[dgit import tarball python-pysam 0.14+ds-2 python-pysam_0.14+ds-2.debian.tar.xz]
--- /dev/null
+python-pysam (0.14+ds-2) unstable; urgency=medium
+
+ * Team upload
+ * Add Python 2.7 compatibility symlink for libchtslib.so (Closes: #890748)
+ * Update Vcs-* URIs for move to salsa.debian.org
+ * Remove trailing whitespace from debian/changelog
+
+ -- Graham Inggs <ginggs@debian.org> Mon, 19 Feb 2018 10:11:17 +0000
+
+python-pysam (0.14+ds-1) unstable; urgency=medium
+
+ * New upstream version
+ * d/rules: Exclude tests using http access
+ * Bump versioned dependencies to samtools and related from 1.6 to 1.7
+ * cme fix dpkg-control
+ * debhelper 11
+ * do not remove samtools/tmp_file.h in clean target
+ * do not depend from non-existing data file in make test target
+ * Update d/copyright
+ * Update lintian overrides
+
+ -- Andreas Tille <tille@debian.org> Sat, 17 Feb 2018 21:45:07 +0100
+
+python-pysam (0.13.0+ds-1) unstable; urgency=medium
+
+ * New upstream version
+ * Bump versioned Build-Depends on libhts-dev, samtools and bcftools to 1.6
+ * Exclude tests accessing remote http sites
+ * Lintian-override for false positive
+ * Remove unused paragraphs from d/copyright
+
+ -- Andreas Tille <tille@debian.org> Thu, 14 Dec 2017 16:36:43 +0100
+
+python-pysam (0.12.0.1+ds-4) unstable; urgency=medium
+
+ * Team upload.
+ * Revert "Skip tests on ppc64el to avoid build-dep on bcftools currently
+ uninstallable". It seems to be installable now, and anyway now that the
+ python3 transition is done we should fix it properly anyway.
+ * d/control:
+ + Bump the libhts-dev buil-dep to 1.5-3, to make sure we gain appropriate
+ versioned symbols and therefore an appropriate versioned dependency on
+ libhts2. Closes: #879867
+ + Bump Standards-Version to 4.1.1.
+
+ -- Mattia Rizzolo <mattia@debian.org> Fri, 10 Nov 2017 12:56:10 +0100
+
+python-pysam (0.12.0.1+ds-3) unstable; urgency=medium
+
+ * Team upload.
+ * Support DEB_BUILD_OPTIONS=nocheck.
+ * Skip tests on ppc64el to avoid build-dep on bcftools which is currently
+ uninstallable.
+ Hopefully this will help unstuck the current python3 transition.
+
+ -- Mattia Rizzolo <mattia@debian.org> Tue, 24 Oct 2017 18:54:29 +0200
+
+python-pysam (0.12.0.1+ds-2) unstable; urgency=low
+
+ * Update autopkgtest for new test suite driver
+
+ -- Afif Elghraoui <afif@debian.org> Fri, 06 Oct 2017 23:38:45 -0400
+
+python-pysam (0.12.0.1+ds-1) unstable; urgency=medium
+
+ [ Andreas Tille ]
+ * Drop patch applied upstream
+ * Standards-Version: 4.1.0 (no changes needed)
+ * Apply upstream patch to fix test suite
+ * Use pytest instead of nosetest
+
+ [ Afif Elghraoui ]
+ * New upstream version
+ Closes: #871083, #834856
+ * Bump htslib suite minimum versions
+ * Use Build Profiles to mark build-dependencies needed only for tests
+ * Temporarily skip a failing test (reported upstream)
+
+ [ Steffen Moeller ]
+ * created debian/upstream/metadata: references to registries
+
+ -- Afif Elghraoui <afif@debian.org> Sun, 01 Oct 2017 12:30:30 -0400
+
+python-pysam (0.11.2.2+ds-3) unstable; urgency=medium
+
+ * Team upload
+ * Link with -Wl,--as-needed and avoid another Python 2.7
+ compatibility symlink for libchtslib.so
+
+ -- Graham Inggs <ginggs@debian.org> Tue, 01 Aug 2017 14:15:58 +0200
+
+python-pysam (0.11.2.2+ds-2) unstable; urgency=medium
+
+ * Team upload
+ * Mark debian/python-pysam.links executable for dh-exec
+ * Drop exclude_test_tyring_to_access_remote_ftpserver.patch,
+ fixed upstream
+ * Drop pysam_stdout_linkage.patch, not needed since
+ compatibility symlinks were added
+
+ -- Graham Inggs <ginggs@debian.org> Mon, 31 Jul 2017 14:05:22 +0200
+
+python-pysam (0.11.2.2+ds-1) unstable; urgency=medium
+
+ [ Afif Elghraoui ]
+ * Imported Upstream version 0.11.2.2+ds
+ * Update patches
+
+ [ Andreas Tille ]
