
> for append in (True, False):
> out_path = op.join(tmp, "test.cool")
> with h5py.File(out_path, "w") as f:
> f.attrs["xxxx"] = True
> kwargs = dict(
> metadata=None,
> assembly="hg19",
> chunksize=int(20e6),
> field=(),
> count_as_float=False,
> one_based=False,
> comment_char="#",
> input_copy_status="unique",
> no_symmetric_upper=False,
> temp_dir=None,
> no_delete_temp=False,
> storage_options=None,
> append=append,
> )
> > load.callback(
> op.join(testdir, "data", "hg19.bins.2000kb.bed.gz"),
> op.join(testdir, "data", "hg19.GM12878-MboI.matrix.2000kb.coo.txt"),
> out_path,
> format="coo",
> **kwargs
> )
>
> tests/test_create_ingest.py:588:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> cooler/cli/load.py:339: in load
> create_from_unordered(
> cooler/create/_create.py:723: in create_from_unordered
> create(uri, bins, chunk, columns=columns, dtypes=dtypes, mode="a", **kwargs)
> cooler/create/_create.py:514: in create
> from dask.dataframe import DataFrame as dask_df
> /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:81: in <module>
> from dask.dataframe import backends, dispatch, rolling
> /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in <module>
> from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame
> /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in <module>
> from dask.dataframe import methods
> /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in <module>
> from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like
> /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in <module>
> from dask.dataframe import ( # noqa: F401 register pandas extension types
> /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in <module>
> from dask.dataframe.extensions import make_array_nonempty, make_scalar
> /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in <module>
> from dask.dataframe.accessor import (
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in <module>
> class DatetimeAccessor(Accessor):
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__
> _bind_property(cls, pd_cls, attr, min_version)
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property
> setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func)))
> /usr/lib/python3/dist-packages/dask/utils.py:858: in wrapper
> method.__doc__ = _derived_from(
> /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from
> method_args = get_named_args(method)
> /usr/lib/python3/dist-packages/dask/utils.py:572: in get_named_args
> s = inspect.signature(func)
> /usr/lib/python3.12/inspect.py:3310: in signature
> return Signature.from_callable(obj, follow_wrapped=follow_wrapped,
> /usr/lib/python3.12/inspect.py:3054: in from_callable
> return _signature_from_callable(obj, sigcls=cls,
> /usr/lib/python3.12/inspect.py:2642: in _signature_from_callable
> call = _descriptor_get(call, obj)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> descriptor = <slot wrapper '__call__' of 'type' objects>
> obj = <property object at 0xffffa8eeed90>
>
> def _descriptor_get(descriptor, obj):
> if isclass(descriptor):
> return descriptor
> get = getattr(type(descriptor), '__get__', _sentinel)
> if get is _sentinel:
> return descriptor
> > return get(descriptor, obj, type(obj))
> E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
>
> /usr/lib/python3.12/inspect.py:2467: TypeError
> ___________________________ test_load_custom_tempdir ___________________________
>
> def test_load_custom_tempdir():
> for temp_dir in [op.join(testdir, "data"), "-"]:
> > load.callback(
> op.join(testdir, "data", "hg19.bins.2000kb.bed.gz"),
> op.join(testdir, "data", "hg19.GM12878-MboI.matrix.2000kb.coo.txt"),
> testcool_path,
> format="coo",
> metadata=None,
> assembly="hg19",
> chunksize=int(20e6),
> field=(),
> count_as_float=False,
> one_based=False,
> comment_char="#",
> input_copy_status="unique",
> no_symmetric_upper=False,
> temp_dir=temp_dir,
> no_delete_temp=False,
> storage_options=None,
> append=False,
>
> )
>
> tests/test_create_ingest.py:608:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> cooler/cli/load.py:339: in load
> create_from_unordered(
> cooler/create/_create.py:723: in create_from_unordered
> create(uri, bins, chunk, columns=columns, dtypes=dtypes, mode="a", **kwargs)
> cooler/create/_create.py:514: in create
> from dask.dataframe import DataFrame as dask_df
> /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:81: in <module>
> from dask.dataframe import backends, dispatch, rolling
> /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in <module>
> from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame
> /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in <module>
> from dask.dataframe import methods
> /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in <module>
> from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like
> /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in <module>
> from dask.dataframe import ( # noqa: F401 register pandas extension types
> /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in <module>
> from dask.dataframe.extensions import make_array_nonempty, make_scalar
> /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in <module>
> from dask.dataframe.accessor import (
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in <module>
> class DatetimeAccessor(Accessor):
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__
> _bind_property(cls, pd_cls, attr, min_version)
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property
> setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func)))
> /usr/lib/python3/dist-packages/dask/utils.py:858: in wrapper
> method.__doc__ = _derived_from(
> /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from
> method_args = get_named_args(method)
> /usr/lib/python3/dist-packages/dask/utils.py:572: in get_named_args
> s = inspect.signature(func)
> /usr/lib/python3.12/inspect.py:3310: in signature
> return Signature.from_callable(obj, follow_wrapped=follow_wrapped,
> /usr/lib/python3.12/inspect.py:3054: in from_callable
> return _signature_from_callable(obj, sigcls=cls,
> /usr/lib/python3.12/inspect.py:2642: in _signature_from_callable
> call = _descriptor_get(call, obj)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> descriptor = <slot wrapper '__call__' of 'type' objects>
> obj = <property object at 0xffffa8eeed90>
>
> def _descriptor_get(descriptor, obj):
> if isclass(descriptor):
> return descriptor
> get = getattr(type(descriptor), '__get__', _sentinel)
> if get is _sentinel:
> return descriptor
> > return get(descriptor, obj, type(obj))
> E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
>
> /usr/lib/python3.12/inspect.py:2467: TypeError
> _ test_merge[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool] _
>
> path1 = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool'
> path2 = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool'
>
> @pytest.mark.parametrize(
> "path1,path2",
> [
> (
> op.join(datadir, "hg19.GM12878-MboI.matrix.2000kb.cool"),
> op.join(datadir, "hg19.GM12878-MboI.matrix.2000kb.cool"),
> ),
> (
> op.join(datadir, "toy.asymm.2.cool"),
> op.join(datadir, "toy.asymm.2.cool")
> )
> ],
> )
> def test_merge(path1, path2):
> with isolated_filesystem():
> > merge_coolers("test.cool", [path1, path2], mergebuf=int(15e6))
>
> tests/test_reduce.py:30:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> cooler/reduce.py:253: in merge_coolers
> create(
> cooler/create/_create.py:514: in create
> from dask.dataframe import DataFrame as dask_df
> /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:81: in <module>
> from dask.dataframe import backends, dispatch, rolling
> /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in <module>
> from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame
> /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in <module>
> from dask.dataframe import methods
> /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in <module>
> from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like
> /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in <module>
> from dask.dataframe import ( # noqa: F401 register pandas extension types
> /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in <module>
> from dask.dataframe.extensions import make_array_nonempty, make_scalar
> /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in <module>
> from dask.dataframe.accessor import (
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in <module>
> class DatetimeAccessor(Accessor):
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__
> _bind_property(cls, pd_cls, attr, min_version)
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property
> setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func)))
> /usr/lib/python3/dist-packages/dask/utils.py:858: in wrapper
> method.__doc__ = _derived_from(
> /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from
> method_args = get_named_args(method)
> /usr/lib/python3/dist-packages/dask/utils.py:572: in get_named_args
> s = inspect.signature(func)
> /usr/lib/python3.12/inspect.py:3310: in signature
> return Signature.from_callable(obj, follow_wrapped=follow_wrapped,
> /usr/lib/python3.12/inspect.py:3054: in from_callable
> return _signature_from_callable(obj, sigcls=cls,
> /usr/lib/python3.12/inspect.py:2642: in _signature_from_callable
> call = _descriptor_get(call, obj)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> descriptor = <slot wrapper '__call__' of 'type' objects>
> obj = <property object at 0xffffa8eeed90>
>
> def _descriptor_get(descriptor, obj):
> if isclass(descriptor):
> return descriptor
> get = getattr(type(descriptor), '__get__', _sentinel)
> if get is _sentinel:
> return descriptor
> > return get(descriptor, obj, type(obj))
> E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
>
> /usr/lib/python3.12/inspect.py:2467: TypeError
> _ test_merge[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.asymm.2.cool-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.asymm.2.cool] _
>
> path1 = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.asymm.2.cool'
> path2 = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.asymm.2.cool'
>
> @pytest.mark.parametrize(
> "path1,path2",
> [
> (
> op.join(datadir, "hg19.GM12878-MboI.matrix.2000kb.cool"),
> op.join(datadir, "hg19.GM12878-MboI.matrix.2000kb.cool"),
> ),
> (
> op.join(datadir, "toy.asymm.2.cool"),
> op.join(datadir, "toy.asymm.2.cool")
> )
> ],
> )
> def test_merge(path1, path2):
> with isolated_filesystem():
> > merge_coolers("test.cool", [path1, path2], mergebuf=int(15e6))
>
> tests/test_reduce.py:30:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> cooler/reduce.py:253: in merge_coolers
> create(
> cooler/create/_create.py:514: in create
> from dask.dataframe import DataFrame as dask_df
> /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:81: in <module>
> from dask.dataframe import backends, dispatch, rolling
> /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in <module>
> from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame
> /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in <module>
> from dask.dataframe import methods
> /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in <module>
> from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like
> /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in <module>
> from dask.dataframe import ( # noqa: F401 register pandas extension types
> /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in <module>
> from dask.dataframe.extensions import make_array_nonempty, make_scalar
> /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in <module>
> from dask.dataframe.accessor import (
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in <module>
> class DatetimeAccessor(Accessor):
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__
> _bind_property(cls, pd_cls, attr, min_version)
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property
> setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func)))
> /usr/lib/python3/dist-packages/dask/utils.py:858: in wrapper
> method.__doc__ = _derived_from(
> /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from
> method_args = get_named_args(method)
> /usr/lib/python3/dist-packages/dask/utils.py:572: in get_named_args
> s = inspect.signature(func)
> /usr/lib/python3.12/inspect.py:3310: in signature
> return Signature.from_callable(obj, follow_wrapped=follow_wrapped,
> /usr/lib/python3.12/inspect.py:3054: in from_callable
> return _signature_from_callable(obj, sigcls=cls,
> /usr/lib/python3.12/inspect.py:2642: in _signature_from_callable
> call = _descriptor_get(call, obj)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> descriptor = <slot wrapper '__call__' of 'type' objects>
> obj = <property object at 0xffffa8eeed90>
>
> def _descriptor_get(descriptor, obj):
> if isclass(descriptor):
> return descriptor
> get = getattr(type(descriptor), '__get__', _sentinel)
> if get is _sentinel:
> return descriptor
> > return get(descriptor, obj, type(obj))
> E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
>
> /usr/lib/python3.12/inspect.py:2467: TypeError
> _________________________________ test_merge2 __________________________________
>
> def test_merge2():
> with isolated_filesystem():
> path1 = op.join(datadir, "toy.symm.upper.2.cool")
> path2 = op.join(datadir, "toy.symm.upper.2.cool")
> > merge_coolers(
> "test.cool", [path1, path2], mergebuf=3, agg={'count': 'mean'}
> )
>
> tests/test_reduce.py:42:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> cooler/reduce.py:253: in merge_coolers
> create(
> cooler/create/_create.py:514: in create
> from dask.dataframe import DataFrame as dask_df
> /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:81: in <module>
> from dask.dataframe import backends, dispatch, rolling
> /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in <module>
> from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame
> /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in <module>
> from dask.dataframe import methods
> /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in <module>
> from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like
> /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in <module>
> from dask.dataframe import ( # noqa: F401 register pandas extension types
> /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in <module>
> from dask.dataframe.extensions import make_array_nonempty, make_scalar
> /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in <module>
> from dask.dataframe.accessor import (
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in <module>
> class DatetimeAccessor(Accessor):
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__
> _bind_property(cls, pd_cls, attr, min_version)
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property
> setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func)))
> /usr/lib/python3/dist-packages/dask/utils.py:858: in wrapper
> method.__doc__ = _derived_from(
> /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from
> method_args = get_named_args(method)
> /usr/lib/python3/dist-packages/dask/utils.py:572: in get_named_args
> s = inspect.signature(func)
> /usr/lib/python3.12/inspect.py:3310: in signature
> return Signature.from_callable(obj, follow_wrapped=follow_wrapped,
> /usr/lib/python3.12/inspect.py:3054: in from_callable
> return _signature_from_callable(obj, sigcls=cls,
> /usr/lib/python3.12/inspect.py:2642: in _signature_from_callable
> call = _descriptor_get(call, obj)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> descriptor = <slot wrapper '__call__' of 'type' objects>
> obj = <property object at 0xffffa8eeed90>
>
> def _descriptor_get(descriptor, obj):
> if isclass(descriptor):
> return descriptor
> get = getattr(type(descriptor), '__get__', _sentinel)
> if get is _sentinel:
> return descriptor
> > return get(descriptor, obj, type(obj))
> E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
>
> /usr/lib/python3.12/inspect.py:2467: TypeError
> _ test_coarsen[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.symm.upper.2.cool-2-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.symm.upper.4.cool] _
>
> input_uri = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.symm.upper.2.cool'
> factor = 2
> ref_uri = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.symm.upper.4.cool'
>
> @pytest.mark.parametrize(
> "input_uri,factor,ref_uri",
> [
> (
> op.join(datadir, "toy.symm.upper.2.cool"),
> 2,
> op.join(datadir, "toy.symm.upper.4.cool"),
> ),
> (
> op.join(datadir, "toy.asymm.2.cool"),
> 2,
> op.join(datadir, "toy.asymm.4.cool")
> ),
> (
> op.join(datadir, "toy.symm.upper.var.cool"),
> 2,
> op.join(datadir, "toy.symm.upper.var2x.cool"),
> ),
> ],
> )
> def test_coarsen(input_uri, factor, ref_uri):
>
> with isolated_filesystem():
> kwargs = dict(
> chunksize=10, nproc=1, columns=None, dtypes=None, agg=None
> )
> > coarsen_cooler(input_uri, "test.cool", factor, **kwargs)
>
> tests/test_reduce.py:109:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> cooler/reduce.py:712: in coarsen_cooler
> create(
> cooler/create/_create.py:514: in create
> from dask.dataframe import DataFrame as dask_df
> /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:81: in <module>
> from dask.dataframe import backends, dispatch, rolling
> /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in <module>
> from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame
> /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in <module>
> from dask.dataframe import methods
> /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in <module>
> from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like
> /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in <module>
> from dask.dataframe import ( # noqa: F401 register pandas extension types
> /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in <module>
> from dask.dataframe.extensions import make_array_nonempty, make_scalar
> /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in <module>
> from dask.dataframe.accessor import (
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in <module>
> class DatetimeAccessor(Accessor):
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__
> _bind_property(cls, pd_cls, attr, min_version)
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property
> setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func)))
> /usr/lib/python3/dist-packages/dask/utils.py:858: in wrapper
> method.__doc__ = _derived_from(
> /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from
> method_args = get_named_args(method)
> /usr/lib/python3/dist-packages/dask/utils.py:572: in get_named_args
> s = inspect.signature(func)
> /usr/lib/python3.12/inspect.py:3310: in signature
> return Signature.from_callable(obj, follow_wrapped=follow_wrapped,
> /usr/lib/python3.12/inspect.py:3054: in from_callable
> return _signature_from_callable(obj, sigcls=cls,
> /usr/lib/python3.12/inspect.py:2642: in _signature_from_callable
> call = _descriptor_get(call, obj)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> descriptor = <slot wrapper '__call__' of 'type' objects>
> obj = <property object at 0xffffa8eeed90>
>
> def _descriptor_get(descriptor, obj):
> if isclass(descriptor):
> return descriptor
> get = getattr(type(descriptor), '__get__', _sentinel)
> if get is _sentinel:
> return descriptor
> > return get(descriptor, obj, type(obj))
> E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
>
> /usr/lib/python3.12/inspect.py:2467: TypeError
> _ test_coarsen[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.asymm.2.cool-2-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.asymm.4.cool] _
>
> input_uri = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.asymm.2.cool'
> factor = 2
> ref_uri = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.asymm.4.cool'
>
> @pytest.mark.parametrize(
> "input_uri,factor,ref_uri",
> [
> (
> op.join(datadir, "toy.symm.upper.2.cool"),
> 2,
> op.join(datadir, "toy.symm.upper.4.cool"),
> ),
> (
> op.join(datadir, "toy.asymm.2.cool"),
> 2,
> op.join(datadir, "toy.asymm.4.cool")
> ),
> (
> op.join(datadir, "toy.symm.upper.var.cool"),
> 2,
> op.join(datadir, "toy.symm.upper.var2x.cool"),
> ),
> ],
> )
> def test_coarsen(input_uri, factor, ref_uri):
>
> with isolated_filesystem():
> kwargs = dict(
> chunksize=10, nproc=1, columns=None, dtypes=None, agg=None
> )
> > coarsen_cooler(input_uri, "test.cool", factor, **kwargs)
>
> tests/test_reduce.py:109:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> cooler/reduce.py:712: in coarsen_cooler
> create(
> cooler/create/_create.py:514: in create
> from dask.dataframe import DataFrame as dask_df
> /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:81: in <module>
> from dask.dataframe import backends, dispatch, rolling
> /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in <module>
> from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame
> /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in <module>
> from dask.dataframe import methods
> /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in <module>
> from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like
> /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in <module>
> from dask.dataframe import ( # noqa: F401 register pandas extension types
> /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in <module>
> from dask.dataframe.extensions import make_array_nonempty, make_scalar
> /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in <module>
> from dask.dataframe.accessor import (
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in <module>
> class DatetimeAccessor(Accessor):
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__
> _bind_property(cls, pd_cls, attr, min_version)
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property
> setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func)))
> /usr/lib/python3/dist-packages/dask/utils.py:858: in wrapper
> method.__doc__ = _derived_from(
> /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from
> method_args = get_named_args(method)
> /usr/lib/python3/dist-packages/dask/utils.py:572: in get_named_args
> s = inspect.signature(func)
> /usr/lib/python3.12/inspect.py:3310: in signature
> return Signature.from_callable(obj, follow_wrapped=follow_wrapped,
> /usr/lib/python3.12/inspect.py:3054: in from_callable
> return _signature_from_callable(obj, sigcls=cls,
> /usr/lib/python3.12/inspect.py:2642: in _signature_from_callable
> call = _descriptor_get(call, obj)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> descriptor = <slot wrapper '__call__' of 'type' objects>
> obj = <property object at 0xffffa8eeed90>
>
> def _descriptor_get(descriptor, obj):
> if isclass(descriptor):
> return descriptor
> get = getattr(type(descriptor), '__get__', _sentinel)
> if get is _sentinel:
> return descriptor
> > return get(descriptor, obj, type(obj))
> E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
>
> /usr/lib/python3.12/inspect.py:2467: TypeError
> _ test_coarsen[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.symm.upper.var.cool-2-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.symm.upper.var2x.cool] _
>
> input_uri = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.symm.upper.var.cool'
> factor = 2
> ref_uri = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.symm.upper.var2x.cool'
>
> @pytest.mark.parametrize(
> "input_uri,factor,ref_uri",
> [
> (
> op.join(datadir, "toy.symm.upper.2.cool"),
> 2,
> op.join(datadir, "toy.symm.upper.4.cool"),
> ),
> (
> op.join(datadir, "toy.asymm.2.cool"),
> 2,
> op.join(datadir, "toy.asymm.4.cool")
> ),
> (
> op.join(datadir, "toy.symm.upper.var.cool"),
> 2,
> op.join(datadir, "toy.symm.upper.var2x.cool"),
> ),
> ],
> )
> def test_coarsen(input_uri, factor, ref_uri):
>
> with isolated_filesystem():
> kwargs = dict(
> chunksize=10, nproc=1, columns=None, dtypes=None, agg=None
> )
> > coarsen_cooler(input_uri, "test.cool", factor, **kwargs)
>
> tests/test_reduce.py:109:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> cooler/reduce.py:712: in coarsen_cooler
> create(
> cooler/create/_create.py:514: in create
