[Debian-med-packaging] Bug#1136139: python-biom-format: FTBFS with python3-click 8.3.3: ModuleNotFoundError: No module named 'biom._filter'
Sérgio Cipriano
cipriano at debian.org
Sun May 10 04:39:26 BST 2026
Source: python-biom-format
Version: 2.1.17-1
Severity: normal
Justification: FTBFS
Tags: ftbfs experimental
User: debian-python at lists.debian.org
Usertags: python3-click-8.3.3
Hi,
I have completed a rebuild of the reverse dependencies of python3-click in
order to add support for version 8.3.3. The package python-biom-format was found to
fail to build in that situation.
To reproduce this locally, you need to install python3-click from experimental
on an unstable system or build chroot. Like this:
sbuild --extra-repository='deb http://deb.debian.org/debian experimental main' --starting-build-commands='apt-get update && apt-get -t experimental install --only-upgrade -y python-click'
Relevant part (hopefully):
> make[1]: Entering directory '/build/reproducible-path/python-biom-format-2.1.17'
> # arch
> USE_CYTHON=true dh_auto_build
> pybuild --build -i python{version} -p "3.14 3.13" --parallel=8
> I: pybuild plugin_pyproject:142: Building wheel for python3.14 with "build" module
> I: pybuild base:385: python3.14 -m build --skip-dependency-check --no-isolation --wheel --outdir /build/reproducible-path/python-biom-format-2.1.17/.pybuild/cpython3_3.14_biom-format
> * Building wheel...
> [1/3] Cythonizing biom/_filter.pyx
> [2/3] Cythonizing biom/_subsample.pyx
> [3/3] Cythonizing biom/_transform.pyx
> /usr/lib/python3/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated
> !!
>
> ********************************************************************************
> Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0).
>
> This deprecation is overdue, please update your project and remove deprecated
> calls to avoid build errors in the future.
>
> See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
> ********************************************************************************
>
> !!
> corresp(dist, value, root_dir)
> /usr/lib/python3/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated.
> !!
>
> ********************************************************************************
> Please consider removing the following classifiers in favor of a SPDX license expression:
>
> License :: OSI Approved :: BSD License
>
> See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
> ********************************************************************************
>
> !!
> dist._finalize_license_expression()
> /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
> !!
>
> ********************************************************************************
> Please consider removing the following classifiers in favor of a SPDX license expression:
>
> License :: OSI Approved :: BSD License
>
> See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
> ********************************************************************************
>
> !!
> self._finalize_license_expression()
> running bdist_wheel
> running build
> running build_py
> creating build/lib.linux-x86_64-cpython-314/doc
> copying doc/conf.py -> build/lib.linux-x86_64-cpython-314/doc
> creating build/lib.linux-x86_64-cpython-314/biom
> copying biom/__init__.py -> build/lib.linux-x86_64-cpython-314/biom
> copying biom/util.py -> build/lib.linux-x86_64-cpython-314/biom
> copying biom/table.py -> build/lib.linux-x86_64-cpython-314/biom
> copying biom/parse.py -> build/lib.linux-x86_64-cpython-314/biom
> copying biom/exception.py -> build/lib.linux-x86_64-cpython-314/biom
> copying biom/err.py -> build/lib.linux-x86_64-cpython-314/biom
> creating build/lib.linux-x86_64-cpython-314/doc/sphinxext/numpydoc/numpydoc
> copying doc/sphinxext/numpydoc/numpydoc/numpydoc.py -> build/lib.linux-x86_64-cpython-314/doc/sphinxext/numpydoc/numpydoc
> copying doc/sphinxext/numpydoc/numpydoc/linkcode.py -> build/lib.linux-x86_64-cpython-314/doc/sphinxext/numpydoc/numpydoc
> copying doc/sphinxext/numpydoc/numpydoc/__init__.py -> build/lib.linux-x86_64-cpython-314/doc/sphinxext/numpydoc/numpydoc
> copying doc/sphinxext/numpydoc/numpydoc/traitsdoc.py -> build/lib.linux-x86_64-cpython-314/doc/sphinxext/numpydoc/numpydoc
> copying doc/sphinxext/numpydoc/numpydoc/plot_directive.py -> build/lib.linux-x86_64-cpython-314/doc/sphinxext/numpydoc/numpydoc
> copying doc/sphinxext/numpydoc/numpydoc/phantom_import.py -> build/lib.linux-x86_64-cpython-314/doc/sphinxext/numpydoc/numpydoc
> copying doc/sphinxext/numpydoc/numpydoc/docscrape_sphinx.py -> build/lib.linux-x86_64-cpython-314/doc/sphinxext/numpydoc/numpydoc
> copying doc/sphinxext/numpydoc/numpydoc/docscrape.py -> build/lib.linux-x86_64-cpython-314/doc/sphinxext/numpydoc/numpydoc
> copying doc/sphinxext/numpydoc/numpydoc/compiler_unparse.py -> build/lib.linux-x86_64-cpython-314/doc/sphinxext/numpydoc/numpydoc
> copying doc/sphinxext/numpydoc/numpydoc/comment_eater.py -> build/lib.linux-x86_64-cpython-314/doc/sphinxext/numpydoc/numpydoc
> creating build/lib.linux-x86_64-cpython-314/doc/sphinxext/numpydoc/numpydoc/tests
> copying doc/sphinxext/numpydoc/numpydoc/tests/test_traitsdoc.py -> build/lib.linux-x86_64-cpython-314/doc/sphinxext/numpydoc/numpydoc/tests
> copying doc/sphinxext/numpydoc/numpydoc/tests/test_plot_directive.py -> build/lib.linux-x86_64-cpython-314/doc/sphinxext/numpydoc/numpydoc/tests
> copying doc/sphinxext/numpydoc/numpydoc/tests/test_phantom_import.py -> build/lib.linux-x86_64-cpython-314/doc/sphinxext/numpydoc/numpydoc/tests
> copying doc/sphinxext/numpydoc/numpydoc/tests/test_linkcode.py -> build/lib.linux-x86_64-cpython-314/doc/sphinxext/numpydoc/numpydoc/tests
> copying doc/sphinxext/numpydoc/numpydoc/tests/test_docscrape.py -> build/lib.linux-x86_64-cpython-314/doc/sphinxext/numpydoc/numpydoc/tests
> creating build/lib.linux-x86_64-cpython-314/biom/tests
> copying biom/tests/test_util.py -> build/lib.linux-x86_64-cpython-314/biom/tests
> copying biom/tests/test_table.py -> build/lib.linux-x86_64-cpython-314/biom/tests
> copying biom/tests/test_parse.py -> build/lib.linux-x86_64-cpython-314/biom/tests
> copying biom/tests/test_err.py -> build/lib.linux-x86_64-cpython-314/biom/tests
> copying biom/tests/long_lines.py -> build/lib.linux-x86_64-cpython-314/biom/tests
> copying biom/tests/__init__.py -> build/lib.linux-x86_64-cpython-314/biom/tests
> creating build/lib.linux-x86_64-cpython-314/biom/cli
> copying biom/cli/util.py -> build/lib.linux-x86_64-cpython-314/biom/cli
> copying biom/cli/uc_processor.py -> build/lib.linux-x86_64-cpython-314/biom/cli
> copying biom/cli/table_validator.py -> build/lib.linux-x86_64-cpython-314/biom/cli
> copying biom/cli/table_summarizer.py -> build/lib.linux-x86_64-cpython-314/biom/cli
> copying biom/cli/table_subsetter.py -> build/lib.linux-x86_64-cpython-314/biom/cli
> copying biom/cli/table_normalizer.py -> build/lib.linux-x86_64-cpython-314/biom/cli
> copying biom/cli/table_ids.py -> build/lib.linux-x86_64-cpython-314/biom/cli
> copying biom/cli/table_head.py -> build/lib.linux-x86_64-cpython-314/biom/cli
> copying biom/cli/table_converter.py -> build/lib.linux-x86_64-cpython-314/biom/cli
> copying biom/cli/metadata_exporter.py -> build/lib.linux-x86_64-cpython-314/biom/cli
> copying biom/cli/metadata_adder.py -> build/lib.linux-x86_64-cpython-314/biom/cli
> copying biom/cli/installation_informer.py -> build/lib.linux-x86_64-cpython-314/biom/cli
> copying biom/cli/__init__.py -> build/lib.linux-x86_64-cpython-314/biom/cli
> creating build/lib.linux-x86_64-cpython-314/biom/assets
> copying biom/assets/exercise_api.py -> build/lib.linux-x86_64-cpython-314/biom/assets
> creating build/lib.linux-x86_64-cpython-314/biom/tests/test_data
> copying biom/tests/test_data/__init__.py -> build/lib.linux-x86_64-cpython-314/biom/tests/test_data
> creating build/lib.linux-x86_64-cpython-314/biom/tests/test_cli
> copying biom/tests/test_cli/test_validate_table.py -> build/lib.linux-x86_64-cpython-314/biom/tests/test_cli
> copying biom/tests/test_cli/test_uc_processor.py -> build/lib.linux-x86_64-cpython-314/biom/tests/test_cli
> copying biom/tests/test_cli/test_table_normalizer.py -> build/lib.linux-x86_64-cpython-314/biom/tests/test_cli
> copying biom/tests/test_cli/test_table_converter.py -> build/lib.linux-x86_64-cpython-314/biom/tests/test_cli
> copying biom/tests/test_cli/test_summarize_table.py -> build/lib.linux-x86_64-cpython-314/biom/tests/test_cli
> copying biom/tests/test_cli/test_subset_table.py -> build/lib.linux-x86_64-cpython-314/biom/tests/test_cli
> copying biom/tests/test_cli/test_show_install_info.py -> build/lib.linux-x86_64-cpython-314/biom/tests/test_cli
> copying biom/tests/test_cli/test_add_metadata.py -> build/lib.linux-x86_64-cpython-314/biom/tests/test_cli
> copying biom/tests/test_cli/__init__.py -> build/lib.linux-x86_64-cpython-314/biom/tests/test_cli
> running egg_info
> creating biom_format.egg-info
> writing biom_format.egg-info/PKG-INFO
> writing dependency_links to biom_format.egg-info/dependency_links.txt
> writing entry points to biom_format.egg-info/entry_points.txt
> writing requirements to biom_format.egg-info/requires.txt
> writing top-level names to biom_format.egg-info/top_level.txt
> writing manifest file 'biom_format.egg-info/SOURCES.txt'
> dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
> dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
> dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
> dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
> dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
> dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
> dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
> dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
> dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
> dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
> dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
> dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
> dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
> dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
> dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
> reading manifest file 'biom_format.egg-info/SOURCES.txt'
> reading manifest template 'MANIFEST.in'
> warning: no directories found matching 'support_files'
> warning: no directories found matching 'tests/test_data'
> no previously-included directories found matching 'docs/_build'
> warning: no previously-included files matching '*.pyc' found anywhere in distribution
> warning: no previously-included files matching '*.pyo' found anywhere in distribution
> warning: no previously-included files matching '.git' found anywhere in distribution
> warning: no previously-included files matching '*.so' found anywhere in distribution
> warning: no previously-included files matching '.*.swp' found anywhere in distribution
> adding license file 'COPYING.txt'
> writing manifest file 'biom_format.egg-info/SOURCES.txt'
> creating build/lib.linux-x86_64-cpython-314/licenses
> copying licenses/numpydoc.txt -> build/lib.linux-x86_64-cpython-314/licenses
> copying licenses/scikit-learn.txt -> build/lib.linux-x86_64-cpython-314/licenses
> copying licenses/scipy.txt -> build/lib.linux-x86_64-cpython-314/licenses
> creating build/lib.linux-x86_64-cpython-314/examples
> copying examples/min_sparse_otu_table.biom -> build/lib.linux-x86_64-cpython-314/examples
> copying examples/min_sparse_otu_table_hdf5.biom -> build/lib.linux-x86_64-cpython-314/examples
> copying examples/obs_md.txt -> build/lib.linux-x86_64-cpython-314/examples
> copying examples/rich_sparse_otu_table.biom -> build/lib.linux-x86_64-cpython-314/examples
> copying examples/rich_sparse_otu_table_hdf5.biom -> build/lib.linux-x86_64-cpython-314/examples
> copying examples/rich_sparse_otu_table_hdf5_group_metadata.biom -> build/lib.linux-x86_64-cpython-314/examples
> copying examples/sam_md.txt -> build/lib.linux-x86_64-cpython-314/examples
> copying doc/BIOM_LICENSE.rst -> build/lib.linux-x86_64-cpython-314/doc
> copying doc/Makefile -> build/lib.linux-x86_64-cpython-314/doc
> copying doc/index.rst -> build/lib.linux-x86_64-cpython-314/doc
> copying biom/_filter.pyx -> build/lib.linux-x86_64-cpython-314/biom
> copying biom/_subsample.pyx -> build/lib.linux-x86_64-cpython-314/biom
> copying biom/_transform.pyx -> build/lib.linux-x86_64-cpython-314/biom
> creating build/lib.linux-x86_64-cpython-314/doc/documentation
> copying doc/documentation/adding_metadata.rst -> build/lib.linux-x86_64-cpython-314/doc/documentation
> copying doc/documentation/biom_conversion.rst -> build/lib.linux-x86_64-cpython-314/doc/documentation
> copying doc/documentation/biom_format.rst -> build/lib.linux-x86_64-cpython-314/doc/documentation
> copying doc/documentation/index.rst -> build/lib.linux-x86_64-cpython-314/doc/documentation
> copying doc/documentation/quick_usage_examples.rst -> build/lib.linux-x86_64-cpython-314/doc/documentation
> copying doc/documentation/summarizing_biom_tables.rst -> build/lib.linux-x86_64-cpython-314/doc/documentation
> copying doc/documentation/table_objects.rst -> build/lib.linux-x86_64-cpython-314/doc/documentation
> creating build/lib.linux-x86_64-cpython-314/doc/_static
> copying doc/_static/biom-format.png -> build/lib.linux-x86_64-cpython-314/doc/_static
> copying doc/_static/copybutton.js -> build/lib.linux-x86_64-cpython-314/doc/_static
> copying doc/sphinxext/numpydoc/LICENSE.txt -> build/lib.linux-x86_64-cpython-314/doc/sphinxext/numpydoc
> copying doc/sphinxext/numpydoc/README.rst -> build/lib.linux-x86_64-cpython-314/doc/sphinxext/numpydoc
> creating build/lib.linux-x86_64-cpython-314/doc/documentation/format_versions
> copying doc/documentation/format_versions/biom-1.0.rst -> build/lib.linux-x86_64-cpython-314/doc/documentation/format_versions
> copying doc/documentation/format_versions/biom-2.0.rst -> build/lib.linux-x86_64-cpython-314/doc/documentation/format_versions
> copying doc/documentation/format_versions/biom-2.1.rst -> build/lib.linux-x86_64-cpython-314/doc/documentation/format_versions
> creating build/lib.linux-x86_64-cpython-314/doc/_templates/autosummary
> copying doc/_templates/autosummary/attribute.rst -> build/lib.linux-x86_64-cpython-314/doc/_templates/autosummary
> copying doc/_templates/autosummary/class.rst -> build/lib.linux-x86_64-cpython-314/doc/_templates/autosummary
> copying doc/_templates/autosummary/method.rst -> build/lib.linux-x86_64-cpython-314/doc/_templates/autosummary
> copying biom/assets/exercise_cli.sh -> build/lib.linux-x86_64-cpython-314/biom/assets
> copying biom/tests/test_data/bad_table.txt -> build/lib.linux-x86_64-cpython-314/biom/tests/test_data
> copying biom/tests/test_data/bad_table.txt.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/test_data
> copying biom/tests/test_data/edgecase_issue_952.biom -> build/lib.linux-x86_64-cpython-314/biom/tests/test_data
> copying biom/tests/test_data/empty.biom -> build/lib.linux-x86_64-cpython-314/biom/tests/test_data
> copying biom/tests/test_data/no-contents.biom -> build/lib.linux-x86_64-cpython-314/biom/tests/test_data
> copying biom/tests/test_data/test.biom -> build/lib.linux-x86_64-cpython-314/biom/tests/test_data
> copying biom/tests/test_data/test.json -> build/lib.linux-x86_64-cpython-314/biom/tests/test_data
> copying biom/tests/test_data/test.json.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/test_data
> copying biom/tests/test_data/test_grp_metadata.biom -> build/lib.linux-x86_64-cpython-314/biom/tests/test_data
> creating build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x10000x0.001_bench.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x10000x0.001_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x10000x0.010_bench.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x10000x0.010_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x10000x0.100_bench.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x10000x0.100_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x1000x0.001_bench.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x1000x0.001_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x1000x0.010_bench.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x1000x0.010_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x1000x0.100_bench.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x1000x0.100_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x100x0.001_bench.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x100x0.001_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x100x0.010_bench.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x100x0.010_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x100x0.100_bench.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x100x0.100_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x10x0.001_bench.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x10x0.001_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x10x0.010_bench.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x10x0.010_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x10x0.100_bench.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x10x0.100_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x10000x0.001_bench.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x10000x0.001_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x10000x0.010_bench.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x10000x0.010_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x10000x0.100_bench.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x10000x0.100_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x1000x0.001_bench.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x1000x0.001_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x1000x0.010_bench.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x1000x0.010_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x1000x0.100_bench.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x1000x0.100_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x100x0.001_bench.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x100x0.001_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x100x0.010_bench.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x100x0.010_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x100x0.100_bench.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x100x0.100_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x10x0.001_bench.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x10x0.001_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x10x0.010_bench.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x10x0.010_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x10x0.100_bench.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x10x0.100_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x10000x0.001_bench.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x10000x0.001_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x10000x0.010_bench.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x10000x0.010_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x10000x0.100_bench.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x10000x0.100_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x1000x0.001_bench.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x1000x0.001_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x1000x0.010_bench.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x1000x0.010_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x1000x0.100_bench.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x1000x0.100_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x100x0.001_bench.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x100x0.001_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x100x0.010_bench.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x100x0.010_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x100x0.100_bench.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x100x0.100_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x10x0.001_bench.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x10x0.001_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x10x0.010_bench.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x10x0.010_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x10x0.100_bench.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x10x0.100_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x10000x0.001_bench.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x10000x0.001_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x10000x0.010_bench.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x10000x0.010_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x10000x0.100_bench.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x10000x0.100_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x1000x0.001_bench.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x1000x0.001_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x1000x0.010_bench.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x1000x0.010_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x1000x0.100_bench.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x1000x0.100_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x100x0.001_bench.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x100x0.001_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x100x0.010_bench.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x100x0.010_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x100x0.100_bench.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x100x0.100_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x10x0.001_bench.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x10x0.001_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x10x0.010_bench.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x10x0.010_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x10x0.100_bench.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x10x0.100_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables
> creating build/lib.linux-x86_64-cpython-314/biom/tests/test_cli/test_data
> copying biom/tests/test_cli/test_data/json_obs_collapsed.biom -> build/lib.linux-x86_64-cpython-314/biom/tests/test_cli/test_data
> copying biom/tests/test_cli/test_data/json_sample_collapsed.biom -> build/lib.linux-x86_64-cpython-314/biom/tests/test_cli/test_data
> copying biom/tests/test_cli/test_data/test.biom -> build/lib.linux-x86_64-cpython-314/biom/tests/test_cli/test_data
> copying biom/tests/test_cli/test_data/test.json -> build/lib.linux-x86_64-cpython-314/biom/tests/test_cli/test_data
> running build_ext
> building 'biom._filter' extension
> creating build/temp.linux-x86_64-cpython-314/biom
> x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-biom-format-2.1.17=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c biom/_filter.c -o build/temp.linux-x86_64-cpython-314/biom/_filter.o