+ * Apply patches suggested by Steve Langasek (thanks for this Steve)
+ Closes: #867017, LP: #1701268
+ * debhelper 10
+ * Standards-Version: 4.0.0 (no changes needed)
+ * Add some symlinks to run autopkgtests correctly
+
+ -- Andreas Tille <tille@debian.org> Sat, 29 Jul 2017 09:03:05 +0200
+
+python-pysam (0.10.0+ds-2) unstable; urgency=medium
+
+ * d/rules:
+ - Add some files that need to be removed after running tests
+ - Remove other autogenerated files to build twice in a row
+ * Exclude test tyring to access remote ftpserver
+ Closes: #861496
+
+ -- Andreas Tille <tille@debian.org> Thu, 04 May 2017 15:06:21 +0200
+
+python-pysam (0.10.0+ds-1) unstable; urgency=medium
+
+ [ Afif Elghraoui ]
+ * New upstream release
+ * Update patches
+
+ [ Andreas Tille ]
+ * d/rules: Remove redundant get-orig-source target
+ * hardening=+all
+ * Fix lintian overrides
+
+ [ Afif Elghraoui ]
+ * Do not use internal htslib
+
+ -- Afif Elghraoui <afif@debian.org> Thu, 26 Jan 2017 04:36:11 -0800
+
+python-pysam (0.9.1.4+ds-1) unstable; urgency=medium
+
+ * Imported Upstream version 0.9.1.4+ds
+ * Drop patch applied upstream
+ * Drop unused lintian overrides
+ * Fix spelling issues
+
+ -- Afif Elghraoui <afif@debian.org> Sat, 23 Jul 2016 18:47:31 -0700
+
+python-pysam (0.9.1+ds-1) unstable; urgency=medium
+
+ * Imported Upstream version 0.9.1+ds
+ * Force at least matching versions of the samtools suite
+ * Bump Standards-Version to 3.9.8
+ * Globally use C.UTF-8 locale
+ * Update patch for external htslib
+ * Refresh patch
+ * Drop obsolete patches
+ * Fix handling of configuration headers generated at build time
+ * Rely more on pybuild for build-time tests and respect exit code
+ * Fix autopkgtests
+
+ -- Afif Elghraoui <afif@debian.org> Sun, 19 Jun 2016 18:43:53 -0700
+
+python-pysam (0.9.0+ds-1) unstable; urgency=medium
+
+ * Add filenamemangle to d/watch and space out content
+ * Imported Upstream version 0.9.0+ds (Closes: #814765)
+ * Bump htslib and samtools minimum versions
+ * Update policy statndards-version to 3.9.7
+ * Use encrypted protocols for Vcs URLs in d/control
+ * Use readthedocs page as pysam's homepage
+ * Update packaging for external htslib link
+ * Refresh patches
+ * Delete obsolete patch
+
+ -- Afif Elghraoui <afif@debian.org> Wed, 09 Mar 2016 23:43:59 -0800
+
+python-pysam (0.8.4+ds-1) unstable; urgency=medium
+
+ * Add version constraints to build-dependencies.
+ * Drop ds suffix versioning.
+ * Imported Upstream version 0.8.4+ds
+ * Remove patches applied upstream
+ * Refresh existing patches
+ * Refine d/rules
+ * Set Vcs-Browser to point to cgit rather than gitweb
+ * Reduce dependencies in autopktest dependencies
+ * Replace patch for network-dependent tests
+ * Add new lintian overrides
+
+ -- Afif Elghraoui <afif@ghraoui.name> Fri, 13 Nov 2015 22:15:14 -0800
+
+python-pysam (0.8.3+ds1-3) unstable; urgency=medium
+
+ * Backport upstream commit 6efb22b to permit building with Cython 0.23.x
+ (Closes: 800794)
+ * Revise lintian overrides.
+
+ -- Afif Elghraoui <afif@ghraoui.name> Tue, 06 Oct 2015 00:57:19 -0700
+
+python-pysam (0.8.3+ds1-2) unstable; urgency=medium
+
+ [ Afif Elghraoui ]
+ * Improve python3 compatibility for upstream test sources
+ * Refresh older patches
+ * Fix autopkgtests
+ * Fix error in sam_mpileup.patch
+ * Remove unused lintian override
+
+ [ Andreas Tille ]
+ * Remove tests relying on online connection from test suite
+ * For the moment do some dirty tricks in test run script
+ * The automatic nosetest trigger does not work and this it is
+ switched back to manual nosetests invocation
+
+ -- Afif Elghraoui <afif@ghraoui.name> Fri, 24 Jul 2015 10:12:41 +0200
+
+python-pysam (0.8.3+ds1-1) experimental; urgency=medium
+
+ * Team upload.
+
+ [ Jorge Soares ]
+ * New upstream version
+ * provide python3-pysam
+
+ [ Charles Plessy ]
+ * Requires Python 2.7 or higher.