> from dask.dataframe import DataFrame as dask_df
> /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:81: in <module>
> from dask.dataframe import backends, dispatch, rolling
> /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in <module>
> from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame
> /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in <module>
> from dask.dataframe import methods
> /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in <module>
> from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like
> /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in <module>
> from dask.dataframe import ( # noqa: F401 register pandas extension types
> /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in <module>
> from dask.dataframe.extensions import make_array_nonempty, make_scalar
> /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in <module>
> from dask.dataframe.accessor import (
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in <module>
> class DatetimeAccessor(Accessor):
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__
> _bind_property(cls, pd_cls, attr, min_version)
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property
> setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func)))
> /usr/lib/python3/dist-packages/dask/utils.py:858: in wrapper
> method.__doc__ = _derived_from(
> /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from
> method_args = get_named_args(method)
> /usr/lib/python3/dist-packages/dask/utils.py:572: in get_named_args
> s = inspect.signature(func)
> /usr/lib/python3.12/inspect.py:3310: in signature
> return Signature.from_callable(obj, follow_wrapped=follow_wrapped,
> /usr/lib/python3.12/inspect.py:3054: in from_callable
> return _signature_from_callable(obj, sigcls=cls,
> /usr/lib/python3.12/inspect.py:2642: in _signature_from_callable
> call = _descriptor_get(call, obj)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> descriptor = <slot wrapper '__call__' of 'type' objects>
> obj = <property object at 0xffffa8eeed90>
>
> def _descriptor_get(descriptor, obj):
> if isclass(descriptor):
> return descriptor
> get = getattr(type(descriptor), '__get__', _sentinel)
> if get is _sentinel:
> return descriptor
> > return get(descriptor, obj, type(obj))
> E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
>
> /usr/lib/python3.12/inspect.py:2467: TypeError
> ______________________ test_coarsen_partitions_correctly _______________________
>
> def test_coarsen_partitions_correctly():
> kwargs = dict(nproc=1, columns=None, dtypes=None, agg=None)
> with isolated_filesystem():
> f_ref = op.join(datadir, "odd.4.cool")
> f_in = op.join(datadir, "odd.1.cool")
> > coarsen_cooler(f_in, "odd.1.coarsen_4.cool", factor=4, chunksize=2, **kwargs)
>
> tests/test_reduce.py:145:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> cooler/reduce.py:712: in coarsen_cooler
> create(
> cooler/create/_create.py:514: in create
> from dask.dataframe import DataFrame as dask_df
> /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:81: in <module>
> from dask.dataframe import backends, dispatch, rolling
> /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in <module>
> from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame
> /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in <module>
> from dask.dataframe import methods
> /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in <module>
> from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like
> /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in <module>
> from dask.dataframe import ( # noqa: F401 register pandas extension types
> /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in <module>
> from dask.dataframe.extensions import make_array_nonempty, make_scalar
> /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in <module>
> from dask.dataframe.accessor import (
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in <module>
> class DatetimeAccessor(Accessor):
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__
> _bind_property(cls, pd_cls, attr, min_version)
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property
> setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func)))
> /usr/lib/python3/dist-packages/dask/utils.py:858: in wrapper
> method.__doc__ = _derived_from(
> /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from
> method_args = get_named_args(method)
> /usr/lib/python3/dist-packages/dask/utils.py:572: in get_named_args
> s = inspect.signature(func)
> /usr/lib/python3.12/inspect.py:3310: in signature
> return Signature.from_callable(obj, follow_wrapped=follow_wrapped,
> /usr/lib/python3.12/inspect.py:3054: in from_callable
> return _signature_from_callable(obj, sigcls=cls,
> /usr/lib/python3.12/inspect.py:2642: in _signature_from_callable
> call = _descriptor_get(call, obj)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> descriptor = <slot wrapper '__call__' of 'type' objects>
> obj = <property object at 0xffffa8eeed90>
>
> def _descriptor_get(descriptor, obj):
> if isclass(descriptor):
> return descriptor
> get = getattr(type(descriptor), '__get__', _sentinel)
> if get is _sentinel:
> return descriptor
> > return get(descriptor, obj, type(obj))
> E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
>
> /usr/lib/python3.12/inspect.py:2467: TypeError
> _________________________________ test_zoomify _________________________________
>
> def test_zoomify():
> kwargs = dict(chunksize=10, nproc=1, columns=None, dtypes=None, agg=None)
> with isolated_filesystem():
> > zoomify_cooler(
> op.join(datadir, "toy.asymm.2.cool"),
> "test.2.mcool",
> resolutions=[4, 8, 16, 32],
> **kwargs
> )
>
> tests/test_reduce.py:156:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> cooler/reduce.py:832: in zoomify_cooler
> coarsen_cooler(
> cooler/reduce.py:712: in coarsen_cooler
> create(
> cooler/create/_create.py:514: in create
> from dask.dataframe import DataFrame as dask_df
> /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:81: in <module>
> from dask.dataframe import backends, dispatch, rolling
> /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in <module>
> from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame
> /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in <module>
> from dask.dataframe import methods
> /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in <module>
> from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like
> /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in <module>
> from dask.dataframe import ( # noqa: F401 register pandas extension types
> /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in <module>
> from dask.dataframe.extensions import make_array_nonempty, make_scalar
> /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in <module>
> from dask.dataframe.accessor import (
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in <module>
> class DatetimeAccessor(Accessor):
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__
> _bind_property(cls, pd_cls, attr, min_version)
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property
> setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func)))
> /usr/lib/python3/dist-packages/dask/utils.py:858: in wrapper
> method.__doc__ = _derived_from(
> /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from
> method_args = get_named_args(method)
> /usr/lib/python3/dist-packages/dask/utils.py:572: in get_named_args
> s = inspect.signature(func)
> /usr/lib/python3.12/inspect.py:3310: in signature
> return Signature.from_callable(obj, follow_wrapped=follow_wrapped,
> /usr/lib/python3.12/inspect.py:3054: in from_callable
> return _signature_from_callable(obj, sigcls=cls,
> /usr/lib/python3.12/inspect.py:2642: in _signature_from_callable
> call = _descriptor_get(call, obj)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> descriptor = <slot wrapper '__call__' of 'type' objects>
> obj = <property object at 0xffffa8eeed90>
>
> def _descriptor_get(descriptor, obj):
> if isclass(descriptor):
> return descriptor
> get = getattr(type(descriptor), '__get__', _sentinel)
> if get is _sentinel:
> return descriptor
> > return get(descriptor, obj, type(obj))
> E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
>
> /usr/lib/python3.12/inspect.py:2467: TypeError
> _____________________________ test_legacy_zoomify ______________________________
>
> def test_legacy_zoomify():
> infile = op.join(datadir, "hg19.GM12878-MboI.matrix.2000kb.cool")
> chunksize = int(10e6)
> # n_zooms = 2
> n_cpus = 1
> with isolated_filesystem():
> > legacy_zoomify(infile, "test.multires.cool", n_cpus, chunksize)
>
> tests/test_reduce.py:197:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> cooler/reduce.py:900: in legacy_zoomify
> coarsen_cooler(
> cooler/reduce.py:712: in coarsen_cooler
> create(
> cooler/create/_create.py:514: in create
> from dask.dataframe import DataFrame as dask_df
> /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:81: in <module>
> from dask.dataframe import backends, dispatch, rolling
> /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in <module>
> from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame
> /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in <module>
> from dask.dataframe import methods
> /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in <module>
> from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like
> /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in <module>
> from dask.dataframe import ( # noqa: F401 register pandas extension types
> /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in <module>
> from dask.dataframe.extensions import make_array_nonempty, make_scalar
> /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in <module>
> from dask.dataframe.accessor import (
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in <module>
> class DatetimeAccessor(Accessor):
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__
> _bind_property(cls, pd_cls, attr, min_version)
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property
> setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func)))
> /usr/lib/python3/dist-packages/dask/utils.py:858: in wrapper
> method.__doc__ = _derived_from(
> /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from
> method_args = get_named_args(method)
> /usr/lib/python3/dist-packages/dask/utils.py:572: in get_named_args
> s = inspect.signature(func)
> /usr/lib/python3.12/inspect.py:3310: in signature
> return Signature.from_callable(obj, follow_wrapped=follow_wrapped,
> /usr/lib/python3.12/inspect.py:3054: in from_callable
> return _signature_from_callable(obj, sigcls=cls,
> /usr/lib/python3.12/inspect.py:2642: in _signature_from_callable
> call = _descriptor_get(call, obj)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> descriptor = <slot wrapper '__call__' of 'type' objects>
> obj = <property object at 0xffffa8eeed90>
>
> def _descriptor_get(descriptor, obj):
> if isclass(descriptor):
> return descriptor
> get = getattr(type(descriptor), '__get__', _sentinel)
> if get is _sentinel:
> return descriptor
> > return get(descriptor, obj, type(obj))
> E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
>
> /usr/lib/python3.12/inspect.py:2467: TypeError
> _______________________________ test_append_mode _______________________________
>
> def test_append_mode():
> # merge
> path1 = path2 = op.join(datadir, "toy.asymm.2.cool")
> out_path = "test.cool"
> for append in (True, False):
> with isolated_filesystem():
> with h5py.File("test.cool", "w") as f:
> f.attrs["xxxx"] = True
> > merge_coolers(
> out_path,
> [path1, path2],
> mergebuf=int(15e6),
> mode="a" if append else "w"
> )
>
> tests/test_reduce.py:208:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> cooler/reduce.py:253: in merge_coolers
> create(
> cooler/create/_create.py:514: in create
> from dask.dataframe import DataFrame as dask_df
> /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:81: in <module>
> from dask.dataframe import backends, dispatch, rolling
> /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in <module>
> from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame
> /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in <module>
> from dask.dataframe import methods
> /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in <module>
> from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like
> /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in <module>
> from dask.dataframe import ( # noqa: F401 register pandas extension types
> /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in <module>
> from dask.dataframe.extensions import make_array_nonempty, make_scalar
> /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in <module>
> from dask.dataframe.accessor import (
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in <module>
> class DatetimeAccessor(Accessor):
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__
> _bind_property(cls, pd_cls, attr, min_version)
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property
> setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func)))
> /usr/lib/python3/dist-packages/dask/utils.py:858: in wrapper
> method.__doc__ = _derived_from(
> /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from
> method_args = get_named_args(method)
> /usr/lib/python3/dist-packages/dask/utils.py:572: in get_named_args
> s = inspect.signature(func)
> /usr/lib/python3.12/inspect.py:3310: in signature
> return Signature.from_callable(obj, follow_wrapped=follow_wrapped,
> /usr/lib/python3.12/inspect.py:3054: in from_callable
> return _signature_from_callable(obj, sigcls=cls,
> /usr/lib/python3.12/inspect.py:2642: in _signature_from_callable
> call = _descriptor_get(call, obj)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> descriptor = <slot wrapper '__call__' of 'type' objects>
> obj = <property object at 0xffffa8eeed90>
>
> def _descriptor_get(descriptor, obj):
> if isclass(descriptor):
> return descriptor
> get = getattr(type(descriptor), '__get__', _sentinel)
> if get is _sentinel:
> return descriptor
> > return get(descriptor, obj, type(obj))
> E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
>
> /usr/lib/python3.12/inspect.py:2467: TypeError
> =============================== warnings summary ===============================
> tests/test_api.py::test_bintable_many_contigs
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/test_api.py:44: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
> assert pd.api.types.is_categorical_dtype(bins["chrom"].dtype)
>
> tests/test_api.py::test_bintable_many_contigs
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/test_api.py:47: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
> assert pd.api.types.is_categorical_dtype(bins["chrom"].dtype)
>
> tests/test_api.py::test_bintable_many_contigs
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/test_api.py:51: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
> assert pd.api.types.is_categorical_dtype(chroms.dtype)
>
> tests/test_balance.py::test_balancing_other_options[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.symm.upper.2.cool-0.01]
> tests/test_cli_ops.py::test_zoomify
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/cooler/balance.py:112: RuntimeWarning: Mean of empty slice.
> scale = nzmarg.mean()
>
> tests/test_balance.py::test_balancing_other_options[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.symm.upper.2.cool-0.01]
> tests/test_cli_ops.py::test_zoomify
> /usr/lib/python3/dist-packages/numpy/core/_methods.py:129: RuntimeWarning: invalid value encountered in scalar divide
> ret = ret.dtype.type(ret / rcount)
>
> tests/test_cli.py::test_makebins
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/cooler/cli/makebins.py:55: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
> bins["id"] = bins.groupby("chrom").cumcount()
>
> tests/test_cli_ingest.py: 11 warnings
> tests/test_cli_ops.py: 2 warnings
> tests/test_create_ingest.py: 13 warnings
> tests/test_create_sanitize.py: 18 warnings
> tests/test_reduce.py: 6 warnings
> tests/test_util.py: 2 warnings
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/cooler/util.py:730: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
> is_cat = pd.api.types.is_categorical_dtype(bins["chrom"])
>
> tests/test_cli_ingest.py: 11 warnings
> tests/test_cli_ops.py: 2 warnings
> tests/test_create_ingest.py: 13 warnings
> tests/test_create_sanitize.py: 18 warnings
> tests/test_reduce.py: 6 warnings
> tests/test_util.py: 1 warning
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/cooler/util.py:771: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
> self._bins_grouped = bins.groupby("chrom", sort=False)
>
> tests/test_cli_ingest.py: 11 warnings
> tests/test_cli_ops.py: 2 warnings
> tests/test_create_ingest.py: 13 warnings
> tests/test_create_sanitize.py: 18 warnings
> tests/test_reduce.py: 6 warnings
> tests/test_util.py: 2 warnings
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/cooler/util.py:395: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
> for _chrom, group in bins.groupby("chrom"):
>
> tests/test_cli_ingest.py: 11 warnings
> tests/test_create_ingest.py: 8 warnings
> tests/test_create_sanitize.py: 9 warnings
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/cooler/create/_ingest.py:133: FutureWarning: Series.__getitem__ treating keys as positions is deprecated. In a future version, integer keys will always be treated as labels (consistent with DataFrame behavior). To access a value by position, use `ser.iloc[pos]`
> chromsizes1 = gs.chromsizes[chrom1_ids].values
>
> tests/test_cli_ingest.py: 11 warnings
> tests/test_create_ingest.py: 8 warnings
> tests/test_create_sanitize.py: 9 warnings
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/cooler/create/_ingest.py:134: FutureWarning: Series.__getitem__ treating keys as positions is deprecated. In a future version, integer keys will always be treated as labels (consistent with DataFrame behavior). To access a value by position, use `ser.iloc[pos]`
> chromsizes2 = gs.chromsizes[chrom2_ids].values
>
> tests/test_cli_ops.py::test_coarsen
> tests/test_cli_ops.py::test_zoomify
> tests/test_reduce.py::test_coarsen[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.symm.upper.2.cool-2-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.symm.upper.4.cool]
> tests/test_reduce.py::test_coarsen[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.asymm.2.cool-2-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.asymm.4.cool]
> tests/test_reduce.py::test_coarsen[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.symm.upper.var.cool-2-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.symm.upper.var2x.cool]
> tests/test_reduce.py::test_coarsen_partitions_correctly
> tests/test_reduce.py::test_zoomify
> tests/test_reduce.py::test_legacy_zoomify
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/cooler/reduce.py:548: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
> return old_bins.groupby("chrom").apply(_each).reset_index(drop=True)
>
> tests/test_cli_ops.py::test_zoomify
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/cooler/cli/zoomify.py:198: UserWarning: Map is already < 256 x 256. Provide resolutions explicitly if you want to coarsen more.
> warnings.warn(
>
> tests/test_cli_ops.py::test_zoomify
> tests/test_cli_ops.py::test_zoomify
> tests/test_reduce.py::test_zoomify
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/cooler/reduce.py:792: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
> n_bins_longest_chrom[base_binsize] = clr.bins()[:].groupby("chrom").size().max()
>
> tests/test_cli_ops.py::test_balance
> tests/test_cli_ops.py::test_balance
> tests/test_cli_ops.py::test_balance
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/cooler/balance.py:108: ConvergenceWarning: Iteration limit reached without convergence.
> warnings.warn(
>
> tests/test_cli_ops.py::test_balance
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/cooler/cli/balance.py:183: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
> bins_grouped = clr.bins()[:].groupby('chrom')
>
> tests/test_core.py::test_put
> tests/test_core.py::test_put
> tests/test_core.py::test_put
> tests/test_core.py::test_put
> tests/test_core.py::test_put
> tests/test_core.py::test_put
> tests/test_create.py::test_write
> tests/test_create.py::test_write
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/cooler/core/_tableops.py:120: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
> elif is_categorical_dtype(data):
>
> tests/test_core.py::test_put
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/test_core.py:94: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
> assert pd.api.types.is_categorical_dtype(out['chrom_enum'].dtype)
>
> tests/test_core.py::test_put
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/test_core.py:104: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
> assert not pd.api.types.is_categorical_dtype(out['chrom_string'].dtype)
>
> tests/test_create.py::test_rename_chroms
> tests/test_create.py::test_many_contigs
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/cooler/create/_create.py:349: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
> if is_categorical_dtype(bins["chrom"]):
>
> tests/test_reduce.py::test_merge[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool]
> tests/test_reduce.py::test_merge[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.asymm.2.cool-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.asymm.2.cool]
> tests/test_reduce.py::test_merge2
> tests/test_reduce.py::test_append_mode
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/cooler/reduce.py:247: DeprecationWarning: np.find_common_type is deprecated. Please use `np.result_type` or `np.promote_types`.
> See https://numpy.org/devdocs/release/1.25.0-notes.html and the docs for more information. (Deprecated NumPy 1.25)
> dtypes[col] = np.find_common_type(dtype_map[col], [])
>
> tests/test_util.py::test_bedslice
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/test_util.py:234: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
> grouped = bins.groupby('chrom')
>
> tests/test_util.py::test_check_bins
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/test_util.py:312: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
> assert pd.api.types.is_categorical_dtype(bins["chrom"])
>
> -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
> =========================== short test summary info ============================
> FAILED tests/test_cli_export.py::test_dump - TypeError: descriptor '__call__'...
> FAILED tests/test_cli_ingest.py::test_cload_symm_asymm[symm.upper-extra_args0]
> FAILED tests/test_cli_ingest.py::test_cload_symm_asymm[symm.upper-extra_args1]
> FAILED tests/test_cli_ingest.py::test_cload_symm_asymm[asymm-extra_args2] - a...
> FAILED tests/test_cli_ingest.py::test_cload_mergepass[symm.upper-extra_args0]
> FAILED tests/test_cli_ingest.py::test_cload_field - assert 1 == 0
> FAILED tests/test_cli_ingest.py::test_cload_other_options - assert 1 == 0
> FAILED tests/test_cli_ingest.py::test_load_symm_asymm[symm.upper-extra_args0]
> FAILED tests/test_cli_ingest.py::test_load_symm_asymm[symm.upper-extra_args1]
> FAILED tests/test_cli_ingest.py::test_load_symm_asymm[asymm-extra_args2] - as...
> FAILED tests/test_cli_ingest.py::test_load_field - assert 1 == 0
> FAILED tests/test_cli_ingest.py::test_load_field2 - assert 1 == 0
> FAILED tests/test_cli_ops.py::test_merge - assert 1 == 0
> FAILED tests/test_cli_ops.py::test_coarsen - assert 1 == 0
> FAILED tests/test_cli_ops.py::test_zoomify - assert 1 == 0
> FAILED tests/test_create.py::test_create_append[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool]
> FAILED tests/test_create.py::test_create_custom_cols - TypeError: descriptor ...
> FAILED tests/test_create.py::test_create_cooler - TypeError: descriptor '__ca...
> FAILED tests/test_create.py::test_create_cooler_from_dask - TypeError: descri...
> FAILED tests/test_create.py::test_create_scool[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool]
> FAILED tests/test_create_ingest.py::test_from_hdf5_pairs - TypeError: descrip...
