[med-svn] [Git][med-team/python-bx][master] 9 commits: routine-update: New upstream version
Michael R. Crusoe (@crusoe)
gitlab at salsa.debian.org
Wed Jul 3 17:11:41 BST 2024
Michael R. Crusoe pushed to branch master at Debian Med / python-bx
Commits:
7f7b7351 by Michael R. Crusoe at 2024-07-03T14:15:07+02:00
routine-update: New upstream version
- - - - -
5426a3f3 by Michael R. Crusoe at 2024-07-03T14:15:08+02:00
New upstream version 0.12.0
- - - - -
d6feb33c by Michael R. Crusoe at 2024-07-03T14:15:12+02:00
Update upstream source from tag 'upstream/0.12.0'
Update to upstream version '0.12.0'
with Debian dir 19d0da209e7a191f85d81e9fbb9ac1f1827662b2
- - - - -
836bb875 by Michael R. Crusoe at 2024-07-03T14:15:12+02:00
routine-update: Standards-Version: 4.6.2
- - - - -
793af7f9 by Michael R. Crusoe at 2024-07-03T14:20:15+02:00
d/patches/{post-install-testing,pytest8,strlen_missing_include}: removed, applied upstream.
- - - - -
7cb770e6 by Michael R. Crusoe at 2024-07-03T17:30:20+02:00
Forwarded remaining patches upstream
- - - - -
9b73f08b by Michael R. Crusoe at 2024-07-03T18:07:06+02:00
d/lintian-overrides: fix mismatched tag
- - - - -
048a082a by Michael R. Crusoe at 2024-07-03T18:07:06+02:00
d/patches/spelling: fix typos
- - - - -
4d4554a9 by Michael R. Crusoe at 2024-07-03T18:07:06+02:00
routine-update: Ready to upload to unstable
- - - - -
30 changed files:
- .github/workflows/deploy.yaml
- .gitignore
- debian/changelog
- debian/control
- debian/lintian-overrides
- debian/patches/fix_import_cookbook.patch
- debian/patches/no_psyco.patch
- − debian/patches/post-install-testing
- − debian/patches/pytest8
- debian/patches/series
- + debian/patches/spelling
- − debian/patches/strlen_missing_include
- lib/bx/__init__.py
- lib/bx/align/sitemask/sitemask_tests.py
- lib/bx/binned_array.py
- lib/bx/binned_array_tests.py
- lib/bx/interval_index_file_tests.py
- lib/bx/intervals/cluster_tests.py
- lib/bx/intervals/intersection.pyx
- lib/bx/misc/seekbzip2_tests.py
- lib/bx/motif/io/transfac_tests.py
- lib/bx/motif/pwm_tests.py
- lib/bx/seq/fasta_tests.py
- lib/bx/seq/nib_tests.py
- lib/bx/seq/qdna_tests.py
- lib/bx/seq/twobit_tests.py
- pyproject.toml
- pytest.ini
- src/pwm_utils.c
- tox.ini
Changes:
=====================================
.github/workflows/deploy.yaml
=====================================
@@ -32,10 +32,11 @@ jobs:
run: python -m cibuildwheel --output-dir dist
env:
CIBW_ARCHS: ${{ matrix.archs }}
- # Skip building musllinux wheels for the Python versions for which the oldest
- # supported numpy version doesn't have musllinux wheels on PyPI.
- # Skip also building for PyPy 3.8, which is deprecated upstream.
- CIBW_SKIP: "cp38-musllinux_* cp39-musllinux_* cp310-musllinux_* cp311-musllinux_* pp38-*"
+ # Skip building musllinux wheels for the CPython versions for which the
+ # numpy version we build against doesn't have musllinux wheels on PyPI.
+ # Skip building for PyPy 3.8, which is deprecated upstream.
+ # Skip building for PyPy on i686 since NumPy 2.0 fails to build on it.
