[Debian-med-packaging] Bug#867017: src:python-pysam: FTBFS during rebuild for python3.6 transition
Steve Langasek
steve.langasek at canonical.com
Sat Jul 29 06:37:38 UTC 2017
On Fri, Jul 28, 2017 at 01:37:54PM -0700, Steve Langasek wrote:
> One additional patch required: the previous version built fine locally in a
> terminal, but when dispatched to a builder, the build failed because the
> test suite is testing functions that only output anything when stdin is a
> tty. Since this is clearly deliberate behavior in the code, I'm updating
> the test suite to match.
Well, and one more. This package now built fine, but the autopkgtests
correctly caught that the python2 module was unusable because library
dependencies could not be resolved. Adding some compat symlinks solves
this.
The python3 package was unaffected by this because python3 has native
support for the collision-free library naming.
Attached is now a complete debdiff.
--
Steve Langasek Give me a lever long enough and a Free OS
Debian Developer to set it on, and I can move the world.
Ubuntu Developer http://www.debian.org/
slangasek at ubuntu.com vorlon at debian.org
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diff -Nru python-pysam-0.10.0+ds/debian/control python-pysam-0.11.2.2/debian/control
--- python-pysam-0.10.0+ds/debian/control 2017-05-04 06:06:21.000000000 -0700
+++ python-pysam-0.11.2.2/debian/control 2017-07-28 18:55:54.000000000 -0700
@@ -8,6 +8,7 @@
Priority: optional
Build-Depends:
debhelper (>= 9),
+ dh-exec,
dh-python,
libhts-dev (>= 1.3.2),
zlib1g-dev,
diff -Nru python-pysam-0.10.0+ds/debian/patches/exclude_test_tyring_to_access_remote_ftpserver.patch python-pysam-0.11.2.2/debian/patches/exclude_test_tyring_to_access_remote_ftpserver.patch
--- python-pysam-0.10.0+ds/debian/patches/exclude_test_tyring_to_access_remote_ftpserver.patch 2017-05-04 06:06:21.000000000 -0700
+++ python-pysam-0.11.2.2/debian/patches/exclude_test_tyring_to_access_remote_ftpserver.patch 1969-12-31 16:00:00.000000000 -0800
@@ -1,29 +0,0 @@
-Description: Exclude test tyring to access remote ftpserver
-Bug-Debian: https://bugs.debian.org/861496
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Thu, 04 May 2017 12:50:22 +0200
-
---- a/tests/faidx_test.py
-+++ b/tests/faidx_test.py
-@@ -216,21 +216,5 @@ class TestFastxFileWithEmptySequence(uni
- self.assertEqual(ref_num, l)
-
-
--class TestRemoteFileFTP(unittest.TestCase):
-- '''test remote access.
-- '''
--
-- url = "ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/reference/GRCh38_reference_genome/GRCh38_full_analysis_set_plus_decoy_hla.fa"
--
--
-- def testFTPView(self):
-- if not checkURL(self.url):
-- return
-- with pysam.Fastafile(self.url) as f:
-- self.assertEqual(
-- len(f.fetch("chr1", 0, 1000)),
-- 1000)
--
--
- if __name__ == "__main__":
- unittest.main()
diff -Nru python-pysam-0.10.0+ds/debian/patches/htslib-external-config.patch python-pysam-0.11.2.2/debian/patches/htslib-external-config.patch
--- python-pysam-0.10.0+ds/debian/patches/htslib-external-config.patch 2017-05-04 06:06:21.000000000 -0700
+++ python-pysam-0.11.2.2/debian/patches/htslib-external-config.patch 1969-12-31 16:00:00.000000000 -0800
@@ -1,15 +0,0 @@
-Description: Do not use internal htslib library
-Author: Afif Elghraoui <afif at debian.org>
-Forwarded: not-needed
-Last-Update: 2017-01-26
---- python-pysam.orig/setup.py
-+++ python-pysam/setup.py
-@@ -255,7 +255,7 @@
- else:
- raise ValueError("unknown HTSLIB value '%s'" % HTSLIB_MODE)
-
--internal_htslib_libraries = [os.path.splitext("chtslib{}".format(sysconfig.get_config_var('SO')))[0]]
-+internal_htslib_libraries = []
-
- # build config.py
- with open(os.path.join("pysam", "config.py"), "w") as outf:
diff -Nru python-pysam-0.10.0+ds/debian/patches/no-usage-test-without-tty.patch python-pysam-0.11.2.2/debian/patches/no-usage-test-without-tty.patch
--- python-pysam-0.10.0+ds/debian/patches/no-usage-test-without-tty.patch 1969-12-31 16:00:00.000000000 -0800
+++ python-pysam-0.11.2.2/debian/patches/no-usage-test-without-tty.patch 2017-07-28 13:36:09.000000000 -0700
@@ -0,0 +1,21 @@
+Description: skip usage() tests on autobuilders
+ The usage() functions check whether stdin is a tty before displaying usage
+ information. Therefore, we should not test this code when running on an
+ autobuilder without a tty.
+ .
+ Clever allocation of a pty from within the test suite itself for purposes
+ of testing this path is left as an exercise for the reader.