> FAILED tests/test_create_ingest.py::test_cload_tabix[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/hg19.bins.2000kb.bed.gz-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/hg19.GM12878-MboI.pairs.subsample.sorted.txt.gz-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool]
> FAILED tests/test_create_ingest.py::test_cload_pairix[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/hg19.bins.2000kb.bed.gz-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/hg19.GM12878-MboI.pairs.subsample.blksrt.txt.gz-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool]
> FAILED tests/test_create_ingest.py::test_cload_pairs[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.bins.var.bed-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.pairs-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.symm.upper.var.cool]
> FAILED tests/test_create_ingest.py::test_cload_pairs[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.bins.var.bed-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy_hash.pairs-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.symm.upper.var.cool]
> FAILED tests/test_create_ingest.py::test_cload_pairs[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.bins.var.bed-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy_hash.pairs.gz-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.symm.upper.var.cool]
> FAILED tests/test_create_ingest.py::test_cload_field[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.chrom.sizes:2-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.pairs]
> FAILED tests/test_create_ingest.py::test_cload_custom_tempdir[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.chrom.sizes:2-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.pairs]
> FAILED tests/test_create_ingest.py::test_load_bg2_vs_coo - TypeError: descrip...
> FAILED tests/test_create_ingest.py::test_load_zero_one_based_bg2 - TypeError:...
> FAILED tests/test_create_ingest.py::test_load_zero_one_based_coo - TypeError:...
> FAILED tests/test_create_ingest.py::test_cload_append_mode - TypeError: descr...
> FAILED tests/test_create_ingest.py::test_load_append_mode - TypeError: descri...
> FAILED tests/test_create_ingest.py::test_load_custom_tempdir - TypeError: des...
> FAILED tests/test_reduce.py::test_merge[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool]
> FAILED tests/test_reduce.py::test_merge[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.asymm.2.cool-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.asymm.2.cool]
> FAILED tests/test_reduce.py::test_merge2 - TypeError: descriptor '__call__' f...
> FAILED tests/test_reduce.py::test_coarsen[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.symm.upper.2.cool-2-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.symm.upper.4.cool]
> FAILED tests/test_reduce.py::test_coarsen[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.asymm.2.cool-2-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.asymm.4.cool]
> FAILED tests/test_reduce.py::test_coarsen[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.symm.upper.var.cool-2-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.symm.upper.var2x.cool]
> FAILED tests/test_reduce.py::test_coarsen_partitions_correctly - TypeError: d...
> FAILED tests/test_reduce.py::test_zoomify - TypeError: descriptor '__call__' ...
> FAILED tests/test_reduce.py::test_legacy_zoomify - TypeError: descriptor '__c...
> FAILED tests/test_reduce.py::test_append_mode - TypeError: descriptor '__call...
> =========== 44 failed, 86 passed, 6 skipped, 253 warnings in 19.76s ============
> E: pybuild pybuild:389: test: plugin pyproject failed with: exit code=1: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cooler/build; python3.12 -m pytest tests
> I: pybuild base:311: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build; python3.11 -m pytest tests
> ============================= test session starts ==============================
> platform linux -- Python 3.11.9, pytest-8.1.1, pluggy-1.4.0
> rootdir: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build
> configfile: pyproject.toml
> collected 136 items
>
> tests/test_api.py .......... [ 7%]
> tests/test_balance.py .... [ 10%]
> tests/test_cli.py .s..s..... [ 17%]
> tests/test_cli_export.py .Fs [ 19%]
> tests/test_cli_fileops.py .... [ 22%]
> tests/test_cli_ingest.py FFFFException ignored in: <function _TemporaryFileCloser.__del__ at 0xffffb8971440>
> Traceback (most recent call last):
> File "/usr/lib/python3.11/tempfile.py", line 606, in __del__
> self.close()
> File "/usr/lib/python3.11/tempfile.py", line 602, in close
> unlink(self.name)
> FileNotFoundError: [Errno 2] No such file or directory: '/tmp/tmpiskg6ace/tmpks7k1q8c.multi.cool'
> FFFFFFF [ 30%]
> tests/test_cli_ops.py FFF. [ 33%]
> tests/test_core.py ........... [ 41%]
> tests/test_create.py Exception ignored in: <function _TemporaryFileCloser.__del__ at 0xffffb8971440>
> Traceback (most recent call last):
> File "/usr/lib/python3.11/tempfile.py", line 606, in __del__
> self.close()
> File "/usr/lib/python3.11/tempfile.py", line 602, in close
> unlink(self.name)
> FileNotFoundError: [Errno 2] No such file or directory: '/tmp/tmpo52wzfwe/tmps6xvgd0f.multi.cool'
> Fs.F..FFF [ 48%]
> tests/test_create_ingest.py FFFFFFFFFFF.FFF [ 59%]
> tests/test_create_sanitize.py ........ [ 65%]
> tests/test_fileops.py ........s.. [ 73%]
> tests/test_parallel.py ... [ 75%]
> tests/test_reduce.py FFFFFFFFFF [ 83%]
> tests/test_util.py .........s............. [100%]
>
> =================================== FAILURES ===================================
> __________________________________ test_dump ___________________________________
>
> def test_dump():
> runner = CliRunner()
> with runner.isolated_filesystem():
> f_in = op.join(datadir, "toy.symm.upper.2.cool")
> result = runner.invoke(dump, [f_in])
> assert result.exit_code == 0
> result = runner.invoke(dump, [f_in, "-t", "chroms", "--columns", "length"])
> assert result.exit_code == 0
> result = runner.invoke(dump, [f_in, "-t", "bins", "--columns", "chrom,start"])
> assert result.exit_code == 0
> result = runner.invoke(dump, [f_in, "-r", "chr1"])
> assert result.exit_code == 0
> result = runner.invoke(dump, [f_in, "-r", "chr1:0-16", "-r2", "chr1:10-25"])
> assert result.exit_code == 0
> result = runner.invoke(dump, [f_in, "-r", "chr1:10-25", "-r2", "chr1:0-5"])
> assert result.exit_code == 0
> result = runner.invoke(dump, [f_in, "--join"])
> assert result.exit_code == 0
> result = runner.invoke(dump, [f_in, "--join", "--one-based-ids"])
> assert result.exit_code == 0
> result = runner.invoke(dump, [f_in, "--join", "--one-based-starts"])
> assert result.exit_code == 0
> result = runner.invoke(dump, [f_in, "--annotate", "chrom", "--one-based-starts"])
> assert result.exit_code == 0
>
> # unbalanced file
> result = runner.invoke(dump, [f_in, "-b"])
> assert result.exit_code == 1
>
> # roundtrip symm-upper data
> result = runner.invoke(dump, [f_in, "-H", "-t", "bins"])
> bins = pd.read_csv(StringIO(result.output), sep="\t")
> result = runner.invoke(dump, [f_in, "-H"])
> pixels = pd.read_csv(StringIO(result.output), sep="\t")
> > cooler.create_cooler("out.cool", bins, pixels, symmetric_upper=True)
>
> tests/test_cli_export.py:74:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> cooler/create/_create.py:1024: in create_cooler
> create(
> cooler/create/_create.py:514: in create
> from dask.dataframe import DataFrame as dask_df
> /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:81: in <module>
> from dask.dataframe import backends, dispatch, rolling
> /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in <module>
> from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame
> /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in <module>
> from dask.dataframe import methods
> /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in <module>
> from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like
> /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in <module>
> from dask.dataframe import ( # noqa: F401 register pandas extension types
> /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in <module>
> from dask.dataframe.extensions import make_array_nonempty, make_scalar
> /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in <module>
> from dask.dataframe.accessor import (
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in <module>
> class DatetimeAccessor(Accessor):
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__
> _bind_property(cls, pd_cls, attr, min_version)
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property
> setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func)))
> /usr/lib/python3/dist-packages/dask/utils.py:858: in wrapper
> method.__doc__ = _derived_from(
> /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from
> method_args = get_named_args(method)
> /usr/lib/python3/dist-packages/dask/utils.py:572: in get_named_args
> s = inspect.signature(func)
> /usr/lib/python3.11/inspect.py:3263: in signature
> return Signature.from_callable(obj, follow_wrapped=follow_wrapped,
> /usr/lib/python3.11/inspect.py:3011: in from_callable
> return _signature_from_callable(obj, sigcls=cls,
> /usr/lib/python3.11/inspect.py:2599: in _signature_from_callable
> call = _descriptor_get(call, obj)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> descriptor = <slot wrapper '__call__' of 'type' objects>
> obj = <property object at 0xffffb19c2200>
>
> def _descriptor_get(descriptor, obj):
> if isclass(descriptor):
> return descriptor
> get = getattr(type(descriptor), '__get__', _sentinel)
> if get is _sentinel:
> return descriptor
> > return get(descriptor, obj, type(obj))
> E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
>
> /usr/lib/python3.11/inspect.py:2432: TypeError
> ________________ test_cload_symm_asymm[symm.upper-extra_args0] _________________
>
> ref = 'symm.upper', extra_args = []
>
> @pytest.mark.parametrize(
> "ref,extra_args",
> [
> ("symm.upper", []), # reflect triu pairs
> ("symm.upper", ["--input-copy-status", "unique"]), # reflect triu pairs
> ("asymm", ["--no-symmetric-upper"]),
> ],
> )
> def test_cload_symm_asymm(ref, extra_args):
> runner = CliRunner()
> with runner.isolated_filesystem():
> result = _run_cload_pairs(runner, 2, extra_args)
> > assert result.exit_code == 0
> E assert 1 == 0
> E + where 1 = <Result TypeError("descriptor '__call__' for 'type' objects doesn't apply to a 'property' object")>.exit_code
>
> tests/test_cli_ingest.py:72: AssertionError
> ________________ test_cload_symm_asymm[symm.upper-extra_args1] _________________
>
> ref = 'symm.upper', extra_args = ['--input-copy-status', 'unique']
>
> @pytest.mark.parametrize(
> "ref,extra_args",
> [
> ("symm.upper", []), # reflect triu pairs
> ("symm.upper", ["--input-copy-status", "unique"]), # reflect triu pairs
> ("asymm", ["--no-symmetric-upper"]),
> ],
> )
> def test_cload_symm_asymm(ref, extra_args):
> runner = CliRunner()
> with runner.isolated_filesystem():
> result = _run_cload_pairs(runner, 2, extra_args)
> > assert result.exit_code == 0
> E assert 1 == 0
> E + where 1 = <Result TypeError("descriptor '__call__' for 'type' objects doesn't apply to a 'property' object")>.exit_code
>
> tests/test_cli_ingest.py:72: AssertionError
> ___________________ test_cload_symm_asymm[asymm-extra_args2] ___________________
>
> ref = 'asymm', extra_args = ['--no-symmetric-upper']
>
> @pytest.mark.parametrize(
> "ref,extra_args",
> [
> ("symm.upper", []), # reflect triu pairs
> ("symm.upper", ["--input-copy-status", "unique"]), # reflect triu pairs
> ("asymm", ["--no-symmetric-upper"]),
> ],
> )
> def test_cload_symm_asymm(ref, extra_args):
> runner = CliRunner()
> with runner.isolated_filesystem():
> result = _run_cload_pairs(runner, 2, extra_args)
> > assert result.exit_code == 0
> E assert 1 == 0
> E + where 1 = <Result TypeError("descriptor '__call__' for 'type' objects doesn't apply to a 'property' object")>.exit_code
>
> tests/test_cli_ingest.py:72: AssertionError
> _________________ test_cload_mergepass[symm.upper-extra_args0] _________________
>
> ref = 'symm.upper', extra_args = ['--temp-dir', '.', '--no-delete-temp']
>
> @pytest.mark.parametrize(
> "ref,extra_args", [("symm.upper", ["--temp-dir", ".", "--no-delete-temp"])]
> )
> def test_cload_mergepass(ref, extra_args):
> runner = CliRunner()
> with runner.isolated_filesystem():
> result = _run_cload_pairs(runner, 2, extra_args)
> > assert result.exit_code == 0
> E assert 1 == 0
> E + where 1 = <Result TypeError("descriptor '__call__' for 'type' objects doesn't apply to a 'property' object")>.exit_code
>
> tests/test_cli_ingest.py:86: AssertionError
> _______________________________ test_cload_field _______________________________
>
> def test_cload_field():
> runner = CliRunner()
> with runner.isolated_filesystem():
> extra_args = ["--field", "score=8"]
> result = _run_cload_pairs(runner, 2, extra_args)
> > assert result.exit_code == 0
> E assert 1 == 0
> E + where 1 = <Result TypeError("descriptor '__call__' for 'type' objects doesn't apply to a 'property' object")>.exit_code
>
> tests/test_cli_ingest.py:98: AssertionError
> ___________________________ test_cload_other_options ___________________________
>
> def test_cload_other_options():
> runner = CliRunner()
> with runner.isolated_filesystem():
> meta = {"foo": "bar", "number": 42}
> with open("meta.json", "w") as f:
> json.dump(meta, f)
> extra_args = [
> "--metadata",
> "meta.json",
> "--zero-based",
> "--storage-options",
> "shuffle=True,fletcher32=True,compression=lzf",
> ]
> result = _run_cload_pairs(runner, 2, extra_args)
> > assert result.exit_code == 0
> E assert 1 == 0
> E + where 1 = <Result TypeError("descriptor '__call__' for 'type' objects doesn't apply to a 'property' object")>.exit_code
>
> tests/test_cli_ingest.py:161: AssertionError
> _________________ test_load_symm_asymm[symm.upper-extra_args0] _________________
>
> ref = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.symm.upper.2.bg2'
> extra_args = []
>
> @pytest.mark.parametrize(
> "ref,extra_args",
> [
> ("symm.upper", []), # reflect tril pairs
> ("symm.upper", ["--one-based", "--input-copy-status", "unique"]), # reflect tril pairs
> ("asymm", ["--one-based", "--no-symmetric-upper"]),
> ],
> )
> def test_load_symm_asymm(ref, extra_args):
> runner = CliRunner()
> with runner.isolated_filesystem():
> ref = op.join(datadir, f"toy.{ref}.2.bg2")
> result = _run_load(runner, ref, "bg2", 2, extra_args)
> > assert result.exit_code == 0
> E assert 1 == 0
> E + where 1 = <Result TypeError("descriptor '__call__' for 'type' objects doesn't apply to a 'property' object")>.exit_code
>
> tests/test_cli_ingest.py:201: AssertionError
> _________________ test_load_symm_asymm[symm.upper-extra_args1] _________________
>
> ref = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.symm.upper.2.bg2'
> extra_args = ['--one-based', '--input-copy-status', 'unique']
>
> @pytest.mark.parametrize(
> "ref,extra_args",
> [
> ("symm.upper", []), # reflect tril pairs
> ("symm.upper", ["--one-based", "--input-copy-status", "unique"]), # reflect tril pairs
> ("asymm", ["--one-based", "--no-symmetric-upper"]),
> ],
> )
> def test_load_symm_asymm(ref, extra_args):
> runner = CliRunner()
> with runner.isolated_filesystem():
> ref = op.join(datadir, f"toy.{ref}.2.bg2")
> result = _run_load(runner, ref, "bg2", 2, extra_args)
> > assert result.exit_code == 0
> E assert 1 == 0
> E + where 1 = <Result TypeError("descriptor '__call__' for 'type' objects doesn't apply to a 'property' object")>.exit_code
>
> tests/test_cli_ingest.py:201: AssertionError
> ___________________ test_load_symm_asymm[asymm-extra_args2] ____________________
>
> ref = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.asymm.2.bg2'
> extra_args = ['--one-based', '--no-symmetric-upper']
>
> @pytest.mark.parametrize(
> "ref,extra_args",
> [
> ("symm.upper", []), # reflect tril pairs
> ("symm.upper", ["--one-based", "--input-copy-status", "unique"]), # reflect tril pairs
> ("asymm", ["--one-based", "--no-symmetric-upper"]),
> ],
> )
> def test_load_symm_asymm(ref, extra_args):
> runner = CliRunner()
> with runner.isolated_filesystem():
> ref = op.join(datadir, f"toy.{ref}.2.bg2")
> result = _run_load(runner, ref, "bg2", 2, extra_args)
> > assert result.exit_code == 0
> E assert 1 == 0
> E + where 1 = <Result TypeError("descriptor '__call__' for 'type' objects doesn't apply to a 'property' object")>.exit_code
>
> tests/test_cli_ingest.py:201: AssertionError
> _______________________________ test_load_field ________________________________
>
> def test_load_field():
> runner = CliRunner()
> with runner.isolated_filesystem():
> extra_args = ["--field", "count=7:dtype=float"]
> result = _run_load(runner, "toy.symm.upper.2.bg2", "bg2", 2, extra_args)
> > assert result.exit_code == 0
> E assert 1 == 0
> E + where 1 = <Result TypeError("descriptor '__call__' for 'type' objects doesn't apply to a 'property' object")>.exit_code
>
> tests/test_cli_ingest.py:211: AssertionError
> _______________________________ test_load_field2 _______________________________
>
> def test_load_field2():
> runner = CliRunner()
> with runner.isolated_filesystem():
> extra_args = ["--count-as-float"]
> result = _run_load(runner, "toy.symm.upper.2.bg2", "bg2", 2, extra_args)
> > assert result.exit_code == 0
> E assert 1 == 0
> E + where 1 = <Result TypeError("descriptor '__call__' for 'type' objects doesn't apply to a 'property' object")>.exit_code
>
> tests/test_cli_ingest.py:225: AssertionError
> __________________________________ test_merge __________________________________
>
> def test_merge():
> runner = CliRunner()
> with runner.isolated_filesystem():
> f_in = op.join(datadir, "toy.symm.upper.2.cool")
> result = runner.invoke(
> merge, ["toy.2.double.cool", f_in, f_in, "--field", "count:dtype=int"]
> )
> > assert result.exit_code == 0
> E assert 1 == 0
> E + where 1 = <Result TypeError("descriptor '__call__' for 'type' objects doesn't apply to a 'property' object")>.exit_code
>
> tests/test_cli_ops.py:31: AssertionError
> _________________________________ test_coarsen _________________________________
>
> def test_coarsen():
> runner = CliRunner()
> with runner.isolated_filesystem():
> f_in = op.join(datadir, "toy.symm.upper.2.cool")
> f_ref = op.join(datadir, "toy.symm.upper.4.cool")
> result = runner.invoke(
> coarsen, [
> f_in,
> "--factor", "2",
> "--nproc", "2",
> "-o", "toy.2.coarsen_2.cool"
> ],
> )
> > assert result.exit_code == 0
> E assert 1 == 0
> E + where 1 = <Result TypeError("descriptor '__call__' for 'type' objects doesn't apply to a 'property' object")>.exit_code
>
> tests/test_cli_ops.py:50: AssertionError
> _________________________________ test_zoomify _________________________________
>
> def test_zoomify():
> runner = CliRunner()
>
> with runner.isolated_filesystem():
> f_in = op.join(datadir, "toy.symm.upper.2.cool")
> result = runner.invoke(
> zoomify, [f_in, "--balance", "--legacy", "-o", "toy.2.mcool"]
> )
> assert result.exit_code == 0
>
> f_in = op.join(datadir, "toy.symm.upper.2.cool")
> result = runner.invoke(
> zoomify, [
> f_in,
> "--balance",
> "--nproc", "2",
> "-o", "toy.2.mcool"
> ]
> )
> assert result.exit_code == 0
>
> f_in = op.join(datadir, "toy.symm.upper.2.cool")
> result = runner.invoke(
> zoomify, [
> f_in,
> "--balance",
> "--resolutions", "2,4,8",
> "-o", "toy.2.mcool"
> ]
> )
> > assert result.exit_code == 0
> E assert 1 == 0
> E + where 1 = <Result TypeError("descriptor '__call__' for 'type' objects doesn't apply to a 'property' object")>.exit_code
>
> tests/test_cli_ops.py:98: AssertionError
> _ test_create_append[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool] _
>
> fp = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool'
>
> @pytest.mark.parametrize(
> "fp", [op.join(datadir, "hg19.GM12878-MboI.matrix.2000kb.cool")]
> )
> def test_create_append(fp):
> > import dask.dataframe as dd
>
> tests/test_create.py:24:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:81: in <module>
> from dask.dataframe import backends, dispatch, rolling
> /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in <module>
> from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame
> /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in <module>
> from dask.dataframe import methods
> /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in <module>
> from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like
> /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in <module>
> from dask.dataframe import ( # noqa: F401 register pandas extension types
> /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in <module>
> from dask.dataframe.extensions import make_array_nonempty, make_scalar
> /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in <module>
> from dask.dataframe.accessor import (
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in <module>
> class DatetimeAccessor(Accessor):
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__
> _bind_property(cls, pd_cls, attr, min_version)
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property
> setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func)))
> /usr/lib/python3/dist-packages/dask/utils.py:858: in wrapper
> method.__doc__ = _derived_from(
> /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from
> method_args = get_named_args(method)
> /usr/lib/python3/dist-packages/dask/utils.py:572: in get_named_args
> s = inspect.signature(func)
> /usr/lib/python3.11/inspect.py:3263: in signature
> return Signature.from_callable(obj, follow_wrapped=follow_wrapped,
> /usr/lib/python3.11/inspect.py:3011: in from_callable
> return _signature_from_callable(obj, sigcls=cls,
> /usr/lib/python3.11/inspect.py:2599: in _signature_from_callable
> call = _descriptor_get(call, obj)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> descriptor = <slot wrapper '__call__' of 'type' objects>
> obj = <property object at 0xffffb19c2200>
>
> def _descriptor_get(descriptor, obj):
> if isclass(descriptor):
> return descriptor
> get = getattr(type(descriptor), '__get__', _sentinel)
> if get is _sentinel:
> return descriptor
> > return get(descriptor, obj, type(obj))
> E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
>
> /usr/lib/python3.11/inspect.py:2432: TypeError
> ___________________________ test_create_custom_cols ____________________________
>
> def test_create_custom_cols():
>
> with isolated_filesystem():
> df = pd.DataFrame(
> {
> "bin1_id": [0, 1, 1, 1, 2, 2, 3, 4, 5],
> "bin2_id": [1, 1, 3, 4, 5, 6, 7, 8, 9],
> "foo": [1, 1, 1, 1, 1, 2, 2, 2, 2],
> "bar": [0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9],
> },
> columns=["bin1_id", "bin2_id", "foo", "bar"],
> )
> bins = pd.DataFrame(
> {
> "chrom": ["chr1"] * 5 + ["chr2"] * 5,
> "start": list(range(5)) * 2,
> "end": list(range(1, 6)) * 2,
> }
> )
> # works in unordered mode
> > cooler.create_cooler("test.cool", bins, df, columns=["foo", "bar"])
>
> tests/test_create.py:159:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> cooler/create/_create.py:1024: in create_cooler
> create(
> cooler/create/_create.py:514: in create
> from dask.dataframe import DataFrame as dask_df