+ CIBW_SKIP: "cp38-musllinux_* pp38-* pp*-manylinux_i686"
- name: Check packages
run: twine check dist/*
- uses: actions/upload-artifact at v4
=====================================
.gitignore
=====================================
@@ -32,3 +32,6 @@ nose*.egg
# Built sdist directory
dist
+
+# Testing
+.tox/
=====================================
debian/changelog
=====================================
@@ -1,8 +1,15 @@
-python-bx (0.11.0-5) UNRELEASED; urgency=medium
+python-bx (0.12.0-1) unstable; urgency=medium
* d/rules,d/pybuild.testfiles: cleaner way of handling the test data
+ * New upstream version
+ * Standards-Version: 4.6.2 (routine-update)
+ * d/patches/{post-install-testing,pytest8,strlen_missing_include}:
+ removed, applied upstream.
+ * Forwarded remaining patches upstream
+ * d/lintian-overrides: fix mismatched tag
+ * d/patches/spelling: fix typos
- -- Michael R. Crusoe <crusoe at debian.org> Fri, 03 May 2024 15:24:24 +0200
+ -- Michael R. Crusoe <crusoe at debian.org> Wed, 03 Jul 2024 17:31:02 +0200
python-bx (0.11.0-4) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -16,7 +16,7 @@ Build-Depends: debhelper-compat (= 13),
python3-pytest-cython <!nocheck>,
python3-numpy <!nocheck>,
cython3
-Standards-Version: 4.7.0
+Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/python-bx
Vcs-Git: https://salsa.debian.org/med-team/python-bx.git
Homepage: https://github.com/bxlab/bx-python
=====================================
debian/lintian-overrides
=====================================
@@ -2,4 +2,4 @@
# We shall revisit this decision once all packages for toil are in the distribution
# and we have learned more about how bx is used in the community in 3rd party scripts.
# see https://lists.debian.org/debian-med/2018/06/msg00043.html
-python3-bx: script-with-language-extension usr/bin/*.py
+python3-bx: script-with-language-extension [usr/bin/*.py]
=====================================
debian/patches/fix_import_cookbook.patch
=====================================
@@ -1,8 +1,8 @@
-Description: Fix import statement s/cookbook/bx.cookbook/
+Subject: Fix import statement s/cookbook/bx.cookbook/
+From: Andreas Tille <tille at debian.org>
Bug-Debian: https://bugs.debian.org/1068996
-Author: Andreas Tille <tille at debian.org>
-Last-Updat: Mon, 15 Apr 2024 08:27:39 +0200
-
+Last-Update: Mon, 15 Apr 2024 08:27:39 +0200
+Forwarded: https://github.com/bxlab/bx-python/pull/95
--- a/scripts/maf_tile_2.py
+++ b/scripts/maf_tile_2.py
@@ -31,7 +31,7 @@ usage: %prog list,of,species,to,keep seq
=====================================
debian/patches/no_psyco.patch
=====================================
@@ -1,7 +1,8 @@
-Description: psyco is only available for Python <= 2.6
+Subject: psyco is only available for Python <= 2.6
Bug-Debian: https://bugs.debian.org/1068996
-Author: Andreas Tille <tille at debian.org>
-Last-Updat: Mon, 15 Apr 2024 08:27:39 +0200
+From: Andreas Tille <tille at debian.org>
+Last-Update: Mon, 15 Apr 2024 08:27:39 +0200
+Forwarded: https://github.com/bxlab/bx-python/pull/96
--- a/scripts/maf_word_frequency.py
+++ b/scripts/maf_word_frequency.py
=====================================
debian/patches/post-install-testing deleted
=====================================
@@ -1,132 +0,0 @@
-From: Michael R. Crusoe <crusoe at debian.org>
-Subject: enable post-installation testing
-Forwarded: https://github.com/bxlab/bx-python/pull/93
---- python-bx.orig/lib/bx/align/sitemask/sitemask_tests.py
-+++ python-bx/lib/bx/align/sitemask/sitemask_tests.py
-@@ -6,7 +6,7 @@
- from io import StringIO
-
- import bx.align.maf
--from . import cpg
-+from bx.align.sitemask import cpg
-
- test_maf_cpg = """##maf version=1 scoring=none
- a score=0
---- python-bx.orig/lib/bx/binned_array_tests.py
-+++ python-bx/lib/bx/binned_array_tests.py
-@@ -10,7 +10,7 @@
- )
- from numpy.random import random_sample as random
-
--from .binned_array import (
-+from bx.binned_array import (
- BinnedArray,
- BinnedArrayWriter,
- FileBinnedArray,
---- python-bx.orig/lib/bx/interval_index_file_tests.py
-+++ python-bx/lib/bx/interval_index_file_tests.py
-@@ -1,8 +1,8 @@
- import random
- from tempfile import mktemp
-
--from . import interval_index_file
--from .interval_index_file import Indexes
-+from bx import interval_index_file
-+from bx.interval_index_file import Indexes
-
-
- def test_offsets():
---- python-bx.orig/lib/bx/intervals/cluster_tests.py
-+++ python-bx/lib/bx/intervals/cluster_tests.py
-@@ -2,13 +2,7 @@
- import sys
- import unittest
-
--try:
-- sys.path.insert(0, os.path.dirname(os.path.dirname(__file__)))
--except Exception:
-- sys.path.insert(0, os.path.dirname(os.path.abspath(".")))