> building 'biom._transform' extension
> x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-biom-format-2.1.17=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c biom/_transform.c -o build/temp.linux-x86_64-cpython-314/biom/_transform.o
> building 'biom._subsample' extension
> x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-biom-format-2.1.17=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.14 -c biom/_subsample.c -o build/temp.linux-x86_64-cpython-314/biom/_subsample.o
> x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-biom-format-2.1.17=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-314/biom/_transform.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-314/biom/_transform.cpython-314-x86_64-linux-gnu.so
> x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-biom-format-2.1.17=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-314/biom/_subsample.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-314/biom/_subsample.cpython-314-x86_64-linux-gnu.so
> x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-biom-format-2.1.17=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-314/biom/_filter.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-314/biom/_filter.cpython-314-x86_64-linux-gnu.so
> installing to build/bdist.linux-x86_64/wheel
> running install
> running install_lib
> creating build/bdist.linux-x86_64/wheel
> creating build/bdist.linux-x86_64/wheel/examples
> copying build/lib.linux-x86_64-cpython-314/examples/sam_md.txt -> build/bdist.linux-x86_64/wheel/./examples
> copying build/lib.linux-x86_64-cpython-314/examples/rich_sparse_otu_table_hdf5_group_metadata.biom -> build/bdist.linux-x86_64/wheel/./examples
> copying build/lib.linux-x86_64-cpython-314/examples/rich_sparse_otu_table_hdf5.biom -> build/bdist.linux-x86_64/wheel/./examples
> copying build/lib.linux-x86_64-cpython-314/examples/rich_sparse_otu_table.biom -> build/bdist.linux-x86_64/wheel/./examples
> copying build/lib.linux-x86_64-cpython-314/examples/obs_md.txt -> build/bdist.linux-x86_64/wheel/./examples
> copying build/lib.linux-x86_64-cpython-314/examples/min_sparse_otu_table_hdf5.biom -> build/bdist.linux-x86_64/wheel/./examples
> copying build/lib.linux-x86_64-cpython-314/examples/min_sparse_otu_table.biom -> build/bdist.linux-x86_64/wheel/./examples
> creating build/bdist.linux-x86_64/wheel/licenses
> copying build/lib.linux-x86_64-cpython-314/licenses/scipy.txt -> build/bdist.linux-x86_64/wheel/./licenses
> copying build/lib.linux-x86_64-cpython-314/licenses/scikit-learn.txt -> build/bdist.linux-x86_64/wheel/./licenses
> copying build/lib.linux-x86_64-cpython-314/licenses/numpydoc.txt -> build/bdist.linux-x86_64/wheel/./licenses
> creating build/bdist.linux-x86_64/wheel/biom
> copying build/lib.linux-x86_64-cpython-314/biom/_filter.cpython-314-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./biom
> copying build/lib.linux-x86_64-cpython-314/biom/_subsample.cpython-314-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./biom
> copying build/lib.linux-x86_64-cpython-314/biom/_transform.cpython-314-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./biom
> copying build/lib.linux-x86_64-cpython-314/biom/_transform.pyx -> build/bdist.linux-x86_64/wheel/./biom
> copying build/lib.linux-x86_64-cpython-314/biom/_subsample.pyx -> build/bdist.linux-x86_64/wheel/./biom
> copying build/lib.linux-x86_64-cpython-314/biom/_filter.pyx -> build/bdist.linux-x86_64/wheel/./biom
> creating build/bdist.linux-x86_64/wheel/biom/assets
> copying build/lib.linux-x86_64-cpython-314/biom/assets/exercise_cli.sh -> build/bdist.linux-x86_64/wheel/./biom/assets
> copying build/lib.linux-x86_64-cpython-314/biom/assets/exercise_api.py -> build/bdist.linux-x86_64/wheel/./biom/assets
> creating build/bdist.linux-x86_64/wheel/biom/cli
> copying build/lib.linux-x86_64-cpython-314/biom/cli/__init__.py -> build/bdist.linux-x86_64/wheel/./biom/cli
> copying build/lib.linux-x86_64-cpython-314/biom/cli/installation_informer.py -> build/bdist.linux-x86_64/wheel/./biom/cli
> copying build/lib.linux-x86_64-cpython-314/biom/cli/metadata_adder.py -> build/bdist.linux-x86_64/wheel/./biom/cli
> copying build/lib.linux-x86_64-cpython-314/biom/cli/metadata_exporter.py -> build/bdist.linux-x86_64/wheel/./biom/cli
> copying build/lib.linux-x86_64-cpython-314/biom/cli/table_converter.py -> build/bdist.linux-x86_64/wheel/./biom/cli
> copying build/lib.linux-x86_64-cpython-314/biom/cli/table_head.py -> build/bdist.linux-x86_64/wheel/./biom/cli
> copying build/lib.linux-x86_64-cpython-314/biom/cli/table_ids.py -> build/bdist.linux-x86_64/wheel/./biom/cli
> copying build/lib.linux-x86_64-cpython-314/biom/cli/table_normalizer.py -> build/bdist.linux-x86_64/wheel/./biom/cli
> copying build/lib.linux-x86_64-cpython-314/biom/cli/table_subsetter.py -> build/bdist.linux-x86_64/wheel/./biom/cli
> copying build/lib.linux-x86_64-cpython-314/biom/cli/table_summarizer.py -> build/bdist.linux-x86_64/wheel/./biom/cli
> copying build/lib.linux-x86_64-cpython-314/biom/cli/table_validator.py -> build/bdist.linux-x86_64/wheel/./biom/cli
> copying build/lib.linux-x86_64-cpython-314/biom/cli/uc_processor.py -> build/bdist.linux-x86_64/wheel/./biom/cli
> copying build/lib.linux-x86_64-cpython-314/biom/cli/util.py -> build/bdist.linux-x86_64/wheel/./biom/cli
> creating build/bdist.linux-x86_64/wheel/biom/tests
> creating build/bdist.linux-x86_64/wheel/biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/10x10x0.100_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/10x10x0.100_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/10x10x0.010_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/10x10x0.010_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/10x10x0.001_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/10x10x0.001_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/10x100x0.100_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/10x100x0.100_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/10x100x0.010_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/10x100x0.010_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/10x100x0.001_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/10x100x0.001_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/10x1000x0.100_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/10x1000x0.100_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/10x1000x0.010_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/10x1000x0.010_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/10x1000x0.001_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/10x1000x0.001_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/10x10000x0.100_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/10x10000x0.100_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/10x10000x0.010_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/10x10000x0.010_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/10x10000x0.001_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/10x10000x0.001_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/100x10x0.100_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/100x10x0.100_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/100x10x0.010_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/100x10x0.010_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/100x10x0.001_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/100x10x0.001_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/100x100x0.100_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/100x100x0.100_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/100x100x0.010_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/100x100x0.010_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/100x100x0.001_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/100x100x0.001_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/100x1000x0.100_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/100x1000x0.100_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/100x1000x0.010_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/100x1000x0.010_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/100x1000x0.001_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/100x1000x0.001_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/100x10000x0.100_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/100x10000x0.100_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/100x10000x0.010_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/100x10000x0.010_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/100x10000x0.001_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/100x10000x0.001_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/1000x10x0.100_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/1000x10x0.100_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/1000x10x0.010_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/1000x10x0.010_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/1000x10x0.001_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/1000x10x0.001_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/1000x100x0.100_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/1000x100x0.100_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/1000x100x0.010_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/1000x100x0.010_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/1000x100x0.001_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/1000x100x0.001_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/1000x1000x0.100_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/1000x1000x0.100_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/1000x1000x0.010_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/1000x1000x0.010_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/1000x1000x0.001_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/1000x1000x0.001_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/1000x10000x0.100_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/1000x10000x0.100_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/1000x10000x0.010_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/1000x10000x0.010_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/1000x10000x0.001_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/1000x10000x0.001_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/10000x10x0.100_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/10000x10x0.100_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/10000x10x0.010_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/10000x10x0.010_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/10000x10x0.001_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/10000x10x0.001_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/10000x100x0.100_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/10000x100x0.100_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/10000x100x0.010_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/10000x100x0.010_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/10000x100x0.001_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/10000x100x0.001_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/10000x1000x0.100_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/10000x1000x0.100_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/10000x1000x0.010_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/10000x1000x0.010_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/10000x1000x0.001_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/10000x1000x0.001_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/10000x10000x0.100_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/10000x10000x0.100_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/10000x10000x0.010_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/10000x10000x0.010_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/10000x10000x0.001_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-314/biom/tests/bench_tables/10000x10000x0.001_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> creating build/bdist.linux-x86_64/wheel/biom/tests/test_cli
> creating build/bdist.linux-x86_64/wheel/biom/tests/test_cli/test_data
> copying build/lib.linux-x86_64-cpython-314/biom/tests/test_cli/test_data/test.json -> build/bdist.linux-x86_64/wheel/./biom/tests/test_cli/test_data
> copying build/lib.linux-x86_64-cpython-314/biom/tests/test_cli/test_data/test.biom -> build/bdist.linux-x86_64/wheel/./biom/tests/test_cli/test_data
> copying build/lib.linux-x86_64-cpython-314/biom/tests/test_cli/test_data/json_sample_collapsed.biom -> build/bdist.linux-x86_64/wheel/./biom/tests/test_cli/test_data
> copying build/lib.linux-x86_64-cpython-314/biom/tests/test_cli/test_data/json_obs_collapsed.biom -> build/bdist.linux-x86_64/wheel/./biom/tests/test_cli/test_data
> copying build/lib.linux-x86_64-cpython-314/biom/tests/test_cli/__init__.py -> build/bdist.linux-x86_64/wheel/./biom/tests/test_cli
> copying build/lib.linux-x86_64-cpython-314/biom/tests/test_cli/test_add_metadata.py -> build/bdist.linux-x86_64/wheel/./biom/tests/test_cli
> copying build/lib.linux-x86_64-cpython-314/biom/tests/test_cli/test_show_install_info.py -> build/bdist.linux-x86_64/wheel/./biom/tests/test_cli
> copying build/lib.linux-x86_64-cpython-314/biom/tests/test_cli/test_subset_table.py -> build/bdist.linux-x86_64/wheel/./biom/tests/test_cli
> copying build/lib.linux-x86_64-cpython-314/biom/tests/test_cli/test_summarize_table.py -> build/bdist.linux-x86_64/wheel/./biom/tests/test_cli
> copying build/lib.linux-x86_64-cpython-314/biom/tests/test_cli/test_table_converter.py -> build/bdist.linux-x86_64/wheel/./biom/tests/test_cli
> copying build/lib.linux-x86_64-cpython-314/biom/tests/test_cli/test_table_normalizer.py -> build/bdist.linux-x86_64/wheel/./biom/tests/test_cli
> copying build/lib.linux-x86_64-cpython-314/biom/tests/test_cli/test_uc_processor.py -> build/bdist.linux-x86_64/wheel/./biom/tests/test_cli
> copying build/lib.linux-x86_64-cpython-314/biom/tests/test_cli/test_validate_table.py -> build/bdist.linux-x86_64/wheel/./biom/tests/test_cli
> creating build/bdist.linux-x86_64/wheel/biom/tests/test_data
> copying build/lib.linux-x86_64-cpython-314/biom/tests/test_data/test_grp_metadata.biom -> build/bdist.linux-x86_64/wheel/./biom/tests/test_data
> copying build/lib.linux-x86_64-cpython-314/biom/tests/test_data/test.json.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/test_data
> copying build/lib.linux-x86_64-cpython-314/biom/tests/test_data/test.json -> build/bdist.linux-x86_64/wheel/./biom/tests/test_data
> copying build/lib.linux-x86_64-cpython-314/biom/tests/test_data/test.biom -> build/bdist.linux-x86_64/wheel/./biom/tests/test_data
> copying build/lib.linux-x86_64-cpython-314/biom/tests/test_data/no-contents.biom -> build/bdist.linux-x86_64/wheel/./biom/tests/test_data
> copying build/lib.linux-x86_64-cpython-314/biom/tests/test_data/empty.biom -> build/bdist.linux-x86_64/wheel/./biom/tests/test_data
> copying build/lib.linux-x86_64-cpython-314/biom/tests/test_data/edgecase_issue_952.biom -> build/bdist.linux-x86_64/wheel/./biom/tests/test_data
> copying build/lib.linux-x86_64-cpython-314/biom/tests/test_data/bad_table.txt.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/test_data
> copying build/lib.linux-x86_64-cpython-314/biom/tests/test_data/bad_table.txt -> build/bdist.linux-x86_64/wheel/./biom/tests/test_data
> copying build/lib.linux-x86_64-cpython-314/biom/tests/test_data/__init__.py -> build/bdist.linux-x86_64/wheel/./biom/tests/test_data
> copying build/lib.linux-x86_64-cpython-314/biom/tests/__init__.py -> build/bdist.linux-x86_64/wheel/./biom/tests
> copying build/lib.linux-x86_64-cpython-314/biom/tests/long_lines.py -> build/bdist.linux-x86_64/wheel/./biom/tests
> copying build/lib.linux-x86_64-cpython-314/biom/tests/test_err.py -> build/bdist.linux-x86_64/wheel/./biom/tests
> copying build/lib.linux-x86_64-cpython-314/biom/tests/test_parse.py -> build/bdist.linux-x86_64/wheel/./biom/tests
> copying build/lib.linux-x86_64-cpython-314/biom/tests/test_table.py -> build/bdist.linux-x86_64/wheel/./biom/tests
> copying build/lib.linux-x86_64-cpython-314/biom/tests/test_util.py -> build/bdist.linux-x86_64/wheel/./biom/tests
> copying build/lib.linux-x86_64-cpython-314/biom/err.py -> build/bdist.linux-x86_64/wheel/./biom
> copying build/lib.linux-x86_64-cpython-314/biom/exception.py -> build/bdist.linux-x86_64/wheel/./biom
> copying build/lib.linux-x86_64-cpython-314/biom/parse.py -> build/bdist.linux-x86_64/wheel/./biom
> copying build/lib.linux-x86_64-cpython-314/biom/table.py -> build/bdist.linux-x86_64/wheel/./biom
> copying build/lib.linux-x86_64-cpython-314/biom/util.py -> build/bdist.linux-x86_64/wheel/./biom
> copying build/lib.linux-x86_64-cpython-314/biom/__init__.py -> build/bdist.linux-x86_64/wheel/./biom
> creating build/bdist.linux-x86_64/wheel/doc
> creating build/bdist.linux-x86_64/wheel/doc/_templates
> creating build/bdist.linux-x86_64/wheel/doc/_templates/autosummary
> copying build/lib.linux-x86_64-cpython-314/doc/_templates/autosummary/method.rst -> build/bdist.linux-x86_64/wheel/./doc/_templates/autosummary
> copying build/lib.linux-x86_64-cpython-314/doc/_templates/autosummary/class.rst -> build/bdist.linux-x86_64/wheel/./doc/_templates/autosummary
> copying build/lib.linux-x86_64-cpython-314/doc/_templates/autosummary/attribute.rst -> build/bdist.linux-x86_64/wheel/./doc/_templates/autosummary
> creating build/bdist.linux-x86_64/wheel/doc/_static
> copying build/lib.linux-x86_64-cpython-314/doc/_static/copybutton.js -> build/bdist.linux-x86_64/wheel/./doc/_static
> copying build/lib.linux-x86_64-cpython-314/doc/_static/biom-format.png -> build/bdist.linux-x86_64/wheel/./doc/_static
> creating build/bdist.linux-x86_64/wheel/doc/documentation
> creating build/bdist.linux-x86_64/wheel/doc/documentation/format_versions
> copying build/lib.linux-x86_64-cpython-314/doc/documentation/format_versions/biom-2.1.rst -> build/bdist.linux-x86_64/wheel/./doc/documentation/format_versions
> copying build/lib.linux-x86_64-cpython-314/doc/documentation/format_versions/biom-2.0.rst -> build/bdist.linux-x86_64/wheel/./doc/documentation/format_versions
> copying build/lib.linux-x86_64-cpython-314/doc/documentation/format_versions/biom-1.0.rst -> build/bdist.linux-x86_64/wheel/./doc/documentation/format_versions
> copying build/lib.linux-x86_64-cpython-314/doc/documentation/table_objects.rst -> build/bdist.linux-x86_64/wheel/./doc/documentation
> copying build/lib.linux-x86_64-cpython-314/doc/documentation/summarizing_biom_tables.rst -> build/bdist.linux-x86_64/wheel/./doc/documentation
> copying build/lib.linux-x86_64-cpython-314/doc/documentation/quick_usage_examples.rst -> build/bdist.linux-x86_64/wheel/./doc/documentation
> copying build/lib.linux-x86_64-cpython-314/doc/documentation/index.rst -> build/bdist.linux-x86_64/wheel/./doc/documentation
> copying build/lib.linux-x86_64-cpython-314/doc/documentation/biom_format.rst -> build/bdist.linux-x86_64/wheel/./doc/documentation
> copying build/lib.linux-x86_64-cpython-314/doc/documentation/biom_conversion.rst -> build/bdist.linux-x86_64/wheel/./doc/documentation
> copying build/lib.linux-x86_64-cpython-314/doc/documentation/adding_metadata.rst -> build/bdist.linux-x86_64/wheel/./doc/documentation
> copying build/lib.linux-x86_64-cpython-314/doc/index.rst -> build/bdist.linux-x86_64/wheel/./doc
> copying build/lib.linux-x86_64-cpython-314/doc/Makefile -> build/bdist.linux-x86_64/wheel/./doc
> copying build/lib.linux-x86_64-cpython-314/doc/BIOM_LICENSE.rst -> build/bdist.linux-x86_64/wheel/./doc
> creating build/bdist.linux-x86_64/wheel/doc/sphinxext
> creating build/bdist.linux-x86_64/wheel/doc/sphinxext/numpydoc
> copying build/lib.linux-x86_64-cpython-314/doc/sphinxext/numpydoc/README.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinxext/numpydoc
> copying build/lib.linux-x86_64-cpython-314/doc/sphinxext/numpydoc/LICENSE.txt -> build/bdist.linux-x86_64/wheel/./doc/sphinxext/numpydoc
> creating build/bdist.linux-x86_64/wheel/doc/sphinxext/numpydoc/numpydoc
> creating build/bdist.linux-x86_64/wheel/doc/sphinxext/numpydoc/numpydoc/tests
> copying build/lib.linux-x86_64-cpython-314/doc/sphinxext/numpydoc/numpydoc/tests/test_docscrape.py -> build/bdist.linux-x86_64/wheel/./doc/sphinxext/numpydoc/numpydoc/tests
> copying build/lib.linux-x86_64-cpython-314/doc/sphinxext/numpydoc/numpydoc/tests/test_linkcode.py -> build/bdist.linux-x86_64/wheel/./doc/sphinxext/numpydoc/numpydoc/tests
> copying build/lib.linux-x86_64-cpython-314/doc/sphinxext/numpydoc/numpydoc/tests/test_phantom_import.py -> build/bdist.linux-x86_64/wheel/./doc/sphinxext/numpydoc/numpydoc/tests
> copying build/lib.linux-x86_64-cpython-314/doc/sphinxext/numpydoc/numpydoc/tests/test_plot_directive.py -> build/bdist.linux-x86_64/wheel/./doc/sphinxext/numpydoc/numpydoc/tests
> copying build/lib.linux-x86_64-cpython-314/doc/sphinxext/numpydoc/numpydoc/tests/test_traitsdoc.py -> build/bdist.linux-x86_64/wheel/./doc/sphinxext/numpydoc/numpydoc/tests
> copying build/lib.linux-x86_64-cpython-314/doc/sphinxext/numpydoc/numpydoc/comment_eater.py -> build/bdist.linux-x86_64/wheel/./doc/sphinxext/numpydoc/numpydoc
> copying build/lib.linux-x86_64-cpython-314/doc/sphinxext/numpydoc/numpydoc/compiler_unparse.py -> build/bdist.linux-x86_64/wheel/./doc/sphinxext/numpydoc/numpydoc
> copying build/lib.linux-x86_64-cpython-314/doc/sphinxext/numpydoc/numpydoc/docscrape.py -> build/bdist.linux-x86_64/wheel/./doc/sphinxext/numpydoc/numpydoc
> copying build/lib.linux-x86_64-cpython-314/doc/sphinxext/numpydoc/numpydoc/docscrape_sphinx.py -> build/bdist.linux-x86_64/wheel/./doc/sphinxext/numpydoc/numpydoc
> copying build/lib.linux-x86_64-cpython-314/doc/sphinxext/numpydoc/numpydoc/phantom_import.py -> build/bdist.linux-x86_64/wheel/./doc/sphinxext/numpydoc/numpydoc
> copying build/lib.linux-x86_64-cpython-314/doc/sphinxext/numpydoc/numpydoc/plot_directive.py -> build/bdist.linux-x86_64/wheel/./doc/sphinxext/numpydoc/numpydoc
> copying build/lib.linux-x86_64-cpython-314/doc/sphinxext/numpydoc/numpydoc/traitsdoc.py -> build/bdist.linux-x86_64/wheel/./doc/sphinxext/numpydoc/numpydoc
> copying build/lib.linux-x86_64-cpython-314/doc/sphinxext/numpydoc/numpydoc/__init__.py -> build/bdist.linux-x86_64/wheel/./doc/sphinxext/numpydoc/numpydoc
> copying build/lib.linux-x86_64-cpython-314/doc/sphinxext/numpydoc/numpydoc/linkcode.py -> build/bdist.linux-x86_64/wheel/./doc/sphinxext/numpydoc/numpydoc
> copying build/lib.linux-x86_64-cpython-314/doc/sphinxext/numpydoc/numpydoc/numpydoc.py -> build/bdist.linux-x86_64/wheel/./doc/sphinxext/numpydoc/numpydoc
> copying build/lib.linux-x86_64-cpython-314/doc/conf.py -> build/bdist.linux-x86_64/wheel/./doc
> running install_egg_info
> Copying biom_format.egg-info to build/bdist.linux-x86_64/wheel/./biom_format-2.1.17.egg-info