> /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:81: in <module>
> from dask.dataframe import backends, dispatch, rolling
> /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in <module>
> from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame
> /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in <module>
> from dask.dataframe import methods
> /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in <module>
> from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like
> /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in <module>
> from dask.dataframe import ( # noqa: F401 register pandas extension types
> /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in <module>
> from dask.dataframe.extensions import make_array_nonempty, make_scalar
> /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in <module>
> from dask.dataframe.accessor import (
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in <module>
> class DatetimeAccessor(Accessor):
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__
> _bind_property(cls, pd_cls, attr, min_version)
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property
> setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func)))
> /usr/lib/python3/dist-packages/dask/utils.py:858: in wrapper
> method.__doc__ = _derived_from(
> /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from
> method_args = get_named_args(method)
> /usr/lib/python3/dist-packages/dask/utils.py:572: in get_named_args
> s = inspect.signature(func)
> /usr/lib/python3.11/inspect.py:3263: in signature
> return Signature.from_callable(obj, follow_wrapped=follow_wrapped,
> /usr/lib/python3.11/inspect.py:3011: in from_callable
> return _signature_from_callable(obj, sigcls=cls,
> /usr/lib/python3.11/inspect.py:2599: in _signature_from_callable
> call = _descriptor_get(call, obj)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> descriptor = <slot wrapper '__call__' of 'type' objects>
> obj = <property object at 0xffffb19c2200>
>
> def _descriptor_get(descriptor, obj):
> if isclass(descriptor):
> return descriptor
> get = getattr(type(descriptor), '__get__', _sentinel)
> if get is _sentinel:
> return descriptor
> > return get(descriptor, obj, type(obj))
> E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
>
> /usr/lib/python3.11/inspect.py:2432: TypeError
> ______________________________ test_create_cooler ______________________________
>
> def test_create_cooler():
> chromsizes = cooler.util.read_chromsizes(
> op.join(datadir, "toy.chrom.sizes")
> )
> bins = cooler.util.binnify(chromsizes, 1)
> pixels = pd.read_csv(
> op.join(datadir, "toy.symm.upper.1.zb.coo"),
> sep='\t',
> names=['bin1_id', 'bin2_id', 'count']
> )
> pixels['foo'] = 42.0
>
> with isolated_filesystem():
> > cooler.create.create_cooler(
> "test.cool",
> bins,
> pixels,
> assembly='toy',
> metadata={'hello': 'world', 'list': [1, 2, 3]},
> )
>
> tests/test_create.py:304:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> cooler/create/_create.py:1024: in create_cooler
> create(
> cooler/create/_create.py:514: in create
> from dask.dataframe import DataFrame as dask_df
> /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:81: in <module>
> from dask.dataframe import backends, dispatch, rolling
> /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in <module>
> from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame
> /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in <module>
> from dask.dataframe import methods
> /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in <module>
> from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like
> /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in <module>
> from dask.dataframe import ( # noqa: F401 register pandas extension types
> /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in <module>
> from dask.dataframe.extensions import make_array_nonempty, make_scalar
> /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in <module>
> from dask.dataframe.accessor import (
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in <module>
> class DatetimeAccessor(Accessor):
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__
> _bind_property(cls, pd_cls, attr, min_version)
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property
> setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func)))
> /usr/lib/python3/dist-packages/dask/utils.py:858: in wrapper
> method.__doc__ = _derived_from(
> /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from
> method_args = get_named_args(method)
> /usr/lib/python3/dist-packages/dask/utils.py:572: in get_named_args
> s = inspect.signature(func)
> /usr/lib/python3.11/inspect.py:3263: in signature
> return Signature.from_callable(obj, follow_wrapped=follow_wrapped,
> /usr/lib/python3.11/inspect.py:3011: in from_callable
> return _signature_from_callable(obj, sigcls=cls,
> /usr/lib/python3.11/inspect.py:2599: in _signature_from_callable
> call = _descriptor_get(call, obj)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> descriptor = <slot wrapper '__call__' of 'type' objects>
> obj = <property object at 0xffffb19c2200>
>
> def _descriptor_get(descriptor, obj):
> if isclass(descriptor):
> return descriptor
> get = getattr(type(descriptor), '__get__', _sentinel)
> if get is _sentinel:
> return descriptor
> > return get(descriptor, obj, type(obj))
> E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
>
> /usr/lib/python3.11/inspect.py:2432: TypeError
> _________________________ test_create_cooler_from_dask _________________________
>
> def test_create_cooler_from_dask():
> > dd = pytest.importorskip("dask.dataframe")
>
> tests/test_create.py:405:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:81: in <module>
> from dask.dataframe import backends, dispatch, rolling
> /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in <module>
> from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame
> /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in <module>
> from dask.dataframe import methods
> /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in <module>
> from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like
> /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in <module>
> from dask.dataframe import ( # noqa: F401 register pandas extension types
> /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in <module>
> from dask.dataframe.extensions import make_array_nonempty, make_scalar
> /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in <module>
> from dask.dataframe.accessor import (
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in <module>
> class DatetimeAccessor(Accessor):
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__
> _bind_property(cls, pd_cls, attr, min_version)
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property
> setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func)))
> /usr/lib/python3/dist-packages/dask/utils.py:858: in wrapper
> method.__doc__ = _derived_from(
> /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from
> method_args = get_named_args(method)
> /usr/lib/python3/dist-packages/dask/utils.py:572: in get_named_args
> s = inspect.signature(func)
> /usr/lib/python3.11/inspect.py:3263: in signature
> return Signature.from_callable(obj, follow_wrapped=follow_wrapped,
> /usr/lib/python3.11/inspect.py:3011: in from_callable
> return _signature_from_callable(obj, sigcls=cls,
> /usr/lib/python3.11/inspect.py:2599: in _signature_from_callable
> call = _descriptor_get(call, obj)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> descriptor = <slot wrapper '__call__' of 'type' objects>
> obj = <property object at 0xffffb19c2200>
>
> def _descriptor_get(descriptor, obj):
> if isclass(descriptor):
> return descriptor
> get = getattr(type(descriptor), '__get__', _sentinel)
> if get is _sentinel:
> return descriptor
> > return get(descriptor, obj, type(obj))
> E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
>
> /usr/lib/python3.11/inspect.py:2432: TypeError
> _ test_create_scool[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool] _
>
> fp = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool'
>
> @pytest.mark.parametrize(
> "fp", [op.join(datadir, "hg19.GM12878-MboI.matrix.2000kb.cool")]
> )
> def test_create_scool(fp):
> c = cooler.Cooler(fp)
> # chromsizes = c.chromsizes
> bins = c.bins()[:]
> pixels = c.pixels()[:]
>
> # random and different content to prove only chrom, start, end is linked and the rest is independent for each cell
> from copy import deepcopy
> bins_cell1 = deepcopy(bins)
> bins_cell2 = deepcopy(bins)
> bins_cell3 = deepcopy(bins)
> bins_cell1['weight'] = np.array([0] * len(bins_cell1["start"]))
> bins_cell2['weight'] = np.array([1] * len(bins_cell1["start"]))
> bins_cell3['weight'] = np.array([2] * len(bins_cell1["start"]))
>
> bins_cell1['KR'] = np.array([3] * len(bins_cell1["start"]))
> bins_cell2['KR'] = np.array([4] * len(bins_cell1["start"]))
> bins_cell3['KR'] = np.array([5] * len(bins_cell1["start"]))
>
> name_pixel_dict = {'cell1': pixels, 'cell2': pixels, 'cell3': pixels}
> name_bins_dict = {'cell1': bins_cell1, 'cell2': bins_cell2, 'cell3': bins_cell3}
>
> with isolated_filesystem():
> > cooler.create_scool('outfile_test.scool', name_bins_dict, name_pixel_dict)
>
> tests/test_create.py:461:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> cooler/create/_create.py:1237: in create_scool
> create(
> cooler/create/_create.py:514: in create
> from dask.dataframe import DataFrame as dask_df
> /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:81: in <module>
> from dask.dataframe import backends, dispatch, rolling
> /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in <module>
> from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame
> /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in <module>
> from dask.dataframe import methods
> /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in <module>
> from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like
> /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in <module>
> from dask.dataframe import ( # noqa: F401 register pandas extension types
> /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in <module>
> from dask.dataframe.extensions import make_array_nonempty, make_scalar
> /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in <module>
> from dask.dataframe.accessor import (
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in <module>
> class DatetimeAccessor(Accessor):
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__
> _bind_property(cls, pd_cls, attr, min_version)
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property
> setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func)))
> /usr/lib/python3/dist-packages/dask/utils.py:858: in wrapper
> method.__doc__ = _derived_from(
> /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from
> method_args = get_named_args(method)
> /usr/lib/python3/dist-packages/dask/utils.py:572: in get_named_args
> s = inspect.signature(func)
> /usr/lib/python3.11/inspect.py:3263: in signature
> return Signature.from_callable(obj, follow_wrapped=follow_wrapped,
> /usr/lib/python3.11/inspect.py:3011: in from_callable
> return _signature_from_callable(obj, sigcls=cls,
> /usr/lib/python3.11/inspect.py:2599: in _signature_from_callable
> call = _descriptor_get(call, obj)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> descriptor = <slot wrapper '__call__' of 'type' objects>
> obj = <property object at 0xffffb19c2200>
>
> def _descriptor_get(descriptor, obj):
> if isclass(descriptor):
> return descriptor
> get = getattr(type(descriptor), '__get__', _sentinel)
> if get is _sentinel:
> return descriptor
> > return get(descriptor, obj, type(obj))
> E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
>
> /usr/lib/python3.11/inspect.py:2432: TypeError
> _____________________________ test_from_hdf5_pairs _____________________________
>
> def test_from_hdf5_pairs():
> def should_not_depend_on_chunksize(chromsizes, bintable, mock_pairs):
> # try different chunk sizes
> binner = cooler.create.HDF5Aggregator(
> mock_pairs, chromsizes, bintable, chunksize=66
> )
> cooler.create.create(testcool_path, bintable, binner)
> with h5py.File(testcool_path, "r") as h5:
> oc1 = h5["indexes"]["chrom_offset"][:]
> ob1 = h5["indexes"]["bin1_offset"][:]
> p1 = cooler.api.pixels(h5, join=False)
>
> binner = cooler.create.HDF5Aggregator(
> mock_pairs, chromsizes, bintable, chunksize=666
> )
> cooler.create.create(testcool_path, bintable, binner)
> with h5py.File(testcool_path, "r") as h5:
> oc2 = h5["indexes"]["chrom_offset"][:]
> ob2 = h5["indexes"]["bin1_offset"][:]
> p2 = cooler.api.pixels(h5, join=False)
>
> assert np.all(oc1 == oc2)
> assert np.all(ob1 == ob2)
> assert np.all(p1.values == p2.values)
>
> def should_raise_if_input_not_sorted(chromsizes, bintable, mock_pairs):
> # not sorted by chrm1
> # with h5py.File(testcool_path, 'w') as h5:
> bad_reads = {
> "chrms1": mock_pairs["chrms2"],
> "cuts1": mock_pairs["cuts2"],
> "chrms2": mock_pairs["chrms1"],
> "cuts2": mock_pairs["cuts1"],
> }
> with pytest.raises(ValueError):
> cooler.create.HDF5Aggregator(bad_reads, chromsizes, bintable, chunksize=66)
>
> # not triu
> bad_reads = {
> "chrms1": mock_pairs["chrms1"].copy(),
> "cuts1": mock_pairs["cuts1"].copy(),
> "chrms2": mock_pairs["chrms2"].copy(),
> "cuts2": mock_pairs["cuts2"].copy(),
> }
> bad_reads["chrms1"][0] = 0
> bad_reads["chrms2"][0] = 0
> bad_reads["cuts1"][0] = 10
> bad_reads["cuts2"][0] = 9
> binner = cooler.create.HDF5Aggregator(
> bad_reads, chromsizes, bintable, chunksize=66
> )
> with pytest.raises(ValueError):
> cooler.create.create(testcool_path, bintable, binner)
>
> def should_work_with_int32_cols(chromsizes, bintable, mock_pairs):
> # int64
> binner = cooler.create.HDF5Aggregator(
> mock_pairs, chromsizes, bintable, chunksize=66
> )
> cooler.create.create(testcool_path, bintable, binner)
> with h5py.File(testcool_path, "r") as h5:
> oc1 = h5["indexes"]["chrom_offset"][:]
> ob1 = h5["indexes"]["bin1_offset"][:]
> p1 = cooler.api.pixels(h5, join=False)
>
> # int32
> mock_pairs32 = {
> "chrms1": mock_pairs["chrms1"].astype(np.int32),
> "cuts1": mock_pairs["cuts1"].astype(np.int32),
> "chrms2": mock_pairs["chrms2"].astype(np.int32),
> "cuts2": mock_pairs["cuts2"].astype(np.int32),
> }
> binner = cooler.create.HDF5Aggregator(
> mock_pairs32, chromsizes, bintable, chunksize=66
> )
> cooler.create.create(testcool_path, bintable, binner)
> with h5py.File(testcool_path, "r") as h5:
> oc2 = h5["indexes"]["chrom_offset"][:]
> ob2 = h5["indexes"]["bin1_offset"][:]
> p2 = cooler.api.pixels(h5, join=False)
>
> assert np.all(oc1 == oc2)
> assert np.all(ob1 == ob2)
> assert np.all(p1.values == p2.values)
>
> def _mock_hdf5_pairs():
> np.random.seed(1)
> chrms = np.random.randint(0, n_chroms, n_records * 2)
> cuts = np.random.randint(0, clen, n_records * 2)
> abs_cuts = np.array([clen * chrm + cut for chrm, cut in zip(chrms, cuts)])
> abs_cuts1, abs_cuts2 = abs_cuts[:n_records], abs_cuts[n_records:]
> mock_pairs = {
> "chrms1": chrms[:n_records],
> "cuts1": cuts[:n_records],
> "chrms2": chrms[n_records:],
> "cuts2": cuts[n_records:],
> }
> # Triu-sort
> mask = abs_cuts1 > abs_cuts2
> mock_pairs["chrms1"][mask], mock_pairs["chrms2"][mask] = (
> mock_pairs["chrms2"][mask],
> mock_pairs["chrms1"][mask],
> )
> mock_pairs["cuts1"][mask], mock_pairs["cuts2"][mask] = (
> mock_pairs["cuts2"][mask],
> mock_pairs["cuts1"][mask],
> )
> abs_cuts1[mask], abs_cuts2[mask] = abs_cuts2[mask], abs_cuts1[mask]
> idx = np.lexsort([abs_cuts2, abs_cuts1])
> for key in mock_pairs:
> mock_pairs[key] = mock_pairs[key][idx]
> return mock_pairs
>
> n_chroms = 2
> clen = 2000
> n_records = 3000
> chromsizes = pd.Series(index=["chr1", "chr2"], data=[clen, clen])
> mock_pairs = _mock_hdf5_pairs()
>
> # uniform bins
> bintable = cooler.binnify(chromsizes, 100)
> > should_not_depend_on_chunksize(chromsizes, bintable, mock_pairs)
>
> tests/test_create_ingest.py:167:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> tests/test_create_ingest.py:52: in should_not_depend_on_chunksize
> cooler.create.create(testcool_path, bintable, binner)
> cooler/create/_create.py:514: in create
> from dask.dataframe import DataFrame as dask_df
> /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:81: in <module>
> from dask.dataframe import backends, dispatch, rolling
> /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in <module>
> from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame
> /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in <module>
> from dask.dataframe import methods
> /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in <module>
> from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like
> /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in <module>
> from dask.dataframe import ( # noqa: F401 register pandas extension types
> /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in <module>
> from dask.dataframe.extensions import make_array_nonempty, make_scalar
> /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in <module>
> from dask.dataframe.accessor import (
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in <module>
> class DatetimeAccessor(Accessor):
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__
> _bind_property(cls, pd_cls, attr, min_version)
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property
> setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func)))
> /usr/lib/python3/dist-packages/dask/utils.py:858: in wrapper
> method.__doc__ = _derived_from(
> /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from
> method_args = get_named_args(method)
> /usr/lib/python3/dist-packages/dask/utils.py:572: in get_named_args
> s = inspect.signature(func)
> /usr/lib/python3.11/inspect.py:3263: in signature
> return Signature.from_callable(obj, follow_wrapped=follow_wrapped,
> /usr/lib/python3.11/inspect.py:3011: in from_callable
> return _signature_from_callable(obj, sigcls=cls,
> /usr/lib/python3.11/inspect.py:2599: in _signature_from_callable
> call = _descriptor_get(call, obj)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> descriptor = <slot wrapper '__call__' of 'type' objects>
> obj = <property object at 0xffffb19c2200>
>
> def _descriptor_get(descriptor, obj):
> if isclass(descriptor):
> return descriptor
> get = getattr(type(descriptor), '__get__', _sentinel)
> if get is _sentinel:
> return descriptor
> > return get(descriptor, obj, type(obj))
> E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
>
> /usr/lib/python3.11/inspect.py:2432: TypeError
> _ test_cload_tabix[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/hg19.bins.2000kb.bed.gz-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/hg19.GM12878-MboI.pairs.subsample.sorted.txt.gz-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool] _
>
> bins_path = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/hg19.bins.2000kb.bed.gz'
> pairs_path = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/hg19.GM12878-MboI.pairs.subsample.sorted.txt.gz'
> ref_path = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool'
>
> @pytest.mark.filterwarnings("ignore")
> @pytest.mark.parametrize(
> "bins_path,pairs_path,ref_path",
> [
> (
> op.join(testdir, "data", "hg19.bins.2000kb.bed.gz"),
> op.join(testdir, "data", "hg19.GM12878-MboI.pairs.subsample.sorted.txt.gz"),
> op.join(testdir, "data", "hg19.GM12878-MboI.matrix.2000kb.cool"),
> )
> ],
> )
> def test_cload_tabix(bins_path, pairs_path, ref_path):
> > cload_tabix.callback(
> bins_path,
> pairs_path,
> testcool_path,
> metadata=None,
> assembly="hg19",
> nproc=8,
> zero_based=False,
> max_split=2,
> )
>
> tests/test_create_ingest.py:190:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> cooler/cli/cload.py:240: in tabix
> create_cooler(
> cooler/create/_create.py:1024: in create_cooler
> create(
> cooler/create/_create.py:514: in create
> from dask.dataframe import DataFrame as dask_df
> /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:81: in <module>
> from dask.dataframe import backends, dispatch, rolling
> /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in <module>
> from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame
> /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in <module>
> from dask.dataframe import methods
> /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in <module>
> from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like
> /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in <module>
> from dask.dataframe import ( # noqa: F401 register pandas extension types
> /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in <module>
> from dask.dataframe.extensions import make_array_nonempty, make_scalar
> /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in <module>
> from dask.dataframe.accessor import (
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in <module>
> class DatetimeAccessor(Accessor):
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__
> _bind_property(cls, pd_cls, attr, min_version)
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property
> setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func)))
> /usr/lib/python3/dist-packages/dask/utils.py:858: in wrapper
> method.__doc__ = _derived_from(
> /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from
> method_args = get_named_args(method)
> /usr/lib/python3/dist-packages/dask/utils.py:572: in get_named_args
> s = inspect.signature(func)
> /usr/lib/python3.11/inspect.py:3263: in signature
> return Signature.from_callable(obj, follow_wrapped=follow_wrapped,
> /usr/lib/python3.11/inspect.py:3011: in from_callable
> return _signature_from_callable(obj, sigcls=cls,
> /usr/lib/python3.11/inspect.py:2599: in _signature_from_callable
> call = _descriptor_get(call, obj)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> descriptor = <slot wrapper '__call__' of 'type' objects>
> obj = <property object at 0xffffb19c2200>
>
> def _descriptor_get(descriptor, obj):
> if isclass(descriptor):
> return descriptor
> get = getattr(type(descriptor), '__get__', _sentinel)
> if get is _sentinel:
> return descriptor
> > return get(descriptor, obj, type(obj))
> E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
>
> /usr/lib/python3.11/inspect.py:2432: TypeError
> _ test_cload_pairix[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/hg19.bins.2000kb.bed.gz-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/hg19.GM12878-MboI.pairs.subsample.blksrt.txt.gz-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool] _
>
> bins_path = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/hg19.bins.2000kb.bed.gz'
> pairs_path = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/hg19.GM12878-MboI.pairs.subsample.blksrt.txt.gz'
> ref_path = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool'
>
> @pytest.mark.parametrize(
> "bins_path,pairs_path,ref_path",
> [
> (
> op.join(testdir, "data", "hg19.bins.2000kb.bed.gz"),
> op.join(testdir, "data", "hg19.GM12878-MboI.pairs.subsample.blksrt.txt.gz"),
> op.join(testdir, "data", "hg19.GM12878-MboI.matrix.2000kb.cool"),
> )
> ],
> )
