Package: python-pysam
Version: 0.10.0+ds-2
Followup-For: Bug #867017
User: ubuntu-de...@lists.ubuntu.com
Usertags: origin-ubuntu artful ubuntu-patch
Hi folks,
I've looked into updating python-pysam to the new upstream version to
correct the issue with htslib 1.4 compatibility. The existing patches
against upstream can/must all be dropped, but an additional patch is needed
for the new upstream to ensure proper linkage of all the .so's.
Please find attached a debdiff against the packaging to allow an update to
pysam 0.11.2. I have uploaded this debdiff to Ubuntu, where it is now
building.
By way of explanation, here is the accompanying changelog for that upload:
* New upstream release.
- Fixes compatibility with htslib 1.4. Closes: #867017, LP: #1701268.
* debian/patches/exclude_test_tyring_to_access_remote_ftpserver.patch:
drop, fixed upstream.
* debian/patches/rpath.patch: drop, this actually now breaks the libraries
which need to find one another on the path.
* debian/patches/htslib-external-config.patch: drop, the
HTSLIB_MODE=external already ensures we aren't using the internal copy.
* debian/patches/pysam_stdout_linkage.patch: fix missing symbols in
libcsamtools and libcbcftools libraries.
Hope that helps,
--
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/
slanga...@ubuntu.com vor...@debian.org
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 <ti...@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 <a...@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/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.langa...@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 <a...@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 2017-07-27 23:49:17.000000000
-0700
@@ -1,3 +1 @@
-rpath.patch
-htslib-external-config.patch
-exclude_test_tyring_to_access_remote_ftpserver.patch
+pysam_stdout_linkage.patch