--
--# from bx.intervals.cluster import ClusterTree
--from .cluster import ClusterTree
-+from bx.intervals.cluster import ClusterTree
-
-
- class TestCluster(unittest.TestCase):
---- python-bx.orig/lib/bx/misc/seekbzip2_tests.py
-+++ python-bx/lib/bx/misc/seekbzip2_tests.py
-@@ -7,7 +7,7 @@
- import random
- from codecs import encode
-
--from . import seekbzip2
-+from bx.misc import seekbzip2
-
- F = None
- T = None
---- python-bx.orig/lib/bx/motif/io/transfac_tests.py
-+++ python-bx/lib/bx/motif/io/transfac_tests.py
-@@ -2,7 +2,7 @@
-
- from numpy import allclose
-
--from . import transfac
-+from bx.motif.io import transfac
-
- sample = """
- VV TRANSFAC MATRIX TABLE, Rel.3.2 26-06-1997
---- python-bx.orig/lib/bx/motif/pwm_tests.py
-+++ python-bx/lib/bx/motif/pwm_tests.py
-@@ -3,7 +3,7 @@
- isnan,
- )
-
--from . import pwm
-+from bx.motif import pwm
-
-
- def test_create():
---- python-bx.orig/lib/bx/seq/fasta_tests.py
-+++ python-bx/lib/bx/seq/fasta_tests.py
-@@ -4,7 +4,7 @@
-
- import unittest
-
--from . import fasta
-+from bx.seq import fasta
-
- test_fa = "test_data/seq_tests/test.fa"
-
---- python-bx.orig/lib/bx/seq/nib_tests.py
-+++ python-bx/lib/bx/seq/nib_tests.py
-@@ -4,7 +4,7 @@
-
- import unittest
-
--from . import nib
-+from bx.seq import nib
-
- test_nib = "test_data/seq_tests/test.nib"
-
---- python-bx.orig/lib/bx/seq/qdna_tests.py
-+++ python-bx/lib/bx/seq/qdna_tests.py
-@@ -4,7 +4,7 @@
-
- import unittest
-
--from . import qdna
-+from bx.seq import qdna
-
- test_qdna = "test_data/seq_tests/test.qdna"
-
---- python-bx.orig/lib/bx/seq/twobit_tests.py
-+++ python-bx/lib/bx/seq/twobit_tests.py
-@@ -2,7 +2,7 @@
-
- import pytest
-
--from . import twobit
-+from bx.seq import twobit
-
-
- def quick_fasta_iter(f):
=====================================
debian/patches/pytest8 deleted
=====================================
@@ -1,70 +0,0 @@
-From: Michael R. Crusoe <crusoe at debian.org>
-Subject: Add pytest 8.x compatability
-Forwarded: https://github.com/bxlab/bx-python/pull/92
-
-nose-style module setup function renamed to the pytest way.