+Author: Steve Langasek <steve.langasek at canonical.com>
+
+Index: python-pysam-0.11.2.2/tests/samtools_test.py
+===================================================================
+--- python-pysam-0.11.2.2.orig/tests/samtools_test.py
++++ python-pysam-0.11.2.2/tests/samtools_test.py
+@@ -245,6 +245,7 @@
+ self.check_statement(statement)
+
+ @unittest.skipIf(sys.platform == "darwin", "not supported, pattern does not match")
++ @unittest.skipIf(not sys.stdin.isatty(), "skipping usage tests, stdin is not a tty")
+ def testUsage(self):
+ if self.executable == "bcftools":
+ # bcftools usage messages end with exit(1)
diff -Nru python-pysam-0.10.0+ds/debian/patches/pysam_stdout_linkage.patch python-pysam-0.11.2.2/debian/patches/pysam_stdout_linkage.patch
--- python-pysam-0.10.0+ds/debian/patches/pysam_stdout_linkage.patch 1969-12-31 16:00:00.000000000 -0800
+++ python-pysam-0.11.2.2/debian/patches/pysam_stdout_linkage.patch 2017-07-28 10:12:35.000000000 -0700
@@ -0,0 +1,28 @@
+Description: fix missing symbols in libcsamtools and libcbcftools libraries
+ Building on Ubuntu fails because a couple of the .sos wind up with
+ unresolved references to symbols found elsewhere in the tree. Fix their
+ linkage so that they load cleanly.
+Author: Steve Langasek <steve.langasek at canonical.com>
+
+Index: python-pysam-0.11.2.2/setup.py
+===================================================================
+--- python-pysam-0.11.2.2.orig/setup.py
++++ python-pysam-0.11.2.2/setup.py
+@@ -463,6 +463,7 @@
+ csamtools = Extension(
+ "pysam.libcsamtools",
+ [source_pattern % "samtools"] +
++ ["pysam/pysam_util.c"] +
+ glob.glob(os.path.join("samtools", "*.pysam.c")) +
+ htslib_sources +
+ os_c_files,
+@@ -484,7 +485,8 @@
+ library_dirs=["pysam"] + htslib_library_dirs,
+ include_dirs=["bcftools", "pysam", "."] +
+ include_os + htslib_include_dirs,
+- libraries=external_htslib_libraries + internal_htslib_libraries,
++ libraries=external_htslib_libraries + internal_htslib_libraries + \
++ [os.path.splitext("csamtools{}".format(suffix))[0]],
+ language="c",
+ extra_compile_args=extra_compile_args,
+ define_macros=define_macros
diff -Nru python-pysam-0.10.0+ds/debian/patches/rpath.patch python-pysam-0.11.2.2/debian/patches/rpath.patch
--- python-pysam-0.10.0+ds/debian/patches/rpath.patch 2017-05-04 06:06:21.000000000 -0700
+++ python-pysam-0.11.2.2/debian/patches/rpath.patch 1969-12-31 16:00:00.000000000 -0800
@@ -1,32 +0,0 @@
-Description: Disable setting rpath
-Author: Afif Elghraoui <afif at debian.org>
-Forwarded: not-needed
-Last-Update: 2016-03-05
---- python-pysam.orig/cy_build.py
-+++ python-pysam/cy_build.py
-@@ -57,7 +57,7 @@
- ext._init_func(ext)
-
- if not self.inplace:
-- ext.library_dirs.append(os.path.join(self.build_lib, "pysam"))
-+ pass
-
- if sys.platform == 'darwin':
- relative_module_path = ext.name.replace(".", os.sep) + get_config_vars()["SO"]
-@@ -85,6 +85,5 @@
- if not ext.extra_link_args:
- ext.extra_link_args = []
-
-- ext.extra_link_args += ['-Wl,-rpath,$ORIGIN']
-
- build_ext.build_extension(self, ext)
---- python-pysam.orig/setup.py
-+++ python-pysam/setup.py
-@@ -353,7 +353,6 @@
- shared_htslib_sources +
- os_c_files,
- library_dirs=htslib_library_dirs,
-- runtime_library_dirs=htslib_library_dirs,
- include_dirs=["pysam", "."] + include_os + htslib_include_dirs,
- libraries=external_htslib_libraries,
- language="c",
diff -Nru python-pysam-0.10.0+ds/debian/patches/series python-pysam-0.11.2.2/debian/patches/series
--- python-pysam-0.10.0+ds/debian/patches/series 2017-05-04 06:06:21.000000000 -0700
+++ python-pysam-0.11.2.2/debian/patches/series 2017-07-28 13:32:34.000000000 -0700
@@ -1,3 +1,2 @@
-rpath.patch
-htslib-external-config.patch
-exclude_test_tyring_to_access_remote_ftpserver.patch
+pysam_stdout_linkage.patch
+no-usage-test-without-tty.patch
diff -Nru python-pysam-0.10.0+ds/debian/python-pysam.links python-pysam-0.11.2.2/debian/python-pysam.links
--- python-pysam-0.10.0+ds/debian/python-pysam.links 1969-12-31 16:00:00.000000000 -0800
+++ python-pysam-0.11.2.2/debian/python-pysam.links 2017-07-28 19:53:07.000000000 -0700
@@ -0,0 +1,3 @@
+#!/usr/bin/dh-exec
+/usr/lib/python2.7/dist-packages/pysam/libcsamtools.${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
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