+
+ [ Andreas Tille ]
+ * Link against htslib
+ * d/watch: dversionmangle
+
+ [ Afif Elghraoui ]
+ * New upstream releases (Closes: #763218)
+ * Remove unnecessary test-suite declaration in d/control
+ * Remove nonexistent files from copyright explanations
+ * Allow building of the package when non-ASCII characters are in the path
+ * Add to package long description
+ * Resolve lintian "duplicated-compressed-file"
+ * Make package descriptions unique
+ * Remove extra license definitions from d/copyright
+ * Fix spelling errors in source distribution (forwarded upstream as well)
+ * Add lintian overrides
+ * Exclude bundled htslib convenience-copy
+ * Provide get-orig-source rule
+ * Support building with missing htslib directory
+ * Add dependency on cython for autopkgtests to provide pyximport
+ * Revamp debian/copyright
+
+ -- Afif Elghraoui <afif@ghraoui.name> Thu, 25 Jun 2015 10:44:30 +0200
+
+python-pysam (0.7.7-1) unstable; urgency=medium
+
+ * New upstream releases.
+ * Upstream source code moved to GitHub.
+ * Watch the Python Package Index since there are no relevant tags on GitHub.
+ * Added a git-buildpackage configuration file to mark its usage.
+ * Build-depend samtools (>= 0.1.19); this is needed for the regression tests
+ in Wheezy.
+ * debian/patches/offline-tests.patch: correction from a later release.
+
+ -- Charles Plessy <plessy@debian.org> Sat, 19 Apr 2014 14:17:42 +0900
+
+python-pysam (0.7.5-5) unstable; urgency=medium
+
+ * Add make to autopkgtest dependencies
+ Closes: #741274
+
+ -- Andreas Tille <tille@debian.org> Wed, 19 Mar 2014 13:30:15 +0100
+
+python-pysam (0.7.5-4) unstable; urgency=medium
+
+ * Fix autotest
+ Closes: #741274
+
+ -- Andreas Tille <tille@debian.org> Tue, 11 Mar 2014 20:08:15 +0100
+
+python-pysam (0.7.5-3) unstable; urgency=medium
+
+ * Do not install tests in world writable dir
+ Closes: #739575
+
+ -- Andreas Tille <tille@debian.org> Sat, 01 Mar 2014 23:40:21 +0100
+
+python-pysam (0.7.5-2) unstable; urgency=medium
+
+ * debian/rules: Set PYTHONPATH correctly using dh_python
+ (thanks to Piotr Ożarowski <piotr@debian.org> for the patch)
+ Closes: #739631
+
+ -- Andreas Tille <tille@debian.org> Thu, 20 Feb 2014 19:01:46 +0100
+
+python-pysam (0.7.5-1) unstable; urgency=low
+
+ * Initial release (Closes: #738665)
+
+ -- Andreas Tille <tille@debian.org> Fri, 07 Feb 2014 18:29:40 +0100
--- /dev/null
+tests/GRCh38_full_analysis_set_plus_decoy_hla.fa.fai
+tests/pysam_data/ex1.fa.gz
+tests/pysam_data/ex1.fa.gz.gzi
+tests/pysam_data/ex1_csi.bam.csi
--- /dev/null
+Source: python-pysam
+Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+Uploaders: Charles Plessy <plessy@debian.org>,
+ Andreas Tille <tille@debian.org>,
+ Afif Elghraoui <afif@debian.org>
+Section: python
+Priority: optional
+Build-Depends: debhelper (>= 11~),
+ dh-exec,
+ dh-python,
+ libhts-dev (>= 1.7),
+ zlib1g-dev,
+ python-all-dev,
+ python-setuptools,
+ cython (>= 0.23),
+ python3-all-dev,
+ python3-setuptools,
+ cython3 (>= 0.23),
+ tabix <!nocheck>,
+ samtools (>= 1.7) <!nocheck>,
+ bcftools (>= 1.7) <!nocheck>,
+ python-pytest <!nocheck>,
+ python3-pytest <!nocheck>
+Standards-Version: 4.1.3
+Vcs-Browser: https://salsa.debian.org/med-team/python-pysam
+Vcs-Git: https://salsa.debian.org/med-team/python-pysam.git
+Homepage: http://pysam.readthedocs.org/en/latest
+X-Python-Version: >= 2.7
+X-Python3-Version: >= 3.2
+
+Package: python-pysam
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends},
+ ${python:Depends}
+Description: interface for the SAM/BAM sequence alignment and mapping format (Python 2)
+ Pysam is a Python module for reading and manipulating Samfiles. It's a
+ lightweight wrapper of the samtools C-API. Pysam also includes an interface
+ for tabix.
+ .
+ This package installs the module for Python 2.
+
+Package: python3-pysam
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends},
+ ${python3:Depends}
+Description: interface for the SAM/BAM sequence alignment and mapping format (Python 3)
+ Pysam is a Python module for reading and manipulating Samfiles. It's a
+ lightweight wrapper of the samtools C-API. Pysam also includes an interface
+ for tabix.