> running install_scripts
> creating build/bdist.linux-x86_64/wheel/biom_format-2.1.17.dist-info/WHEEL
> creating '/build/reproducible-path/python-biom-format-2.1.17/.pybuild/cpython3_3.14_biom-format/.tmp-fcsgf4uu/biom_format-2.1.17-cp314-cp314-linux_x86_64.whl' and adding 'build/bdist.linux-x86_64/wheel' to it
> adding 'biom/__init__.py'
> adding 'biom/_filter.cpython-314-x86_64-linux-gnu.so'
> adding 'biom/_filter.pyx'
> adding 'biom/_subsample.cpython-314-x86_64-linux-gnu.so'
> adding 'biom/_subsample.pyx'
> adding 'biom/_transform.cpython-314-x86_64-linux-gnu.so'
> adding 'biom/_transform.pyx'
> adding 'biom/err.py'
> adding 'biom/exception.py'
> adding 'biom/parse.py'
> adding 'biom/table.py'
> adding 'biom/util.py'
> adding 'biom/assets/exercise_api.py'
> adding 'biom/assets/exercise_cli.sh'
> adding 'biom/cli/__init__.py'
> adding 'biom/cli/installation_informer.py'
> adding 'biom/cli/metadata_adder.py'
> adding 'biom/cli/metadata_exporter.py'
> adding 'biom/cli/table_converter.py'
> adding 'biom/cli/table_head.py'
> adding 'biom/cli/table_ids.py'
> adding 'biom/cli/table_normalizer.py'
> adding 'biom/cli/table_subsetter.py'
> adding 'biom/cli/table_summarizer.py'
> adding 'biom/cli/table_validator.py'
> adding 'biom/cli/uc_processor.py'
> adding 'biom/cli/util.py'
> adding 'biom/tests/__init__.py'
> adding 'biom/tests/long_lines.py'
> adding 'biom/tests/test_err.py'
> adding 'biom/tests/test_parse.py'
> adding 'biom/tests/test_table.py'
> adding 'biom/tests/test_util.py'
> adding 'biom/tests/bench_tables/10000x10000x0.001_bench.biom.gz'
> adding 'biom/tests/bench_tables/10000x10000x0.001_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/10000x10000x0.010_bench.biom.gz'
> adding 'biom/tests/bench_tables/10000x10000x0.010_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/10000x10000x0.100_bench.biom.gz'
> adding 'biom/tests/bench_tables/10000x10000x0.100_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/10000x1000x0.001_bench.biom.gz'
> adding 'biom/tests/bench_tables/10000x1000x0.001_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/10000x1000x0.010_bench.biom.gz'
> adding 'biom/tests/bench_tables/10000x1000x0.010_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/10000x1000x0.100_bench.biom.gz'
> adding 'biom/tests/bench_tables/10000x1000x0.100_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/10000x100x0.001_bench.biom.gz'
> adding 'biom/tests/bench_tables/10000x100x0.001_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/10000x100x0.010_bench.biom.gz'
> adding 'biom/tests/bench_tables/10000x100x0.010_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/10000x100x0.100_bench.biom.gz'
> adding 'biom/tests/bench_tables/10000x100x0.100_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/10000x10x0.001_bench.biom.gz'
> adding 'biom/tests/bench_tables/10000x10x0.001_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/10000x10x0.010_bench.biom.gz'
> adding 'biom/tests/bench_tables/10000x10x0.010_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/10000x10x0.100_bench.biom.gz'
> adding 'biom/tests/bench_tables/10000x10x0.100_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/1000x10000x0.001_bench.biom.gz'
> adding 'biom/tests/bench_tables/1000x10000x0.001_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/1000x10000x0.010_bench.biom.gz'
> adding 'biom/tests/bench_tables/1000x10000x0.010_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/1000x10000x0.100_bench.biom.gz'
> adding 'biom/tests/bench_tables/1000x10000x0.100_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/1000x1000x0.001_bench.biom.gz'
> adding 'biom/tests/bench_tables/1000x1000x0.001_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/1000x1000x0.010_bench.biom.gz'
> adding 'biom/tests/bench_tables/1000x1000x0.010_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/1000x1000x0.100_bench.biom.gz'
> adding 'biom/tests/bench_tables/1000x1000x0.100_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/1000x100x0.001_bench.biom.gz'
> adding 'biom/tests/bench_tables/1000x100x0.001_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/1000x100x0.010_bench.biom.gz'
> adding 'biom/tests/bench_tables/1000x100x0.010_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/1000x100x0.100_bench.biom.gz'
> adding 'biom/tests/bench_tables/1000x100x0.100_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/1000x10x0.001_bench.biom.gz'
> adding 'biom/tests/bench_tables/1000x10x0.001_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/1000x10x0.010_bench.biom.gz'
> adding 'biom/tests/bench_tables/1000x10x0.010_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/1000x10x0.100_bench.biom.gz'
> adding 'biom/tests/bench_tables/1000x10x0.100_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/100x10000x0.001_bench.biom.gz'
> adding 'biom/tests/bench_tables/100x10000x0.001_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/100x10000x0.010_bench.biom.gz'
> adding 'biom/tests/bench_tables/100x10000x0.010_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/100x10000x0.100_bench.biom.gz'
> adding 'biom/tests/bench_tables/100x10000x0.100_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/100x1000x0.001_bench.biom.gz'
> adding 'biom/tests/bench_tables/100x1000x0.001_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/100x1000x0.010_bench.biom.gz'
> adding 'biom/tests/bench_tables/100x1000x0.010_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/100x1000x0.100_bench.biom.gz'
> adding 'biom/tests/bench_tables/100x1000x0.100_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/100x100x0.001_bench.biom.gz'
> adding 'biom/tests/bench_tables/100x100x0.001_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/100x100x0.010_bench.biom.gz'
> adding 'biom/tests/bench_tables/100x100x0.010_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/100x100x0.100_bench.biom.gz'
> adding 'biom/tests/bench_tables/100x100x0.100_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/100x10x0.001_bench.biom.gz'
> adding 'biom/tests/bench_tables/100x10x0.001_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/100x10x0.010_bench.biom.gz'
> adding 'biom/tests/bench_tables/100x10x0.010_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/100x10x0.100_bench.biom.gz'
> adding 'biom/tests/bench_tables/100x10x0.100_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/10x10000x0.001_bench.biom.gz'
> adding 'biom/tests/bench_tables/10x10000x0.001_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/10x10000x0.010_bench.biom.gz'
> adding 'biom/tests/bench_tables/10x10000x0.010_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/10x10000x0.100_bench.biom.gz'
> adding 'biom/tests/bench_tables/10x10000x0.100_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/10x1000x0.001_bench.biom.gz'
> adding 'biom/tests/bench_tables/10x1000x0.001_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/10x1000x0.010_bench.biom.gz'
> adding 'biom/tests/bench_tables/10x1000x0.010_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/10x1000x0.100_bench.biom.gz'
> adding 'biom/tests/bench_tables/10x1000x0.100_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/10x100x0.001_bench.biom.gz'
> adding 'biom/tests/bench_tables/10x100x0.001_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/10x100x0.010_bench.biom.gz'
> adding 'biom/tests/bench_tables/10x100x0.010_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/10x100x0.100_bench.biom.gz'
> adding 'biom/tests/bench_tables/10x100x0.100_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/10x10x0.001_bench.biom.gz'
> adding 'biom/tests/bench_tables/10x10x0.001_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/10x10x0.010_bench.biom.gz'
> adding 'biom/tests/bench_tables/10x10x0.010_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/10x10x0.100_bench.biom.gz'
> adding 'biom/tests/bench_tables/10x10x0.100_bench_hdf5.biom.gz'
> adding 'biom/tests/test_cli/__init__.py'
> adding 'biom/tests/test_cli/test_add_metadata.py'
> adding 'biom/tests/test_cli/test_show_install_info.py'
> adding 'biom/tests/test_cli/test_subset_table.py'
> adding 'biom/tests/test_cli/test_summarize_table.py'
> adding 'biom/tests/test_cli/test_table_converter.py'
> adding 'biom/tests/test_cli/test_table_normalizer.py'
> adding 'biom/tests/test_cli/test_uc_processor.py'
> adding 'biom/tests/test_cli/test_validate_table.py'
> adding 'biom/tests/test_cli/test_data/json_obs_collapsed.biom'
> adding 'biom/tests/test_cli/test_data/json_sample_collapsed.biom'
> adding 'biom/tests/test_cli/test_data/test.biom'
> adding 'biom/tests/test_cli/test_data/test.json'
> adding 'biom/tests/test_data/__init__.py'
> adding 'biom/tests/test_data/bad_table.txt'
> adding 'biom/tests/test_data/bad_table.txt.gz'
> adding 'biom/tests/test_data/edgecase_issue_952.biom'
> adding 'biom/tests/test_data/empty.biom'
> adding 'biom/tests/test_data/no-contents.biom'
> adding 'biom/tests/test_data/test.biom'
> adding 'biom/tests/test_data/test.json'
> adding 'biom/tests/test_data/test.json.gz'
> adding 'biom/tests/test_data/test_grp_metadata.biom'
> adding 'biom_format-2.1.17.dist-info/licenses/COPYING.txt'
> adding 'doc/BIOM_LICENSE.rst'
> adding 'doc/Makefile'
> adding 'doc/conf.py'
> adding 'doc/index.rst'
> adding 'doc/_static/biom-format.png'
> adding 'doc/_static/copybutton.js'
> adding 'doc/_templates/autosummary/attribute.rst'
> adding 'doc/_templates/autosummary/class.rst'
> adding 'doc/_templates/autosummary/method.rst'
> adding 'doc/documentation/adding_metadata.rst'
> adding 'doc/documentation/biom_conversion.rst'
> adding 'doc/documentation/biom_format.rst'
> adding 'doc/documentation/index.rst'
> adding 'doc/documentation/quick_usage_examples.rst'
> adding 'doc/documentation/summarizing_biom_tables.rst'
> adding 'doc/documentation/table_objects.rst'
> adding 'doc/documentation/format_versions/biom-1.0.rst'
> adding 'doc/documentation/format_versions/biom-2.0.rst'
> adding 'doc/documentation/format_versions/biom-2.1.rst'
> adding 'doc/sphinxext/numpydoc/LICENSE.txt'
> adding 'doc/sphinxext/numpydoc/README.rst'
> adding 'doc/sphinxext/numpydoc/numpydoc/__init__.py'
> adding 'doc/sphinxext/numpydoc/numpydoc/comment_eater.py'
> adding 'doc/sphinxext/numpydoc/numpydoc/compiler_unparse.py'
> adding 'doc/sphinxext/numpydoc/numpydoc/docscrape.py'
> adding 'doc/sphinxext/numpydoc/numpydoc/docscrape_sphinx.py'
> adding 'doc/sphinxext/numpydoc/numpydoc/linkcode.py'
> adding 'doc/sphinxext/numpydoc/numpydoc/numpydoc.py'
> adding 'doc/sphinxext/numpydoc/numpydoc/phantom_import.py'
> adding 'doc/sphinxext/numpydoc/numpydoc/plot_directive.py'
> adding 'doc/sphinxext/numpydoc/numpydoc/traitsdoc.py'
> adding 'doc/sphinxext/numpydoc/numpydoc/tests/test_docscrape.py'
> adding 'doc/sphinxext/numpydoc/numpydoc/tests/test_linkcode.py'
> adding 'doc/sphinxext/numpydoc/numpydoc/tests/test_phantom_import.py'
> adding 'doc/sphinxext/numpydoc/numpydoc/tests/test_plot_directive.py'
> adding 'doc/sphinxext/numpydoc/numpydoc/tests/test_traitsdoc.py'
> adding 'examples/min_sparse_otu_table.biom'
> adding 'examples/min_sparse_otu_table_hdf5.biom'
> adding 'examples/obs_md.txt'
> adding 'examples/rich_sparse_otu_table.biom'
> adding 'examples/rich_sparse_otu_table_hdf5.biom'
> adding 'examples/rich_sparse_otu_table_hdf5_group_metadata.biom'
> adding 'examples/sam_md.txt'
> adding 'licenses/numpydoc.txt'
> adding 'licenses/scikit-learn.txt'
> adding 'licenses/scipy.txt'
> adding 'biom_format-2.1.17.dist-info/METADATA'
> adding 'biom_format-2.1.17.dist-info/WHEEL'
> adding 'biom_format-2.1.17.dist-info/entry_points.txt'
> adding 'biom_format-2.1.17.dist-info/top_level.txt'
> adding 'biom_format-2.1.17.dist-info/RECORD'
> removing build/bdist.linux-x86_64/wheel
> Successfully built biom_format-2.1.17-cp314-cp314-linux_x86_64.whl
> I: pybuild plugin_pyproject:168: Unpacking wheel built for python3.14 with "installer" module
> I: pybuild plugin_pyproject:142: Building wheel for python3.13 with "build" module
> I: pybuild base:385: python3.13 -m build --skip-dependency-check --no-isolation --wheel --outdir /build/reproducible-path/python-biom-format-2.1.17/.pybuild/cpython3_3.13_biom-format
> * Building wheel...
> [1/3] Cythonizing biom/_filter.pyx
> [2/3] Cythonizing biom/_subsample.pyx
> [3/3] Cythonizing biom/_transform.pyx
> /usr/lib/python3/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated
> !!
>
> ********************************************************************************
> Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0).
>
> This deprecation is overdue, please update your project and remove deprecated
> calls to avoid build errors in the future.
>
> See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
> ********************************************************************************
>
> !!
> corresp(dist, value, root_dir)
> /usr/lib/python3/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated.
> !!
>
> ********************************************************************************
> Please consider removing the following classifiers in favor of a SPDX license expression:
>
> License :: OSI Approved :: BSD License
>
> See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
> ********************************************************************************
>
> !!
> dist._finalize_license_expression()
> /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
> !!
>
> ********************************************************************************
> Please consider removing the following classifiers in favor of a SPDX license expression:
>
> License :: OSI Approved :: BSD License
>
> See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
> ********************************************************************************
>
> !!
> self._finalize_license_expression()
> running bdist_wheel
> running build
> running build_py
> creating build/lib.linux-x86_64-cpython-313/doc
> copying doc/conf.py -> build/lib.linux-x86_64-cpython-313/doc
> creating build/lib.linux-x86_64-cpython-313/biom
> copying biom/__init__.py -> build/lib.linux-x86_64-cpython-313/biom
> copying biom/util.py -> build/lib.linux-x86_64-cpython-313/biom
> copying biom/table.py -> build/lib.linux-x86_64-cpython-313/biom
> copying biom/parse.py -> build/lib.linux-x86_64-cpython-313/biom
> copying biom/exception.py -> build/lib.linux-x86_64-cpython-313/biom
> copying biom/err.py -> build/lib.linux-x86_64-cpython-313/biom
> creating build/lib.linux-x86_64-cpython-313/doc/sphinxext/numpydoc/numpydoc
> copying doc/sphinxext/numpydoc/numpydoc/numpydoc.py -> build/lib.linux-x86_64-cpython-313/doc/sphinxext/numpydoc/numpydoc
> copying doc/sphinxext/numpydoc/numpydoc/linkcode.py -> build/lib.linux-x86_64-cpython-313/doc/sphinxext/numpydoc/numpydoc
> copying doc/sphinxext/numpydoc/numpydoc/__init__.py -> build/lib.linux-x86_64-cpython-313/doc/sphinxext/numpydoc/numpydoc
> copying doc/sphinxext/numpydoc/numpydoc/traitsdoc.py -> build/lib.linux-x86_64-cpython-313/doc/sphinxext/numpydoc/numpydoc
> copying doc/sphinxext/numpydoc/numpydoc/plot_directive.py -> build/lib.linux-x86_64-cpython-313/doc/sphinxext/numpydoc/numpydoc
> copying doc/sphinxext/numpydoc/numpydoc/phantom_import.py -> build/lib.linux-x86_64-cpython-313/doc/sphinxext/numpydoc/numpydoc
> copying doc/sphinxext/numpydoc/numpydoc/docscrape_sphinx.py -> build/lib.linux-x86_64-cpython-313/doc/sphinxext/numpydoc/numpydoc
> copying doc/sphinxext/numpydoc/numpydoc/docscrape.py -> build/lib.linux-x86_64-cpython-313/doc/sphinxext/numpydoc/numpydoc
> copying doc/sphinxext/numpydoc/numpydoc/compiler_unparse.py -> build/lib.linux-x86_64-cpython-313/doc/sphinxext/numpydoc/numpydoc
> copying doc/sphinxext/numpydoc/numpydoc/comment_eater.py -> build/lib.linux-x86_64-cpython-313/doc/sphinxext/numpydoc/numpydoc
> creating build/lib.linux-x86_64-cpython-313/doc/sphinxext/numpydoc/numpydoc/tests
> copying doc/sphinxext/numpydoc/numpydoc/tests/test_traitsdoc.py -> build/lib.linux-x86_64-cpython-313/doc/sphinxext/numpydoc/numpydoc/tests
> copying doc/sphinxext/numpydoc/numpydoc/tests/test_plot_directive.py -> build/lib.linux-x86_64-cpython-313/doc/sphinxext/numpydoc/numpydoc/tests
> copying doc/sphinxext/numpydoc/numpydoc/tests/test_phantom_import.py -> build/lib.linux-x86_64-cpython-313/doc/sphinxext/numpydoc/numpydoc/tests
> copying doc/sphinxext/numpydoc/numpydoc/tests/test_linkcode.py -> build/lib.linux-x86_64-cpython-313/doc/sphinxext/numpydoc/numpydoc/tests
> copying doc/sphinxext/numpydoc/numpydoc/tests/test_docscrape.py -> build/lib.linux-x86_64-cpython-313/doc/sphinxext/numpydoc/numpydoc/tests
> creating build/lib.linux-x86_64-cpython-313/biom/tests
> copying biom/tests/test_util.py -> build/lib.linux-x86_64-cpython-313/biom/tests
> copying biom/tests/test_table.py -> build/lib.linux-x86_64-cpython-313/biom/tests
> copying biom/tests/test_parse.py -> build/lib.linux-x86_64-cpython-313/biom/tests
> copying biom/tests/test_err.py -> build/lib.linux-x86_64-cpython-313/biom/tests
> copying biom/tests/long_lines.py -> build/lib.linux-x86_64-cpython-313/biom/tests
> copying biom/tests/__init__.py -> build/lib.linux-x86_64-cpython-313/biom/tests
> creating build/lib.linux-x86_64-cpython-313/biom/cli
> copying biom/cli/util.py -> build/lib.linux-x86_64-cpython-313/biom/cli
> copying biom/cli/uc_processor.py -> build/lib.linux-x86_64-cpython-313/biom/cli
> copying biom/cli/table_validator.py -> build/lib.linux-x86_64-cpython-313/biom/cli
> copying biom/cli/table_summarizer.py -> build/lib.linux-x86_64-cpython-313/biom/cli
> copying biom/cli/table_subsetter.py -> build/lib.linux-x86_64-cpython-313/biom/cli
> copying biom/cli/table_normalizer.py -> build/lib.linux-x86_64-cpython-313/biom/cli
> copying biom/cli/table_ids.py -> build/lib.linux-x86_64-cpython-313/biom/cli
> copying biom/cli/table_head.py -> build/lib.linux-x86_64-cpython-313/biom/cli
> copying biom/cli/table_converter.py -> build/lib.linux-x86_64-cpython-313/biom/cli
> copying biom/cli/metadata_exporter.py -> build/lib.linux-x86_64-cpython-313/biom/cli
> copying biom/cli/metadata_adder.py -> build/lib.linux-x86_64-cpython-313/biom/cli
> copying biom/cli/installation_informer.py -> build/lib.linux-x86_64-cpython-313/biom/cli
> copying biom/cli/__init__.py -> build/lib.linux-x86_64-cpython-313/biom/cli
> creating build/lib.linux-x86_64-cpython-313/biom/assets
> copying biom/assets/exercise_api.py -> build/lib.linux-x86_64-cpython-313/biom/assets
> creating build/lib.linux-x86_64-cpython-313/biom/tests/test_data
> copying biom/tests/test_data/__init__.py -> build/lib.linux-x86_64-cpython-313/biom/tests/test_data
> creating build/lib.linux-x86_64-cpython-313/biom/tests/test_cli
> copying biom/tests/test_cli/test_validate_table.py -> build/lib.linux-x86_64-cpython-313/biom/tests/test_cli
> copying biom/tests/test_cli/test_uc_processor.py -> build/lib.linux-x86_64-cpython-313/biom/tests/test_cli
> copying biom/tests/test_cli/test_table_normalizer.py -> build/lib.linux-x86_64-cpython-313/biom/tests/test_cli
> copying biom/tests/test_cli/test_table_converter.py -> build/lib.linux-x86_64-cpython-313/biom/tests/test_cli
> copying biom/tests/test_cli/test_summarize_table.py -> build/lib.linux-x86_64-cpython-313/biom/tests/test_cli
> copying biom/tests/test_cli/test_subset_table.py -> build/lib.linux-x86_64-cpython-313/biom/tests/test_cli
> copying biom/tests/test_cli/test_show_install_info.py -> build/lib.linux-x86_64-cpython-313/biom/tests/test_cli
> copying biom/tests/test_cli/test_add_metadata.py -> build/lib.linux-x86_64-cpython-313/biom/tests/test_cli
> copying biom/tests/test_cli/__init__.py -> build/lib.linux-x86_64-cpython-313/biom/tests/test_cli
> running egg_info
> writing biom_format.egg-info/PKG-INFO
> writing dependency_links to biom_format.egg-info/dependency_links.txt
> writing entry points to biom_format.egg-info/entry_points.txt
> writing requirements to biom_format.egg-info/requires.txt
> writing top-level names to biom_format.egg-info/top_level.txt
> dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
> dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
> dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
> dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
> dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
> dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
> dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
> dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
> dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
> dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
> dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
> dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
> dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
> dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
> dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
> reading manifest file 'biom_format.egg-info/SOURCES.txt'
> reading manifest template 'MANIFEST.in'
> warning: no directories found matching 'support_files'
> warning: no directories found matching 'tests/test_data'
> no previously-included directories found matching 'docs/_build'
> warning: no previously-included files matching '*.pyc' found anywhere in distribution
> warning: no previously-included files matching '*.pyo' found anywhere in distribution
> warning: no previously-included files matching '.git' found anywhere in distribution
> warning: no previously-included files matching '*.so' found anywhere in distribution
> warning: no previously-included files matching '.*.swp' found anywhere in distribution
> adding license file 'COPYING.txt'
> writing manifest file 'biom_format.egg-info/SOURCES.txt'
> creating build/lib.linux-x86_64-cpython-313/licenses
> copying licenses/numpydoc.txt -> build/lib.linux-x86_64-cpython-313/licenses
> copying licenses/scikit-learn.txt -> build/lib.linux-x86_64-cpython-313/licenses
> copying licenses/scipy.txt -> build/lib.linux-x86_64-cpython-313/licenses
> creating build/lib.linux-x86_64-cpython-313/examples
> copying examples/min_sparse_otu_table.biom -> build/lib.linux-x86_64-cpython-313/examples
> copying examples/min_sparse_otu_table_hdf5.biom -> build/lib.linux-x86_64-cpython-313/examples
> copying examples/obs_md.txt -> build/lib.linux-x86_64-cpython-313/examples
> copying examples/rich_sparse_otu_table.biom -> build/lib.linux-x86_64-cpython-313/examples
> copying examples/rich_sparse_otu_table_hdf5.biom -> build/lib.linux-x86_64-cpython-313/examples
> copying examples/rich_sparse_otu_table_hdf5_group_metadata.biom -> build/lib.linux-x86_64-cpython-313/examples
> copying examples/sam_md.txt -> build/lib.linux-x86_64-cpython-313/examples
> copying doc/BIOM_LICENSE.rst -> build/lib.linux-x86_64-cpython-313/doc
> copying doc/Makefile -> build/lib.linux-x86_64-cpython-313/doc
> copying doc/index.rst -> build/lib.linux-x86_64-cpython-313/doc
> copying biom/_filter.pyx -> build/lib.linux-x86_64-cpython-313/biom
> copying biom/_subsample.pyx -> build/lib.linux-x86_64-cpython-313/biom