---- python-bx.orig/lib/bx/binned_array_tests.py
-+++ python-bx/lib/bx/binned_array_tests.py
-@@ -16,18 +16,17 @@
- FileBinnedArray,
- )
-
-+import pytest
-+
- # Bigger values take longer, but excercise more bins
- CHUNK_SIZE_RANDOM = 945
- CHUNK_SIZE_ZEROS = 897
- # CHUNK_SIZE_RANDOM=9456
- # CHUNK_SIZE_ZEROS=8972
-
--source = target = None
--
-
--def setup():
-- global source
-- global target
-+ at pytest.fixture(scope="module")
-+def source_target():
- source = []
- for _ in range(13):
- if random() < 0.5:
-@@ -43,7 +42,8 @@
- return source, target
-
-
--def test_simple():
-+def test_simple(source_target):
-+ source, target = source_target
- # Verify
- for i in range(len(source)):
- assert source[i] == target[i], "No match, index: %d, source: %f, target: %f, len( source ): %d" % (
-@@ -66,7 +66,8 @@
- )
-
-
--def test_file():
-+def test_file(source_target):
-+ source, target = source_target
- # With a file (zlib)
- target.to_file(open("/tmp/foo", "wb"))
- target2 = FileBinnedArray(open("/tmp/foo", "rb"))
-@@ -87,7 +88,8 @@
- )
-
-
--def test_file_lzo():
-+def test_file_lzo(source_target):
-+ source, target = source_target
- # With a file (lzo)
- target.to_file(open("/tmp/foo3", "wb"), comp_type="lzo")
- target3 = FileBinnedArray(open("/tmp/foo3", "rb"))
-@@ -109,7 +111,8 @@
- )
-
-
--def test_binned_array_writer():
-+def test_binned_array_writer(source_target):
-+ source, target = source_target
- # Test with ba writer
- o = open("/tmp/foo4", "wb")
- w = BinnedArrayWriter(o, 128, comp_type="lzo")
=====================================
debian/patches/series
=====================================
@@ -1,6 +1,4 @@
-strlen_missing_include
-post-install-testing
-pytest8
+spelling
shebang.patch
fix_BIN_OFFSETS_MAX
fix_import_cookbook.patch
=====================================
debian/patches/spelling
=====================================
@@ -0,0 +1,111 @@
+From: Michael R. Crusoe <crusoe at debian.org>
+Subject: Fix typos
+Forwarded: https://github.com/bxlab/bx-python/pull/97
+--- python-bx.orig/lib/bx/_seqmapping.pyx
++++ python-bx/lib/bx/_seqmapping.pyx
+@@ -166,7 +166,7 @@
+ return copy
+
+ def expand( self, int x ):
+- """Grow the alphabet by making 'a' a seperate symbol. If it already mapped to a single symbol, do nothing"""
++ """Grow the alphabet by making 'a' a separate symbol. If it already mapped to a single symbol, do nothing"""
+ cdef int i, count, a, b
+ cdef IntToIntMapping copy
+ # Get the symbol x maps to
+--- python-bx.orig/lib/bx/align/_epo.pyx
++++ python-bx/lib/bx/align/_epo.pyx
+@@ -165,9 +165,9 @@
+
+ #@cython.wraparound(False)
+ #@cython.boundscheck(False)
+-cpdef numpy.ndarray[numpy.int64_t, ndim=2] cummulative_intervals(numpy.ndarray[numpy.int64_t, ndim=1] S,
++cpdef numpy.ndarray[numpy.int64_t, ndim=2] cumulative_intervals(numpy.ndarray[numpy.int64_t, ndim=1] S,
+ numpy.ndarray[numpy.int64_t, ndim=1] D ):
+- """compute cummulative intervals for this side of an aligmnent. S and D are one side of
++ """compute cumulative intervals for this side of an aligmnent. S and D are one side of
+ the alignment as described in the chain file format"""
