Bug#861828: unblock: python-pysam/0.10.0+ds-2
Package: release.debian.org
Severity: normal
User: release.debian.org@packages.debian.org
Usertags: unblock
Please unblock package python-pysam
The package exludes a test trying to access a remote ftpserver
and thus closes bug #861496.
When working on the package I noticed that the clean target is
missing some files that should be deleted to build twice in a
row. I took the freedom to avoid freeze policy and fixed this
issue as well (the file debian/clean is useless since I later
followed the maintainers way and added the files to d/rules -
please excuse that I forgot to remove it).
Kind regards and thanks for your work for the Debian release
Andreas.
unblock python-pysam/0.10.0+ds-2
-- System Information:
Debian Release: 8.7
APT prefers stable-updates
APT policy: (500, 'stable-updates'), (500, 'stable')
Architecture: amd64 (x86_64)
Kernel: Linux 3.16.0-4-amd64 (SMP w/1 CPU core)
Locale: LANG=de_DE.UTF-8, LC_CTYPE=de_DE.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
diff -Nru python-pysam-0.10.0+ds/debian/changelog python-pysam-0.10.0+ds/debian/changelog
--- python-pysam-0.10.0+ds/debian/changelog 2017-01-26 13:36:47.000000000 +0100
+++ python-pysam-0.10.0+ds/debian/changelog 2017-05-04 15:06:21.000000000 +0200
@@ -1,3 +1,13 @@
+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 ]
diff -Nru python-pysam-0.10.0+ds/debian/clean python-pysam-0.10.0+ds/debian/clean
--- python-pysam-0.10.0+ds/debian/clean 1970-01-01 01:00:00.000000000 +0100
+++ python-pysam-0.10.0+ds/debian/clean 2017-05-04 12:46:49.000000000 +0200
@@ -0,0 +1,4 @@
+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
diff -Nru python-pysam-0.10.0+ds/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
--- python-pysam-0.10.0+ds/debian/patches/exclude_test_tyring_to_access_remote_ftpserver.patch 1970-01-01 01:00:00.000000000 +0100
+++ python-pysam-0.10.0+ds/debian/patches/exclude_test_tyring_to_access_remote_ftpserver.patch 2017-05-04 15:06:21.000000000 +0200
@@ -0,0 +1,29 @@
+Description: Exclude test tyring to access remote ftpserver
+Bug-Debian: https://bugs.debian.org/861496
+Author: Andreas Tille <tille@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/series python-pysam-0.10.0+ds/debian/patches/series
--- python-pysam-0.10.0+ds/debian/patches/series 2017-01-26 07:32:37.000000000 +0100
+++ python-pysam-0.10.0+ds/debian/patches/series 2017-05-04 15:06:21.000000000 +0200
@@ -1,2 +1,3 @@
rpath.patch
htslib-external-config.patch
+exclude_test_tyring_to_access_remote_ftpserver.patch
diff -Nru python-pysam-0.10.0+ds/debian/rules python-pysam-0.10.0+ds/debian/rules
--- python-pysam-0.10.0+ds/debian/rules 2017-01-26 07:16:06.000000000 +0100
+++ python-pysam-0.10.0+ds/debian/rules 2017-05-04 15:06:21.000000000 +0200
@@ -42,7 +42,9 @@
$(RM) \
pysam/config.py \
pysam/config.h \
+ pysam/lib*.c \
samtools/config.h
+ rm -rf pysam.egg-info
.PHONY: pysam_data.% cbcf_data.%
cbcf_data.%:
@@ -66,4 +68,9 @@
tests/pysam_ex2.sam \
tests/__pycache__ \
pysam/calignmentfile.c \
- pysam/cbcf.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
+
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