> copying biom/_transform.pyx -> build/lib.linux-x86_64-cpython-313/biom
> creating build/lib.linux-x86_64-cpython-313/doc/documentation
> copying doc/documentation/adding_metadata.rst -> build/lib.linux-x86_64-cpython-313/doc/documentation
> copying doc/documentation/biom_conversion.rst -> build/lib.linux-x86_64-cpython-313/doc/documentation
> copying doc/documentation/biom_format.rst -> build/lib.linux-x86_64-cpython-313/doc/documentation
> copying doc/documentation/index.rst -> build/lib.linux-x86_64-cpython-313/doc/documentation
> copying doc/documentation/quick_usage_examples.rst -> build/lib.linux-x86_64-cpython-313/doc/documentation
> copying doc/documentation/summarizing_biom_tables.rst -> build/lib.linux-x86_64-cpython-313/doc/documentation
> copying doc/documentation/table_objects.rst -> build/lib.linux-x86_64-cpython-313/doc/documentation
> creating build/lib.linux-x86_64-cpython-313/doc/_static
> copying doc/_static/biom-format.png -> build/lib.linux-x86_64-cpython-313/doc/_static
> copying doc/_static/copybutton.js -> build/lib.linux-x86_64-cpython-313/doc/_static
> copying doc/sphinxext/numpydoc/LICENSE.txt -> build/lib.linux-x86_64-cpython-313/doc/sphinxext/numpydoc
> copying doc/sphinxext/numpydoc/README.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinxext/numpydoc
> creating build/lib.linux-x86_64-cpython-313/doc/documentation/format_versions
> copying doc/documentation/format_versions/biom-1.0.rst -> build/lib.linux-x86_64-cpython-313/doc/documentation/format_versions
> copying doc/documentation/format_versions/biom-2.0.rst -> build/lib.linux-x86_64-cpython-313/doc/documentation/format_versions
> copying doc/documentation/format_versions/biom-2.1.rst -> build/lib.linux-x86_64-cpython-313/doc/documentation/format_versions
> creating build/lib.linux-x86_64-cpython-313/doc/_templates/autosummary
> copying doc/_templates/autosummary/attribute.rst -> build/lib.linux-x86_64-cpython-313/doc/_templates/autosummary
> copying doc/_templates/autosummary/class.rst -> build/lib.linux-x86_64-cpython-313/doc/_templates/autosummary
> copying doc/_templates/autosummary/method.rst -> build/lib.linux-x86_64-cpython-313/doc/_templates/autosummary
> copying biom/assets/exercise_cli.sh -> build/lib.linux-x86_64-cpython-313/biom/assets
> copying biom/tests/test_data/bad_table.txt -> build/lib.linux-x86_64-cpython-313/biom/tests/test_data
> copying biom/tests/test_data/bad_table.txt.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/test_data
> copying biom/tests/test_data/edgecase_issue_952.biom -> build/lib.linux-x86_64-cpython-313/biom/tests/test_data
> copying biom/tests/test_data/empty.biom -> build/lib.linux-x86_64-cpython-313/biom/tests/test_data
> copying biom/tests/test_data/no-contents.biom -> build/lib.linux-x86_64-cpython-313/biom/tests/test_data
> copying biom/tests/test_data/test.biom -> build/lib.linux-x86_64-cpython-313/biom/tests/test_data
> copying biom/tests/test_data/test.json -> build/lib.linux-x86_64-cpython-313/biom/tests/test_data
> copying biom/tests/test_data/test.json.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/test_data
> copying biom/tests/test_data/test_grp_metadata.biom -> build/lib.linux-x86_64-cpython-313/biom/tests/test_data
> creating build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x10000x0.001_bench.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x10000x0.001_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x10000x0.010_bench.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x10000x0.010_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x10000x0.100_bench.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x10000x0.100_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x1000x0.001_bench.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x1000x0.001_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x1000x0.010_bench.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x1000x0.010_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x1000x0.100_bench.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x1000x0.100_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x100x0.001_bench.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x100x0.001_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x100x0.010_bench.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x100x0.010_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x100x0.100_bench.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x100x0.100_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x10x0.001_bench.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x10x0.001_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x10x0.010_bench.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x10x0.010_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x10x0.100_bench.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x10x0.100_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x10000x0.001_bench.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x10000x0.001_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x10000x0.010_bench.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x10000x0.010_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x10000x0.100_bench.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x10000x0.100_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x1000x0.001_bench.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x1000x0.001_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x1000x0.010_bench.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x1000x0.010_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x1000x0.100_bench.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x1000x0.100_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x100x0.001_bench.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x100x0.001_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x100x0.010_bench.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x100x0.010_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x100x0.100_bench.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x100x0.100_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x10x0.001_bench.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x10x0.001_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x10x0.010_bench.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x10x0.010_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x10x0.100_bench.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x10x0.100_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x10000x0.001_bench.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x10000x0.001_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x10000x0.010_bench.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x10000x0.010_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x10000x0.100_bench.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x10000x0.100_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x1000x0.001_bench.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x1000x0.001_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x1000x0.010_bench.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x1000x0.010_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x1000x0.100_bench.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x1000x0.100_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x100x0.001_bench.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x100x0.001_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x100x0.010_bench.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x100x0.010_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x100x0.100_bench.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x100x0.100_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x10x0.001_bench.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x10x0.001_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x10x0.010_bench.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x10x0.010_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x10x0.100_bench.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x10x0.100_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x10000x0.001_bench.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x10000x0.001_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x10000x0.010_bench.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x10000x0.010_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x10000x0.100_bench.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x10000x0.100_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x1000x0.001_bench.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x1000x0.001_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x1000x0.010_bench.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x1000x0.010_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x1000x0.100_bench.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x1000x0.100_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x100x0.001_bench.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x100x0.001_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x100x0.010_bench.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x100x0.010_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x100x0.100_bench.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x100x0.100_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x10x0.001_bench.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x10x0.001_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x10x0.010_bench.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x10x0.010_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x10x0.100_bench.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x10x0.100_bench_hdf5.biom.gz -> build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables
> creating build/lib.linux-x86_64-cpython-313/biom/tests/test_cli/test_data
> copying biom/tests/test_cli/test_data/json_obs_collapsed.biom -> build/lib.linux-x86_64-cpython-313/biom/tests/test_cli/test_data
> copying biom/tests/test_cli/test_data/json_sample_collapsed.biom -> build/lib.linux-x86_64-cpython-313/biom/tests/test_cli/test_data
> copying biom/tests/test_cli/test_data/test.biom -> build/lib.linux-x86_64-cpython-313/biom/tests/test_cli/test_data
> copying biom/tests/test_cli/test_data/test.json -> build/lib.linux-x86_64-cpython-313/biom/tests/test_cli/test_data
> running build_ext
> building 'biom._transform' extension
> creating build/temp.linux-x86_64-cpython-313/biom
> building 'biom._filter' extension
> creating build/temp.linux-x86_64-cpython-313/biom
> x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-biom-format-2.1.17=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c biom/_filter.c -o build/temp.linux-x86_64-cpython-313/biom/_filter.o
> building 'biom._subsample' extension
> x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-biom-format-2.1.17=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c biom/_subsample.c -o build/temp.linux-x86_64-cpython-313/biom/_subsample.o
> x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-biom-format-2.1.17=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c biom/_transform.c -o build/temp.linux-x86_64-cpython-313/biom/_transform.o
> x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-biom-format-2.1.17=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/biom/_transform.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/biom/_transform.cpython-313-x86_64-linux-gnu.so
> x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-biom-format-2.1.17=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/biom/_subsample.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/biom/_subsample.cpython-313-x86_64-linux-gnu.so
> x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-biom-format-2.1.17=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/biom/_filter.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/biom/_filter.cpython-313-x86_64-linux-gnu.so
> installing to build/bdist.linux-x86_64/wheel
> running install
> running install_lib
> creating build/bdist.linux-x86_64/wheel
> creating build/bdist.linux-x86_64/wheel/examples
> copying build/lib.linux-x86_64-cpython-313/examples/sam_md.txt -> build/bdist.linux-x86_64/wheel/./examples
> copying build/lib.linux-x86_64-cpython-313/examples/rich_sparse_otu_table_hdf5_group_metadata.biom -> build/bdist.linux-x86_64/wheel/./examples
> copying build/lib.linux-x86_64-cpython-313/examples/rich_sparse_otu_table_hdf5.biom -> build/bdist.linux-x86_64/wheel/./examples
> copying build/lib.linux-x86_64-cpython-313/examples/rich_sparse_otu_table.biom -> build/bdist.linux-x86_64/wheel/./examples
> copying build/lib.linux-x86_64-cpython-313/examples/obs_md.txt -> build/bdist.linux-x86_64/wheel/./examples
> copying build/lib.linux-x86_64-cpython-313/examples/min_sparse_otu_table_hdf5.biom -> build/bdist.linux-x86_64/wheel/./examples
> copying build/lib.linux-x86_64-cpython-313/examples/min_sparse_otu_table.biom -> build/bdist.linux-x86_64/wheel/./examples
> creating build/bdist.linux-x86_64/wheel/licenses
> copying build/lib.linux-x86_64-cpython-313/licenses/scipy.txt -> build/bdist.linux-x86_64/wheel/./licenses
> copying build/lib.linux-x86_64-cpython-313/licenses/scikit-learn.txt -> build/bdist.linux-x86_64/wheel/./licenses
> copying build/lib.linux-x86_64-cpython-313/licenses/numpydoc.txt -> build/bdist.linux-x86_64/wheel/./licenses
> creating build/bdist.linux-x86_64/wheel/biom
> copying build/lib.linux-x86_64-cpython-313/biom/_filter.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./biom
> copying build/lib.linux-x86_64-cpython-313/biom/_subsample.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./biom
> copying build/lib.linux-x86_64-cpython-313/biom/_transform.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./biom
> copying build/lib.linux-x86_64-cpython-313/biom/_transform.pyx -> build/bdist.linux-x86_64/wheel/./biom
> copying build/lib.linux-x86_64-cpython-313/biom/_subsample.pyx -> build/bdist.linux-x86_64/wheel/./biom
> copying build/lib.linux-x86_64-cpython-313/biom/_filter.pyx -> build/bdist.linux-x86_64/wheel/./biom
> creating build/bdist.linux-x86_64/wheel/biom/assets
> copying build/lib.linux-x86_64-cpython-313/biom/assets/exercise_cli.sh -> build/bdist.linux-x86_64/wheel/./biom/assets
> copying build/lib.linux-x86_64-cpython-313/biom/assets/exercise_api.py -> build/bdist.linux-x86_64/wheel/./biom/assets
> creating build/bdist.linux-x86_64/wheel/biom/cli
> copying build/lib.linux-x86_64-cpython-313/biom/cli/__init__.py -> build/bdist.linux-x86_64/wheel/./biom/cli
> copying build/lib.linux-x86_64-cpython-313/biom/cli/installation_informer.py -> build/bdist.linux-x86_64/wheel/./biom/cli
> copying build/lib.linux-x86_64-cpython-313/biom/cli/metadata_adder.py -> build/bdist.linux-x86_64/wheel/./biom/cli
> copying build/lib.linux-x86_64-cpython-313/biom/cli/metadata_exporter.py -> build/bdist.linux-x86_64/wheel/./biom/cli
> copying build/lib.linux-x86_64-cpython-313/biom/cli/table_converter.py -> build/bdist.linux-x86_64/wheel/./biom/cli
> copying build/lib.linux-x86_64-cpython-313/biom/cli/table_head.py -> build/bdist.linux-x86_64/wheel/./biom/cli
> copying build/lib.linux-x86_64-cpython-313/biom/cli/table_ids.py -> build/bdist.linux-x86_64/wheel/./biom/cli
> copying build/lib.linux-x86_64-cpython-313/biom/cli/table_normalizer.py -> build/bdist.linux-x86_64/wheel/./biom/cli
> copying build/lib.linux-x86_64-cpython-313/biom/cli/table_subsetter.py -> build/bdist.linux-x86_64/wheel/./biom/cli
> copying build/lib.linux-x86_64-cpython-313/biom/cli/table_summarizer.py -> build/bdist.linux-x86_64/wheel/./biom/cli
> copying build/lib.linux-x86_64-cpython-313/biom/cli/table_validator.py -> build/bdist.linux-x86_64/wheel/./biom/cli
> copying build/lib.linux-x86_64-cpython-313/biom/cli/uc_processor.py -> build/bdist.linux-x86_64/wheel/./biom/cli
> copying build/lib.linux-x86_64-cpython-313/biom/cli/util.py -> build/bdist.linux-x86_64/wheel/./biom/cli
> creating build/bdist.linux-x86_64/wheel/biom/tests
> creating build/bdist.linux-x86_64/wheel/biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/10x10x0.100_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/10x10x0.100_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/10x10x0.010_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/10x10x0.010_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/10x10x0.001_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/10x10x0.001_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/10x100x0.100_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/10x100x0.100_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/10x100x0.010_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/10x100x0.010_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/10x100x0.001_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/10x100x0.001_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/10x1000x0.100_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/10x1000x0.100_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/10x1000x0.010_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/10x1000x0.010_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/10x1000x0.001_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/10x1000x0.001_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/10x10000x0.100_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/10x10000x0.100_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/10x10000x0.010_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/10x10000x0.010_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/10x10000x0.001_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/10x10000x0.001_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/100x10x0.100_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/100x10x0.100_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/100x10x0.010_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/100x10x0.010_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/100x10x0.001_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/100x10x0.001_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/100x100x0.100_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/100x100x0.100_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/100x100x0.010_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/100x100x0.010_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/100x100x0.001_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/100x100x0.001_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/100x1000x0.100_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/100x1000x0.100_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/100x1000x0.010_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/100x1000x0.010_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/100x1000x0.001_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/100x1000x0.001_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/100x10000x0.100_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/100x10000x0.100_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/100x10000x0.010_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/100x10000x0.010_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/100x10000x0.001_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/100x10000x0.001_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/1000x10x0.100_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/1000x10x0.100_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/1000x10x0.010_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/1000x10x0.010_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/1000x10x0.001_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/1000x10x0.001_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/1000x100x0.100_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/1000x100x0.100_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/1000x100x0.010_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/1000x100x0.010_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/1000x100x0.001_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/1000x100x0.001_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/1000x1000x0.100_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/1000x1000x0.100_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/1000x1000x0.010_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/1000x1000x0.010_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/1000x1000x0.001_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/1000x1000x0.001_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/1000x10000x0.100_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/1000x10000x0.100_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/1000x10000x0.010_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/1000x10000x0.010_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/1000x10000x0.001_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/1000x10000x0.001_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/10000x10x0.100_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/10000x10x0.100_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/10000x10x0.010_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/10000x10x0.010_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/10000x10x0.001_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/10000x10x0.001_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/10000x100x0.100_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/10000x100x0.100_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/10000x100x0.010_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/10000x100x0.010_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/10000x100x0.001_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/10000x100x0.001_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/10000x1000x0.100_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/10000x1000x0.100_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/10000x1000x0.010_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/10000x1000x0.010_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/10000x1000x0.001_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/10000x1000x0.001_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/10000x10000x0.100_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/10000x10000x0.100_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/10000x10000x0.010_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/10000x10000x0.010_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/10000x10000x0.001_bench_hdf5.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> copying build/lib.linux-x86_64-cpython-313/biom/tests/bench_tables/10000x10000x0.001_bench.biom.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/bench_tables
> creating build/bdist.linux-x86_64/wheel/biom/tests/test_cli
