New upstream version 0.15.3+ds (169a6288) · Commits · Debian Med / python-pysam

.gitignore

+3 −1

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		@@ -17,11 +17,13 @@ tests/cbcf_data
		tests/tabix_data

		samtools/config.h
		bcftools/config.g
		bcftools/config.h
		htslib/config.status
		htslib/config.h
		htslib/config.log
		htslib/config.mk
		htslib/htslib.pc.tmp
		htslib/htslib-uninstalled.pc
		pysam/config.py

		# linking tests

+50 −3

Original line number	Diff line number	Diff line
		os:
		- linx
		- linux
		- osx

		language: c
		@@ -7,11 +7,58 @@ language: c
		env:
		matrix:
		- CONDA_PY=2.7
		- CONDA_PY=3.4
		- CONDA_PY=3.5
		- CONDA_PY=3.6
		- CONDA_PY=3.7
		global:
		- PYSAM_LINKING_TEST=1
		- TWINE_USERNAME=grepall
		- secure: 'OcwwP8/o21+SGW0UVAnnCQwllhGSCq2HJzpI9EhX3kh6J9RTkyx/+drkg45bx1Z5u8zymuAFappEYzlpzqZE886XezkjOYGVa/u+Coqr1oT/BEJHFCkCA4o26yESp7Zy8aNj/juhB7Rfa77pIDXBayqTzbALz/AURMtZapasB18='

		_deploy_common: &deploy_common
		if: tag IS present
		install:
		- python3 -m pip install cibuildwheel twine

		matrix:
		include:
		- stage: deploy
		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:
		- gcc
		- g++
		- libcurl4-openssl-dev # for libcurl support in sdist
		- libssl-dev # for s3 support in sdist
		<<: *deploy_common
		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/*
		- stage: deploy
		os: osx
		language: generic
		env:
		- CIBW_BEFORE_BUILD="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/*

		addons:
		apt:

+20 −0

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		@@ -5,6 +5,26 @@ http://pysam.readthedocs.io/en/latest/release.html
		Release notes
		=============

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

		Bugfix release.

		* [#824] allow reading of UTF-8 encoded text in VCF/BCF files.
		* [#780] close all filehandles before opening new ones in pysam_dispatch
		* [#773] do not cache VariantRecord.id to avoid memory leak
		* [#781] default of multiple_iterators=True is changed to False for
		CRAM files.
		* [#825] fix collections.abc import
		* [#825] use bcf_hdr_format instead of bcf_hdr_fmt_text, fix memcpy
		bug when setting FORMAT fields.
		* [#804] Use HTSlib's kstring_t, which reallocates and enlarges its
		memory as needed, rather than a fixed-size char buffer.
		* [#814] Build wheels and upload them to PyPI
		* [#755] Allow passing flags and arguments to index methods
		* [#763] Strip \0 in header check
		* [#761] Test Tabix index contents, not the compression

		Release 0.15.2
		==============

+2 −0

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		@@ -25,6 +25,8 @@ as it resolves non-python dependencies and uses pre-configured
		compilation options. Especially for OS X this will potentially save a
		lot of trouble.

		The current version of pysam wraps 3rd-party code from htslib-1.9, samtools-1.9, and bcftools-1.9.

		Pysam is available through `pypi
		<https://pypi.python.org/pypi/pysam>`_. To install, type::

+6 −11

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		@@ -10,7 +10,6 @@
		FILE * bcftools_stderr = NULL;
		FILE * bcftools_stdout = NULL;
		const char * bcftools_stdout_fn = NULL;
		int bcftools_stdout_fileno = STDOUT_FILENO;


		FILE * bcftools_set_stderr(int fd)
		@@ -21,11 +20,10 @@ FILE * bcftools_set_stderr(int fd)
		return bcftools_stderr;
		}

		void bcftools_unset_stderr(void)
		void bcftools_close_stderr(void)
		{
		if (bcftools_stderr != NULL)
		fclose(bcftools_stderr);
		bcftools_stderr = fopen("/dev/null", "w");
		bcftools_stderr = NULL;
		}

		FILE * bcftools_set_stdout(int fd)
		@@ -37,7 +35,6 @@ FILE * bcftools_set_stdout(int fd)
		{
		fprintf(bcftools_stderr, "could not set stdout to fd %i", fd);
		}
		bcftools_stdout_fileno = fd;
		return bcftools_stdout;
		}

		@@ -46,12 +43,10 @@ void bcftools_set_stdout_fn(const char *fn)
		bcftools_stdout_fn = fn;
		}

		void bcftools_unset_stdout(void)
		void bcftools_close_stdout(void)
		{
		if (bcftools_stdout != NULL)
		fclose(bcftools_stdout);
		bcftools_stdout = fopen("/dev/null", "w");
		bcftools_stdout_fileno = STDOUT_FILENO;
		bcftools_stdout = NULL;
		}

		int bcftools_puts(const char *s)