New upstream version 0.15.4+ds (f4cfe1fb) · Commits · Debian Med / python-pysam

.travis.yml

+42 −20

Original line number	Diff line number	Diff line
		@@ -4,6 +4,11 @@ os:

		language: c

		stages:
		- test
		- name: deploy
		if: tag IS present

		env:
		matrix:
		- CONDA_PY=2.7
		@@ -12,12 +17,26 @@ env:
		global:
		- PYSAM_LINKING_TEST=1
		- TWINE_USERNAME=grepall
		- secure: 'OcwwP8/o21+SGW0UVAnnCQwllhGSCq2HJzpI9EhX3kh6J9RTkyx/+drkg45bx1Z5u8zymuAFappEYzlpzqZE886XezkjOYGVa/u+Coqr1oT/BEJHFCkCA4o26yESp7Zy8aNj/juhB7Rfa77pIDXBayqTzbALz/AURMtZapasB18='
		- secure: bTbky3Un19NAl62lix8bMLmBv9IGNhFkRXlZH+B253nYub7jwQwPQKum3ct9ea+XHJT5//uM0B8WAF6eyugpNkPQ7+S7SEH5BJuCt30nv6qvGhSO2AffZKeHEDnfW2kqGrivn87TqeomlSBlO742CD/V0wOIUwkTT9tutd+E7FU=

		_deploy_common: &deploy_common
		if: tag IS present
		_cibw_common: &cibw_common
		addons: {}
		install:
		- python3 -m pip install cibuildwheel twine
		- python3 -m pip install cibuildwheel>=1.1.0 twine
		script:
		- set -e
		- cibuildwheel --output-dir dist
		- twine check dist/*
		- twine upload --skip-existing dist/*

		_cibw_linux: &cibw_linux
		stage: deploy
		os: linux
		language: python
		python: '3.5'
		services:
		- docker
		<<: *cibw_common

		matrix:
		include:
		@@ -25,11 +44,6 @@ matrix:
		os: linux
		language: python
		python: '3.5'
		services:
		- docker
		env:
		- CIBW_BEFORE_BUILD="yum install -y zlib-devel bzip2-devel xz-devel && pip install -r requirements.txt"
		- CIBW_ENVIRONMENT='HTSLIB_CONFIGURE_OPTIONS="--disable-libcurl"'
		addons:
		apt:
		packages:
		@@ -37,28 +51,36 @@ matrix:
		- g++
		- libcurl4-openssl-dev # for libcurl support in sdist
		- libssl-dev # for s3 support in sdist
		<<: *deploy_common
		install:
		- python3 -m pip install Cython twine
		script:
		- set -e
		- cibuildwheel --output-dir dist
		- python3 -m pip install Cython
		- python3 setup.py build_ext --inplace
		- python3 setup.py sdist
		- twine check dist/*
		- twine upload --skip-existing dist/*
		- <<: *cibw_linux
		env:
		- CIBW_BUILD="*_x86_64"
		- CIBW_BEFORE_BUILD="yum install -y zlib-devel bzip2-devel xz-devel && python -m pip install -r requirements.txt"
		- CIBW_ENVIRONMENT='HTSLIB_CONFIGURE_OPTIONS="--disable-libcurl"'
		- CIBW_REPAIR_WHEEL_COMMAND_LINUX='auditwheel repair -L . -w {dest_dir} {wheel}'
		- CIBW_TEST_COMMAND='python -c "import pysam"'
		- <<: *cibw_linux
		env:
		- CIBW_BUILD="*_i686"
		- CIBW_BEFORE_BUILD="yum install -y zlib-devel bzip2-devel xz-devel && python -m pip install -r requirements.txt"
		- CIBW_ENVIRONMENT='HTSLIB_CONFIGURE_OPTIONS="--disable-libcurl"'
		- CIBW_REPAIR_WHEEL_COMMAND_LINUX='auditwheel repair -L . -w {dest_dir} {wheel}'
		- CIBW_TEST_COMMAND='python -c "import pysam"'
		- stage: deploy
		os: osx
		language: generic
		env:
		- CIBW_BEFORE_BUILD="pip install -r requirements.txt"
		- CIBW_BEFORE_BUILD="python -m pip install -r requirements.txt"
		- CIBW_ENVIRONMENT='HTSLIB_CONFIGURE_OPTIONS="--disable-libcurl"'
		addons: {}
		<<: *deploy_common
		script:
		- set -e
		- cibuildwheel --output-dir dist
		- twine check dist/*
		- twine upload --skip-existing dist/*
		- CIBW_TEST_COMMAND='python -c "import pysam"'
		<<: *cibw_common

		addons:
		apt:

doc/release.rst

+20 −0

Original line number	Diff line number	Diff line
		@@ -2,6 +2,26 @@
		Release notes
		=============

		Release 0.15.4
		==============

		Bugfix release. Principal reason for release is to update cython
		version in order to fix pip install pysam with python 3.8.