> def test_cload_pairix(bins_path, pairs_path, ref_path):
> > cload_pairix.callback(
> bins_path,
> pairs_path,
> testcool_path,
> metadata=None,
> assembly="hg19",
> nproc=8,
> zero_based=False,
> max_split=2,
> )
>
> tests/test_create_ingest.py:221:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> cooler/cli/cload.py:308: in pairix
> create_cooler(
> cooler/create/_create.py:1024: in create_cooler
> create(
> cooler/create/_create.py:514: in create
> from dask.dataframe import DataFrame as dask_df
> /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:81: in <module>
> from dask.dataframe import backends, dispatch, rolling
> /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in <module>
> from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame
> /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in <module>
> from dask.dataframe import methods
> /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in <module>
> from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like
> /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in <module>
> from dask.dataframe import ( # noqa: F401 register pandas extension types
> /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in <module>
> from dask.dataframe.extensions import make_array_nonempty, make_scalar
> /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in <module>
> from dask.dataframe.accessor import (
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in <module>
> class DatetimeAccessor(Accessor):
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__
> _bind_property(cls, pd_cls, attr, min_version)
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property
> setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func)))
> /usr/lib/python3/dist-packages/dask/utils.py:858: in wrapper
> method.__doc__ = _derived_from(
> /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from
> method_args = get_named_args(method)
> /usr/lib/python3/dist-packages/dask/utils.py:572: in get_named_args
> s = inspect.signature(func)
> /usr/lib/python3.11/inspect.py:3263: in signature
> return Signature.from_callable(obj, follow_wrapped=follow_wrapped,
> /usr/lib/python3.11/inspect.py:3011: in from_callable
> return _signature_from_callable(obj, sigcls=cls,
> /usr/lib/python3.11/inspect.py:2599: in _signature_from_callable
> call = _descriptor_get(call, obj)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> descriptor = <slot wrapper '__call__' of 'type' objects>
> obj = <property object at 0xffffb19c2200>
>
> def _descriptor_get(descriptor, obj):
> if isclass(descriptor):
> return descriptor
> get = getattr(type(descriptor), '__get__', _sentinel)
> if get is _sentinel:
> return descriptor
> > return get(descriptor, obj, type(obj))
> E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
>
> /usr/lib/python3.11/inspect.py:2432: TypeError
> _ test_cload_pairs[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.bins.var.bed-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.pairs-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.symm.upper.var.cool] _
>
> bins_path = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.bins.var.bed'
> pairs_path = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.pairs'
> ref_path = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.symm.upper.var.cool'
>
> @pytest.mark.skipif(
> _pandas_major_version < 1,
> reason="hash fix only works with pandas >= 1.0"
> )
> @pytest.mark.parametrize(
> "bins_path,pairs_path,ref_path",
> [
> (
> op.join(testdir, "data", "toy.bins.var.bed"),
> op.join(testdir, "data", "toy.pairs"),
> op.join(testdir, "data", "toy.symm.upper.var.cool"),
> ),
> (
> op.join(testdir, "data", "toy.bins.var.bed"),
> op.join(testdir, "data", "toy_hash.pairs"),
> op.join(testdir, "data", "toy.symm.upper.var.cool"),
> ),
> (
> op.join(testdir, "data", "toy.bins.var.bed"),
> op.join(testdir, "data", "toy_hash.pairs.gz"),
> op.join(testdir, "data", "toy.symm.upper.var.cool"),
> )
> ],
> )
> def test_cload_pairs(bins_path, pairs_path, ref_path):
> kwargs = dict(
> metadata=None,
> assembly="hg19",
> chunksize=int(15e6),
> zero_based=False,
> comment_char="#",
> input_copy_status="unique",
> no_symmetric_upper=False,
> field=(),
> temp_dir=None,
> no_delete_temp=False,
> storage_options=None,
> no_count=False,
> max_merge=200,
> chrom1=2,
> pos1=3,
> chrom2=4,
> pos2=5,
> append=False,
> )
> > cload_pairs.callback(bins_path, pairs_path, testcool_path, **kwargs)
>
> tests/test_create_ingest.py:286:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> cooler/cli/cload.py:584: in pairs
> create_cooler(
> cooler/create/_create.py:1042: in create_cooler
> create_from_unordered(
> cooler/create/_create.py:723: in create_from_unordered
> create(uri, bins, chunk, columns=columns, dtypes=dtypes, mode="a", **kwargs)
> cooler/create/_create.py:514: in create
> from dask.dataframe import DataFrame as dask_df
> /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:81: in <module>
> from dask.dataframe import backends, dispatch, rolling
> /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in <module>
> from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame
> /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in <module>
> from dask.dataframe import methods
> /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in <module>
> from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like
> /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in <module>
> from dask.dataframe import ( # noqa: F401 register pandas extension types
> /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in <module>
> from dask.dataframe.extensions import make_array_nonempty, make_scalar
> /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in <module>
> from dask.dataframe.accessor import (
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in <module>
> class DatetimeAccessor(Accessor):
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__
> _bind_property(cls, pd_cls, attr, min_version)
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property
> setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func)))
> /usr/lib/python3/dist-packages/dask/utils.py:858: in wrapper
> method.__doc__ = _derived_from(
> /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from
> method_args = get_named_args(method)
> /usr/lib/python3/dist-packages/dask/utils.py:572: in get_named_args
> s = inspect.signature(func)
> /usr/lib/python3.11/inspect.py:3263: in signature
> return Signature.from_callable(obj, follow_wrapped=follow_wrapped,
> /usr/lib/python3.11/inspect.py:3011: in from_callable
> return _signature_from_callable(obj, sigcls=cls,
> /usr/lib/python3.11/inspect.py:2599: in _signature_from_callable
> call = _descriptor_get(call, obj)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> descriptor = <slot wrapper '__call__' of 'type' objects>
> obj = <property object at 0xffffb19c2200>
>
> def _descriptor_get(descriptor, obj):
> if isclass(descriptor):
> return descriptor
> get = getattr(type(descriptor), '__get__', _sentinel)
> if get is _sentinel:
> return descriptor
> > return get(descriptor, obj, type(obj))
> E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
>
> /usr/lib/python3.11/inspect.py:2432: TypeError
> _ test_cload_pairs[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.bins.var.bed-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy_hash.pairs-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.symm.upper.var.cool] _
>
> bins_path = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.bins.var.bed'
> pairs_path = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy_hash.pairs'
> ref_path = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.symm.upper.var.cool'
>
> @pytest.mark.skipif(
> _pandas_major_version < 1,
> reason="hash fix only works with pandas >= 1.0"
> )
> @pytest.mark.parametrize(
> "bins_path,pairs_path,ref_path",
> [
> (
> op.join(testdir, "data", "toy.bins.var.bed"),
> op.join(testdir, "data", "toy.pairs"),
> op.join(testdir, "data", "toy.symm.upper.var.cool"),
> ),
> (
> op.join(testdir, "data", "toy.bins.var.bed"),
> op.join(testdir, "data", "toy_hash.pairs"),
> op.join(testdir, "data", "toy.symm.upper.var.cool"),
> ),
> (
> op.join(testdir, "data", "toy.bins.var.bed"),
> op.join(testdir, "data", "toy_hash.pairs.gz"),
> op.join(testdir, "data", "toy.symm.upper.var.cool"),
> )
> ],
> )
> def test_cload_pairs(bins_path, pairs_path, ref_path):
> kwargs = dict(
> metadata=None,
> assembly="hg19",
> chunksize=int(15e6),
> zero_based=False,
> comment_char="#",
> input_copy_status="unique",
> no_symmetric_upper=False,
> field=(),
> temp_dir=None,
> no_delete_temp=False,
> storage_options=None,
> no_count=False,
> max_merge=200,
> chrom1=2,
> pos1=3,
> chrom2=4,
> pos2=5,
> append=False,
> )
> > cload_pairs.callback(bins_path, pairs_path, testcool_path, **kwargs)
>
> tests/test_create_ingest.py:286:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> cooler/cli/cload.py:584: in pairs
> create_cooler(
> cooler/create/_create.py:1042: in create_cooler
> create_from_unordered(
> cooler/create/_create.py:723: in create_from_unordered
> create(uri, bins, chunk, columns=columns, dtypes=dtypes, mode="a", **kwargs)
> cooler/create/_create.py:514: in create
> from dask.dataframe import DataFrame as dask_df
> /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:81: in <module>
> from dask.dataframe import backends, dispatch, rolling
> /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in <module>
> from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame
> /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in <module>
> from dask.dataframe import methods
> /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in <module>
> from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like
> /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in <module>
> from dask.dataframe import ( # noqa: F401 register pandas extension types
> /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in <module>
> from dask.dataframe.extensions import make_array_nonempty, make_scalar
> /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in <module>
> from dask.dataframe.accessor import (
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in <module>
> class DatetimeAccessor(Accessor):
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__
> _bind_property(cls, pd_cls, attr, min_version)
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property
> setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func)))
> /usr/lib/python3/dist-packages/dask/utils.py:858: in wrapper
> method.__doc__ = _derived_from(
> /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from
> method_args = get_named_args(method)
> /usr/lib/python3/dist-packages/dask/utils.py:572: in get_named_args
> s = inspect.signature(func)
> /usr/lib/python3.11/inspect.py:3263: in signature
> return Signature.from_callable(obj, follow_wrapped=follow_wrapped,
> /usr/lib/python3.11/inspect.py:3011: in from_callable
> return _signature_from_callable(obj, sigcls=cls,
> /usr/lib/python3.11/inspect.py:2599: in _signature_from_callable
> call = _descriptor_get(call, obj)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> descriptor = <slot wrapper '__call__' of 'type' objects>
> obj = <property object at 0xffffb19c2200>
>
> def _descriptor_get(descriptor, obj):
> if isclass(descriptor):
> return descriptor
> get = getattr(type(descriptor), '__get__', _sentinel)
> if get is _sentinel:
> return descriptor
> > return get(descriptor, obj, type(obj))
> E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
>
> /usr/lib/python3.11/inspect.py:2432: TypeError
> _ test_cload_pairs[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.bins.var.bed-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy_hash.pairs.gz-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.symm.upper.var.cool] _
>
> bins_path = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.bins.var.bed'
> pairs_path = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy_hash.pairs.gz'
> ref_path = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.symm.upper.var.cool'
>
> @pytest.mark.skipif(
> _pandas_major_version < 1,
> reason="hash fix only works with pandas >= 1.0"
> )
> @pytest.mark.parametrize(
> "bins_path,pairs_path,ref_path",
> [
> (
> op.join(testdir, "data", "toy.bins.var.bed"),
> op.join(testdir, "data", "toy.pairs"),
> op.join(testdir, "data", "toy.symm.upper.var.cool"),
> ),
> (
> op.join(testdir, "data", "toy.bins.var.bed"),
> op.join(testdir, "data", "toy_hash.pairs"),
> op.join(testdir, "data", "toy.symm.upper.var.cool"),
> ),
> (
> op.join(testdir, "data", "toy.bins.var.bed"),
> op.join(testdir, "data", "toy_hash.pairs.gz"),
> op.join(testdir, "data", "toy.symm.upper.var.cool"),
> )
> ],
> )
> def test_cload_pairs(bins_path, pairs_path, ref_path):
> kwargs = dict(
> metadata=None,
> assembly="hg19",
> chunksize=int(15e6),
> zero_based=False,
> comment_char="#",
> input_copy_status="unique",
> no_symmetric_upper=False,
> field=(),
> temp_dir=None,
> no_delete_temp=False,
> storage_options=None,
> no_count=False,
> max_merge=200,
> chrom1=2,
> pos1=3,
> chrom2=4,
> pos2=5,
> append=False,
> )
> > cload_pairs.callback(bins_path, pairs_path, testcool_path, **kwargs)
>
> tests/test_create_ingest.py:286:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> cooler/cli/cload.py:584: in pairs
> create_cooler(
> cooler/create/_create.py:1042: in create_cooler
> create_from_unordered(
> cooler/create/_create.py:723: in create_from_unordered
> create(uri, bins, chunk, columns=columns, dtypes=dtypes, mode="a", **kwargs)
> cooler/create/_create.py:514: in create
> from dask.dataframe import DataFrame as dask_df
> /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:81: in <module>
> from dask.dataframe import backends, dispatch, rolling
> /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in <module>
> from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame
> /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in <module>
> from dask.dataframe import methods
> /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in <module>
> from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like
> /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in <module>
> from dask.dataframe import ( # noqa: F401 register pandas extension types
> /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in <module>
> from dask.dataframe.extensions import make_array_nonempty, make_scalar
> /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in <module>
> from dask.dataframe.accessor import (
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in <module>
> class DatetimeAccessor(Accessor):
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__
> _bind_property(cls, pd_cls, attr, min_version)
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property
> setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func)))
> /usr/lib/python3/dist-packages/dask/utils.py:858: in wrapper
> method.__doc__ = _derived_from(
> /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from
> method_args = get_named_args(method)
> /usr/lib/python3/dist-packages/dask/utils.py:572: in get_named_args
> s = inspect.signature(func)
> /usr/lib/python3.11/inspect.py:3263: in signature
> return Signature.from_callable(obj, follow_wrapped=follow_wrapped,
> /usr/lib/python3.11/inspect.py:3011: in from_callable
> return _signature_from_callable(obj, sigcls=cls,
> /usr/lib/python3.11/inspect.py:2599: in _signature_from_callable
> call = _descriptor_get(call, obj)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> descriptor = <slot wrapper '__call__' of 'type' objects>
> obj = <property object at 0xffffb19c2200>
>
> def _descriptor_get(descriptor, obj):
> if isclass(descriptor):
> return descriptor
> get = getattr(type(descriptor), '__get__', _sentinel)
> if get is _sentinel:
> return descriptor
> > return get(descriptor, obj, type(obj))
> E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
>
> /usr/lib/python3.11/inspect.py:2432: TypeError
> _ test_cload_field[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.chrom.sizes:2-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.pairs] _
>
> bins_path = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.chrom.sizes:2'
> pairs_path = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.pairs'
>
> @pytest.mark.parametrize(
> "bins_path,pairs_path",
> [
> (
> op.join(testdir, "data", "toy.chrom.sizes") + ":2",
> op.join(testdir, "data", "toy.pairs"),
> )
> ],
> )
> def test_cload_field(bins_path, pairs_path):
> kwargs = dict(
> metadata=None,
> assembly="toy",
> chunksize=10,
> zero_based=False,
> comment_char="#",
> input_copy_status="unique",
> no_symmetric_upper=False,
> temp_dir=None,
> no_delete_temp=False,
> storage_options=None,
> no_count=True,
> max_merge=200,
> chrom1=2,
> pos1=3,
> chrom2=4,
> pos2=5,
> append=False,
> )
> > cload_pairs.callback(
> bins_path, pairs_path, testcool_path, field=("score=8:dtype=float",), **kwargs
> )
>
> tests/test_create_ingest.py:326:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> cooler/cli/cload.py:584: in pairs
> create_cooler(
> cooler/create/_create.py:1042: in create_cooler
> create_from_unordered(
> cooler/create/_create.py:723: in create_from_unordered
> create(uri, bins, chunk, columns=columns, dtypes=dtypes, mode="a", **kwargs)
> cooler/create/_create.py:514: in create
> from dask.dataframe import DataFrame as dask_df
> /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:81: in <module>
> from dask.dataframe import backends, dispatch, rolling
> /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in <module>
> from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame
> /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in <module>
> from dask.dataframe import methods
> /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in <module>
> from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like
> /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in <module>
> from dask.dataframe import ( # noqa: F401 register pandas extension types
> /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in <module>
> from dask.dataframe.extensions import make_array_nonempty, make_scalar
> /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in <module>
> from dask.dataframe.accessor import (
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in <module>
> class DatetimeAccessor(Accessor):
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__
> _bind_property(cls, pd_cls, attr, min_version)
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property
> setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func)))
> /usr/lib/python3/dist-packages/dask/utils.py:858: in wrapper
> method.__doc__ = _derived_from(
> /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from
> method_args = get_named_args(method)
> /usr/lib/python3/dist-packages/dask/utils.py:572: in get_named_args
> s = inspect.signature(func)
> /usr/lib/python3.11/inspect.py:3263: in signature
> return Signature.from_callable(obj, follow_wrapped=follow_wrapped,
> /usr/lib/python3.11/inspect.py:3011: in from_callable
> return _signature_from_callable(obj, sigcls=cls,
> /usr/lib/python3.11/inspect.py:2599: in _signature_from_callable
> call = _descriptor_get(call, obj)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> descriptor = <slot wrapper '__call__' of 'type' objects>
> obj = <property object at 0xffffb19c2200>
>
> def _descriptor_get(descriptor, obj):
> if isclass(descriptor):
> return descriptor
> get = getattr(type(descriptor), '__get__', _sentinel)
> if get is _sentinel:
> return descriptor
> > return get(descriptor, obj, type(obj))
> E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
>
> /usr/lib/python3.11/inspect.py:2432: TypeError
> _ test_cload_custom_tempdir[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.chrom.sizes:2-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.pairs] _
>
> bins_path = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.chrom.sizes:2'
> pairs_path = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.pairs'
>
> @pytest.mark.parametrize(
> "bins_path,pairs_path",
> [
> (
> op.join(testdir, "data", "toy.chrom.sizes") + ":2",
> op.join(testdir, "data", "toy.pairs"),
> )
> ],
> )
> def test_cload_custom_tempdir(bins_path, pairs_path):
> for temp_dir in [op.join(testdir, "data"), "-"]:
> > cload_pairs.callback(
> bins_path,
> pairs_path,
> testcool_path,
> metadata=None,
> assembly="toy",
> chunksize=10,
> zero_based=False,
> comment_char="#",
> input_copy_status="unique",
> no_symmetric_upper=False,
> field=(),
> temp_dir=temp_dir,
> no_delete_temp=False,
> storage_options=None,
> no_count=True,
> max_merge=200,
> chrom1=2,
> pos1=3,
> chrom2=4,
> pos2=5,
> append=False,
> )
>
> tests/test_create_ingest.py:345:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> cooler/cli/cload.py:584: in pairs
> create_cooler(
> cooler/create/_create.py:1042: in create_cooler
> create_from_unordered(
> cooler/create/_create.py:723: in create_from_unordered
> create(uri, bins, chunk, columns=columns, dtypes=dtypes, mode="a", **kwargs)
> cooler/create/_create.py:514: in create
> from dask.dataframe import DataFrame as dask_df
> /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:81: in <module>
> from dask.dataframe import backends, dispatch, rolling
> /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in <module>
> from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame
> /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in <module>
> from dask.dataframe import methods
> /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in <module>
> from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like
> /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in <module>
> from dask.dataframe import ( # noqa: F401 register pandas extension types
> /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in <module>
> from dask.dataframe.extensions import make_array_nonempty, make_scalar
> /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in <module>
> from dask.dataframe.accessor import (
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in <module>
> class DatetimeAccessor(Accessor):
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__
> _bind_property(cls, pd_cls, attr, min_version)
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property
> setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func)))
> /usr/lib/python3/dist-packages/dask/utils.py:858: in wrapper
> method.__doc__ = _derived_from(
> /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from
> method_args = get_named_args(method)
> /usr/lib/python3/dist-packages/dask/utils.py:572: in get_named_args
> s = inspect.signature(func)
> /usr/lib/python3.11/inspect.py:3263: in signature
> return Signature.from_callable(obj, follow_wrapped=follow_wrapped,
> /usr/lib/python3.11/inspect.py:3011: in from_callable
> return _signature_from_callable(obj, sigcls=cls,
> /usr/lib/python3.11/inspect.py:2599: in _signature_from_callable
> call = _descriptor_get(call, obj)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> descriptor = <slot wrapper '__call__' of 'type' objects>