+ .
+ This package installs the module for Python 3.
+
+Package: python-pysam-tests
+Architecture: all
+Depends: ${misc:Depends}
+Enhances: python-pysam
+Description: interface for the SAM/BAM sequence alignment and mapping format (test data)
+ Pysam is a Python module for reading and manipulating Samfiles. It's a
+ lightweight wrapper of the samtools C-API. Pysam also includes an interface
+ for tabix.
+ .
+ This package contains the data provided by upstream to run the pysam
+ test suite.
--- /dev/null
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: pysam
+Upstream-Contact: Andreas Heger <andreas.heger@gmail.com>
+Source: https://github.com/pysam-developers/pysam
+Files-Excluded: htslib/*
+
+Files: *
+Copyright: 2009-2018 Andreas Heger,
+ Tildon Grant Belgrad,
+ Martin Goodson,
+ Kevin Jacobs <jacobs@bionformed.com>
+ 2008-2010 Genome Research Ltd.
+License: MIT
+
+Files: bcftools/*
+Copyright:
+ 2013-2018 Genome Research Ltd.
+ 2010-2011 Broad Institute
+License: MIT
+
+Files: samtools/*
+Copyright: 2009-2012 Broad Institute
+ 2008-2014 Genome Research Ltd.
+License: MIT
+
+Files: samtools/bam_cat.*
+Copyright: 2008-2009, 2011-2013 Genome Research Ltd.
+ 2010 Illumina, Inc.
+License: MIT
+
+Files: samtools/bam_color.*
+Copyright: 2009, 2012 University of California - Los Angeles
+License: MIT
+
+Files: samtools/bam_index.*
+ samtools/bam_mate.*
+Copyright: 2008-2014 Genome Research Ltd.
+ 2010-2011 Broad Institute
+ 2012-2013 Peter Cock, The James Hutton Institute
+License: MIT
+
+Files: samtools/misc/ace2sam.*
+Copyright: 2011 Heng Li
+License: MIT
+
+Files: samtools/padding.*
+Copyright: 2011-2012 Broad Institute
+ 2014 Genome Research Ltd.
+ 2012-2013 Peter Cock, The James Hutton Institute
+License: MIT
+
+Files: samtools/win32/zconf.h samtools/win32/zlib.h
+Copyright: 1995-2005 Jean-loup Gailly <jloup@gzip.org> and Mark Adler <madler@alumni.caltech.edu>
+License: BSDlike2
+ This software is provided 'as-is', without any express or implied
+ warranty. In no event will the authors be held liable for any damages
+ arising from the use of this software.
+ .
+ Permission is granted to anyone to use this software for any purpose,
+ including commercial applications, and to alter it and redistribute it
+ freely, subject to the following restrictions:
+ .
+ 1. The origin of this software must not be misrepresented; you must not
+ claim that you wrote the original software. If you use this software
+ in a product, an acknowledgment in the product documentation would be
+ appreciated but is not required.
+ 2. Altered source versions must be plainly marked as such, and must not be
+ misrepresented as being the original software.
+ 3. This notice may not be removed or altered from any source distribution.
+Comment: These files are not used and could be stripped from the source
+
+Files: samtools/win32/xcurses.h
+Copyright: 2008 wmcbrine
+License: public-domain
+Comment: These files are not used and could be stripped from the source
+
+Files: win32/stdint.h
+Copyright: 2005-2007 Paul Hsieh
+License: BSD-3-clause
+
+Files: win32/getopt.*
+Copyright: 1987-2001 Free Software Foundation, Inc.
+License: LGPL-2.1+
+
+Files: debian/*
+Copyright:
+ 2015-2016 Afif Elghraoui <afif@debian.org>
+ 2015 Jorge Soares <j.s.soares@gmail.com>
+ 2014-2015 Charles Plessy <plessy@debian.org>
+ 2014-2018 Andreas Tille <tille@debian.org>
+License: MIT
+
+License: BSD-3-clause
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+ 2. Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions and the following disclaimer in the
+ documentation and/or other materials provided with the distribution.
+ 3. Neither the name of the University nor the names of its contributors
+ may be used to endorse or promote products derived from this software
+ without specific prior written permission.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+ LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+ A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE HOLDERS OR
+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+ EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+ PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+ PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+ LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+ NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+ SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+License: MIT
+ Permission is hereby granted, free of charge, to any person obtaining a copy
+ of this software and associated documentation files (the "Software"), to deal
+ in the Software without restriction, including without limitation the rights
+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ copies of the Software, and to permit persons to whom the Software is
+ furnished to do so, subject to the following conditions:
+ .
+ The above copyright notice and this permission notice shall be included in
+ all copies or substantial portions of the Software.
+ .
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ THE SOFTWARE.
+
+License: public-domain
+ No copyright is claimed.
+ This code is in the public domain; do with it what you wish.