+
+ cdef int N = S.shape[0]
+--- python-bx.orig/lib/bx/align/epo.py
++++ python-bx/lib/bx/align/epo.py
+@@ -8,7 +8,7 @@
+
+ from ._epo import ( # noqa: F401
+ bed_union,
+- cummulative_intervals,
++ cumulative_intervals,
+ fastLoadChain,
+ rem_dash,
+ )
+--- python-bx.orig/lib/bx/align/epo_tests.py
++++ python-bx/lib/bx/align/epo_tests.py
+@@ -8,7 +8,7 @@
+
+ from bx.align._epo import (
+ bed_union,
+- cummulative_intervals,
++ cumulative_intervals,
+ )
+ from bx.align.epo import (
+ Chain,
+@@ -26,7 +26,7 @@
+ S.append(random.randint(10, 50))
+ D.append(random.randint(10, 50))
+ D[-1] = 0
+- C = cummulative_intervals(np.array(S, dtype=np.int64), np.array(D, dtype=np.int64))
++ C = cumulative_intervals(np.array(S, dtype=np.int64), np.array(D, dtype=np.int64))
+ for i in range(self.N):
+ assert C[i, 1] - C[i, 0] == S[i]
+ for i in range(1, self.N):
+--- python-bx.orig/scripts/bnMapper.py
++++ python-bx/scripts/bnMapper.py
+@@ -292,14 +292,14 @@
+
+ EPO = epo.Chain._parse_file(path, True)
+ # convert coordinates w.r.t the forward strand (into slices)
+- # compute cummulative intervals
++ # compute cumulative intervals
+ for i in range(len(EPO)):
+ ch, S, T, Q = EPO[i]
+ if ch.tStrand == "-":
+ ch = ch._replace(tEnd=ch.tSize - ch.tStart, tStart=ch.tSize - ch.tEnd)
+ if ch.qStrand == "-":
+ ch = ch._replace(qEnd=ch.qSize - ch.qStart, qStart=ch.qSize - ch.qEnd)
+- EPO[i] = (ch, epo.cummulative_intervals(S, T), epo.cummulative_intervals(S, Q))
++ EPO[i] = (ch, epo.cumulative_intervals(S, T), epo.cumulative_intervals(S, Q))
+ # now each element of epo is (chain_header, target_intervals, query_intervals)
+ assert all(t[0].tStrand == "+" for t in EPO), "all target strands should be +"
+ return EPO
+--- python-bx.orig/scripts/maf_tile_2.py
++++ python-bx/scripts/maf_tile_2.py
+@@ -186,7 +186,7 @@
+ # Store the size of the reference sequence for building fake block
+ if ref_src_size is None:
+ ref_src_size = ref.src_size
+- # Handle the reference component seperately, it has no synteny status
++ # Handle the reference component separately, it has no synteny status
+ # but we will try to fill in missing sequence
+ if ref.start > last_stop:
+ # Need to fill in some reference sequence
+--- python-bx.orig/scripts/maf_tile_2bit.py
++++ python-bx/scripts/maf_tile_2bit.py
+@@ -178,7 +178,7 @@
+ # Store the size of the reference sequence for building fake block
+ if ref_src_size is None:
+ ref_src_size = ref.src_size
+- # Handle the reference component seperately, it has no synteny status
++ # Handle the reference component separately, it has no synteny status
+ # but we will try to fill in missing sequence
+ if ref.start > last_stop:
+ # Need to fill in some reference sequence
+--- python-bx.orig/scripts/mask_quality.py
++++ python-bx/scripts/mask_quality.py
+@@ -12,7 +12,7 @@
+ -m, --mask=N: Character to use as mask character
+ -q, --quality=N: Min quality allowed
+ -t, --type=N: base_pair or nqs
+- -l, --list=N: colon seperated list of species,len_file[,qualityfile].
++ -l, --list=N: colon separated list of species,len_file[,qualityfile].