> obj = <property object at 0xffffb19c2200>
>
> def _descriptor_get(descriptor, obj):
> if isclass(descriptor):
> return descriptor
> get = getattr(type(descriptor), '__get__', _sentinel)
> if get is _sentinel:
> return descriptor
> > return get(descriptor, obj, type(obj))
> E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
>
> /usr/lib/python3.11/inspect.py:2432: TypeError
> _____________________________ test_load_bg2_vs_coo _____________________________
>
> def test_load_bg2_vs_coo():
> kwargs = dict(
> metadata=None,
> assembly="hg19",
> chunksize=int(20e6),
> field=(),
> count_as_float=False,
> one_based=False,
> comment_char="#",
> input_copy_status="unique",
> no_symmetric_upper=False,
> temp_dir=None,
> no_delete_temp=False,
> storage_options=None,
> append=False,
> )
>
> out_path1 = op.join(tmp, "test1.cool")
> out_path2 = op.join(tmp, "test2.cool")
>
> > load.callback(
> op.join(testdir, "data", "hg19.bins.2000kb.bed.gz"),
> op.join(testdir, "data", "hg19.GM12878-MboI.matrix.2000kb.bg2.gz"),
> out_path1,
> format="bg2",
> **kwargs
> )
>
> tests/test_create_ingest.py:394:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> cooler/cli/load.py:339: in load
> create_from_unordered(
> cooler/create/_create.py:723: in create_from_unordered
> create(uri, bins, chunk, columns=columns, dtypes=dtypes, mode="a", **kwargs)
> cooler/create/_create.py:514: in create
> from dask.dataframe import DataFrame as dask_df
> /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:81: in <module>
> from dask.dataframe import backends, dispatch, rolling
> /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in <module>
> from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame
> /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in <module>
> from dask.dataframe import methods
> /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in <module>
> from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like
> /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in <module>
> from dask.dataframe import ( # noqa: F401 register pandas extension types
> /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in <module>
> from dask.dataframe.extensions import make_array_nonempty, make_scalar
> /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in <module>
> from dask.dataframe.accessor import (
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in <module>
> class DatetimeAccessor(Accessor):
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__
> _bind_property(cls, pd_cls, attr, min_version)
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property
> setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func)))
> /usr/lib/python3/dist-packages/dask/utils.py:858: in wrapper
> method.__doc__ = _derived_from(
> /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from
> method_args = get_named_args(method)
> /usr/lib/python3/dist-packages/dask/utils.py:572: in get_named_args
> s = inspect.signature(func)
> /usr/lib/python3.11/inspect.py:3263: in signature
> return Signature.from_callable(obj, follow_wrapped=follow_wrapped,
> /usr/lib/python3.11/inspect.py:3011: in from_callable
> return _signature_from_callable(obj, sigcls=cls,
> /usr/lib/python3.11/inspect.py:2599: in _signature_from_callable
> call = _descriptor_get(call, obj)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> descriptor = <slot wrapper '__call__' of 'type' objects>
> obj = <property object at 0xffffb19c2200>
>
> def _descriptor_get(descriptor, obj):
> if isclass(descriptor):
> return descriptor
> get = getattr(type(descriptor), '__get__', _sentinel)
> if get is _sentinel:
> return descriptor
> > return get(descriptor, obj, type(obj))
> E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
>
> /usr/lib/python3.11/inspect.py:2432: TypeError
> _________________________ test_load_zero_one_based_bg2 _________________________
>
> def test_load_zero_one_based_bg2():
> kwargs = dict(
> format="bg2",
> metadata=None,
> assembly="toy",
> chunksize=10,
> field=(),
> count_as_float=False,
> comment_char="#",
> input_copy_status="unique",
> no_symmetric_upper=False,
> temp_dir=None,
> no_delete_temp=False,
> storage_options=None,
> append=False,
> )
> # 1-based-start BG2 input
> ref = "toy.symm.upper.1.ob.bg2"
> bins_path = op.join(testdir, "data", "toy.chrom.sizes") + ":1"
> pixels_path = op.join(testdir, "data", ref)
> > load.callback(bins_path, pixels_path, testcool_path, one_based=True, **kwargs)
>
> tests/test_create_ingest.py:441:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> cooler/cli/load.py:339: in load
> create_from_unordered(
> cooler/create/_create.py:723: in create_from_unordered
> create(uri, bins, chunk, columns=columns, dtypes=dtypes, mode="a", **kwargs)
> cooler/create/_create.py:514: in create
> from dask.dataframe import DataFrame as dask_df
> /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:81: in <module>
> from dask.dataframe import backends, dispatch, rolling
> /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in <module>
> from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame
> /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in <module>
> from dask.dataframe import methods
> /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in <module>
> from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like
> /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in <module>
> from dask.dataframe import ( # noqa: F401 register pandas extension types
> /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in <module>
> from dask.dataframe.extensions import make_array_nonempty, make_scalar
> /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in <module>
> from dask.dataframe.accessor import (
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in <module>
> class DatetimeAccessor(Accessor):
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__
> _bind_property(cls, pd_cls, attr, min_version)
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property
> setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func)))
> /usr/lib/python3/dist-packages/dask/utils.py:858: in wrapper
> method.__doc__ = _derived_from(
> /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from
> method_args = get_named_args(method)
> /usr/lib/python3/dist-packages/dask/utils.py:572: in get_named_args
> s = inspect.signature(func)
> /usr/lib/python3.11/inspect.py:3263: in signature
> return Signature.from_callable(obj, follow_wrapped=follow_wrapped,
> /usr/lib/python3.11/inspect.py:3011: in from_callable
> return _signature_from_callable(obj, sigcls=cls,
> /usr/lib/python3.11/inspect.py:2599: in _signature_from_callable
> call = _descriptor_get(call, obj)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> descriptor = <slot wrapper '__call__' of 'type' objects>
> obj = <property object at 0xffffb19c2200>
>
> def _descriptor_get(descriptor, obj):
> if isclass(descriptor):
> return descriptor
> get = getattr(type(descriptor), '__get__', _sentinel)
> if get is _sentinel:
> return descriptor
> > return get(descriptor, obj, type(obj))
> E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
>
> /usr/lib/python3.11/inspect.py:2432: TypeError
> _________________________ test_load_zero_one_based_coo _________________________
>
> def test_load_zero_one_based_coo():
> kwargs = dict(
> format="coo",
> metadata=None,
> assembly="toy",
> chunksize=10,
> field=(),
> count_as_float=False,
> comment_char="#",
> input_copy_status="unique",
> no_symmetric_upper=False,
> temp_dir=None,
> no_delete_temp=False,
> storage_options=None,
> append=False,
> )
> # 1-based-start COO input
> ref = "toy.symm.upper.1.ob.coo"
> bins_path = op.join(testdir, "data", "toy.chrom.sizes") + ":1"
> pixels_path = op.join(testdir, "data", ref)
> > load.callback(bins_path, pixels_path, testcool_path, one_based=True, **kwargs)
>
> tests/test_create_ingest.py:490:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> cooler/cli/load.py:339: in load
> create_from_unordered(
> cooler/create/_create.py:723: in create_from_unordered
> create(uri, bins, chunk, columns=columns, dtypes=dtypes, mode="a", **kwargs)
> cooler/create/_create.py:514: in create
> from dask.dataframe import DataFrame as dask_df
> /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:81: in <module>
> from dask.dataframe import backends, dispatch, rolling
> /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in <module>
> from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame
> /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in <module>
> from dask.dataframe import methods
> /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in <module>
> from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like
> /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in <module>
> from dask.dataframe import ( # noqa: F401 register pandas extension types
> /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in <module>
> from dask.dataframe.extensions import make_array_nonempty, make_scalar
> /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in <module>
> from dask.dataframe.accessor import (
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in <module>
> class DatetimeAccessor(Accessor):
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__
> _bind_property(cls, pd_cls, attr, min_version)
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property
> setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func)))
> /usr/lib/python3/dist-packages/dask/utils.py:858: in wrapper
> method.__doc__ = _derived_from(
> /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from
> method_args = get_named_args(method)
> /usr/lib/python3/dist-packages/dask/utils.py:572: in get_named_args
> s = inspect.signature(func)
> /usr/lib/python3.11/inspect.py:3263: in signature
> return Signature.from_callable(obj, follow_wrapped=follow_wrapped,
> /usr/lib/python3.11/inspect.py:3011: in from_callable
> return _signature_from_callable(obj, sigcls=cls,
> /usr/lib/python3.11/inspect.py:2599: in _signature_from_callable
> call = _descriptor_get(call, obj)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> descriptor = <slot wrapper '__call__' of 'type' objects>
> obj = <property object at 0xffffb19c2200>
>
> def _descriptor_get(descriptor, obj):
> if isclass(descriptor):
> return descriptor
> get = getattr(type(descriptor), '__get__', _sentinel)
> if get is _sentinel:
> return descriptor
> > return get(descriptor, obj, type(obj))
> E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
>
> /usr/lib/python3.11/inspect.py:2432: TypeError
> ____________________________ test_cload_append_mode ____________________________
>
> def test_cload_append_mode():
> for append in (True, False):
> out_path = op.join(tmp, "test.cool")
> with h5py.File(out_path, "w") as f:
> f.attrs["xxxx"] = True
> kwargs = dict(
> metadata=None,
> assembly="hg19",
> chunksize=int(15e6),
> zero_based=False,
> comment_char="#",
> input_copy_status="unique",
> no_symmetric_upper=False,
> field=(),
> temp_dir=None,
> no_delete_temp=False,
> storage_options=None,
> no_count=False,
> max_merge=200,
> chrom1=2,
> pos1=3,
> chrom2=4,
> pos2=5,
> append=append,
> )
> > cload_pairs.callback(
> op.join(testdir, "data", "toy.bins.var.bed"),
> op.join(testdir, "data", "toy.pairs"),
> out_path,
> **kwargs
> )
>
> tests/test_create_ingest.py:551:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> cooler/cli/cload.py:584: in pairs
> create_cooler(
> cooler/create/_create.py:1042: in create_cooler
> create_from_unordered(
> cooler/create/_create.py:723: in create_from_unordered
> create(uri, bins, chunk, columns=columns, dtypes=dtypes, mode="a", **kwargs)
> cooler/create/_create.py:514: in create
> from dask.dataframe import DataFrame as dask_df
> /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:81: in <module>
> from dask.dataframe import backends, dispatch, rolling
> /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in <module>
> from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame
> /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in <module>
> from dask.dataframe import methods
> /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in <module>
> from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like
> /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in <module>
> from dask.dataframe import ( # noqa: F401 register pandas extension types
> /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in <module>
> from dask.dataframe.extensions import make_array_nonempty, make_scalar
> /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in <module>
> from dask.dataframe.accessor import (
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in <module>
> class DatetimeAccessor(Accessor):
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__
> _bind_property(cls, pd_cls, attr, min_version)
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property
> setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func)))
> /usr/lib/python3/dist-packages/dask/utils.py:858: in wrapper
> method.__doc__ = _derived_from(
> /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from
> method_args = get_named_args(method)
> /usr/lib/python3/dist-packages/dask/utils.py:572: in get_named_args
> s = inspect.signature(func)
> /usr/lib/python3.11/inspect.py:3263: in signature
> return Signature.from_callable(obj, follow_wrapped=follow_wrapped,
> /usr/lib/python3.11/inspect.py:3011: in from_callable
> return _signature_from_callable(obj, sigcls=cls,
> /usr/lib/python3.11/inspect.py:2599: in _signature_from_callable
> call = _descriptor_get(call, obj)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> descriptor = <slot wrapper '__call__' of 'type' objects>
> obj = <property object at 0xffffb19c2200>
>
> def _descriptor_get(descriptor, obj):
> if isclass(descriptor):
> return descriptor
> get = getattr(type(descriptor), '__get__', _sentinel)
> if get is _sentinel:
> return descriptor
> > return get(descriptor, obj, type(obj))
> E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
>
> /usr/lib/python3.11/inspect.py:2432: TypeError
> ____________________________ test_load_append_mode _____________________________
>
> def test_load_append_mode():
> for append in (True, False):
> out_path = op.join(tmp, "test.cool")
> with h5py.File(out_path, "w") as f:
> f.attrs["xxxx"] = True
> kwargs = dict(
> metadata=None,
> assembly="hg19",
> chunksize=int(20e6),
> field=(),
> count_as_float=False,
> one_based=False,
> comment_char="#",
> input_copy_status="unique",
> no_symmetric_upper=False,
> temp_dir=None,
> no_delete_temp=False,
> storage_options=None,
> append=append,
> )
> > load.callback(
> op.join(testdir, "data", "hg19.bins.2000kb.bed.gz"),
> op.join(testdir, "data", "hg19.GM12878-MboI.matrix.2000kb.coo.txt"),
> out_path,
> format="coo",
> **kwargs
> )
>
> tests/test_create_ingest.py:588:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> cooler/cli/load.py:339: in load
> create_from_unordered(
> cooler/create/_create.py:723: in create_from_unordered
> create(uri, bins, chunk, columns=columns, dtypes=dtypes, mode="a", **kwargs)
> cooler/create/_create.py:514: in create
> from dask.dataframe import DataFrame as dask_df
> /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:81: in <module>
> from dask.dataframe import backends, dispatch, rolling
> /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in <module>
> from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame
> /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in <module>
> from dask.dataframe import methods
> /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in <module>
> from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like
> /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in <module>
> from dask.dataframe import ( # noqa: F401 register pandas extension types
> /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in <module>
> from dask.dataframe.extensions import make_array_nonempty, make_scalar
> /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in <module>
> from dask.dataframe.accessor import (
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in <module>
> class DatetimeAccessor(Accessor):
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__
> _bind_property(cls, pd_cls, attr, min_version)
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property
> setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func)))
> /usr/lib/python3/dist-packages/dask/utils.py:858: in wrapper
> method.__doc__ = _derived_from(
> /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from
> method_args = get_named_args(method)
> /usr/lib/python3/dist-packages/dask/utils.py:572: in get_named_args
> s = inspect.signature(func)
> /usr/lib/python3.11/inspect.py:3263: in signature
> return Signature.from_callable(obj, follow_wrapped=follow_wrapped,
> /usr/lib/python3.11/inspect.py:3011: in from_callable
> return _signature_from_callable(obj, sigcls=cls,
> /usr/lib/python3.11/inspect.py:2599: in _signature_from_callable
> call = _descriptor_get(call, obj)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> descriptor = <slot wrapper '__call__' of 'type' objects>
> obj = <property object at 0xffffb19c2200>
>
> def _descriptor_get(descriptor, obj):
> if isclass(descriptor):
> return descriptor
> get = getattr(type(descriptor), '__get__', _sentinel)
> if get is _sentinel:
> return descriptor
> > return get(descriptor, obj, type(obj))
> E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
>
> /usr/lib/python3.11/inspect.py:2432: TypeError
> ___________________________ test_load_custom_tempdir ___________________________
>
> def test_load_custom_tempdir():
> for temp_dir in [op.join(testdir, "data"), "-"]:
> > load.callback(
> op.join(testdir, "data", "hg19.bins.2000kb.bed.gz"),
> op.join(testdir, "data", "hg19.GM12878-MboI.matrix.2000kb.coo.txt"),
> testcool_path,
> format="coo",
> metadata=None,
> assembly="hg19",
> chunksize=int(20e6),
> field=(),
> count_as_float=False,
> one_based=False,
> comment_char="#",
> input_copy_status="unique",
> no_symmetric_upper=False,
> temp_dir=temp_dir,
> no_delete_temp=False,
> storage_options=None,
> append=False,
>
> )
>
> tests/test_create_ingest.py:608:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> cooler/cli/load.py:339: in load
> create_from_unordered(
> cooler/create/_create.py:723: in create_from_unordered
> create(uri, bins, chunk, columns=columns, dtypes=dtypes, mode="a", **kwargs)
> cooler/create/_create.py:514: in create
> from dask.dataframe import DataFrame as dask_df
> /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:81: in <module>
> from dask.dataframe import backends, dispatch, rolling
> /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in <module>
> from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame
> /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in <module>
> from dask.dataframe import methods
> /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in <module>
> from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like
> /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in <module>
> from dask.dataframe import ( # noqa: F401 register pandas extension types
> /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in <module>
> from dask.dataframe.extensions import make_array_nonempty, make_scalar
> /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in <module>
> from dask.dataframe.accessor import (
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in <module>
> class DatetimeAccessor(Accessor):
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__
> _bind_property(cls, pd_cls, attr, min_version)
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property
> setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func)))
> /usr/lib/python3/dist-packages/dask/utils.py:858: in wrapper
> method.__doc__ = _derived_from(
> /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from
> method_args = get_named_args(method)
> /usr/lib/python3/dist-packages/dask/utils.py:572: in get_named_args
> s = inspect.signature(func)
> /usr/lib/python3.11/inspect.py:3263: in signature
> return Signature.from_callable(obj, follow_wrapped=follow_wrapped,
> /usr/lib/python3.11/inspect.py:3011: in from_callable
> return _signature_from_callable(obj, sigcls=cls,
> /usr/lib/python3.11/inspect.py:2599: in _signature_from_callable
> call = _descriptor_get(call, obj)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> descriptor = <slot wrapper '__call__' of 'type' objects>
> obj = <property object at 0xffffb19c2200>
>
> def _descriptor_get(descriptor, obj):
> if isclass(descriptor):
> return descriptor
> get = getattr(type(descriptor), '__get__', _sentinel)
> if get is _sentinel:
> return descriptor
> > return get(descriptor, obj, type(obj))
> E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
>
> /usr/lib/python3.11/inspect.py:2432: TypeError
> _ test_merge[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool] _
>
> path1 = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool'
> path2 = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool'
>
> @pytest.mark.parametrize(
> "path1,path2",
> [
> (
> op.join(datadir, "hg19.GM12878-MboI.matrix.2000kb.cool"),
> op.join(datadir, "hg19.GM12878-MboI.matrix.2000kb.cool"),
> ),
> (
> op.join(datadir, "toy.asymm.2.cool"),
> op.join(datadir, "toy.asymm.2.cool")
> )
> ],
> )
> def test_merge(path1, path2):
> with isolated_filesystem():
> > merge_coolers("test.cool", [path1, path2], mergebuf=int(15e6))
>
> tests/test_reduce.py:30:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> cooler/reduce.py:253: in merge_coolers
> create(
> cooler/create/_create.py:514: in create
> from dask.dataframe import DataFrame as dask_df
> /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:81: in <module>
> from dask.dataframe import backends, dispatch, rolling
> /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in <module>
> from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame
> /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in <module>
> from dask.dataframe import methods
> /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in <module>
> from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like
> /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in <module>
> from dask.dataframe import ( # noqa: F401 register pandas extension types
> /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in <module>
> from dask.dataframe.extensions import make_array_nonempty, make_scalar
> /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in <module>
> from dask.dataframe.accessor import (
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in <module>
> class DatetimeAccessor(Accessor):
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__
> _bind_property(cls, pd_cls, attr, min_version)
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property
> setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func)))
> /usr/lib/python3/dist-packages/dask/utils.py:858: in wrapper
> method.__doc__ = _derived_from(
> /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from
> method_args = get_named_args(method)
> /usr/lib/python3/dist-packages/dask/utils.py:572: in get_named_args