+
+License: LGPL-2.1+
+ This package is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 2.1 of the License, or (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+ .
+ On Debian systems, the complete text of the GNU Lesser General
+ Public License can be found in "/usr/share/common-licenses/LGPL-2.1".
--- /dev/null
+# This source package is managed with git-buildpackage and pristine-tar.
+
+[DEFAULT]
+# use pristine-tar:
+pristine-tar = True
--- /dev/null
+Author: Andreas Tille <tille@debian.org>
+Last-Update: Wed, 13 Dec 2017 13:03:50 +0100
+Description: Exclude tests trying to access remote http sites and thus need
+ to fail in a chroot without network access.
+ .
+ Remark: Any more elegant method than dumb removal to exclude the tests would
+ be welcome.
+
+--- a/save/pysam_test2.6.py
++++ b/save/pysam_test2.6.py
+@@ -1284,61 +1284,6 @@ class TestDoubleFetch(unittest.TestCase)
+ samfile1.fetch( until_eof = True )):
+ self.assertEqual( a.compare( b), 0 )
+
+-class TestRemoteFileFTP(unittest.TestCase):
+- '''test remote access.
+-
+- '''
+-
+- # Need to find an ftp server without password on standard
+- # port.
+-
+- url = "ftp://ftp.sanger.ac.uk/pub/rd/humanSequences/CV.bam"
+- region = "1:1-1000"
+-
+- def testFTPView( self ):
+- return
+- result = pysam.view( self.url, self.region )
+- self.assertEqual( len(result), 36 )
+-
+- def testFTPFetch( self ):
+- return
+- samfile = pysam.Samfile(self.url, "rb")
+- result = list(samfile.fetch( region = self.region ))
+- self.assertEqual( len(result), 36 )
+-
+-class TestRemoteFileHTTP( unittest.TestCase):
+-
+- url = "http://genserv.anat.ox.ac.uk/downloads/pysam/test/ex1.bam"
+- region = "chr1:1-1000"
+- local = "ex1.bam"
+-
+- def testView( self ):
+- samfile_local = pysam.Samfile(self.local, "rb")
+- ref = list(samfile_local.fetch( region = self.region ))
+-
+- result = pysam.view( self.url, self.region )
+- self.assertEqual( len(result), len(ref) )
+-
+- def testFetch( self ):
+- samfile = pysam.Samfile(self.url, "rb")
+- result = list(samfile.fetch( region = self.region ))
+- samfile_local = pysam.Samfile(self.local, "rb")
+- ref = list(samfile_local.fetch( region = self.region ))
+-
+- self.assertEqual( len(ref), len(result) )
+- for x, y in zip(result, ref):
+- self.assertEqual( x.compare( y ), 0 )
+-
+- def testFetchAll( self ):
+- samfile = pysam.Samfile(self.url, "rb")
+- result = list(samfile.fetch())
+- samfile_local = pysam.Samfile(self.local, "rb")
+- ref = list(samfile_local.fetch() )
+-
+- self.assertEqual( len(ref), len(result) )
+- for x, y in zip(result, ref):
+- self.assertEqual( x.compare( y ), 0 )
+-
+ class TestLargeOptValues( unittest.TestCase ):
+
+ ints = ( 65536, 214748, 2147484, 2147483647 )
+--- a/tests/AlignmentFile_test.py
++++ b/tests/AlignmentFile_test.py
+@@ -1559,81 +1559,6 @@ class TestDoubleFetchCRAMWithReference(T
+ reference_filename = os.path.join(BAM_DATADIR, 'ex1.fa')
+
+
+-class TestRemoteFileFTP(unittest.TestCase):
+-
+- '''test remote access.
+-
+- '''
+-
+- # Need to find an ftp server without password on standard
+- # port.