> creating build/bdist.linux-x86_64/wheel/biom/tests/test_cli/test_data
> copying build/lib.linux-x86_64-cpython-313/biom/tests/test_cli/test_data/test.json -> build/bdist.linux-x86_64/wheel/./biom/tests/test_cli/test_data
> copying build/lib.linux-x86_64-cpython-313/biom/tests/test_cli/test_data/test.biom -> build/bdist.linux-x86_64/wheel/./biom/tests/test_cli/test_data
> copying build/lib.linux-x86_64-cpython-313/biom/tests/test_cli/test_data/json_sample_collapsed.biom -> build/bdist.linux-x86_64/wheel/./biom/tests/test_cli/test_data
> copying build/lib.linux-x86_64-cpython-313/biom/tests/test_cli/test_data/json_obs_collapsed.biom -> build/bdist.linux-x86_64/wheel/./biom/tests/test_cli/test_data
> copying build/lib.linux-x86_64-cpython-313/biom/tests/test_cli/__init__.py -> build/bdist.linux-x86_64/wheel/./biom/tests/test_cli
> copying build/lib.linux-x86_64-cpython-313/biom/tests/test_cli/test_add_metadata.py -> build/bdist.linux-x86_64/wheel/./biom/tests/test_cli
> copying build/lib.linux-x86_64-cpython-313/biom/tests/test_cli/test_show_install_info.py -> build/bdist.linux-x86_64/wheel/./biom/tests/test_cli
> copying build/lib.linux-x86_64-cpython-313/biom/tests/test_cli/test_subset_table.py -> build/bdist.linux-x86_64/wheel/./biom/tests/test_cli
> copying build/lib.linux-x86_64-cpython-313/biom/tests/test_cli/test_summarize_table.py -> build/bdist.linux-x86_64/wheel/./biom/tests/test_cli
> copying build/lib.linux-x86_64-cpython-313/biom/tests/test_cli/test_table_converter.py -> build/bdist.linux-x86_64/wheel/./biom/tests/test_cli
> copying build/lib.linux-x86_64-cpython-313/biom/tests/test_cli/test_table_normalizer.py -> build/bdist.linux-x86_64/wheel/./biom/tests/test_cli
> copying build/lib.linux-x86_64-cpython-313/biom/tests/test_cli/test_uc_processor.py -> build/bdist.linux-x86_64/wheel/./biom/tests/test_cli
> copying build/lib.linux-x86_64-cpython-313/biom/tests/test_cli/test_validate_table.py -> build/bdist.linux-x86_64/wheel/./biom/tests/test_cli
> creating build/bdist.linux-x86_64/wheel/biom/tests/test_data
> copying build/lib.linux-x86_64-cpython-313/biom/tests/test_data/test_grp_metadata.biom -> build/bdist.linux-x86_64/wheel/./biom/tests/test_data
> copying build/lib.linux-x86_64-cpython-313/biom/tests/test_data/test.json.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/test_data
> copying build/lib.linux-x86_64-cpython-313/biom/tests/test_data/test.json -> build/bdist.linux-x86_64/wheel/./biom/tests/test_data
> copying build/lib.linux-x86_64-cpython-313/biom/tests/test_data/test.biom -> build/bdist.linux-x86_64/wheel/./biom/tests/test_data
> copying build/lib.linux-x86_64-cpython-313/biom/tests/test_data/no-contents.biom -> build/bdist.linux-x86_64/wheel/./biom/tests/test_data
> copying build/lib.linux-x86_64-cpython-313/biom/tests/test_data/empty.biom -> build/bdist.linux-x86_64/wheel/./biom/tests/test_data
> copying build/lib.linux-x86_64-cpython-313/biom/tests/test_data/edgecase_issue_952.biom -> build/bdist.linux-x86_64/wheel/./biom/tests/test_data
> copying build/lib.linux-x86_64-cpython-313/biom/tests/test_data/bad_table.txt.gz -> build/bdist.linux-x86_64/wheel/./biom/tests/test_data
> copying build/lib.linux-x86_64-cpython-313/biom/tests/test_data/bad_table.txt -> build/bdist.linux-x86_64/wheel/./biom/tests/test_data
> copying build/lib.linux-x86_64-cpython-313/biom/tests/test_data/__init__.py -> build/bdist.linux-x86_64/wheel/./biom/tests/test_data
> copying build/lib.linux-x86_64-cpython-313/biom/tests/__init__.py -> build/bdist.linux-x86_64/wheel/./biom/tests
> copying build/lib.linux-x86_64-cpython-313/biom/tests/long_lines.py -> build/bdist.linux-x86_64/wheel/./biom/tests
> copying build/lib.linux-x86_64-cpython-313/biom/tests/test_err.py -> build/bdist.linux-x86_64/wheel/./biom/tests
> copying build/lib.linux-x86_64-cpython-313/biom/tests/test_parse.py -> build/bdist.linux-x86_64/wheel/./biom/tests
> copying build/lib.linux-x86_64-cpython-313/biom/tests/test_table.py -> build/bdist.linux-x86_64/wheel/./biom/tests
> copying build/lib.linux-x86_64-cpython-313/biom/tests/test_util.py -> build/bdist.linux-x86_64/wheel/./biom/tests
> copying build/lib.linux-x86_64-cpython-313/biom/err.py -> build/bdist.linux-x86_64/wheel/./biom
> copying build/lib.linux-x86_64-cpython-313/biom/exception.py -> build/bdist.linux-x86_64/wheel/./biom
> copying build/lib.linux-x86_64-cpython-313/biom/parse.py -> build/bdist.linux-x86_64/wheel/./biom
> copying build/lib.linux-x86_64-cpython-313/biom/table.py -> build/bdist.linux-x86_64/wheel/./biom
> copying build/lib.linux-x86_64-cpython-313/biom/util.py -> build/bdist.linux-x86_64/wheel/./biom
> copying build/lib.linux-x86_64-cpython-313/biom/__init__.py -> build/bdist.linux-x86_64/wheel/./biom
> creating build/bdist.linux-x86_64/wheel/doc
> creating build/bdist.linux-x86_64/wheel/doc/_templates
> creating build/bdist.linux-x86_64/wheel/doc/_templates/autosummary
> copying build/lib.linux-x86_64-cpython-313/doc/_templates/autosummary/method.rst -> build/bdist.linux-x86_64/wheel/./doc/_templates/autosummary
> copying build/lib.linux-x86_64-cpython-313/doc/_templates/autosummary/class.rst -> build/bdist.linux-x86_64/wheel/./doc/_templates/autosummary
> copying build/lib.linux-x86_64-cpython-313/doc/_templates/autosummary/attribute.rst -> build/bdist.linux-x86_64/wheel/./doc/_templates/autosummary
> creating build/bdist.linux-x86_64/wheel/doc/_static
> copying build/lib.linux-x86_64-cpython-313/doc/_static/copybutton.js -> build/bdist.linux-x86_64/wheel/./doc/_static
> copying build/lib.linux-x86_64-cpython-313/doc/_static/biom-format.png -> build/bdist.linux-x86_64/wheel/./doc/_static
> creating build/bdist.linux-x86_64/wheel/doc/documentation
> creating build/bdist.linux-x86_64/wheel/doc/documentation/format_versions
> copying build/lib.linux-x86_64-cpython-313/doc/documentation/format_versions/biom-2.1.rst -> build/bdist.linux-x86_64/wheel/./doc/documentation/format_versions
> copying build/lib.linux-x86_64-cpython-313/doc/documentation/format_versions/biom-2.0.rst -> build/bdist.linux-x86_64/wheel/./doc/documentation/format_versions
> copying build/lib.linux-x86_64-cpython-313/doc/documentation/format_versions/biom-1.0.rst -> build/bdist.linux-x86_64/wheel/./doc/documentation/format_versions
> copying build/lib.linux-x86_64-cpython-313/doc/documentation/table_objects.rst -> build/bdist.linux-x86_64/wheel/./doc/documentation
> copying build/lib.linux-x86_64-cpython-313/doc/documentation/summarizing_biom_tables.rst -> build/bdist.linux-x86_64/wheel/./doc/documentation
> copying build/lib.linux-x86_64-cpython-313/doc/documentation/quick_usage_examples.rst -> build/bdist.linux-x86_64/wheel/./doc/documentation
> copying build/lib.linux-x86_64-cpython-313/doc/documentation/index.rst -> build/bdist.linux-x86_64/wheel/./doc/documentation
> copying build/lib.linux-x86_64-cpython-313/doc/documentation/biom_format.rst -> build/bdist.linux-x86_64/wheel/./doc/documentation
> copying build/lib.linux-x86_64-cpython-313/doc/documentation/biom_conversion.rst -> build/bdist.linux-x86_64/wheel/./doc/documentation
> copying build/lib.linux-x86_64-cpython-313/doc/documentation/adding_metadata.rst -> build/bdist.linux-x86_64/wheel/./doc/documentation
> copying build/lib.linux-x86_64-cpython-313/doc/index.rst -> build/bdist.linux-x86_64/wheel/./doc
> copying build/lib.linux-x86_64-cpython-313/doc/Makefile -> build/bdist.linux-x86_64/wheel/./doc
> copying build/lib.linux-x86_64-cpython-313/doc/BIOM_LICENSE.rst -> build/bdist.linux-x86_64/wheel/./doc
> creating build/bdist.linux-x86_64/wheel/doc/sphinxext
> creating build/bdist.linux-x86_64/wheel/doc/sphinxext/numpydoc
> copying build/lib.linux-x86_64-cpython-313/doc/sphinxext/numpydoc/README.rst -> build/bdist.linux-x86_64/wheel/./doc/sphinxext/numpydoc
> copying build/lib.linux-x86_64-cpython-313/doc/sphinxext/numpydoc/LICENSE.txt -> build/bdist.linux-x86_64/wheel/./doc/sphinxext/numpydoc
> creating build/bdist.linux-x86_64/wheel/doc/sphinxext/numpydoc/numpydoc
> creating build/bdist.linux-x86_64/wheel/doc/sphinxext/numpydoc/numpydoc/tests
> copying build/lib.linux-x86_64-cpython-313/doc/sphinxext/numpydoc/numpydoc/tests/test_docscrape.py -> build/bdist.linux-x86_64/wheel/./doc/sphinxext/numpydoc/numpydoc/tests
> copying build/lib.linux-x86_64-cpython-313/doc/sphinxext/numpydoc/numpydoc/tests/test_linkcode.py -> build/bdist.linux-x86_64/wheel/./doc/sphinxext/numpydoc/numpydoc/tests
> copying build/lib.linux-x86_64-cpython-313/doc/sphinxext/numpydoc/numpydoc/tests/test_phantom_import.py -> build/bdist.linux-x86_64/wheel/./doc/sphinxext/numpydoc/numpydoc/tests
> copying build/lib.linux-x86_64-cpython-313/doc/sphinxext/numpydoc/numpydoc/tests/test_plot_directive.py -> build/bdist.linux-x86_64/wheel/./doc/sphinxext/numpydoc/numpydoc/tests
> copying build/lib.linux-x86_64-cpython-313/doc/sphinxext/numpydoc/numpydoc/tests/test_traitsdoc.py -> build/bdist.linux-x86_64/wheel/./doc/sphinxext/numpydoc/numpydoc/tests
> copying build/lib.linux-x86_64-cpython-313/doc/sphinxext/numpydoc/numpydoc/comment_eater.py -> build/bdist.linux-x86_64/wheel/./doc/sphinxext/numpydoc/numpydoc
> copying build/lib.linux-x86_64-cpython-313/doc/sphinxext/numpydoc/numpydoc/compiler_unparse.py -> build/bdist.linux-x86_64/wheel/./doc/sphinxext/numpydoc/numpydoc
> copying build/lib.linux-x86_64-cpython-313/doc/sphinxext/numpydoc/numpydoc/docscrape.py -> build/bdist.linux-x86_64/wheel/./doc/sphinxext/numpydoc/numpydoc
> copying build/lib.linux-x86_64-cpython-313/doc/sphinxext/numpydoc/numpydoc/docscrape_sphinx.py -> build/bdist.linux-x86_64/wheel/./doc/sphinxext/numpydoc/numpydoc
> copying build/lib.linux-x86_64-cpython-313/doc/sphinxext/numpydoc/numpydoc/phantom_import.py -> build/bdist.linux-x86_64/wheel/./doc/sphinxext/numpydoc/numpydoc
> copying build/lib.linux-x86_64-cpython-313/doc/sphinxext/numpydoc/numpydoc/plot_directive.py -> build/bdist.linux-x86_64/wheel/./doc/sphinxext/numpydoc/numpydoc
> copying build/lib.linux-x86_64-cpython-313/doc/sphinxext/numpydoc/numpydoc/traitsdoc.py -> build/bdist.linux-x86_64/wheel/./doc/sphinxext/numpydoc/numpydoc
> copying build/lib.linux-x86_64-cpython-313/doc/sphinxext/numpydoc/numpydoc/__init__.py -> build/bdist.linux-x86_64/wheel/./doc/sphinxext/numpydoc/numpydoc
> copying build/lib.linux-x86_64-cpython-313/doc/sphinxext/numpydoc/numpydoc/linkcode.py -> build/bdist.linux-x86_64/wheel/./doc/sphinxext/numpydoc/numpydoc
> copying build/lib.linux-x86_64-cpython-313/doc/sphinxext/numpydoc/numpydoc/numpydoc.py -> build/bdist.linux-x86_64/wheel/./doc/sphinxext/numpydoc/numpydoc
> copying build/lib.linux-x86_64-cpython-313/doc/conf.py -> build/bdist.linux-x86_64/wheel/./doc
> running install_egg_info
> Copying biom_format.egg-info to build/bdist.linux-x86_64/wheel/./biom_format-2.1.17.egg-info
> running install_scripts
> creating build/bdist.linux-x86_64/wheel/biom_format-2.1.17.dist-info/WHEEL
> creating '/build/reproducible-path/python-biom-format-2.1.17/.pybuild/cpython3_3.13_biom-format/.tmp-oyx3qr_3/biom_format-2.1.17-cp313-cp313-linux_x86_64.whl' and adding 'build/bdist.linux-x86_64/wheel' to it
> adding 'biom/__init__.py'
> adding 'biom/_filter.cpython-313-x86_64-linux-gnu.so'
> adding 'biom/_filter.pyx'
> adding 'biom/_subsample.cpython-313-x86_64-linux-gnu.so'
> adding 'biom/_subsample.pyx'
> adding 'biom/_transform.cpython-313-x86_64-linux-gnu.so'
> adding 'biom/_transform.pyx'
> adding 'biom/err.py'
> adding 'biom/exception.py'
> adding 'biom/parse.py'
> adding 'biom/table.py'
> adding 'biom/util.py'
> adding 'biom/assets/exercise_api.py'
> adding 'biom/assets/exercise_cli.sh'
> adding 'biom/cli/__init__.py'
> adding 'biom/cli/installation_informer.py'
> adding 'biom/cli/metadata_adder.py'
> adding 'biom/cli/metadata_exporter.py'
> adding 'biom/cli/table_converter.py'
> adding 'biom/cli/table_head.py'
> adding 'biom/cli/table_ids.py'
> adding 'biom/cli/table_normalizer.py'
> adding 'biom/cli/table_subsetter.py'
> adding 'biom/cli/table_summarizer.py'
> adding 'biom/cli/table_validator.py'
> adding 'biom/cli/uc_processor.py'
> adding 'biom/cli/util.py'
> adding 'biom/tests/__init__.py'
> adding 'biom/tests/long_lines.py'
> adding 'biom/tests/test_err.py'
> adding 'biom/tests/test_parse.py'
> adding 'biom/tests/test_table.py'
> adding 'biom/tests/test_util.py'
> adding 'biom/tests/bench_tables/10000x10000x0.001_bench.biom.gz'
> adding 'biom/tests/bench_tables/10000x10000x0.001_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/10000x10000x0.010_bench.biom.gz'
> adding 'biom/tests/bench_tables/10000x10000x0.010_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/10000x10000x0.100_bench.biom.gz'
> adding 'biom/tests/bench_tables/10000x10000x0.100_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/10000x1000x0.001_bench.biom.gz'
> adding 'biom/tests/bench_tables/10000x1000x0.001_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/10000x1000x0.010_bench.biom.gz'
> adding 'biom/tests/bench_tables/10000x1000x0.010_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/10000x1000x0.100_bench.biom.gz'
> adding 'biom/tests/bench_tables/10000x1000x0.100_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/10000x100x0.001_bench.biom.gz'
> adding 'biom/tests/bench_tables/10000x100x0.001_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/10000x100x0.010_bench.biom.gz'
> adding 'biom/tests/bench_tables/10000x100x0.010_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/10000x100x0.100_bench.biom.gz'
> adding 'biom/tests/bench_tables/10000x100x0.100_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/10000x10x0.001_bench.biom.gz'
> adding 'biom/tests/bench_tables/10000x10x0.001_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/10000x10x0.010_bench.biom.gz'
> adding 'biom/tests/bench_tables/10000x10x0.010_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/10000x10x0.100_bench.biom.gz'
> adding 'biom/tests/bench_tables/10000x10x0.100_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/1000x10000x0.001_bench.biom.gz'
> adding 'biom/tests/bench_tables/1000x10000x0.001_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/1000x10000x0.010_bench.biom.gz'
> adding 'biom/tests/bench_tables/1000x10000x0.010_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/1000x10000x0.100_bench.biom.gz'
> adding 'biom/tests/bench_tables/1000x10000x0.100_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/1000x1000x0.001_bench.biom.gz'
> adding 'biom/tests/bench_tables/1000x1000x0.001_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/1000x1000x0.010_bench.biom.gz'
> adding 'biom/tests/bench_tables/1000x1000x0.010_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/1000x1000x0.100_bench.biom.gz'
> adding 'biom/tests/bench_tables/1000x1000x0.100_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/1000x100x0.001_bench.biom.gz'
> adding 'biom/tests/bench_tables/1000x100x0.001_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/1000x100x0.010_bench.biom.gz'
> adding 'biom/tests/bench_tables/1000x100x0.010_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/1000x100x0.100_bench.biom.gz'
> adding 'biom/tests/bench_tables/1000x100x0.100_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/1000x10x0.001_bench.biom.gz'
> adding 'biom/tests/bench_tables/1000x10x0.001_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/1000x10x0.010_bench.biom.gz'
> adding 'biom/tests/bench_tables/1000x10x0.010_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/1000x10x0.100_bench.biom.gz'
> adding 'biom/tests/bench_tables/1000x10x0.100_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/100x10000x0.001_bench.biom.gz'
> adding 'biom/tests/bench_tables/100x10000x0.001_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/100x10000x0.010_bench.biom.gz'
> adding 'biom/tests/bench_tables/100x10000x0.010_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/100x10000x0.100_bench.biom.gz'
> adding 'biom/tests/bench_tables/100x10000x0.100_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/100x1000x0.001_bench.biom.gz'
> adding 'biom/tests/bench_tables/100x1000x0.001_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/100x1000x0.010_bench.biom.gz'
> adding 'biom/tests/bench_tables/100x1000x0.010_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/100x1000x0.100_bench.biom.gz'
> adding 'biom/tests/bench_tables/100x1000x0.100_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/100x100x0.001_bench.biom.gz'
> adding 'biom/tests/bench_tables/100x100x0.001_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/100x100x0.010_bench.biom.gz'
> adding 'biom/tests/bench_tables/100x100x0.010_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/100x100x0.100_bench.biom.gz'
> adding 'biom/tests/bench_tables/100x100x0.100_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/100x10x0.001_bench.biom.gz'
> adding 'biom/tests/bench_tables/100x10x0.001_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/100x10x0.010_bench.biom.gz'
> adding 'biom/tests/bench_tables/100x10x0.010_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/100x10x0.100_bench.biom.gz'
> adding 'biom/tests/bench_tables/100x10x0.100_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/10x10000x0.001_bench.biom.gz'
> adding 'biom/tests/bench_tables/10x10000x0.001_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/10x10000x0.010_bench.biom.gz'
> adding 'biom/tests/bench_tables/10x10000x0.010_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/10x10000x0.100_bench.biom.gz'
> adding 'biom/tests/bench_tables/10x10000x0.100_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/10x1000x0.001_bench.biom.gz'
> adding 'biom/tests/bench_tables/10x1000x0.001_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/10x1000x0.010_bench.biom.gz'
> adding 'biom/tests/bench_tables/10x1000x0.010_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/10x1000x0.100_bench.biom.gz'
> adding 'biom/tests/bench_tables/10x1000x0.100_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/10x100x0.001_bench.biom.gz'
> adding 'biom/tests/bench_tables/10x100x0.001_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/10x100x0.010_bench.biom.gz'
> adding 'biom/tests/bench_tables/10x100x0.010_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/10x100x0.100_bench.biom.gz'
> adding 'biom/tests/bench_tables/10x100x0.100_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/10x10x0.001_bench.biom.gz'
> adding 'biom/tests/bench_tables/10x10x0.001_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/10x10x0.010_bench.biom.gz'
> adding 'biom/tests/bench_tables/10x10x0.010_bench_hdf5.biom.gz'
> adding 'biom/tests/bench_tables/10x10x0.100_bench.biom.gz'
> adding 'biom/tests/bench_tables/10x10x0.100_bench_hdf5.biom.gz'
> adding 'biom/tests/test_cli/__init__.py'
> adding 'biom/tests/test_cli/test_add_metadata.py'
> adding 'biom/tests/test_cli/test_show_install_info.py'
> adding 'biom/tests/test_cli/test_subset_table.py'
> adding 'biom/tests/test_cli/test_summarize_table.py'
> adding 'biom/tests/test_cli/test_table_converter.py'
> adding 'biom/tests/test_cli/test_table_normalizer.py'
> adding 'biom/tests/test_cli/test_uc_processor.py'
> adding 'biom/tests/test_cli/test_validate_table.py'
> adding 'biom/tests/test_cli/test_data/json_obs_collapsed.biom'
> adding 'biom/tests/test_cli/test_data/json_sample_collapsed.biom'
> adding 'biom/tests/test_cli/test_data/test.biom'
> adding 'biom/tests/test_cli/test_data/test.json'
> adding 'biom/tests/test_data/__init__.py'
> adding 'biom/tests/test_data/bad_table.txt'
> adding 'biom/tests/test_data/bad_table.txt.gz'
> adding 'biom/tests/test_data/edgecase_issue_952.biom'
> adding 'biom/tests/test_data/empty.biom'
> adding 'biom/tests/test_data/no-contents.biom'
> adding 'biom/tests/test_data/test.biom'
> adding 'biom/tests/test_data/test.json'
> adding 'biom/tests/test_data/test.json.gz'
> adding 'biom/tests/test_data/test_grp_metadata.biom'
> adding 'biom_format-2.1.17.dist-info/licenses/COPYING.txt'
> adding 'doc/BIOM_LICENSE.rst'
> adding 'doc/Makefile'
> adding 'doc/conf.py'
> adding 'doc/index.rst'
> adding 'doc/_static/biom-format.png'
> adding 'doc/_static/copybutton.js'
> adding 'doc/_templates/autosummary/attribute.rst'
> adding 'doc/_templates/autosummary/class.rst'
> adding 'doc/_templates/autosummary/method.rst'
> adding 'doc/documentation/adding_metadata.rst'
> adding 'doc/documentation/biom_conversion.rst'
> adding 'doc/documentation/biom_format.rst'
> adding 'doc/documentation/index.rst'
> adding 'doc/documentation/quick_usage_examples.rst'
> adding 'doc/documentation/summarizing_biom_tables.rst'
> adding 'doc/documentation/table_objects.rst'
> adding 'doc/documentation/format_versions/biom-1.0.rst'
> adding 'doc/documentation/format_versions/biom-2.0.rst'
> adding 'doc/documentation/format_versions/biom-2.1.rst'
> adding 'doc/sphinxext/numpydoc/LICENSE.txt'
> adding 'doc/sphinxext/numpydoc/README.rst'
> adding 'doc/sphinxext/numpydoc/numpydoc/__init__.py'
> adding 'doc/sphinxext/numpydoc/numpydoc/comment_eater.py'
> adding 'doc/sphinxext/numpydoc/numpydoc/compiler_unparse.py'
> adding 'doc/sphinxext/numpydoc/numpydoc/docscrape.py'
> adding 'doc/sphinxext/numpydoc/numpydoc/docscrape_sphinx.py'
> adding 'doc/sphinxext/numpydoc/numpydoc/linkcode.py'
> adding 'doc/sphinxext/numpydoc/numpydoc/numpydoc.py'
> adding 'doc/sphinxext/numpydoc/numpydoc/phantom_import.py'
> adding 'doc/sphinxext/numpydoc/numpydoc/plot_directive.py'
> adding 'doc/sphinxext/numpydoc/numpydoc/traitsdoc.py'
> adding 'doc/sphinxext/numpydoc/numpydoc/tests/test_docscrape.py'
> adding 'doc/sphinxext/numpydoc/numpydoc/tests/test_linkcode.py'
> adding 'doc/sphinxext/numpydoc/numpydoc/tests/test_phantom_import.py'
> adding 'doc/sphinxext/numpydoc/numpydoc/tests/test_plot_directive.py'
> adding 'doc/sphinxext/numpydoc/numpydoc/tests/test_traitsdoc.py'
> adding 'examples/min_sparse_otu_table.biom'
> adding 'examples/min_sparse_otu_table_hdf5.biom'
> adding 'examples/obs_md.txt'
> adding 'examples/rich_sparse_otu_table.biom'
> adding 'examples/rich_sparse_otu_table_hdf5.biom'
> adding 'examples/rich_sparse_otu_table_hdf5_group_metadata.biom'
> adding 'examples/sam_md.txt'
> adding 'licenses/numpydoc.txt'
> adding 'licenses/scikit-learn.txt'
> adding 'licenses/scipy.txt'
> adding 'biom_format-2.1.17.dist-info/METADATA'
> adding 'biom_format-2.1.17.dist-info/WHEEL'
> adding 'biom_format-2.1.17.dist-info/entry_points.txt'
> adding 'biom_format-2.1.17.dist-info/top_level.txt'
> adding 'biom_format-2.1.17.dist-info/RECORD'
> removing build/bdist.linux-x86_64/wheel
> Successfully built biom_format-2.1.17-cp313-cp313-linux_x86_64.whl
> I: pybuild plugin_pyproject:168: Unpacking wheel built for python3.13 with "installer" module
> # indep:
> PYTHONPATH=. http_proxy='127.0.0.1:9' sphinx-build -N -b html doc build/html
> Running Sphinx v9.1.0
> loading translations [en]... done
> making output directory... done
> Converting `source_suffix = '.rst'` to `source_suffix = {'.rst': 'restructuredtext'}`.