+ """
+
+ import fileinput
=====================================
debian/patches/strlen_missing_include deleted
=====================================
@@ -1,15 +0,0 @@
-From: Michael R. Crusoe <crusoe at debian.org>
-Subject: add missing include for strlen()
-Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1066569
-Forwarded: https://github.com/bxlab/bx-python/pull/94
---- python-bx.orig/src/pwm_utils.c
-+++ python-bx/src/pwm_utils.c
-@@ -1,7 +1,7 @@
-
- #include <ctype.h>
- #include <stdio.h>
--#include <strings.h>
-+#include <string.h>
-
- int symbol_match( char, char);
- int pattern_match( char*, char*, int);
=====================================
lib/bx/__init__.py
=====================================
@@ -1 +1 @@
-__version__ = "0.11.0"
+__version__ = "0.12.0"
=====================================
lib/bx/align/sitemask/sitemask_tests.py
=====================================
@@ -6,7 +6,7 @@ import tempfile
from io import StringIO
import bx.align.maf
-from . import cpg
+from bx.align.sitemask import cpg
test_maf_cpg = """##maf version=1 scoring=none
a score=0
=====================================
lib/bx/binned_array.py
=====================================
@@ -20,7 +20,7 @@ from numpy import (
array,
concatenate,
frombuffer,
- NaN,
+ nan,
resize,
zeros,
)
@@ -70,7 +70,7 @@ def bytesify(s):
class BinnedArray:
- def __init__(self, bin_size=512 * 1024, default=NaN, max_size=MAX, typecode="f"):
+ def __init__(self, bin_size=512 * 1024, default=nan, max_size=MAX, typecode="f"):
self.max_size = max_size
self.bin_size = bin_size
self.nbins = int(math.ceil(max_size / self.bin_size))
@@ -273,7 +273,7 @@ class FileBinnedArray:
class BinnedArrayWriter:
- def __init__(self, f, bin_size=512 * 1024, default=NaN, max_size=MAX, typecode="f", comp_type="zlib"):
+ def __init__(self, f, bin_size=512 * 1024, default=nan, max_size=MAX, typecode="f", comp_type="zlib"):
# All parameters in the constructor are immutable after creation
self.f = f
self.max_size = max_size
=====================================
lib/bx/binned_array_tests.py
=====================================
@@ -2,15 +2,16 @@
Tests for `bx.binned_array`.
"""
+import pytest
from numpy import (
allclose,
concatenate,
- NaN,
+ nan,
zeros,
)
from numpy.random import random_sample as random
-from .binned_array import (
+from bx.binned_array import (
BinnedArray,
BinnedArrayWriter,
FileBinnedArray,
@@ -22,12 +23,9 @@ CHUNK_SIZE_ZEROS = 897
# CHUNK_SIZE_RANDOM=9456
# CHUNK_SIZE_ZEROS=8972
-source = target = None
-
-def setup():
- global source
- global target
+ at pytest.fixture(scope="module")
+def source_target():
source = []
for _ in range(13):
if random() < 0.5:
@@ -36,14 +34,15 @@ def setup():
source = concatenate((source, zeros(CHUNK_SIZE_ZEROS, "f")))
source = source.astype("f")
# Set on target
- target = BinnedArray(128, NaN, len(source))
+ target = BinnedArray(128, nan, len(source))
for i in range(len(source)):
# if not isNaN( source[i] ):
target[i] = source[i]
return source, target
-def test_simple():
+def test_simple(source_target):
+ source, target = source_target
# Verify
for i in range(len(source)):
assert source[i] == target[i], "No match, index: %d, source: %f, target: %f, len( source ): %d" % (
@@ -66,7 +65,8 @@ def test_simple():
)
-def test_file():
+def test_file(source_target):
+ source, target = source_target
# With a file (zlib)
target.to_file(open("/tmp/foo", "wb"))
target2 = FileBinnedArray(open("/tmp/foo", "rb"))
@@ -87,7 +87,8 @@ def test_file():
)
-def test_file_lzo():
+def test_file_lzo(source_target):
+ source, target = source_target
# With a file (lzo)
target.to_file(open("/tmp/foo3", "wb"), comp_type="lzo")
target3 = FileBinnedArray(open("/tmp/foo3", "rb"))
@@ -109,7 +110,8 @@ def test_file_lzo():
)
-def test_binned_array_writer():
+def test_binned_array_writer(source_target):
+ source, target = source_target
# Test with ba writer
o = open("/tmp/foo4", "wb")
w = BinnedArrayWriter(o, 128, comp_type="lzo")
=====================================
lib/bx/interval_index_file_tests.py
=====================================
@@ -1,8 +1,8 @@
import random
from tempfile import mktemp
-from . import interval_index_file
-from .interval_index_file import Indexes
+from bx import interval_index_file
+from bx.interval_index_file import Indexes
def test_offsets():
=====================================
lib/bx/intervals/cluster_tests.py
=====================================
@@ -1,14 +1,6 @@
-import os
-import sys
import unittest
-try:
- sys.path.insert(0, os.path.dirname(os.path.dirname(__file__)))
-except Exception:
- sys.path.insert(0, os.path.dirname(os.path.abspath(".")))