+-
+- url = "ftp://ftp.sanger.ac.uk/pub/rd/humanSequences/CV.bam"
+- region = "1:1-1000"
+-
+- def testFTPView(self):
+- return
+- if not checkURL(self.url):
+- return
+-
+- result = pysam.samtools.view(self.url, self.region)
+- self.assertEqual(len(result), 36)
+-
+- def testFTPFetch(self):
+- return
+- if not checkURL(self.url):
+- return
+-
+- samfile = pysam.AlignmentFile(self.url, "rb")
+- result = list(samfile.fetch(region=self.region))
+- self.assertEqual(len(result), 36)
+-
+-
+-class TestRemoteFileHTTP(unittest.TestCase):
+-
+- url = "http://genserv.anat.ox.ac.uk/downloads/pysam/test/ex1.bam"
+- region = "chr1:1-1000"
+- local = os.path.join(BAM_DATADIR, "ex1.bam")
+-
+- def testView(self):
+- if not checkURL(self.url):
+- return
+-
+- samfile_local = pysam.AlignmentFile(self.local, "rb")
+- ref = list(samfile_local.fetch(region=self.region))
+-
+- result = pysam.samtools.view(self.url, self.region)
+- self.assertEqual(len(result.splitlines()), len(ref))
+-
+- def testFetch(self):
+- if not checkURL(self.url):
+- return
+-
+- with pysam.AlignmentFile(self.url, "rb") as samfile:
+- result = list(samfile.fetch(region=self.region))
+-
+- with pysam.AlignmentFile(self.local, "rb") as samfile_local:
+- ref = list(samfile_local.fetch(region=self.region))
+-
+- self.assertEqual(len(ref), len(result))
+- for x, y in zip(result, ref):
+- self.assertEqual(x.compare(y), 0)
+-
+- def testFetchAll(self):
+- if not checkURL(self.url):
+- return
+-
+- with pysam.AlignmentFile(self.url, "rb") as samfile:
+- result = list(samfile.fetch())
+-
+- with pysam.AlignmentFile(self.local, "rb") as samfile_local:
+- ref = list(samfile_local.fetch())
+-
+- self.assertEqual(len(ref), len(result))
+- for x, y in zip(result, ref):
+- self.assertEqual(x.compare(y), 0)
+-
+-
+ class TestLargeOptValues(unittest.TestCase):
+
+ ints = (65536, 214748, 2147484, 2147483647)
+--- a/tests/tabix_test.py
++++ b/tests/tabix_test.py
+@@ -1039,66 +1039,6 @@ for vcf_file in vcf_files:
+ globals()[n] = type(n, (TestVCFFromVariantFile,), dict(filename=vcf_file,))
+
+
+-class TestRemoteFileHTTP(unittest.TestCase):
+-
+- url = "http://genserv.anat.ox.ac.uk/downloads/pysam/test/example.gtf.gz"
+- region = "chr1:1-1000"
+- local = os.path.join(TABIX_DATADIR, "example.gtf.gz")
+-
+- def setUp(self):
+- if not pysam.config.HAVE_LIBCURL or not checkURL(self.url):
+- self.remote_file = None
+- else:
+- self.remote_file = pysam.TabixFile(self.url, "r")
+-
+- self.local_file = pysam.TabixFile(self.local, "r")
+-
+- def tearDown(self):
+- if self.remote_file is None:
+- return
+-
+- self.remote_file.close()
+- self.local_file.close()
+-
+- def testFetchAll(self):
+- if self.remote_file is None:
+- return
+-
+- remote_result = list(self.remote_file.fetch())
+- local_result = list(self.local_file.fetch())
+-
+- self.assertEqual(len(remote_result), len(local_result))
+- for x, y in zip(remote_result, local_result):
+- self.assertEqual(x, y)
+-
+- def testHeader(self):
+- if self.remote_file is None:
+- return
+-
+- self.assertEqual(list(self.local_file.header), [])
+-
+-
+-class TestRemoteFileHTTPWithHeader(TestRemoteFileHTTP):
+-
+- url = "http://genserv.anat.ox.ac.uk/downloads/pysam/test/example_comments.gtf.gz"
+- region = "chr1:1-1000"
+- local = os.path.join(TABIX_DATADIR, "example_comments.gtf.gz")
+-
+- def setUp(self):
+- if not pysam.config.HAVE_LIBCURL or not checkURL(self.url):
+- self.remote_file = None
+- else:
+- self.remote_file = pysam.TabixFile(self.url, "r")
+- self.local_file = pysam.TabixFile(self.local, "r")
+-
+- def testHeader(self):
+- if self.remote_file is None:
+- return
+-
+- self.assertEqual(list(self.local_file.header), ["# comment at start"])
+- self.assertEqual(list(self.local_file.header), self.remote_file.header)
+-
+-
+ class TestIndexArgument(unittest.TestCase):
+
+ filename_src = os.path.join(TABIX_DATADIR, "example.vcf.gz")
--- /dev/null