		* [#879] Fix add_meta function in libcbcf.pyx, so meta-information
		lines in header added with this function have double-quoting rules
		in accordance to rules specified in VCF4.2 and VCF4.3 specifications
		* [#863] Force arg to bytes to support non-ASCII encoding
		* [#875] Bump minimum Cython version
		* [#868] Prevent segfault on Python 2.7 AlignedSegment.compare(other=None)
		* [#867] Fix wheel building on TravisCI
		* [#863] Force arg to bytes to support non-ASCII encoding
		* [#799] disambiguate interpretation of bcf_read return code
		* [#841] Fix silent truncation of FASTQ with bad q strings
		* [#846] Prevent segmentation fault on ID, when handling malformed records
		* [#829] Run configure with the correct CC/CFLAGS/LDFLAGS env vars


		Release 0.15.3
		==============

pysam/bcftools.py

+1 −1

Original line number	Diff line number	Diff line
		from utils import PysamDispatcher
		from pysam.utils import PysamDispatcher

		BCFTOOLS_DISPATCH = [
		"index",

pysam/libcalignedsegment.pyx

+89 −88

Original line number	Diff line number	Diff line
		@@ -924,7 +924,8 @@ cdef class AlignedSegment:
		Parameters
		----------

		header -- :class:`~pysam.AlignmentHeader` object to map numerical
		header:
		:class:`~pysam.AlignmentHeader` object to map numerical
		identifiers to chromosome names. If not given, an empty
		header is created.
		'''
		@@ -999,6 +1000,10 @@ cdef class AlignedSegment:
		<,=,> to other
		'''

		# avoid segfault when other equals None
		if other is None:
		return -1

		cdef int retval, x
		cdef bam1_t *t
		cdef bam1_t *o
		@@ -1088,7 +1093,8 @@ cdef class AlignedSegment:

		Parameters
		----------
		sam -- :term:`SAM` formatted string
		sam:
		:term:`SAM` formatted string

		"""
		cdef AlignedSegment dest = cls.__new__(cls)
		@@ -1110,7 +1116,8 @@ cdef class AlignedSegment:
		Parameters
		----------

		htsfile -- (deprecated) AlignmentFile object to map numerical
		htsfile:
		(deprecated) AlignmentFile object to map numerical
		identifiers to chromosome names. This parameter is present
		for backwards compatibility and ignored.
		"""
		@@ -1133,7 +1140,8 @@ cdef class AlignedSegment:

		Parameters
		----------
		sam_dict -- dictionary of alignment values, keys corresponding to output from
		sam_dict:
		dictionary of alignment values, keys corresponding to output from
		:meth:`todict()`.

		"""
		@@ -2075,15 +2083,11 @@ cdef class AlignedSegment:

		If no cigar string is present, empty arrays will be returned.

		Parameters
		----------

		Returns
		-------

		arrays : two arrays. The first contains the nucleotide counts within
		each cigar operation, the second contains the number of blocks for
		each cigar operation.
		Returns:
		arrays :
		two arrays. The first contains the nucleotide counts within
		each cigar operation, the second contains the number of blocks
		for each cigar operation.

		"""

		@@ -2406,24 +2410,21 @@ cdef class AlignedSegment:
		specification) as well as additional value type 'd' as
		implemented in htslib.

		Parameters
		----------
		Parameters:

		tag :
		data tag.

		with_value_type : Optional[bool]
		if set to True, the return value is a tuple of (tag value, type code).
		(default False)
		if set to True, the return value is a tuple of (tag value, type
		code). (default False)

		Returns
		-------
		Returns:

		A python object with the value of the `tag`. The type of the
		object depends on the data type in the data record.

		Raises
		------
		Raises:

		KeyError
		If `tag` is not present, a KeyError is raised.

pysam/libcalignmentfile.pyx

+54 −56

Original line number	Diff line number	Diff line
		@@ -1705,15 +1705,13 @@ cdef class AlignmentFile(HTSFile):
		'''
		write a single :class:`pysam.AlignedSegment` to disk.

		Raises
		------
		Raises:
		ValueError
		if the writing failed

		Returns
		-------

		int : the number of bytes written. If the file is closed,
		Returns:
		int :
		the number of bytes written. If the file is closed,
		this will be 0.
		'''
		if not self.is_open:
		@@ -1800,10 +1798,10 @@ cdef class AlignmentFile(HTSFile):
		"""return statistics about mapped/unmapped reads per chromosome as
		they are stored in the index.

		Returns
		-------
		list : a list of records for each chromosome. Each record has the attributes 'contig',
		'mapped', 'unmapped' and 'total'.
		Returns:
		list :
		a list of records for each chromosome. Each record has the
		attributes 'contig', 'mapped', 'unmapped' and 'total'.
		"""

		self.check_index()