> [autosummary] generating autosummary for: BIOM_LICENSE.rst, documentation/adding_metadata.rst, documentation/biom_conversion.rst, documentation/biom_format.rst, documentation/index.rst, documentation/quick_usage_examples.rst, documentation/summarizing_biom_tables.rst, documentation/table_objects.rst, index.rst
> WARNING: Failed to import biom.table.
> Possible hints:
> * KeyError: 'biom'
> * ModuleNotFoundError: No module named 'biom._filter'
> WARNING: Failed to import biom.
> Possible hints:
> * KeyError: 'biom'
> * ModuleNotFoundError: No module named 'biom._filter'
> building [mo]: targets for 0 po files that are out of date
> writing output...
> building [html]: targets for 12 source files that are out of date
> updating environment: [new config] 12 added, 0 changed, 0 removed
> reading sources... [ 8%] BIOM_LICENSE
> reading sources... [ 17%] documentation/adding_metadata
> reading sources... [ 25%] documentation/biom_conversion
> reading sources... [ 33%] documentation/biom_format
> reading sources... [ 42%] documentation/format_versions/biom-1.0
> reading sources... [ 50%] documentation/format_versions/biom-2.0
> reading sources... [ 58%] documentation/format_versions/biom-2.1
> reading sources... [ 67%] documentation/index
> reading sources... [ 75%] documentation/quick_usage_examples
> reading sources... [ 83%] documentation/summarizing_biom_tables
> reading sources... [ 92%] documentation/table_objects
> reading sources... [100%] index
>
> WARNING: autodoc: failed to import 'biom'; the following exception was raised:
> Traceback (most recent call last):
> File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/_dynamic/_importer.py", line 131, in _import_from_module_and_path
> module = _import_module(module_name, try_reload=True)
> File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/_dynamic/_importer.py", line 221, in _import_module
> module = importlib.import_module(modname)
> File "/usr/lib/python3.13/importlib/__init__.py", line 88, in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> File "<frozen importlib._bootstrap>", line 1387, in _gcd_import
> File "<frozen importlib._bootstrap>", line 1360, in _find_and_load
> File "<frozen importlib._bootstrap>", line 1331, in _find_and_load_unlocked
> File "<frozen importlib._bootstrap>", line 935, in _load_unlocked
> File "<frozen importlib._bootstrap_external>", line 1023, in exec_module
> File "<frozen importlib._bootstrap>", line 488, in _call_with_frames_removed
> File "/build/reproducible-path/python-biom-format-2.1.17/biom/__init__.py", line 51, in <module>
> from .table import Table
> File "/build/reproducible-path/python-biom-format-2.1.17/biom/table.py", line 193, in <module>
> from ._filter import _filter
> ModuleNotFoundError: No module named 'biom._filter'
> [autodoc.import_object]
> WARNING: autodoc: failed to import 'table' from module 'biom'; the following exception was raised:
> Traceback (most recent call last):
> File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/_dynamic/_importer.py", line 131, in _import_from_module_and_path
> module = _import_module(module_name, try_reload=True)
> File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/_dynamic/_importer.py", line 221, in _import_module
> module = importlib.import_module(modname)
> File "/usr/lib/python3.13/importlib/__init__.py", line 88, in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> File "<frozen importlib._bootstrap>", line 1387, in _gcd_import
> File "<frozen importlib._bootstrap>", line 1360, in _find_and_load
> File "<frozen importlib._bootstrap>", line 1331, in _find_and_load_unlocked
> File "<frozen importlib._bootstrap>", line 935, in _load_unlocked
> File "<frozen importlib._bootstrap_external>", line 1023, in exec_module
> File "<frozen importlib._bootstrap>", line 488, in _call_with_frames_removed
> File "/build/reproducible-path/python-biom-format-2.1.17/biom/__init__.py", line 51, in <module>
> from .table import Table
> File "/build/reproducible-path/python-biom-format-2.1.17/biom/table.py", line 193, in <module>
> from ._filter import _filter
> ModuleNotFoundError: No module named 'biom._filter'
> [autodoc.import_object]
> looking for now-outdated files... none found
> pickling environment... done
> checking consistency... done
> preparing documents... done
> copying assets...
> copying static files...
> Writing evaluated template result to /build/reproducible-path/python-biom-format-2.1.17/build/html/_static/language_data.js
> Writing evaluated template result to /build/reproducible-path/python-biom-format-2.1.17/build/html/_static/documentation_options.js
> Writing evaluated template result to /build/reproducible-path/python-biom-format-2.1.17/build/html/_static/basic.css
> Writing evaluated template result to /build/reproducible-path/python-biom-format-2.1.17/build/html/_static/haiku.css
> copying static files: done
> copying extra files...
> copying extra files: done
> copying assets: done
> writing output... [ 8%] BIOM_LICENSE
> writing output... [ 17%] documentation/adding_metadata
> writing output... [ 25%] documentation/biom_conversion
> writing output... [ 33%] documentation/biom_format
> writing output... [ 42%] documentation/format_versions/biom-1.0
> writing output... [ 50%] documentation/format_versions/biom-2.0
> writing output... [ 58%] documentation/format_versions/biom-2.1
> writing output... [ 67%] documentation/index
> writing output... [ 75%] documentation/quick_usage_examples
> writing output... [ 83%] documentation/summarizing_biom_tables
> writing output... [ 92%] documentation/table_objects
> writing output... [100%] index
>
> /build/reproducible-path/python-biom-format-2.1.17/doc/documentation/index.rst:11: WARNING: toctree contains reference to document 'documentation/quick_usage_examples' that doesn't have a title: no link will be generated [toc.no_title]
> /build/reproducible-path/python-biom-format-2.1.17/doc/documentation/index.rst:11: WARNING: toctree contains reference to document 'documentation/table_objects' that doesn't have a title: no link will be generated [toc.no_title]
> /build/reproducible-path/python-biom-format-2.1.17/doc/documentation/index.rst:11: WARNING: toctree contains reference to document 'documentation/quick_usage_examples' that doesn't have a title: no link will be generated [toc.no_title]
> /build/reproducible-path/python-biom-format-2.1.17/doc/documentation/index.rst:11: WARNING: toctree contains reference to document 'documentation/table_objects' that doesn't have a title: no link will be generated [toc.no_title]
> generating indices... done
> writing additional pages... search done
> copying images... [100%] _static/biom-format.png
>
> dumping search index in English (code: en)... done
> dumping object inventory... done
> build succeeded, 8 warnings.
>
> The HTML pages are in build/html.
> PYTHONPATH=. http_proxy='127.0.0.1:9' sphinx-build -N -b man doc build/man
> Running Sphinx v9.1.0
> loading translations [en]... done
> making output directory... done
> Converting `source_suffix = '.rst'` to `source_suffix = {'.rst': 'restructuredtext'}`.
> [autosummary] generating autosummary for: BIOM_LICENSE.rst, documentation/adding_metadata.rst, documentation/biom_conversion.rst, documentation/biom_format.rst, documentation/index.rst, documentation/quick_usage_examples.rst, documentation/summarizing_biom_tables.rst, documentation/table_objects.rst, index.rst
> WARNING: Failed to import biom.table.
> Possible hints:
> * KeyError: 'biom'
> * ModuleNotFoundError: No module named 'biom._filter'
> WARNING: Failed to import biom.
> Possible hints:
> * KeyError: 'biom'
> * ModuleNotFoundError: No module named 'biom._filter'
> building [mo]: targets for 0 po files that are out of date
> writing output...
> building [man]: all manpages
> updating environment: [new config] 12 added, 0 changed, 0 removed
> reading sources... [ 8%] BIOM_LICENSE
> reading sources... [ 17%] documentation/adding_metadata
> reading sources... [ 25%] documentation/biom_conversion
> reading sources... [ 33%] documentation/biom_format
> reading sources... [ 42%] documentation/format_versions/biom-1.0
> reading sources... [ 50%] documentation/format_versions/biom-2.0
> reading sources... [ 58%] documentation/format_versions/biom-2.1
> reading sources... [ 67%] documentation/index
> reading sources... [ 75%] documentation/quick_usage_examples
> reading sources... [ 83%] documentation/summarizing_biom_tables
> reading sources... [ 92%] documentation/table_objects
> reading sources... [100%] index
>
> WARNING: autodoc: failed to import 'biom'; the following exception was raised:
> Traceback (most recent call last):
> File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/_dynamic/_importer.py", line 131, in _import_from_module_and_path
> module = _import_module(module_name, try_reload=True)
> File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/_dynamic/_importer.py", line 221, in _import_module
> module = importlib.import_module(modname)
> File "/usr/lib/python3.13/importlib/__init__.py", line 88, in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> File "<frozen importlib._bootstrap>", line 1387, in _gcd_import
> File "<frozen importlib._bootstrap>", line 1360, in _find_and_load
> File "<frozen importlib._bootstrap>", line 1331, in _find_and_load_unlocked
> File "<frozen importlib._bootstrap>", line 935, in _load_unlocked
> File "<frozen importlib._bootstrap_external>", line 1023, in exec_module
> File "<frozen importlib._bootstrap>", line 488, in _call_with_frames_removed
> File "/build/reproducible-path/python-biom-format-2.1.17/biom/__init__.py", line 51, in <module>
> from .table import Table
> File "/build/reproducible-path/python-biom-format-2.1.17/biom/table.py", line 193, in <module>
> from ._filter import _filter
> ModuleNotFoundError: No module named 'biom._filter'
> [autodoc.import_object]
> WARNING: autodoc: failed to import 'table' from module 'biom'; the following exception was raised:
> Traceback (most recent call last):
> File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/_dynamic/_importer.py", line 131, in _import_from_module_and_path
> module = _import_module(module_name, try_reload=True)
> File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/_dynamic/_importer.py", line 221, in _import_module
> module = importlib.import_module(modname)
> File "/usr/lib/python3.13/importlib/__init__.py", line 88, in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> File "<frozen importlib._bootstrap>", line 1387, in _gcd_import
> File "<frozen importlib._bootstrap>", line 1360, in _find_and_load
> File "<frozen importlib._bootstrap>", line 1331, in _find_and_load_unlocked
> File "<frozen importlib._bootstrap>", line 935, in _load_unlocked
> File "<frozen importlib._bootstrap_external>", line 1023, in exec_module
> File "<frozen importlib._bootstrap>", line 488, in _call_with_frames_removed
> File "/build/reproducible-path/python-biom-format-2.1.17/biom/__init__.py", line 51, in <module>
> from .table import Table
> File "/build/reproducible-path/python-biom-format-2.1.17/biom/table.py", line 193, in <module>
> from ._filter import _filter
> ModuleNotFoundError: No module named 'biom._filter'
> [autodoc.import_object]
> looking for now-outdated files... none found
> pickling environment... done
> checking consistency... done
> preparing documents... done
> copying assets...
> copying assets: done
> writing... biom.1 {
> documentation/index
> documentation/biom_format
> documentation/format_versions/biom-1.0
> documentation/format_versions/biom-2.0
> documentation/format_versions/biom-2.1
> documentation/quick_usage_examples
> documentation/table_objects
> documentation/biom_conversion
> documentation/adding_metadata
> documentation/summarizing_biom_tables
> BIOM_LICENSE
> } done
> build succeeded, 4 warnings.
>
> The manual pages are in build/man.
> make[1]: Leaving directory '/build/reproducible-path/python-biom-format-2.1.17'
> dh_auto_test -O--buildsystem=pybuild
> pybuild --test --test-pytest -i python{version} -p "3.14 3.13" --parallel=8
> I: pybuild pybuild:390: cp -r /build/reproducible-path/python-biom-format-2.1.17/examples /build/reproducible-path/python-biom-format-2.1.17/.pybuild/cpython3_3.14_biom-format/build
> I: pybuild base:385: cd /build/reproducible-path/python-biom-format-2.1.17/.pybuild/cpython3_3.14_biom-format/build; python3.14 -m pytest
> ============================= test session starts ==============================
> platform linux -- Python 3.14.5rc1, pytest-9.0.3, pluggy-1.6.0
> rootdir: /build/reproducible-path/python-biom-format-2.1.17/.pybuild/cpython3_3.14_biom-format/build
> configfile: pyproject.toml
> testpaths: biom
> plugins: cov-5.0.0, typeguard-4.4.4
> collected 384 items
>
> biom/tests/test_cli/test_add_metadata.py .... [ 1%]
> biom/tests/test_cli/test_show_install_info.py . [ 1%]
> biom/tests/test_cli/test_subset_table.py ..F.F [ 2%]
> biom/tests/test_cli/test_summarize_table.py .. [ 3%]
> biom/tests/test_cli/test_table_converter.py ...... [ 4%]
> biom/tests/test_cli/test_table_normalizer.py . [ 4%]
> biom/tests/test_cli/test_uc_processor.py ...... [ 6%]
> biom/tests/test_cli/test_validate_table.py ....................... [ 12%]
> biom/tests/test_err.py ..................... [ 17%]
> biom/tests/test_parse.py ........................... [ 25%]
> biom/tests/test_table.py ............................................... [ 37%]
> ..ssss..........................F.F.F................................... [ 55%]
> ......sss............................................................... [ 74%]
> ........................................................................ [ 93%]
> ..... [ 94%]
> biom/tests/test_util.py .................... [100%]
>
> =================================== FAILURES ===================================
> ________________ TestSubsetTable.test_subset_observations_hdf5 _________________
>
> self = <biom.tests.test_cli.test_subset_table.TestSubsetTable testMethod=test_subset_observations_hdf5>
>
> def test_subset_observations_hdf5(self):
> """Correctly subsets samples in a hdf5 table"""
> cwd = os.getcwd()
> if os.path.sep in __file__:
> os.chdir(os.path.dirname(__file__))
> > obs = _subset_table(hdf5_biom=os.path.join('test_data', 'test.biom'),
> axis='observation',
> ids=['GG_OTU_1', 'GG_OTU_3', 'GG_OTU_5'],
> json_table_str=None)
>
> /build/reproducible-path/python-biom-format-2.1.17/.pybuild/cpython3_3.14_biom-format/build/biom/tests/test_cli/test_subset_table.py:77:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> /build/reproducible-path/python-biom-format-2.1.17/.pybuild/cpython3_3.14_biom-format/build/biom/cli/table_subsetter.py:133: in _subset_table
> table = Table.from_hdf5(f, ids=ids, axis=axis)
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> /build/reproducible-path/python-biom-format-2.1.17/.pybuild/cpython3_3.14_biom-format/build/biom/table.py:4250: in from_hdf5
> obs_ids, obs_idx = _get_ids(obs_ids, obs)
> ^^^^^^^^^^^^^^^^^^^^^^
> /build/reproducible-path/python-biom-format-2.1.17/.pybuild/cpython3_3.14_biom-format/build/biom/table.py:4237: in _get_ids
> idx = np.in1d(source_ids, desired_ids)
> ^^^^^^^
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> attr = 'in1d'
>
> def __getattr__(attr):
> # Warn for expired attributes
> import warnings
>
> if attr == "linalg":
> import numpy.linalg as linalg
> return linalg
> elif attr == "fft":
> import numpy.fft as fft
> return fft
> elif attr == "dtypes":
> import numpy.dtypes as dtypes
> return dtypes
> elif attr == "random":
> import numpy.random as random
> return random
> elif attr == "polynomial":
> import numpy.polynomial as polynomial
> return polynomial
> elif attr == "ma":
> import numpy.ma as ma
> return ma
> elif attr == "ctypeslib":
> import numpy.ctypeslib as ctypeslib
> return ctypeslib
> elif attr == "exceptions":
> import numpy.exceptions as exceptions
> return exceptions
> elif attr == "testing":
> import numpy.testing as testing
> return testing
> elif attr == "matlib":
> import numpy.matlib as matlib
> return matlib
> elif attr == "f2py":
> import numpy.f2py as f2py
> return f2py
> elif attr == "typing":
> import numpy.typing as typing
> return typing
> elif attr == "rec":
> import numpy.rec as rec
> return rec
> elif attr == "char":
> import numpy.char as char
> return char
> elif attr == "array_api":
> raise AttributeError("`numpy.array_api` is not available from "
> "numpy 2.0 onwards", name=None)
> elif attr == "core":
> import numpy.core as core
> return core
> elif attr == "strings":
> import numpy.strings as strings
> return strings
> elif attr == "distutils":
> if 'distutils' in __numpy_submodules__:
> import numpy.distutils as distutils
> return distutils
> else:
> raise AttributeError("`numpy.distutils` is not available from "
> "Python 3.12 onwards", name=None)
>
> if attr in __future_scalars__:
> # And future warnings for those that will change, but also give
> # the AttributeError
> warnings.warn(
> f"In the future `np.{attr}` will be defined as the "
> "corresponding NumPy scalar.", FutureWarning, stacklevel=2)
>
> if attr in __former_attrs__:
> raise AttributeError(__former_attrs__[attr], name=None)
>
> if attr in __expired_attributes__:
> raise AttributeError(
> f"`np.{attr}` was removed in the NumPy 2.0 release. "
> f"{__expired_attributes__[attr]}",
> name=None
> )
>
> if attr == "chararray":
> warnings.warn(
> "`np.chararray` is deprecated and will be removed from "
> "the main namespace in the future. Use an array with a string "
> "or bytes dtype instead.", DeprecationWarning, stacklevel=2)
> import numpy.char as char
> return char.chararray
>
> > raise AttributeError(f"module {__name__!r} has no attribute {attr!r}")
> E AttributeError: module 'numpy' has no attribute 'in1d'. Did you mean: 'int16'?