+From: Andreas Heger <andreas.heger@gmail.com>
+Date: Mon, 18 Sep 2017 11:19:28 +0100
+Bug-Debian: https://bugs.debian.org/871083
+Subject: execute linking tests only when explicitly
+ requested via PYSAM_LINKING_TESTS env var. Keep on travis. Fixes #534
+
+---
+ .travis.yml | 2 ++
+ tests/TestUtils.py | 1 +
+ tests/linking_test.py | 10 ++++++++++
+ 3 files changed, 13 insertions(+)
+
+--- a/.travis.yml
++++ b/.travis.yml
+@@ -11,8 +11,6 @@ env:
+ - CONDA_PY=3.4
+ - CONDA_PY=3.5
+ - CONDA_PY=3.6
+- global:
+- - PYSAM_LINKING_TEST=1
+
+ addons:
+ apt:
--- /dev/null
+execute-linking-tests-only-when-explicitely-reque.patch
+xfail.patch
+exclude_tests_accessing_remote_http.patch
+skip_test_needing_missing_data.patch
--- /dev/null
+Description: do not depend from non-existing data file in make test target
+ (There is no such file example_reverse_complement.bam)
+Author: Andreas Tille <tille@debian.org>
+Last-Update: Sat, 17 Feb 2018 15:24:34 +0100
+Forwarded: https://github.com/pysam-developers/pysam/issues/626
+
+--- a/tests/pysam_data/Makefile
++++ b/tests/pysam_data/Makefile
+@@ -20,8 +20,7 @@ all: ex1.pileup.gz \
+ explicit_index.bam explicit_index.cram \
+ faidx_empty_seq.fq.gz \
+ ex1.fa.gz ex1.fa.gz.csi \
+- ex1_csi.bam \
+- example_reverse_complement.bam
++ ex1_csi.bam
+
+ # ex2.sam - as ex1.sam, but with header
+ ex2.sam.gz: ex1.bam ex1.bam.bai
+--- a/tests/AlignmentFile_test.py
++++ b/tests/AlignmentFile_test.py
+@@ -1361,12 +1361,7 @@ class TestEmptyHeader(unittest.TestCase)
+ 'example_empty_header.bam'))
+ self.assertEqual(s.header.to_dict(), {'SQ': [{'LN': 1000, 'SN': 'chr1'}]})
+
+- def test_bam_without_seq_in_header(self):
+- s = pysam.AlignmentFile(os.path.join(BAM_DATADIR, "example_no_seq_in_header.bam"))
+- self.assertTrue("SQ" in s.header.to_dict())
+- self.assertTrue("@SQ" in str(s.header))
+
+-
+ class TestHeaderWithProgramOptions(unittest.TestCase):
+
+ '''see issue 39.'''
--- /dev/null
+Description: temporarily skip failing test
+ See https://github.com/pysam-developers/pysam/issues/542
+Author: Afif Elghraoui <afif@debian.org>
+Forwarded: not-needed
+Last-Update: 2017-10-01
+--- a/tests/AlignmentFile_test.py
++++ b/tests/AlignmentFile_test.py
+@@ -474,6 +474,7 @@ class TestIO(unittest.TestCase):
+ "tmp_ex2.bam",
+ "rb", "wb")
+
++ @unittest.skip
+ def testCRAM2CRAM(self):
+ # in some systems different reference sequence paths might be
+ # embedded in the CRAM files which will result in different headers
--- /dev/null
+Pysam for Debian
+================
+
+To verify whether your python-pysam and python3-pysam modules are working
+correctly you can run the test suite manually by running the scripts
+run-nose-tests and run-nose3-tests in this directory.
+
+ -- Jorge Soares <j.s.soares@gmail.com> Fri, 28 Nov 2014 14:29:40 +0100
--- /dev/null
+debian/tests/run-nose-tests
+debian/tests/run-nose3-tests
--- /dev/null
+tests usr/share/doc/python-pysam
--- /dev/null
+# These files are intentionally empty to be used for testing
+zero-byte-file-in-doc-directory usr/share/doc/python-pysam/tests/cbcf_data/example_empty.vcf
+zero-byte-file-in-doc-directory usr/share/doc/python-pysam/tests/tabix_data/empty.bed.gz
+# The duplicate is used for testing and needs to be there
+duplicated-compressed-file usr/share/doc/python-pysam/tests/tabix_data/example.bed.gz
\ No newline at end of file
--- /dev/null
+#!/usr/bin/dh-exec
+/usr/lib/python2.7/dist-packages/pysam/libcsamtools.${DEB_HOST_GNU_TYPE}.so /usr/lib/python2.7/dist-packages/pysam/libcsamtools.so
+/usr/lib/python2.7/dist-packages/pysam/libcbcftools.${DEB_HOST_GNU_TYPE}.so /usr/lib/python2.7/dist-packages/pysam/libcbcftools.so
+/usr/lib/python2.7/dist-packages/pysam/libchtslib.${DEB_HOST_GNU_TYPE}.so /usr/lib/python2.7/dist-packages/pysam/libchtslib.so
--- /dev/null
+# These are apparently false-positives
+# Inspection of the build logs shows that these are indeed compiled with
+# -D_FORTIFY_SOURCE=2