> s = inspect.signature(func)
> /usr/lib/python3.11/inspect.py:3263: in signature
> return Signature.from_callable(obj, follow_wrapped=follow_wrapped,
> /usr/lib/python3.11/inspect.py:3011: in from_callable
> return _signature_from_callable(obj, sigcls=cls,
> /usr/lib/python3.11/inspect.py:2599: in _signature_from_callable
> call = _descriptor_get(call, obj)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> descriptor = <slot wrapper '__call__' of 'type' objects>
> obj = <property object at 0xffffb19c2200>
>
> def _descriptor_get(descriptor, obj):
> if isclass(descriptor):
> return descriptor
> get = getattr(type(descriptor), '__get__', _sentinel)
> if get is _sentinel:
> return descriptor
> > return get(descriptor, obj, type(obj))
> E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
>
> /usr/lib/python3.11/inspect.py:2432: TypeError
> _ test_merge[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.asymm.2.cool-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.asymm.2.cool] _
>
> path1 = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.asymm.2.cool'
> path2 = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.asymm.2.cool'
>
> @pytest.mark.parametrize(
> "path1,path2",
> [
> (
> op.join(datadir, "hg19.GM12878-MboI.matrix.2000kb.cool"),
> op.join(datadir, "hg19.GM12878-MboI.matrix.2000kb.cool"),
> ),
> (
> op.join(datadir, "toy.asymm.2.cool"),
> op.join(datadir, "toy.asymm.2.cool")
> )
> ],
> )
> def test_merge(path1, path2):
> with isolated_filesystem():
> > merge_coolers("test.cool", [path1, path2], mergebuf=int(15e6))
>
> tests/test_reduce.py:30:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> cooler/reduce.py:253: in merge_coolers
> create(
> cooler/create/_create.py:514: in create
> from dask.dataframe import DataFrame as dask_df
> /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:81: in <module>
> from dask.dataframe import backends, dispatch, rolling
> /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in <module>
> from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame
> /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in <module>
> from dask.dataframe import methods
> /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in <module>
> from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like
> /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in <module>
> from dask.dataframe import ( # noqa: F401 register pandas extension types
> /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in <module>
> from dask.dataframe.extensions import make_array_nonempty, make_scalar
> /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in <module>
> from dask.dataframe.accessor import (
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in <module>
> class DatetimeAccessor(Accessor):
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__
> _bind_property(cls, pd_cls, attr, min_version)
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property
> setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func)))
> /usr/lib/python3/dist-packages/dask/utils.py:858: in wrapper
> method.__doc__ = _derived_from(
> /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from
> method_args = get_named_args(method)
> /usr/lib/python3/dist-packages/dask/utils.py:572: in get_named_args
> s = inspect.signature(func)
> /usr/lib/python3.11/inspect.py:3263: in signature
> return Signature.from_callable(obj, follow_wrapped=follow_wrapped,
> /usr/lib/python3.11/inspect.py:3011: in from_callable
> return _signature_from_callable(obj, sigcls=cls,
> /usr/lib/python3.11/inspect.py:2599: in _signature_from_callable
> call = _descriptor_get(call, obj)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> descriptor = <slot wrapper '__call__' of 'type' objects>
> obj = <property object at 0xffffb19c2200>
>
> def _descriptor_get(descriptor, obj):
> if isclass(descriptor):
> return descriptor
> get = getattr(type(descriptor), '__get__', _sentinel)
> if get is _sentinel:
> return descriptor
> > return get(descriptor, obj, type(obj))
> E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
>
> /usr/lib/python3.11/inspect.py:2432: TypeError
> _________________________________ test_merge2 __________________________________
>
> def test_merge2():
> with isolated_filesystem():
> path1 = op.join(datadir, "toy.symm.upper.2.cool")
> path2 = op.join(datadir, "toy.symm.upper.2.cool")
> > merge_coolers(
> "test.cool", [path1, path2], mergebuf=3, agg={'count': 'mean'}
> )
>
> tests/test_reduce.py:42:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> cooler/reduce.py:253: in merge_coolers
> create(
> cooler/create/_create.py:514: in create
> from dask.dataframe import DataFrame as dask_df
> /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:81: in <module>
> from dask.dataframe import backends, dispatch, rolling
> /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in <module>
> from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame
> /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in <module>
> from dask.dataframe import methods
> /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in <module>
> from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like
> /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in <module>
> from dask.dataframe import ( # noqa: F401 register pandas extension types
> /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in <module>
> from dask.dataframe.extensions import make_array_nonempty, make_scalar
> /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in <module>
> from dask.dataframe.accessor import (
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in <module>
> class DatetimeAccessor(Accessor):
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__
> _bind_property(cls, pd_cls, attr, min_version)
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property
> setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func)))
> /usr/lib/python3/dist-packages/dask/utils.py:858: in wrapper
> method.__doc__ = _derived_from(
> /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from
> method_args = get_named_args(method)
> /usr/lib/python3/dist-packages/dask/utils.py:572: in get_named_args
> s = inspect.signature(func)
> /usr/lib/python3.11/inspect.py:3263: in signature
> return Signature.from_callable(obj, follow_wrapped=follow_wrapped,
> /usr/lib/python3.11/inspect.py:3011: in from_callable
> return _signature_from_callable(obj, sigcls=cls,
> /usr/lib/python3.11/inspect.py:2599: in _signature_from_callable
> call = _descriptor_get(call, obj)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> descriptor = <slot wrapper '__call__' of 'type' objects>
> obj = <property object at 0xffffb19c2200>
>
> def _descriptor_get(descriptor, obj):
> if isclass(descriptor):
> return descriptor
> get = getattr(type(descriptor), '__get__', _sentinel)
> if get is _sentinel:
> return descriptor
> > return get(descriptor, obj, type(obj))
> E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
>
> /usr/lib/python3.11/inspect.py:2432: TypeError
> _ test_coarsen[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.symm.upper.2.cool-2-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.symm.upper.4.cool] _
>
> input_uri = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.symm.upper.2.cool'
> factor = 2
> ref_uri = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.symm.upper.4.cool'
>
> @pytest.mark.parametrize(
> "input_uri,factor,ref_uri",
> [
> (
> op.join(datadir, "toy.symm.upper.2.cool"),
> 2,
> op.join(datadir, "toy.symm.upper.4.cool"),
> ),
> (
> op.join(datadir, "toy.asymm.2.cool"),
> 2,
> op.join(datadir, "toy.asymm.4.cool")
> ),
> (
> op.join(datadir, "toy.symm.upper.var.cool"),
> 2,
> op.join(datadir, "toy.symm.upper.var2x.cool"),
> ),
> ],
> )
> def test_coarsen(input_uri, factor, ref_uri):
>
> with isolated_filesystem():
> kwargs = dict(
> chunksize=10, nproc=1, columns=None, dtypes=None, agg=None
> )
> > coarsen_cooler(input_uri, "test.cool", factor, **kwargs)
>
> tests/test_reduce.py:109:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> cooler/reduce.py:712: in coarsen_cooler
> create(
> cooler/create/_create.py:514: in create
> from dask.dataframe import DataFrame as dask_df
> /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:81: in <module>
> from dask.dataframe import backends, dispatch, rolling
> /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in <module>
> from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame
> /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in <module>
> from dask.dataframe import methods
> /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in <module>
> from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like
> /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in <module>
> from dask.dataframe import ( # noqa: F401 register pandas extension types
> /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in <module>
> from dask.dataframe.extensions import make_array_nonempty, make_scalar
> /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in <module>
> from dask.dataframe.accessor import (
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in <module>
> class DatetimeAccessor(Accessor):
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__
> _bind_property(cls, pd_cls, attr, min_version)
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property
> setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func)))
> /usr/lib/python3/dist-packages/dask/utils.py:858: in wrapper
> method.__doc__ = _derived_from(
> /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from
> method_args = get_named_args(method)
> /usr/lib/python3/dist-packages/dask/utils.py:572: in get_named_args
> s = inspect.signature(func)
> /usr/lib/python3.11/inspect.py:3263: in signature
> return Signature.from_callable(obj, follow_wrapped=follow_wrapped,
> /usr/lib/python3.11/inspect.py:3011: in from_callable
> return _signature_from_callable(obj, sigcls=cls,
> /usr/lib/python3.11/inspect.py:2599: in _signature_from_callable
> call = _descriptor_get(call, obj)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> descriptor = <slot wrapper '__call__' of 'type' objects>
> obj = <property object at 0xffffb19c2200>
>
> def _descriptor_get(descriptor, obj):
> if isclass(descriptor):
> return descriptor
> get = getattr(type(descriptor), '__get__', _sentinel)
> if get is _sentinel:
> return descriptor
> > return get(descriptor, obj, type(obj))
> E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
>
> /usr/lib/python3.11/inspect.py:2432: TypeError
> _ test_coarsen[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.asymm.2.cool-2-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.asymm.4.cool] _
>
> input_uri = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.asymm.2.cool'
> factor = 2
> ref_uri = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.asymm.4.cool'
>
> @pytest.mark.parametrize(
> "input_uri,factor,ref_uri",
> [
> (
> op.join(datadir, "toy.symm.upper.2.cool"),
> 2,
> op.join(datadir, "toy.symm.upper.4.cool"),
> ),
> (
> op.join(datadir, "toy.asymm.2.cool"),
> 2,
> op.join(datadir, "toy.asymm.4.cool")
> ),
> (
> op.join(datadir, "toy.symm.upper.var.cool"),
> 2,
> op.join(datadir, "toy.symm.upper.var2x.cool"),
> ),
> ],
> )
> def test_coarsen(input_uri, factor, ref_uri):
>
> with isolated_filesystem():
> kwargs = dict(
> chunksize=10, nproc=1, columns=None, dtypes=None, agg=None
> )
> > coarsen_cooler(input_uri, "test.cool", factor, **kwargs)
>
> tests/test_reduce.py:109:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> cooler/reduce.py:712: in coarsen_cooler
> create(
> cooler/create/_create.py:514: in create
> from dask.dataframe import DataFrame as dask_df
> /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:81: in <module>
> from dask.dataframe import backends, dispatch, rolling
> /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in <module>
> from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame
> /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in <module>
> from dask.dataframe import methods
> /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in <module>
> from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like
> /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in <module>
> from dask.dataframe import ( # noqa: F401 register pandas extension types
> /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in <module>
> from dask.dataframe.extensions import make_array_nonempty, make_scalar
> /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in <module>
> from dask.dataframe.accessor import (
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in <module>
> class DatetimeAccessor(Accessor):
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__
> _bind_property(cls, pd_cls, attr, min_version)
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property
> setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func)))
> /usr/lib/python3/dist-packages/dask/utils.py:858: in wrapper
> method.__doc__ = _derived_from(
> /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from
> method_args = get_named_args(method)
> /usr/lib/python3/dist-packages/dask/utils.py:572: in get_named_args
> s = inspect.signature(func)
> /usr/lib/python3.11/inspect.py:3263: in signature
> return Signature.from_callable(obj, follow_wrapped=follow_wrapped,
> /usr/lib/python3.11/inspect.py:3011: in from_callable
> return _signature_from_callable(obj, sigcls=cls,
> /usr/lib/python3.11/inspect.py:2599: in _signature_from_callable
> call = _descriptor_get(call, obj)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> descriptor = <slot wrapper '__call__' of 'type' objects>
> obj = <property object at 0xffffb19c2200>
>
> def _descriptor_get(descriptor, obj):
> if isclass(descriptor):
> return descriptor
> get = getattr(type(descriptor), '__get__', _sentinel)
> if get is _sentinel:
> return descriptor
> > return get(descriptor, obj, type(obj))
> E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
>
> /usr/lib/python3.11/inspect.py:2432: TypeError
> _ test_coarsen[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.symm.upper.var.cool-2-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.symm.upper.var2x.cool] _
>
> input_uri = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.symm.upper.var.cool'
> factor = 2
> ref_uri = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.symm.upper.var2x.cool'
>
> @pytest.mark.parametrize(
> "input_uri,factor,ref_uri",
> [
> (
> op.join(datadir, "toy.symm.upper.2.cool"),
> 2,
> op.join(datadir, "toy.symm.upper.4.cool"),
> ),
> (
> op.join(datadir, "toy.asymm.2.cool"),
> 2,
> op.join(datadir, "toy.asymm.4.cool")
> ),
> (
> op.join(datadir, "toy.symm.upper.var.cool"),
> 2,
> op.join(datadir, "toy.symm.upper.var2x.cool"),
> ),
> ],
> )
> def test_coarsen(input_uri, factor, ref_uri):
>
> with isolated_filesystem():
> kwargs = dict(
> chunksize=10, nproc=1, columns=None, dtypes=None, agg=None
> )
> > coarsen_cooler(input_uri, "test.cool", factor, **kwargs)
>
> tests/test_reduce.py:109:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> cooler/reduce.py:712: in coarsen_cooler
> create(
> cooler/create/_create.py:514: in create
> from dask.dataframe import DataFrame as dask_df
> /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:81: in <module>
> from dask.dataframe import backends, dispatch, rolling
> /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in <module>
> from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame
> /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in <module>
> from dask.dataframe import methods
> /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in <module>
> from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like
> /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in <module>
> from dask.dataframe import ( # noqa: F401 register pandas extension types
> /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in <module>
> from dask.dataframe.extensions import make_array_nonempty, make_scalar
> /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in <module>
> from dask.dataframe.accessor import (
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in <module>
> class DatetimeAccessor(Accessor):
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__
> _bind_property(cls, pd_cls, attr, min_version)
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property
> setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func)))
> /usr/lib/python3/dist-packages/dask/utils.py:858: in wrapper
> method.__doc__ = _derived_from(
> /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from
> method_args = get_named_args(method)
> /usr/lib/python3/dist-packages/dask/utils.py:572: in get_named_args
> s = inspect.signature(func)
> /usr/lib/python3.11/inspect.py:3263: in signature
> return Signature.from_callable(obj, follow_wrapped=follow_wrapped,
> /usr/lib/python3.11/inspect.py:3011: in from_callable
> return _signature_from_callable(obj, sigcls=cls,
> /usr/lib/python3.11/inspect.py:2599: in _signature_from_callable
> call = _descriptor_get(call, obj)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> descriptor = <slot wrapper '__call__' of 'type' objects>
> obj = <property object at 0xffffb19c2200>
>
> def _descriptor_get(descriptor, obj):
> if isclass(descriptor):
> return descriptor
> get = getattr(type(descriptor), '__get__', _sentinel)
> if get is _sentinel:
> return descriptor
> > return get(descriptor, obj, type(obj))
> E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
>
> /usr/lib/python3.11/inspect.py:2432: TypeError
> ______________________ test_coarsen_partitions_correctly _______________________
>
> def test_coarsen_partitions_correctly():
> kwargs = dict(nproc=1, columns=None, dtypes=None, agg=None)
> with isolated_filesystem():
> f_ref = op.join(datadir, "odd.4.cool")
> f_in = op.join(datadir, "odd.1.cool")
> > coarsen_cooler(f_in, "odd.1.coarsen_4.cool", factor=4, chunksize=2, **kwargs)
>
> tests/test_reduce.py:145:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> cooler/reduce.py:712: in coarsen_cooler
> create(
> cooler/create/_create.py:514: in create
> from dask.dataframe import DataFrame as dask_df
> /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:81: in <module>
> from dask.dataframe import backends, dispatch, rolling
> /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in <module>
> from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame
> /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in <module>
> from dask.dataframe import methods
> /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in <module>
> from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like
> /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in <module>
> from dask.dataframe import ( # noqa: F401 register pandas extension types
> /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in <module>
> from dask.dataframe.extensions import make_array_nonempty, make_scalar
> /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in <module>
> from dask.dataframe.accessor import (
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in <module>
> class DatetimeAccessor(Accessor):
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__
> _bind_property(cls, pd_cls, attr, min_version)
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property
> setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func)))
> /usr/lib/python3/dist-packages/dask/utils.py:858: in wrapper
> method.__doc__ = _derived_from(
> /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from
> method_args = get_named_args(method)
> /usr/lib/python3/dist-packages/dask/utils.py:572: in get_named_args
> s = inspect.signature(func)
> /usr/lib/python3.11/inspect.py:3263: in signature
> return Signature.from_callable(obj, follow_wrapped=follow_wrapped,
> /usr/lib/python3.11/inspect.py:3011: in from_callable
> return _signature_from_callable(obj, sigcls=cls,
> /usr/lib/python3.11/inspect.py:2599: in _signature_from_callable
> call = _descriptor_get(call, obj)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> descriptor = <slot wrapper '__call__' of 'type' objects>
> obj = <property object at 0xffffb19c2200>
>
> def _descriptor_get(descriptor, obj):
> if isclass(descriptor):
> return descriptor
> get = getattr(type(descriptor), '__get__', _sentinel)
> if get is _sentinel:
> return descriptor
> > return get(descriptor, obj, type(obj))
> E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
>
> /usr/lib/python3.11/inspect.py:2432: TypeError
> _________________________________ test_zoomify _________________________________
>
> def test_zoomify():
> kwargs = dict(chunksize=10, nproc=1, columns=None, dtypes=None, agg=None)
> with isolated_filesystem():
> > zoomify_cooler(
> op.join(datadir, "toy.asymm.2.cool"),
> "test.2.mcool",
> resolutions=[4, 8, 16, 32],
> **kwargs
> )
>
> tests/test_reduce.py:156:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> cooler/reduce.py:832: in zoomify_cooler
> coarsen_cooler(
> cooler/reduce.py:712: in coarsen_cooler
> create(
> cooler/create/_create.py:514: in create
> from dask.dataframe import DataFrame as dask_df
> /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:81: in <module>
> from dask.dataframe import backends, dispatch, rolling
> /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in <module>
> from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame
> /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in <module>
> from dask.dataframe import methods
> /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in <module>
> from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like
> /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in <module>
> from dask.dataframe import ( # noqa: F401 register pandas extension types
> /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in <module>
> from dask.dataframe.extensions import make_array_nonempty, make_scalar
> /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in <module>
> from dask.dataframe.accessor import (
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in <module>
> class DatetimeAccessor(Accessor):
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__
> _bind_property(cls, pd_cls, attr, min_version)
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property
> setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func)))
> /usr/lib/python3/dist-packages/dask/utils.py:858: in wrapper
> method.__doc__ = _derived_from(
> /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from
> method_args = get_named_args(method)
> /usr/lib/python3/dist-packages/dask/utils.py:572: in get_named_args
> s = inspect.signature(func)
> /usr/lib/python3.11/inspect.py:3263: in signature
> return Signature.from_callable(obj, follow_wrapped=follow_wrapped,
> /usr/lib/python3.11/inspect.py:3011: in from_callable
> return _signature_from_callable(obj, sigcls=cls,
> /usr/lib/python3.11/inspect.py:2599: in _signature_from_callable
> call = _descriptor_get(call, obj)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> descriptor = <slot wrapper '__call__' of 'type' objects>
> obj = <property object at 0xffffb19c2200>