>
> /usr/lib/python3/dist-packages/numpy/__init__.py:792: AttributeError
> ___________________ TestSubsetTable.test_subset_samples_hdf5 ___________________
>
> self = <biom.tests.test_cli.test_subset_table.TestSubsetTable testMethod=test_subset_samples_hdf5>
>
> def test_subset_samples_hdf5(self):
> """Correctly subsets samples in a hdf5 table"""
> cwd = os.getcwd()
> if os.path.sep in __file__:
> os.chdir(os.path.dirname(__file__))
> > obs = _subset_table(hdf5_biom=os.path.join('test_data', 'test.biom'),
> axis='sample',
> ids=['Sample1', 'Sample2', 'Sample3'],
> json_table_str=None)
>
> /build/reproducible-path/python-biom-format-2.1.17/.pybuild/cpython3_3.14_biom-format/build/biom/tests/test_cli/test_subset_table.py:60:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> /build/reproducible-path/python-biom-format-2.1.17/.pybuild/cpython3_3.14_biom-format/build/biom/cli/table_subsetter.py:133: in _subset_table
> table = Table.from_hdf5(f, ids=ids, axis=axis)
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> /build/reproducible-path/python-biom-format-2.1.17/.pybuild/cpython3_3.14_biom-format/build/biom/table.py:4251: in from_hdf5
> samp_ids, samp_idx = _get_ids(samp_ids, samp)
> ^^^^^^^^^^^^^^^^^^^^^^^^
> /build/reproducible-path/python-biom-format-2.1.17/.pybuild/cpython3_3.14_biom-format/build/biom/table.py:4237: in _get_ids
> idx = np.in1d(source_ids, desired_ids)
> ^^^^^^^
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> attr = 'in1d'
>
> def __getattr__(attr):
> # Warn for expired attributes
> import warnings
>
> if attr == "linalg":
> import numpy.linalg as linalg
> return linalg
> elif attr == "fft":
> import numpy.fft as fft
> return fft
> elif attr == "dtypes":
> import numpy.dtypes as dtypes
> return dtypes
> elif attr == "random":
> import numpy.random as random
> return random
> elif attr == "polynomial":
> import numpy.polynomial as polynomial
> return polynomial
> elif attr == "ma":
> import numpy.ma as ma
> return ma
> elif attr == "ctypeslib":
> import numpy.ctypeslib as ctypeslib
> return ctypeslib
> elif attr == "exceptions":
> import numpy.exceptions as exceptions
> return exceptions
> elif attr == "testing":
> import numpy.testing as testing
> return testing
> elif attr == "matlib":
> import numpy.matlib as matlib
> return matlib
> elif attr == "f2py":
> import numpy.f2py as f2py
> return f2py
> elif attr == "typing":
> import numpy.typing as typing
> return typing
> elif attr == "rec":
> import numpy.rec as rec
> return rec
> elif attr == "char":
> import numpy.char as char
> return char
> elif attr == "array_api":
> raise AttributeError("`numpy.array_api` is not available from "
> "numpy 2.0 onwards", name=None)
> elif attr == "core":
> import numpy.core as core
> return core
> elif attr == "strings":
> import numpy.strings as strings
> return strings
> elif attr == "distutils":
> if 'distutils' in __numpy_submodules__:
> import numpy.distutils as distutils
> return distutils
> else:
> raise AttributeError("`numpy.distutils` is not available from "
> "Python 3.12 onwards", name=None)
>
> if attr in __future_scalars__:
> # And future warnings for those that will change, but also give
> # the AttributeError
> warnings.warn(
> f"In the future `np.{attr}` will be defined as the "
> "corresponding NumPy scalar.", FutureWarning, stacklevel=2)
>
> if attr in __former_attrs__:
> raise AttributeError(__former_attrs__[attr], name=None)
>
> if attr in __expired_attributes__:
> raise AttributeError(
> f"`np.{attr}` was removed in the NumPy 2.0 release. "
> f"{__expired_attributes__[attr]}",
> name=None
> )
>
> if attr == "chararray":
> warnings.warn(
> "`np.chararray` is deprecated and will be removed from "
> "the main namespace in the future. Use an array with a string "
> "or bytes dtype instead.", DeprecationWarning, stacklevel=2)
> import numpy.char as char
> return char.chararray
>
> > raise AttributeError(f"module {__name__!r} has no attribute {attr!r}")
> E AttributeError: module 'numpy' has no attribute 'in1d'. Did you mean: 'int16'?
>
> /usr/lib/python3/dist-packages/numpy/__init__.py:792: AttributeError
> _________________ TableTests.test_from_hdf5_observation_subset _________________
>
> self = <biom.tests.test_table.TableTests testMethod=test_from_hdf5_observation_subset>
>
> def test_from_hdf5_observation_subset(self):
> """Parse a observation subset of a hdf5 formatted BIOM table"""
> observations = ['GG_OTU_1', 'GG_OTU_3', 'GG_OTU_5']
>
> cwd = os.getcwd()
> if '/' in __file__:
> os.chdir(__file__.rsplit('/', 1)[0])
> > t = Table.from_hdf5(h5py.File('test_data/test.biom', 'r'),
> ids=observations, axis='observation')
>
> /build/reproducible-path/python-biom-format-2.1.17/.pybuild/cpython3_3.14_biom-format/build/biom/tests/test_table.py:921:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> /build/reproducible-path/python-biom-format-2.1.17/.pybuild/cpython3_3.14_biom-format/build/biom/table.py:4250: in from_hdf5
> obs_ids, obs_idx = _get_ids(obs_ids, obs)
> ^^^^^^^^^^^^^^^^^^^^^^
> /build/reproducible-path/python-biom-format-2.1.17/.pybuild/cpython3_3.14_biom-format/build/biom/table.py:4237: in _get_ids
> idx = np.in1d(source_ids, desired_ids)
> ^^^^^^^
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> attr = 'in1d'
>
> def __getattr__(attr):
> # Warn for expired attributes
> import warnings
>
> if attr == "linalg":
> import numpy.linalg as linalg
> return linalg
> elif attr == "fft":
> import numpy.fft as fft
> return fft
> elif attr == "dtypes":
> import numpy.dtypes as dtypes
> return dtypes
> elif attr == "random":
> import numpy.random as random
> return random
> elif attr == "polynomial":
> import numpy.polynomial as polynomial
> return polynomial
> elif attr == "ma":
> import numpy.ma as ma
> return ma
> elif attr == "ctypeslib":
> import numpy.ctypeslib as ctypeslib
> return ctypeslib
> elif attr == "exceptions":
> import numpy.exceptions as exceptions
> return exceptions
> elif attr == "testing":
> import numpy.testing as testing
> return testing
> elif attr == "matlib":
> import numpy.matlib as matlib
> return matlib
> elif attr == "f2py":
> import numpy.f2py as f2py
> return f2py
> elif attr == "typing":
> import numpy.typing as typing
> return typing
> elif attr == "rec":
> import numpy.rec as rec
> return rec
> elif attr == "char":
> import numpy.char as char
> return char
> elif attr == "array_api":
> raise AttributeError("`numpy.array_api` is not available from "
> "numpy 2.0 onwards", name=None)
> elif attr == "core":
> import numpy.core as core
> return core
> elif attr == "strings":
> import numpy.strings as strings
> return strings
> elif attr == "distutils":
> if 'distutils' in __numpy_submodules__:
> import numpy.distutils as distutils
> return distutils
> else:
> raise AttributeError("`numpy.distutils` is not available from "
> "Python 3.12 onwards", name=None)
>
> if attr in __future_scalars__:
> # And future warnings for those that will change, but also give
> # the AttributeError
> warnings.warn(
> f"In the future `np.{attr}` will be defined as the "
> "corresponding NumPy scalar.", FutureWarning, stacklevel=2)
>
> if attr in __former_attrs__:
> raise AttributeError(__former_attrs__[attr], name=None)
>
> if attr in __expired_attributes__:
> raise AttributeError(
> f"`np.{attr}` was removed in the NumPy 2.0 release. "
> f"{__expired_attributes__[attr]}",
> name=None
> )
>
> if attr == "chararray":
> warnings.warn(
> "`np.chararray` is deprecated and will be removed from "
> "the main namespace in the future. Use an array with a string "
> "or bytes dtype instead.", DeprecationWarning, stacklevel=2)
> import numpy.char as char
> return char.chararray
>
> > raise AttributeError(f"module {__name__!r} has no attribute {attr!r}")
> E AttributeError: module 'numpy' has no attribute 'in1d'. Did you mean: 'int16'?
>
> /usr/lib/python3/dist-packages/numpy/__init__.py:792: AttributeError
> ___________________ TableTests.test_from_hdf5_sample_subset ____________________
>
> self = <biom.tests.test_table.TableTests testMethod=test_from_hdf5_sample_subset>
>
> def test_from_hdf5_sample_subset(self):
> """Parse a sample subset of a hdf5 formatted BIOM table"""
> samples = ['Sample2', 'Sample4', 'Sample6']
>
> cwd = os.getcwd()
> if '/' in __file__:
> os.chdir(__file__.rsplit('/', 1)[0])
> > t = Table.from_hdf5(h5py.File('test_data/test.biom', 'r'), ids=samples)
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>
> /build/reproducible-path/python-biom-format-2.1.17/.pybuild/cpython3_3.14_biom-format/build/biom/tests/test_table.py:822:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> /build/reproducible-path/python-biom-format-2.1.17/.pybuild/cpython3_3.14_biom-format/build/biom/table.py:4251: in from_hdf5
> samp_ids, samp_idx = _get_ids(samp_ids, samp)
> ^^^^^^^^^^^^^^^^^^^^^^^^
> /build/reproducible-path/python-biom-format-2.1.17/.pybuild/cpython3_3.14_biom-format/build/biom/table.py:4237: in _get_ids
> idx = np.in1d(source_ids, desired_ids)
> ^^^^^^^
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> attr = 'in1d'
>
> def __getattr__(attr):
> # Warn for expired attributes
> import warnings
>
> if attr == "linalg":
> import numpy.linalg as linalg
> return linalg
> elif attr == "fft":
> import numpy.fft as fft
> return fft
> elif attr == "dtypes":
> import numpy.dtypes as dtypes
> return dtypes
> elif attr == "random":
> import numpy.random as random
> return random
> elif attr == "polynomial":
> import numpy.polynomial as polynomial
> return polynomial
> elif attr == "ma":
> import numpy.ma as ma
> return ma
> elif attr == "ctypeslib":
> import numpy.ctypeslib as ctypeslib
> return ctypeslib
> elif attr == "exceptions":
> import numpy.exceptions as exceptions
> return exceptions
> elif attr == "testing":
> import numpy.testing as testing
> return testing
> elif attr == "matlib":
> import numpy.matlib as matlib
> return matlib
> elif attr == "f2py":
> import numpy.f2py as f2py
> return f2py
> elif attr == "typing":
> import numpy.typing as typing
> return typing
> elif attr == "rec":
> import numpy.rec as rec
> return rec
> elif attr == "char":
> import numpy.char as char
> return char
> elif attr == "array_api":
> raise AttributeError("`numpy.array_api` is not available from "
> "numpy 2.0 onwards", name=None)
> elif attr == "core":
> import numpy.core as core
> return core
> elif attr == "strings":
> import numpy.strings as strings
> return strings
> elif attr == "distutils":
> if 'distutils' in __numpy_submodules__:
> import numpy.distutils as distutils
> return distutils
> else:
> raise AttributeError("`numpy.distutils` is not available from "
> "Python 3.12 onwards", name=None)
>
> if attr in __future_scalars__:
> # And future warnings for those that will change, but also give
> # the AttributeError
> warnings.warn(
> f"In the future `np.{attr}` will be defined as the "
> "corresponding NumPy scalar.", FutureWarning, stacklevel=2)
>
> if attr in __former_attrs__:
> raise AttributeError(__former_attrs__[attr], name=None)
>
> if attr in __expired_attributes__:
> raise AttributeError(
> f"`np.{attr}` was removed in the NumPy 2.0 release. "
> f"{__expired_attributes__[attr]}",
> name=None
> )
>
> if attr == "chararray":
> warnings.warn(
> "`np.chararray` is deprecated and will be removed from "
> "the main namespace in the future. Use an array with a string "
> "or bytes dtype instead.", DeprecationWarning, stacklevel=2)
> import numpy.char as char
> return char.chararray
>
> > raise AttributeError(f"module {__name__!r} has no attribute {attr!r}")
> E AttributeError: module 'numpy' has no attribute 'in1d'. Did you mean: 'int16'?
>
> /usr/lib/python3/dist-packages/numpy/__init__.py:792: AttributeError
> ____________________ TableTests.test_from_hdf5_subset_error ____________________
>
> self = <biom.tests.test_table.TableTests testMethod=test_from_hdf5_subset_error>
>
> def test_from_hdf5_subset_error(self):
> """hdf5 biom table parse throws error with invalid parameters"""
> cwd = os.getcwd()
> if '/' in __file__:
> os.chdir(__file__.rsplit('/', 1)[0])
>
> # Raises an error if not all the given samples are in the OTU table
> with self.assertRaises(ValueError):
> > Table.from_hdf5(h5py.File('test_data/test.biom', 'r'),
> ids=['Sample2', 'DoesNotExist', 'Sample6'])
>
> /build/reproducible-path/python-biom-format-2.1.17/.pybuild/cpython3_3.14_biom-format/build/biom/tests/test_table.py:990:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> /build/reproducible-path/python-biom-format-2.1.17/.pybuild/cpython3_3.14_biom-format/build/biom/table.py:4251: in from_hdf5
> samp_ids, samp_idx = _get_ids(samp_ids, samp)
> ^^^^^^^^^^^^^^^^^^^^^^^^
> /build/reproducible-path/python-biom-format-2.1.17/.pybuild/cpython3_3.14_biom-format/build/biom/table.py:4237: in _get_ids
> idx = np.in1d(source_ids, desired_ids)
> ^^^^^^^
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> def __getattr__(attr):
> # Warn for expired attributes
> import warnings
>
> if attr == "linalg":
> import numpy.linalg as linalg
> return linalg
> elif attr == "fft":
> import numpy.fft as fft
> return fft
> elif attr == "dtypes":
> import numpy.dtypes as dtypes
> return dtypes
> elif attr == "random":
> import numpy.random as random
> return random
> elif attr == "polynomial":
> import numpy.polynomial as polynomial
> return polynomial
> elif attr == "ma":
> import numpy.ma as ma
> return ma
> elif attr == "ctypeslib":
> import numpy.ctypeslib as ctypeslib
> return ctypeslib
> elif attr == "exceptions":
> import numpy.exceptions as exceptions
> return exceptions
> elif attr == "testing":
> import numpy.testing as testing
> return testing
> elif attr == "matlib":
> import numpy.matlib as matlib
> return matlib
> elif attr == "f2py":
> import numpy.f2py as f2py
> return f2py
> elif attr == "typing":
> import numpy.typing as typing
> return typing
> elif attr == "rec":
> import numpy.rec as rec
> return rec
> elif attr == "char":
> import numpy.char as char
> return char
> elif attr == "array_api":
> raise AttributeError("`numpy.array_api` is not available from "
> "numpy 2.0 onwards", name=None)
> elif attr == "core":
> import numpy.core as core
> return core
> elif attr == "strings":
> import numpy.strings as strings
> return strings
> elif attr == "distutils":
> if 'distutils' in __numpy_submodules__:
> import numpy.distutils as distutils
> return distutils
> else:
> raise AttributeError("`numpy.distutils` is not available from "
> "Python 3.12 onwards", name=None)
>
> if attr in __future_scalars__:
> # And future warnings for those that will change, but also give
> # the AttributeError
> warnings.warn(
> f"In the future `np.{attr}` will be defined as the "
> "corresponding NumPy scalar.", FutureWarning, stacklevel=2)
>
> if attr in __former_attrs__:
> raise AttributeError(__former_attrs__[attr], name=None)
>
> if attr in __expired_attributes__:
> raise AttributeError(
> f"`np.{attr}` was removed in the NumPy 2.0 release. "
> f"{__expired_attributes__[attr]}",
> name=None
> )
>
> if attr == "chararray":
> warnings.warn(
> "`np.chararray` is deprecated and will be removed from "
> "the main namespace in the future. Use an array with a string "
> "or bytes dtype instead.", DeprecationWarning, stacklevel=2)
> import numpy.char as char
> return char.chararray
>
> > raise AttributeError(f"module {__name__!r} has no attribute {attr!r}")
> E AttributeError: module 'numpy' has no attribute 'in1d'. Did you mean: 'int16'?
>
> /usr/lib/python3/dist-packages/numpy/__init__.py:792: AttributeError
> =============================== warnings summary ===============================
> biom/tests/test_cli/test_show_install_info.py::TestShowInstallInfo::test_default
> biom/tests/test_cli/test_show_install_info.py::TestShowInstallInfo::test_default
> /build/reproducible-path/python-biom-format-2.1.17/.pybuild/cpython3_3.14_biom-format/build/biom/cli/installation_informer.py:66: DeprecationWarning: The '__version__' attribute is deprecated and will be removed in Click 9.1. Use feature detection or 'importlib.metadata.version("click")' instead.
> from click import __version__ as click_lib_version
>
> biom/tests/test_table.py::SupportTests::test_remove_empty_both
> biom/tests/test_table.py::SupportTests::test_remove_empty_obs
> biom/tests/test_table.py::SupportTests::test_remove_empty_sample
> /usr/lib/python3/dist-packages/scipy/sparse/_index.py:210: SparseEfficiencyWarning: Changing the sparsity structure of a csr_matrix is expensive. lil and dok are more efficient.
> self._set_arrayXarray(i, j, x)
>
> biom/tests/test_table.py::TableTests::test_nnz_issue_727
> /usr/lib/python3/dist-packages/scipy/sparse/_index.py:168: SparseEfficiencyWarning: Changing the sparsity structure of a csr_matrix is expensive. lil and dok are more efficient.
> self._set_intXint(row, col, x.flat[0])
>
> -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
> =========================== short test summary info ============================
> FAILED biom/tests/test_cli/test_subset_table.py::TestSubsetTable::test_subset_observations_hdf5
> FAILED biom/tests/test_cli/test_subset_table.py::TestSubsetTable::test_subset_samples_hdf5
> FAILED biom/tests/test_table.py::TableTests::test_from_hdf5_observation_subset
> FAILED biom/tests/test_table.py::TableTests::test_from_hdf5_sample_subset - A...
> FAILED biom/tests/test_table.py::TableTests::test_from_hdf5_subset_error - At...
> ============= 5 failed, 372 passed, 7 skipped, 6 warnings in 3.46s =============
> E: pybuild pybuild:485: test: plugin pyproject failed with: exit code=1: cd /build/reproducible-path/python-biom-format-2.1.17/.pybuild/cpython3_3.14_biom-format/build; python3.14 -m pytest
> I: pybuild pybuild:390: cp -r /build/reproducible-path/python-biom-format-2.1.17/examples /build/reproducible-path/python-biom-format-2.1.17/.pybuild/cpython3_3.13_biom-format/build
> I: pybuild base:385: cd /build/reproducible-path/python-biom-format-2.1.17/.pybuild/cpython3_3.13_biom-format/build; python3.13 -m pytest
> ============================= test session starts ==============================
> platform linux -- Python 3.13.12, pytest-9.0.3, pluggy-1.6.0
> rootdir: /build/reproducible-path/python-biom-format-2.1.17/.pybuild/cpython3_3.13_biom-format/build
> configfile: pyproject.toml
> testpaths: biom
> plugins: cov-5.0.0, typeguard-4.4.4
> collected 384 items
>
> biom/tests/test_cli/test_add_metadata.py .... [ 1%]
> biom/tests/test_cli/test_show_install_info.py . [ 1%]
> biom/tests/test_cli/test_subset_table.py ..F.F [ 2%]
> biom/tests/test_cli/test_summarize_table.py .. [ 3%]
> biom/tests/test_cli/test_table_converter.py ...... [ 4%]
> biom/tests/test_cli/test_table_normalizer.py . [ 4%]
> biom/tests/test_cli/test_uc_processor.py ...... [ 6%]
> biom/tests/test_cli/test_validate_table.py ....................... [ 12%]
> biom/tests/test_err.py ..................... [ 17%]
> biom/tests/test_parse.py ........................... [ 25%]
> biom/tests/test_table.py ............................................... [ 37%]
> ..ssss..........................F.F.F................................... [ 55%]
> ......sss............................................................... [ 74%]
> ........................................................................ [ 93%]
> ..... [ 94%]
> biom/tests/test_util.py .................... [100%]
>
> =================================== FAILURES ===================================
> ________________ TestSubsetTable.test_subset_observations_hdf5 _________________
>
> self = <biom.tests.test_cli.test_subset_table.TestSubsetTable testMethod=test_subset_observations_hdf5>
>
> def test_subset_observations_hdf5(self):
> """Correctly subsets samples in a hdf5 table"""
> cwd = os.getcwd()
> if os.path.sep in __file__:
> os.chdir(os.path.dirname(__file__))
> > obs = _subset_table(hdf5_biom=os.path.join('test_data', 'test.biom'),
> axis='observation',
> ids=['GG_OTU_1', 'GG_OTU_3', 'GG_OTU_5'],
> json_table_str=None)
>
> /build/reproducible-path/python-biom-format-2.1.17/.pybuild/cpython3_3.13_biom-format/build/biom/tests/test_cli/test_subset_table.py:77:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> /build/reproducible-path/python-biom-format-2.1.17/.pybuild/cpython3_3.13_biom-format/build/biom/cli/table_subsetter.py:133: in _subset_table
> table = Table.from_hdf5(f, ids=ids, axis=axis)
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> /build/reproducible-path/python-biom-format-2.1.17/.pybuild/cpython3_3.13_biom-format/build/biom/table.py:4250: in from_hdf5
> obs_ids, obs_idx = _get_ids(obs_ids, obs)
> ^^^^^^^^^^^^^^^^^^^^^^
> /build/reproducible-path/python-biom-format-2.1.17/.pybuild/cpython3_3.13_biom-format/build/biom/table.py:4237: in _get_ids
> idx = np.in1d(source_ids, desired_ids)
> ^^^^^^^
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> attr = 'in1d'
>
> def __getattr__(attr):
> # Warn for expired attributes
> import warnings
>
> if attr == "linalg":
> import numpy.linalg as linalg
> return linalg
> elif attr == "fft":
> import numpy.fft as fft
> return fft
> elif attr == "dtypes":
> import numpy.dtypes as dtypes
> return dtypes
> elif attr == "random":
> import numpy.random as random
> return random
> elif attr == "polynomial":
> import numpy.polynomial as polynomial
> return polynomial
> elif attr == "ma":
> import numpy.ma as ma
> return ma
> elif attr == "ctypeslib":
> import numpy.ctypeslib as ctypeslib
> return ctypeslib
> elif attr == "exceptions":
> import numpy.exceptions as exceptions
> return exceptions
> elif attr == "testing":
> import numpy.testing as testing
> return testing
> elif attr == "matlib":
> import numpy.matlib as matlib
> return matlib
> elif attr == "f2py":
> import numpy.f2py as f2py
> return f2py
> elif attr == "typing":
> import numpy.typing as typing
> return typing
> elif attr == "rec":
> import numpy.rec as rec
> return rec
> elif attr == "char":
> import numpy.char as char
> return char
> elif attr == "array_api":
> raise AttributeError("`numpy.array_api` is not available from "
> "numpy 2.0 onwards", name=None)
> elif attr == "core":
> import numpy.core as core
> return core
> elif attr == "strings":
> import numpy.strings as strings
> return strings
> elif attr == "distutils":
> if 'distutils' in __numpy_submodules__:
> import numpy.distutils as distutils
> return distutils
> else:
> raise AttributeError("`numpy.distutils` is not available from "
> "Python 3.12 onwards", name=None)
>
> if attr in __future_scalars__:
> # And future warnings for those that will change, but also give
> # the AttributeError
> warnings.warn(
> f"In the future `np.{attr}` will be defined as the "
> "corresponding NumPy scalar.", FutureWarning, stacklevel=2)
>
> if attr in __former_attrs__:
> raise AttributeError(__former_attrs__[attr], name=None)
>
> if attr in __expired_attributes__:
> raise AttributeError(
> f"`np.{attr}` was removed in the NumPy 2.0 release. "
> f"{__expired_attributes__[attr]}",
> name=None
> )
>
> if attr == "chararray":
> warnings.warn(
> "`np.chararray` is deprecated and will be removed from "
> "the main namespace in the future. Use an array with a string "
> "or bytes dtype instead.", DeprecationWarning, stacklevel=2)
> import numpy.char as char
> return char.chararray
>
> > raise AttributeError(f"module {__name__!r} has no attribute {attr!r}")
> E AttributeError: module 'numpy' has no attribute 'in1d'. Did you mean: 'int16'?