+hardening-no-fortify-functions usr/lib/python2.7/dist-packages/pysam/lib*.so
--- /dev/null
+# These are apparently false-positives
+# Inspection of the build logs shows that these are indeed compiled with
+# -D_FORTIFY_SOURCE=2
+hardening-no-fortify-functions usr/lib/python3/dist-packages/pysam/lib*.so
--- /dev/null
+#!/usr/bin/make -f
+
+include /usr/share/dpkg/default.mk
+
+export PYBUILD_NAME=pysam
+export LC_ALL = C.UTF-8
+
+export DEB_BUILD_MAINT_OPTIONS = hardening=+all
+export DEB_LDFLAGS_MAINT_APPEND=-Wl,--as-needed
+
+TESTPKG := $(DEB_SOURCE)-tests
+
+export HTSLIB_MODE=external
+HTSLIBDIR := /usr/lib/$(DEB_HOST_MULTIARCH)
+export HTSLIB_LIBRARY_DIR=$(HTSLIBDIR)
+export HTSLIB_INCLUDE_DIR=/usr/include
+
+# unfortunately this does not work - any hint to fix this would be really welcome
+#export PYBUILD_TEST_ARGS_python2=-k-XTestRemoteFileHTTP -k-XTestRemoteFileHTTPWithHeader
+#export PYBUILD_TEST_ARGS_python3=-k-XTestRemoteFileHTTP -k-XTestRemoteFileHTTPWithHeader
+
+clean: clean-tests
+%:
+ dh $@ --with python2,python3 --buildsystem=pybuild
+
+override_dh_install: clean-tests
+ dh_install -Xtest.gtf.gz
+
+ifeq (,$(findstring nocheck, $(DEB_BUILD_OPTIONS)))
+override_dh_auto_test: pysam_data.all cbcf_data.all
+ dh_auto_test
+else
+override_dh_auto_test:
+endif
+
+override_dh_auto_clean:
+ dh_auto_clean
+ $(RM) \
+ pysam/config.py \
+ pysam/config.h \
+ pysam/lib*.c \
+ samtools/config.h \
+ bcftools/config.h
+ rm -rf pysam.egg-info
+
+.PHONY: pysam_data.% cbcf_data.%
+cbcf_data.%:
+ cd tests/$(basename $@) && $(MAKE) $*
+pysam_data.%:
+ cd tests/$(basename $@) && $(MAKE) $*
+
+.PHONY: clean-tests
+clean-tests: pysam_data.clean cbcf_data.clean
+ find . -name "*.pyc" -delete
+ find . -name "*.pyxbldc" -delete
+ #find . -name "tmp_*" -delete # This deletes samtools/tmp_file.* which is needed to build successfully
+ find . -name "*.bai*" -delete
+ find . -name "*.cram*" -delete
+ find . -name "*.bam" -delete
+ rm -rf tests/pysam_test_work \
+ tests/example_htslib.gtf.gz.tbi \
+ tests/log.txt \
+ tests/test.bam \
+ tests/_compile_test.c \
+ tests/pysam_ex2.sam \
+ tests/__pycache__ \
+ pysam/calignmentfile.c \
+ pysam/cbcf.c \
+ tests/GRCh38_full_analysis_set_plus_decoy_hla.fa.fai \
+ tests/pysam_data/ex1.fa.gz \
+ tests/pysam_data/ex1.fa.gz.gzi \
+ tests/pysam_data/ex1_csi.bam.csi
+
--- /dev/null
+3.0 (quilt)
--- /dev/null
+Test-Command: make -C tests/pysam_data && make -C tests/cbcf_data && pytest
+Depends: @builddeps@, python-pysam
+Restrictions: allow-stderr, rw-build-tree
+
+Test-Command: make -C tests/pysam_data && make -C tests/cbcf_data && pytest-3
+Depends: @builddeps@, python3-pysam,
+Restrictions: allow-stderr, rw-build-tree
--- /dev/null
+#!/bin/sh -e
+
+if [ "$ADTTMP" = "" ] ; then
+ ADTTMP=`mktemp -d /tmp/python-pysam-test.XXXXXX`
+fi
+cp -ra /usr/share/doc/python-pysam/data/* $ADTTMP
+
+# FIXME!!
+# That's a pretty strange hack but without it the dynamic libraries are not found
+# Need to be tracked down before uploading
+cd /usr/lib/python2.7/dist-packages/pysam
+gnutype=`dpkg-architecture -qDEB_TARGET_GNU_TYPE`
+for so in *.${gnutype}.so ; do sudo ln -sf $so `basename $so .${gnutype}.so`.so ; done
+
+cd $ADTTMP
+find . -name "*.gz" -exec gunzip -f \{\} \;
+
+nosetests --nocapture -v
+cd
+# rm -rf $ADTTMP
+
--- /dev/null
+#!/bin/sh -e
+
+if [ "$ADTTMP" = "" ] ; then
+ ADTTMP=`mktemp -d /tmp/python3-pysam-test.XXXXXX`
+fi
+cd $ADTTMP
+cp -ra /usr/share/doc/python-pysam/tests/* $ADTTMP
+nosetests3 --nocapture
+cd
+rm -rf $ADTTMP
--- /dev/null
+Registry:
+ - Name: OMICtools
+ Entry: OMICS_19073
+ - Name: RRID
+ Entry: NA
+ - Name: bio.tools
+ Entry: pysam
--- /dev/null
+version=3
+
+opts="repacksuffix=+ds,dversionmangle=s/\+ds//g,filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%python-pysam-$1.tar.gz%" \
+ https://github.com/pysam-developers/pysam/tags \
+ (?:.*/)?v?(\d[\d\.]*)\.tar\.gz
projects / python-pysam.git / commitdiff