>
> def _descriptor_get(descriptor, obj):
> if isclass(descriptor):
> return descriptor
> get = getattr(type(descriptor), '__get__', _sentinel)
> if get is _sentinel:
> return descriptor
> > return get(descriptor, obj, type(obj))
> E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
>
> /usr/lib/python3.11/inspect.py:2432: TypeError
> _____________________________ test_legacy_zoomify ______________________________
>
> def test_legacy_zoomify():
> infile = op.join(datadir, "hg19.GM12878-MboI.matrix.2000kb.cool")
> chunksize = int(10e6)
> # n_zooms = 2
> n_cpus = 1
> with isolated_filesystem():
> > legacy_zoomify(infile, "test.multires.cool", n_cpus, chunksize)
>
> tests/test_reduce.py:197:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> cooler/reduce.py:900: in legacy_zoomify
> coarsen_cooler(
> cooler/reduce.py:712: in coarsen_cooler
> create(
> cooler/create/_create.py:514: in create
> from dask.dataframe import DataFrame as dask_df
> /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:81: in <module>
> from dask.dataframe import backends, dispatch, rolling
> /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in <module>
> from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame
> /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in <module>
> from dask.dataframe import methods
> /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in <module>
> from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like
> /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in <module>
> from dask.dataframe import ( # noqa: F401 register pandas extension types
> /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in <module>
> from dask.dataframe.extensions import make_array_nonempty, make_scalar
> /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in <module>
> from dask.dataframe.accessor import (
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in <module>
> class DatetimeAccessor(Accessor):
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__
> _bind_property(cls, pd_cls, attr, min_version)
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property
> setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func)))
> /usr/lib/python3/dist-packages/dask/utils.py:858: in wrapper
> method.__doc__ = _derived_from(
> /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from
> method_args = get_named_args(method)
> /usr/lib/python3/dist-packages/dask/utils.py:572: in get_named_args
> s = inspect.signature(func)
> /usr/lib/python3.11/inspect.py:3263: in signature
> return Signature.from_callable(obj, follow_wrapped=follow_wrapped,
> /usr/lib/python3.11/inspect.py:3011: in from_callable
> return _signature_from_callable(obj, sigcls=cls,
> /usr/lib/python3.11/inspect.py:2599: in _signature_from_callable
> call = _descriptor_get(call, obj)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> descriptor = <slot wrapper '__call__' of 'type' objects>
> obj = <property object at 0xffffb19c2200>
>
> def _descriptor_get(descriptor, obj):
> if isclass(descriptor):
> return descriptor
> get = getattr(type(descriptor), '__get__', _sentinel)
> if get is _sentinel:
> return descriptor
> > return get(descriptor, obj, type(obj))
> E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
>
> /usr/lib/python3.11/inspect.py:2432: TypeError
> _______________________________ test_append_mode _______________________________
>
> def test_append_mode():
> # merge
> path1 = path2 = op.join(datadir, "toy.asymm.2.cool")
> out_path = "test.cool"
> for append in (True, False):
> with isolated_filesystem():
> with h5py.File("test.cool", "w") as f:
> f.attrs["xxxx"] = True
> > merge_coolers(
> out_path,
> [path1, path2],
> mergebuf=int(15e6),
> mode="a" if append else "w"
> )
>
> tests/test_reduce.py:208:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> cooler/reduce.py:253: in merge_coolers
> create(
> cooler/create/_create.py:514: in create
> from dask.dataframe import DataFrame as dask_df
> /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:81: in <module>
> from dask.dataframe import backends, dispatch, rolling
> /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in <module>
> from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame
> /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in <module>
> from dask.dataframe import methods
> /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in <module>
> from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like
> /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in <module>
> from dask.dataframe import ( # noqa: F401 register pandas extension types
> /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in <module>
> from dask.dataframe.extensions import make_array_nonempty, make_scalar
> /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in <module>
> from dask.dataframe.accessor import (
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in <module>
> class DatetimeAccessor(Accessor):
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__
> _bind_property(cls, pd_cls, attr, min_version)
> /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property
> setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func)))
> /usr/lib/python3/dist-packages/dask/utils.py:858: in wrapper
> method.__doc__ = _derived_from(
> /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from
> method_args = get_named_args(method)
> /usr/lib/python3/dist-packages/dask/utils.py:572: in get_named_args
> s = inspect.signature(func)
> /usr/lib/python3.11/inspect.py:3263: in signature
> return Signature.from_callable(obj, follow_wrapped=follow_wrapped,
> /usr/lib/python3.11/inspect.py:3011: in from_callable
> return _signature_from_callable(obj, sigcls=cls,
> /usr/lib/python3.11/inspect.py:2599: in _signature_from_callable
> call = _descriptor_get(call, obj)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> descriptor = <slot wrapper '__call__' of 'type' objects>
> obj = <property object at 0xffffb19c2200>
>
> def _descriptor_get(descriptor, obj):
> if isclass(descriptor):
> return descriptor
> get = getattr(type(descriptor), '__get__', _sentinel)
> if get is _sentinel:
> return descriptor
> > return get(descriptor, obj, type(obj))
> E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
>
> /usr/lib/python3.11/inspect.py:2432: TypeError
> =============================== warnings summary ===============================
> tests/test_api.py::test_bintable_many_contigs
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/test_api.py:44: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
> assert pd.api.types.is_categorical_dtype(bins["chrom"].dtype)
>
> tests/test_api.py::test_bintable_many_contigs
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/test_api.py:47: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
> assert pd.api.types.is_categorical_dtype(bins["chrom"].dtype)
>
> tests/test_api.py::test_bintable_many_contigs
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/test_api.py:51: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
> assert pd.api.types.is_categorical_dtype(chroms.dtype)
>
> tests/test_balance.py::test_balancing_other_options[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.symm.upper.2.cool-0.01]
> tests/test_cli_ops.py::test_zoomify
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/cooler/balance.py:112: RuntimeWarning: Mean of empty slice.
> scale = nzmarg.mean()
>
> tests/test_balance.py::test_balancing_other_options[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.symm.upper.2.cool-0.01]
> tests/test_cli_ops.py::test_zoomify
> /usr/lib/python3/dist-packages/numpy/core/_methods.py:129: RuntimeWarning: invalid value encountered in scalar divide
> ret = ret.dtype.type(ret / rcount)
>
> tests/test_cli.py::test_makebins
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/cooler/cli/makebins.py:55: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
> bins["id"] = bins.groupby("chrom").cumcount()
>
> tests/test_cli_ingest.py: 11 warnings
> tests/test_cli_ops.py: 2 warnings
> tests/test_create_ingest.py: 13 warnings
> tests/test_create_sanitize.py: 18 warnings
> tests/test_reduce.py: 6 warnings
> tests/test_util.py: 2 warnings
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/cooler/util.py:730: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
> is_cat = pd.api.types.is_categorical_dtype(bins["chrom"])
>
> tests/test_cli_ingest.py: 11 warnings
> tests/test_cli_ops.py: 2 warnings
> tests/test_create_ingest.py: 13 warnings
> tests/test_create_sanitize.py: 18 warnings
> tests/test_reduce.py: 6 warnings
> tests/test_util.py: 1 warning
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/cooler/util.py:771: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
> self._bins_grouped = bins.groupby("chrom", sort=False)
>
> tests/test_cli_ingest.py: 11 warnings
> tests/test_cli_ops.py: 2 warnings
> tests/test_create_ingest.py: 13 warnings
> tests/test_create_sanitize.py: 18 warnings
> tests/test_reduce.py: 6 warnings
> tests/test_util.py: 2 warnings
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/cooler/util.py:395: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
> for _chrom, group in bins.groupby("chrom"):
>
> tests/test_cli_ingest.py: 11 warnings
> tests/test_create_ingest.py: 8 warnings
> tests/test_create_sanitize.py: 9 warnings
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/cooler/create/_ingest.py:133: FutureWarning: Series.__getitem__ treating keys as positions is deprecated. In a future version, integer keys will always be treated as labels (consistent with DataFrame behavior). To access a value by position, use `ser.iloc[pos]`
> chromsizes1 = gs.chromsizes[chrom1_ids].values
>
> tests/test_cli_ingest.py: 11 warnings
> tests/test_create_ingest.py: 8 warnings
> tests/test_create_sanitize.py: 9 warnings
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/cooler/create/_ingest.py:134: FutureWarning: Series.__getitem__ treating keys as positions is deprecated. In a future version, integer keys will always be treated as labels (consistent with DataFrame behavior). To access a value by position, use `ser.iloc[pos]`
> chromsizes2 = gs.chromsizes[chrom2_ids].values
>
> tests/test_cli_ingest.py::test_cload_symm_asymm[asymm-extra_args2]
> /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:80: PytestUnraisableExceptionWarning: Exception ignored in: <function _TemporaryFileCloser.__del__ at 0xffffb8971440>
>
> Traceback (most recent call last):
> File "/usr/lib/python3.11/tempfile.py", line 606, in __del__
> self.close()
> File "/usr/lib/python3.11/tempfile.py", line 602, in close
> unlink(self.name)
> FileNotFoundError: [Errno 2] No such file or directory: '/tmp/tmpa3vw1tcx/tmptn4kuii7.multi.cool'
>
> warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
>
> tests/test_cli_ingest.py::test_load_symm_asymm[symm.upper-extra_args1]
> /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:80: PytestUnraisableExceptionWarning: Exception ignored in: <function _TemporaryFileCloser.__del__ at 0xffffb8971440>
>
> Traceback (most recent call last):
> File "/usr/lib/python3.11/tempfile.py", line 606, in __del__
> self.close()
> File "/usr/lib/python3.11/tempfile.py", line 602, in close
> unlink(self.name)
> FileNotFoundError: [Errno 2] No such file or directory: '/tmp/tmp439pwc_k/tmpkmcc2_kc.multi.cool'
>
> warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
>
> tests/test_cli_ingest.py::test_load_field2
> /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:80: PytestUnraisableExceptionWarning: Exception ignored in: <function _TemporaryFileCloser.__del__ at 0xffffb8971440>
>
> Traceback (most recent call last):
> File "/usr/lib/python3.11/tempfile.py", line 606, in __del__
> self.close()
> File "/usr/lib/python3.11/tempfile.py", line 602, in close
> unlink(self.name)
> FileNotFoundError: [Errno 2] No such file or directory: '/tmp/tmpj_7otwlk/tmpu1j_rplz.multi.cool'
>
> warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
>
> tests/test_cli_ops.py::test_coarsen
> tests/test_cli_ops.py::test_zoomify
> tests/test_reduce.py::test_coarsen[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.symm.upper.2.cool-2-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.symm.upper.4.cool]
> tests/test_reduce.py::test_coarsen[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.asymm.2.cool-2-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.asymm.4.cool]
> tests/test_reduce.py::test_coarsen[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.symm.upper.var.cool-2-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.symm.upper.var2x.cool]
> tests/test_reduce.py::test_coarsen_partitions_correctly
> tests/test_reduce.py::test_zoomify
> tests/test_reduce.py::test_legacy_zoomify
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/cooler/reduce.py:548: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
> return old_bins.groupby("chrom").apply(_each).reset_index(drop=True)
>
> tests/test_cli_ops.py::test_zoomify
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/cooler/cli/zoomify.py:198: UserWarning: Map is already < 256 x 256. Provide resolutions explicitly if you want to coarsen more.
> warnings.warn(
>
> tests/test_cli_ops.py::test_zoomify
> tests/test_cli_ops.py::test_zoomify
> tests/test_reduce.py::test_zoomify
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/cooler/reduce.py:792: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
> n_bins_longest_chrom[base_binsize] = clr.bins()[:].groupby("chrom").size().max()
>
> tests/test_cli_ops.py::test_zoomify
> /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:80: PytestUnraisableExceptionWarning: Exception ignored in: <function _TemporaryFileCloser.__del__ at 0xffffb8971440>
>
> Traceback (most recent call last):
> File "/usr/lib/python3.11/tempfile.py", line 606, in __del__
> self.close()
> File "/usr/lib/python3.11/tempfile.py", line 602, in close
> unlink(self.name)
> FileNotFoundError: [Errno 2] No such file or directory: '/tmp/tmpi8kk3ih0/tmp_sf3nv42.multi.cool'
>
> warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
>
> tests/test_cli_ops.py::test_balance
> tests/test_cli_ops.py::test_balance
> tests/test_cli_ops.py::test_balance
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/cooler/balance.py:108: ConvergenceWarning: Iteration limit reached without convergence.
> warnings.warn(
>
> tests/test_cli_ops.py::test_balance
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/cooler/cli/balance.py:183: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
> bins_grouped = clr.bins()[:].groupby('chrom')
>
> tests/test_core.py::test_put
> tests/test_core.py::test_put
> tests/test_core.py::test_put
> tests/test_core.py::test_put
> tests/test_core.py::test_put
> tests/test_core.py::test_put
> tests/test_create.py::test_write
> tests/test_create.py::test_write
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/cooler/core/_tableops.py:120: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
> elif is_categorical_dtype(data):
>
> tests/test_core.py::test_put
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/test_core.py:94: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
> assert pd.api.types.is_categorical_dtype(out['chrom_enum'].dtype)
>
> tests/test_core.py::test_put
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/test_core.py:104: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
> assert not pd.api.types.is_categorical_dtype(out['chrom_string'].dtype)
>
> tests/test_create.py::test_rename_chroms
> tests/test_create.py::test_many_contigs
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/cooler/create/_create.py:349: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
> if is_categorical_dtype(bins["chrom"]):
>
> tests/test_reduce.py::test_merge[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool]
> tests/test_reduce.py::test_merge[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.asymm.2.cool-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.asymm.2.cool]
> tests/test_reduce.py::test_merge2
> tests/test_reduce.py::test_append_mode
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/cooler/reduce.py:247: DeprecationWarning: np.find_common_type is deprecated. Please use `np.result_type` or `np.promote_types`.
> See https://numpy.org/devdocs/release/1.25.0-notes.html and the docs for more information. (Deprecated NumPy 1.25)
> dtypes[col] = np.find_common_type(dtype_map[col], [])
>
> tests/test_util.py::test_bedslice
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/test_util.py:234: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
> grouped = bins.groupby('chrom')
>
> tests/test_util.py::test_check_bins
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/test_util.py:312: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
> assert pd.api.types.is_categorical_dtype(bins["chrom"])
>
> -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
> =========================== short test summary info ============================
> FAILED tests/test_cli_export.py::test_dump - TypeError: descriptor '__call__'...
> FAILED tests/test_cli_ingest.py::test_cload_symm_asymm[symm.upper-extra_args0]
> FAILED tests/test_cli_ingest.py::test_cload_symm_asymm[symm.upper-extra_args1]
> FAILED tests/test_cli_ingest.py::test_cload_symm_asymm[asymm-extra_args2] - a...
> FAILED tests/test_cli_ingest.py::test_cload_mergepass[symm.upper-extra_args0]
> FAILED tests/test_cli_ingest.py::test_cload_field - assert 1 == 0
> FAILED tests/test_cli_ingest.py::test_cload_other_options - assert 1 == 0
> FAILED tests/test_cli_ingest.py::test_load_symm_asymm[symm.upper-extra_args0]
> FAILED tests/test_cli_ingest.py::test_load_symm_asymm[symm.upper-extra_args1]
> FAILED tests/test_cli_ingest.py::test_load_symm_asymm[asymm-extra_args2] - as...
> FAILED tests/test_cli_ingest.py::test_load_field - assert 1 == 0
> FAILED tests/test_cli_ingest.py::test_load_field2 - assert 1 == 0
> FAILED tests/test_cli_ops.py::test_merge - assert 1 == 0
> FAILED tests/test_cli_ops.py::test_coarsen - assert 1 == 0
> FAILED tests/test_cli_ops.py::test_zoomify - assert 1 == 0
> FAILED tests/test_create.py::test_create_append[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool]
> FAILED tests/test_create.py::test_create_custom_cols - TypeError: descriptor ...
> FAILED tests/test_create.py::test_create_cooler - TypeError: descriptor '__ca...
> FAILED tests/test_create.py::test_create_cooler_from_dask - TypeError: descri...
> FAILED tests/test_create.py::test_create_scool[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool]
> FAILED tests/test_create_ingest.py::test_from_hdf5_pairs - TypeError: descrip...
> FAILED tests/test_create_ingest.py::test_cload_tabix[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/hg19.bins.2000kb.bed.gz-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/hg19.GM12878-MboI.pairs.subsample.sorted.txt.gz-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool]
> FAILED tests/test_create_ingest.py::test_cload_pairix[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/hg19.bins.2000kb.bed.gz-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/hg19.GM12878-MboI.pairs.subsample.blksrt.txt.gz-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool]
> FAILED tests/test_create_ingest.py::test_cload_pairs[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.bins.var.bed-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.pairs-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.symm.upper.var.cool]
> FAILED tests/test_create_ingest.py::test_cload_pairs[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.bins.var.bed-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy_hash.pairs-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.symm.upper.var.cool]
> FAILED tests/test_create_ingest.py::test_cload_pairs[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.bins.var.bed-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy_hash.pairs.gz-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.symm.upper.var.cool]
> FAILED tests/test_create_ingest.py::test_cload_field[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.chrom.sizes:2-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.pairs]
> FAILED tests/test_create_ingest.py::test_cload_custom_tempdir[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.chrom.sizes:2-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.pairs]
> FAILED tests/test_create_ingest.py::test_load_bg2_vs_coo - TypeError: descrip...
> FAILED tests/test_create_ingest.py::test_load_zero_one_based_bg2 - TypeError:...
> FAILED tests/test_create_ingest.py::test_load_zero_one_based_coo - TypeError:...
> FAILED tests/test_create_ingest.py::test_cload_append_mode - TypeError: descr...
> FAILED tests/test_create_ingest.py::test_load_append_mode - TypeError: descri...
> FAILED tests/test_create_ingest.py::test_load_custom_tempdir - TypeError: des...
> FAILED tests/test_reduce.py::test_merge[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool]
> FAILED tests/test_reduce.py::test_merge[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.asymm.2.cool-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.asymm.2.cool]
> FAILED tests/test_reduce.py::test_merge2 - TypeError: descriptor '__call__' f...
> FAILED tests/test_reduce.py::test_coarsen[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.symm.upper.2.cool-2-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.symm.upper.4.cool]
> FAILED tests/test_reduce.py::test_coarsen[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.asymm.2.cool-2-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.asymm.4.cool]
> FAILED tests/test_reduce.py::test_coarsen[/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.symm.upper.var.cool-2-/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.symm.upper.var2x.cool]
> FAILED tests/test_reduce.py::test_coarsen_partitions_correctly - TypeError: d...
> FAILED tests/test_reduce.py::test_zoomify - TypeError: descriptor '__call__' ...
> FAILED tests/test_reduce.py::test_legacy_zoomify - TypeError: descriptor '__c...
> FAILED tests/test_reduce.py::test_append_mode - TypeError: descriptor '__call...
> =========== 44 failed, 86 passed, 6 skipped, 257 warnings in 24.41s ============
> E: pybuild pybuild:389: test: plugin pyproject failed with: exit code=1: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cooler/build; python3.11 -m pytest tests
> dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.12 3.11" returned exit code 13
The full build log is available from:
http://qa-logs.debian.net/2024/04/20/python-cooler_0.9.3-1_unstable-arm64.log
All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20240420;users=lucas@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20240420&fusertaguser=lucas@debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results
A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
If you reassign this bug to another package, please mark it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects
If you fail to reproduce this, please provide a build log and diff it with mine
so that we can identify if something relevant changed in the meantime.
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