>
> /usr/lib/python3/dist-packages/numpy/__init__.py:792: AttributeError
> ___________________ TestSubsetTable.test_subset_samples_hdf5 ___________________
>
> self = <biom.tests.test_cli.test_subset_table.TestSubsetTable testMethod=test_subset_samples_hdf5>
>
> def test_subset_samples_hdf5(self):
> """Correctly subsets samples in a hdf5 table"""
> cwd = os.getcwd()
> if os.path.sep in __file__:
> os.chdir(os.path.dirname(__file__))
> > obs = _subset_table(hdf5_biom=os.path.join('test_data', 'test.biom'),
> axis='sample',
> ids=['Sample1', 'Sample2', 'Sample3'],
> json_table_str=None)
>
> /build/reproducible-path/python-biom-format-2.1.17/.pybuild/cpython3_3.13_biom-format/build/biom/tests/test_cli/test_subset_table.py:60:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> /build/reproducible-path/python-biom-format-2.1.17/.pybuild/cpython3_3.13_biom-format/build/biom/cli/table_subsetter.py:133: in _subset_table
> table = Table.from_hdf5(f, ids=ids, axis=axis)
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> /build/reproducible-path/python-biom-format-2.1.17/.pybuild/cpython3_3.13_biom-format/build/biom/table.py:4251: in from_hdf5
> samp_ids, samp_idx = _get_ids(samp_ids, samp)
> ^^^^^^^^^^^^^^^^^^^^^^^^
> /build/reproducible-path/python-biom-format-2.1.17/.pybuild/cpython3_3.13_biom-format/build/biom/table.py:4237: in _get_ids
> idx = np.in1d(source_ids, desired_ids)
> ^^^^^^^
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> attr = 'in1d'
>
> def __getattr__(attr):
> # Warn for expired attributes
> import warnings
>
> if attr == "linalg":
> import numpy.linalg as linalg
> return linalg
> elif attr == "fft":
> import numpy.fft as fft
> return fft
> elif attr == "dtypes":
> import numpy.dtypes as dtypes
> return dtypes
> elif attr == "random":
> import numpy.random as random
> return random
> elif attr == "polynomial":
> import numpy.polynomial as polynomial
> return polynomial
> elif attr == "ma":
> import numpy.ma as ma
> return ma
> elif attr == "ctypeslib":
> import numpy.ctypeslib as ctypeslib
> return ctypeslib
> elif attr == "exceptions":
> import numpy.exceptions as exceptions
> return exceptions
> elif attr == "testing":
> import numpy.testing as testing
> return testing
> elif attr == "matlib":
> import numpy.matlib as matlib
> return matlib
> elif attr == "f2py":
> import numpy.f2py as f2py
> return f2py
> elif attr == "typing":
> import numpy.typing as typing
> return typing
> elif attr == "rec":
> import numpy.rec as rec
> return rec
> elif attr == "char":
> import numpy.char as char
> return char
> elif attr == "array_api":
> raise AttributeError("`numpy.array_api` is not available from "
> "numpy 2.0 onwards", name=None)
> elif attr == "core":
> import numpy.core as core
> return core
> elif attr == "strings":
> import numpy.strings as strings
> return strings
> elif attr == "distutils":
> if 'distutils' in __numpy_submodules__:
> import numpy.distutils as distutils
> return distutils
> else:
> raise AttributeError("`numpy.distutils` is not available from "
> "Python 3.12 onwards", name=None)
>
> if attr in __future_scalars__:
> # And future warnings for those that will change, but also give
> # the AttributeError
> warnings.warn(
> f"In the future `np.{attr}` will be defined as the "
> "corresponding NumPy scalar.", FutureWarning, stacklevel=2)
>
> if attr in __former_attrs__:
> raise AttributeError(__former_attrs__[attr], name=None)
>
> if attr in __expired_attributes__:
> raise AttributeError(
> f"`np.{attr}` was removed in the NumPy 2.0 release. "
> f"{__expired_attributes__[attr]}",
> name=None
> )
>
> if attr == "chararray":
> warnings.warn(
> "`np.chararray` is deprecated and will be removed from "
> "the main namespace in the future. Use an array with a string "
> "or bytes dtype instead.", DeprecationWarning, stacklevel=2)
> import numpy.char as char
> return char.chararray
>
> > raise AttributeError(f"module {__name__!r} has no attribute {attr!r}")
> E AttributeError: module 'numpy' has no attribute 'in1d'. Did you mean: 'int16'?
>
> /usr/lib/python3/dist-packages/numpy/__init__.py:792: AttributeError
> _________________ TableTests.test_from_hdf5_observation_subset _________________
>
> self = <biom.tests.test_table.TableTests testMethod=test_from_hdf5_observation_subset>
>
> def test_from_hdf5_observation_subset(self):
> """Parse a observation subset of a hdf5 formatted BIOM table"""
> observations = ['GG_OTU_1', 'GG_OTU_3', 'GG_OTU_5']
>
> cwd = os.getcwd()
> if '/' in __file__:
> os.chdir(__file__.rsplit('/', 1)[0])
> > t = Table.from_hdf5(h5py.File('test_data/test.biom', 'r'),
> ids=observations, axis='observation')
>
> /build/reproducible-path/python-biom-format-2.1.17/.pybuild/cpython3_3.13_biom-format/build/biom/tests/test_table.py:921:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> /build/reproducible-path/python-biom-format-2.1.17/.pybuild/cpython3_3.13_biom-format/build/biom/table.py:4250: in from_hdf5
> obs_ids, obs_idx = _get_ids(obs_ids, obs)
> ^^^^^^^^^^^^^^^^^^^^^^
> /build/reproducible-path/python-biom-format-2.1.17/.pybuild/cpython3_3.13_biom-format/build/biom/table.py:4237: in _get_ids
> idx = np.in1d(source_ids, desired_ids)
> ^^^^^^^
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> attr = 'in1d'
>
> def __getattr__(attr):
> # Warn for expired attributes
> import warnings
>
> if attr == "linalg":
> import numpy.linalg as linalg
> return linalg
> elif attr == "fft":
> import numpy.fft as fft
> return fft
> elif attr == "dtypes":
> import numpy.dtypes as dtypes
> return dtypes
> elif attr == "random":
> import numpy.random as random
> return random
> elif attr == "polynomial":
> import numpy.polynomial as polynomial
> return polynomial
> elif attr == "ma":
> import numpy.ma as ma
> return ma
> elif attr == "ctypeslib":
> import numpy.ctypeslib as ctypeslib
> return ctypeslib
> elif attr == "exceptions":
> import numpy.exceptions as exceptions
> return exceptions
> elif attr == "testing":
> import numpy.testing as testing
> return testing
> elif attr == "matlib":
> import numpy.matlib as matlib
> return matlib
> elif attr == "f2py":
> import numpy.f2py as f2py
> return f2py
> elif attr == "typing":
> import numpy.typing as typing
> return typing
> elif attr == "rec":
> import numpy.rec as rec
> return rec
> elif attr == "char":
> import numpy.char as char
> return char
> elif attr == "array_api":
> raise AttributeError("`numpy.array_api` is not available from "
> "numpy 2.0 onwards", name=None)
> elif attr == "core":
> import numpy.core as core
> return core
> elif attr == "strings":
> import numpy.strings as strings
> return strings
> elif attr == "distutils":
> if 'distutils' in __numpy_submodules__:
> import numpy.distutils as distutils
> return distutils
> else:
> raise AttributeError("`numpy.distutils` is not available from "
> "Python 3.12 onwards", name=None)
>
> if attr in __future_scalars__:
> # And future warnings for those that will change, but also give
> # the AttributeError
> warnings.warn(
> f"In the future `np.{attr}` will be defined as the "
> "corresponding NumPy scalar.", FutureWarning, stacklevel=2)
>
> if attr in __former_attrs__:
> raise AttributeError(__former_attrs__[attr], name=None)
>
> if attr in __expired_attributes__:
> raise AttributeError(
> f"`np.{attr}` was removed in the NumPy 2.0 release. "
> f"{__expired_attributes__[attr]}",
> name=None
> )
>
> if attr == "chararray":
> warnings.warn(
> "`np.chararray` is deprecated and will be removed from "
> "the main namespace in the future. Use an array with a string "
> "or bytes dtype instead.", DeprecationWarning, stacklevel=2)
> import numpy.char as char
> return char.chararray
>
> > raise AttributeError(f"module {__name__!r} has no attribute {attr!r}")
> E AttributeError: module 'numpy' has no attribute 'in1d'. Did you mean: 'int16'?
>
> /usr/lib/python3/dist-packages/numpy/__init__.py:792: AttributeError
> ___________________ TableTests.test_from_hdf5_sample_subset ____________________
>
> self = <biom.tests.test_table.TableTests testMethod=test_from_hdf5_sample_subset>
>
> def test_from_hdf5_sample_subset(self):
> """Parse a sample subset of a hdf5 formatted BIOM table"""
> samples = ['Sample2', 'Sample4', 'Sample6']
>
> cwd = os.getcwd()
> if '/' in __file__:
> os.chdir(__file__.rsplit('/', 1)[0])
> > t = Table.from_hdf5(h5py.File('test_data/test.biom', 'r'), ids=samples)
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>
> /build/reproducible-path/python-biom-format-2.1.17/.pybuild/cpython3_3.13_biom-format/build/biom/tests/test_table.py:822:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> /build/reproducible-path/python-biom-format-2.1.17/.pybuild/cpython3_3.13_biom-format/build/biom/table.py:4251: in from_hdf5
> samp_ids, samp_idx = _get_ids(samp_ids, samp)
> ^^^^^^^^^^^^^^^^^^^^^^^^
> /build/reproducible-path/python-biom-format-2.1.17/.pybuild/cpython3_3.13_biom-format/build/biom/table.py:4237: in _get_ids
> idx = np.in1d(source_ids, desired_ids)
> ^^^^^^^
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> attr = 'in1d'
>
> def __getattr__(attr):
> # Warn for expired attributes
> import warnings
>
> if attr == "linalg":
> import numpy.linalg as linalg
> return linalg
> elif attr == "fft":
> import numpy.fft as fft
> return fft
> elif attr == "dtypes":
> import numpy.dtypes as dtypes
> return dtypes
> elif attr == "random":
> import numpy.random as random
> return random
> elif attr == "polynomial":
> import numpy.polynomial as polynomial
> return polynomial
> elif attr == "ma":
> import numpy.ma as ma
> return ma
> elif attr == "ctypeslib":
> import numpy.ctypeslib as ctypeslib
> return ctypeslib
> elif attr == "exceptions":
> import numpy.exceptions as exceptions
> return exceptions
> elif attr == "testing":
> import numpy.testing as testing
> return testing
> elif attr == "matlib":
> import numpy.matlib as matlib
> return matlib
> elif attr == "f2py":
> import numpy.f2py as f2py
> return f2py
> elif attr == "typing":
> import numpy.typing as typing
> return typing
> elif attr == "rec":
> import numpy.rec as rec
> return rec
> elif attr == "char":
> import numpy.char as char
> return char
> elif attr == "array_api":
> raise AttributeError("`numpy.array_api` is not available from "
> "numpy 2.0 onwards", name=None)
> elif attr == "core":
> import numpy.core as core
> return core
> elif attr == "strings":
> import numpy.strings as strings
> return strings
> elif attr == "distutils":
> if 'distutils' in __numpy_submodules__:
> import numpy.distutils as distutils
> return distutils
> else:
> raise AttributeError("`numpy.distutils` is not available from "
> "Python 3.12 onwards", name=None)
>
> if attr in __future_scalars__:
> # And future warnings for those that will change, but also give
> # the AttributeError
> warnings.warn(
> f"In the future `np.{attr}` will be defined as the "
> "corresponding NumPy scalar.", FutureWarning, stacklevel=2)
>
> if attr in __former_attrs__:
> raise AttributeError(__former_attrs__[attr], name=None)
>
> if attr in __expired_attributes__:
> raise AttributeError(
> f"`np.{attr}` was removed in the NumPy 2.0 release. "
> f"{__expired_attributes__[attr]}",
> name=None
> )
>
> if attr == "chararray":
> warnings.warn(
> "`np.chararray` is deprecated and will be removed from "
> "the main namespace in the future. Use an array with a string "
> "or bytes dtype instead.", DeprecationWarning, stacklevel=2)
> import numpy.char as char
> return char.chararray
>
> > raise AttributeError(f"module {__name__!r} has no attribute {attr!r}")
> E AttributeError: module 'numpy' has no attribute 'in1d'. Did you mean: 'int16'?
>
> /usr/lib/python3/dist-packages/numpy/__init__.py:792: AttributeError
> ____________________ TableTests.test_from_hdf5_subset_error ____________________
>
> self = <biom.tests.test_table.TableTests testMethod=test_from_hdf5_subset_error>
>
> def test_from_hdf5_subset_error(self):
> """hdf5 biom table parse throws error with invalid parameters"""
> cwd = os.getcwd()
> if '/' in __file__:
> os.chdir(__file__.rsplit('/', 1)[0])
>
> # Raises an error if not all the given samples are in the OTU table
> with self.assertRaises(ValueError):
> > Table.from_hdf5(h5py.File('test_data/test.biom', 'r'),
> ids=['Sample2', 'DoesNotExist', 'Sample6'])
>
> /build/reproducible-path/python-biom-format-2.1.17/.pybuild/cpython3_3.13_biom-format/build/biom/tests/test_table.py:990:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> /build/reproducible-path/python-biom-format-2.1.17/.pybuild/cpython3_3.13_biom-format/build/biom/table.py:4251: in from_hdf5
> samp_ids, samp_idx = _get_ids(samp_ids, samp)
> ^^^^^^^^^^^^^^^^^^^^^^^^
> /build/reproducible-path/python-biom-format-2.1.17/.pybuild/cpython3_3.13_biom-format/build/biom/table.py:4237: in _get_ids
> idx = np.in1d(source_ids, desired_ids)
> ^^^^^^^
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> def __getattr__(attr):
> # Warn for expired attributes
> import warnings
>
> if attr == "linalg":
> import numpy.linalg as linalg
> return linalg
> elif attr == "fft":
> import numpy.fft as fft
> return fft
> elif attr == "dtypes":
> import numpy.dtypes as dtypes
> return dtypes
> elif attr == "random":
> import numpy.random as random
> return random
> elif attr == "polynomial":
> import numpy.polynomial as polynomial
> return polynomial
> elif attr == "ma":
> import numpy.ma as ma
> return ma
> elif attr == "ctypeslib":
> import numpy.ctypeslib as ctypeslib
> return ctypeslib
> elif attr == "exceptions":
> import numpy.exceptions as exceptions
> return exceptions
> elif attr == "testing":
> import numpy.testing as testing
> return testing
> elif attr == "matlib":
> import numpy.matlib as matlib
> return matlib
> elif attr == "f2py":
> import numpy.f2py as f2py
> return f2py
> elif attr == "typing":
> import numpy.typing as typing
> return typing
> elif attr == "rec":
> import numpy.rec as rec
> return rec
> elif attr == "char":
> import numpy.char as char
> return char
> elif attr == "array_api":
> raise AttributeError("`numpy.array_api` is not available from "
> "numpy 2.0 onwards", name=None)
> elif attr == "core":
> import numpy.core as core
> return core
> elif attr == "strings":
> import numpy.strings as strings
> return strings
> elif attr == "distutils":
> if 'distutils' in __numpy_submodules__:
> import numpy.distutils as distutils
> return distutils
> else:
> raise AttributeError("`numpy.distutils` is not available from "
> "Python 3.12 onwards", name=None)
>
> if attr in __future_scalars__:
> # And future warnings for those that will change, but also give
> # the AttributeError
> warnings.warn(
> f"In the future `np.{attr}` will be defined as the "
> "corresponding NumPy scalar.", FutureWarning, stacklevel=2)
>
> if attr in __former_attrs__:
> raise AttributeError(__former_attrs__[attr], name=None)
>
> if attr in __expired_attributes__:
> raise AttributeError(
> f"`np.{attr}` was removed in the NumPy 2.0 release. "
> f"{__expired_attributes__[attr]}",
> name=None
> )
>
> if attr == "chararray":
> warnings.warn(
> "`np.chararray` is deprecated and will be removed from "
> "the main namespace in the future. Use an array with a string "
> "or bytes dtype instead.", DeprecationWarning, stacklevel=2)
> import numpy.char as char
> return char.chararray
>
> > raise AttributeError(f"module {__name__!r} has no attribute {attr!r}")
> E AttributeError: module 'numpy' has no attribute 'in1d'. Did you mean: 'int16'?
>
> /usr/lib/python3/dist-packages/numpy/__init__.py:792: AttributeError
> =============================== warnings summary ===============================
> biom/tests/test_cli/test_show_install_info.py::TestShowInstallInfo::test_default
> biom/tests/test_cli/test_show_install_info.py::TestShowInstallInfo::test_default
> /build/reproducible-path/python-biom-format-2.1.17/.pybuild/cpython3_3.13_biom-format/build/biom/cli/installation_informer.py:66: DeprecationWarning: The '__version__' attribute is deprecated and will be removed in Click 9.1. Use feature detection or 'importlib.metadata.version("click")' instead.
> from click import __version__ as click_lib_version
>
> biom/tests/test_table.py::SupportTests::test_remove_empty_both
> biom/tests/test_table.py::SupportTests::test_remove_empty_obs
> biom/tests/test_table.py::SupportTests::test_remove_empty_sample
> /usr/lib/python3/dist-packages/scipy/sparse/_index.py:210: SparseEfficiencyWarning: Changing the sparsity structure of a csr_matrix is expensive. lil and dok are more efficient.
> self._set_arrayXarray(i, j, x)
>
> biom/tests/test_table.py::TableTests::test_nnz_issue_727
> /usr/lib/python3/dist-packages/scipy/sparse/_index.py:168: SparseEfficiencyWarning: Changing the sparsity structure of a csr_matrix is expensive. lil and dok are more efficient.
> self._set_intXint(row, col, x.flat[0])
>
> -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
> =========================== short test summary info ============================
> FAILED biom/tests/test_cli/test_subset_table.py::TestSubsetTable::test_subset_observations_hdf5
> FAILED biom/tests/test_cli/test_subset_table.py::TestSubsetTable::test_subset_samples_hdf5
> FAILED biom/tests/test_table.py::TableTests::test_from_hdf5_observation_subset
> FAILED biom/tests/test_table.py::TableTests::test_from_hdf5_sample_subset - A...
> FAILED biom/tests/test_table.py::TableTests::test_from_hdf5_subset_error - At...
> ============= 5 failed, 372 passed, 7 skipped, 6 warnings in 3.37s =============
> E: pybuild pybuild:485: test: plugin pyproject failed with: exit code=1: cd /build/reproducible-path/python-biom-format-2.1.17/.pybuild/cpython3_3.13_biom-format/build; python3.13 -m pytest
> rm -fr -- /tmp/dh-xdg-rundir-C7ATozNW
> dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.14 3.13" --parallel=8 returned exit code 13
The full build log is available at
https://people.debian.org/~cipriano/custom-mass-rebuild/python3-click-8.3.3/python-biom-format_2.1.17-1.log
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