-
-# from bx.intervals.cluster import ClusterTree
-from .cluster import ClusterTree
+from bx.intervals.cluster import ClusterTree
class TestCluster(unittest.TestCase):
=====================================
lib/bx/intervals/intersection.pyx
=====================================
@@ -282,8 +282,6 @@ cdef class Interval:
>>> f1 = Interval(23, 36)
>>> f2 = Interval(34, 48, value=OrderedDict([('chr', 12), ('anno', 'transposon')]))
- >>> f2
- Interval(34, 48, value=OrderedDict([('chr', 12), ('anno', 'transposon')]))
"""
cdef public int start, end
=====================================
lib/bx/misc/seekbzip2_tests.py
=====================================
@@ -7,7 +7,7 @@ import os
import random
from codecs import encode
-from . import seekbzip2
+from bx.misc import seekbzip2
F = None
T = None
=====================================
lib/bx/motif/io/transfac_tests.py
=====================================
@@ -2,7 +2,7 @@ from io import StringIO
from numpy import allclose
-from . import transfac
+from bx.motif.io import transfac
sample = """
VV TRANSFAC MATRIX TABLE, Rel.3.2 26-06-1997
=====================================
lib/bx/motif/pwm_tests.py
=====================================
@@ -3,7 +3,7 @@ from numpy import (
isnan,
)
-from . import pwm
+from bx.motif import pwm
def test_create():
=====================================
lib/bx/seq/fasta_tests.py
=====================================
@@ -4,7 +4,7 @@ Tests for `bx.seq.fasta`.
import unittest
-from . import fasta
+from bx.seq import fasta
test_fa = "test_data/seq_tests/test.fa"
=====================================
lib/bx/seq/nib_tests.py
=====================================
@@ -4,7 +4,7 @@ Tests for `bx.seq.nib`.
import unittest
-from . import nib
+from bx.seq import nib
test_nib = "test_data/seq_tests/test.nib"
=====================================
lib/bx/seq/qdna_tests.py
=====================================
@@ -4,7 +4,7 @@ Tests for `bx.seq.qdna`.
import unittest
-from . import qdna
+from bx.seq import qdna
test_qdna = "test_data/seq_tests/test.qdna"
=====================================
lib/bx/seq/twobit_tests.py
=====================================
@@ -2,7 +2,7 @@ import random
import pytest
-from . import twobit
+from bx.seq import twobit
def quick_fasta_iter(f):
=====================================
pyproject.toml
=====================================
@@ -1,5 +1,11 @@
[build-system]
-requires = ["cython", "oldest-supported-numpy", "setuptools", "wheel"]
+requires = [
+ "cython",
+ "numpy>=1.25.0; python_version>='3.9'",
+ "oldest-supported-numpy; python_version<'3.9'",
+ "setuptools",
+ "wheel",
+]
build-backend = "setuptools.build_meta"
[tool.black]
=====================================
pytest.ini
=====================================
@@ -1,5 +1,4 @@
[pytest]
-#addopts = --doctest-cython --doctest-modules # https://github.com/lgpage/pytest-cython/issues/58
-addopts = --doctest-modules
+addopts = --doctest-cython --doctest-modules
python_files = *_tests.py
testpaths = lib script_tests/
=====================================
src/pwm_utils.c
=====================================
@@ -1,7 +1,7 @@
#include <ctype.h>
#include <stdio.h>
-#include <strings.h>
+#include <string.h>
int symbol_match( char, char);
int pattern_match( char*, char*, int);
=====================================
tox.ini
=====================================
@@ -11,7 +11,7 @@ deps =
test: Cython
test: numpy
test: pytest
- test: pytest-cython
+ test: pytest-cython >= 0.2.2 # https://github.com/lgpage/pytest-cython/issues/58
test: python-lzo >= 1.14 # Python 3.10 support
lint: black
lint: flake8
View it on GitLab: https://salsa.debian.org/med-team/python-bx/-/compare/6936d52bd3b842493efca1fbbb205a6fb332a871...4d4554a9a4356d602f3a1d748ad71d2937ab64c4
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