[med-svn] [Git][med-team/python-pybedtools][master] 2 commits: Add back test_issue_178 after upstream provided a patch
Andreas Tille
gitlab at salsa.debian.org
Mon Mar 12 10:09:28 UTC 2018
Andreas Tille pushed to branch master at Debian Med / python-pybedtools
Commits:
1ddd1ca6 by Andreas Tille at 2017-11-09T12:01:45+01:00
Add back test_issue_178 after upstream provided a patch
- - - - -
57355f02 by Andreas Tille at 2017-11-09T12:11:30+01:00
Team upload to unstable
- - - - -
4 changed files:
- debian/changelog
- + debian/patches/c8dff864dbc942bb7adb3e719b0702f7e3989d36.patch
- debian/patches/series
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,8 +1,9 @@
-python-pybedtools (0.7.10-2) UNRELEASED; urgency=medium
+python-pybedtools (0.7.10-2) unstable; urgency=medium
- * Provide link to upstream issue for failed test
+ * Team upload
+ * Add back test_issue_178 after upstream provided a patch
- -- Andreas Tille <tille at debian.org> Wed, 08 Nov 2017 09:25:08 +0100
+ -- Andreas Tille <tille at debian.org> Thu, 09 Nov 2017 12:01:51 +0100
python-pybedtools (0.7.10-1) unstable; urgency=medium
=====================================
debian/patches/c8dff864dbc942bb7adb3e719b0702f7e3989d36.patch
=====================================
--- /dev/null
+++ b/debian/patches/c8dff864dbc942bb7adb3e719b0702f7e3989d36.patch
@@ -0,0 +1,151 @@
+From: Ryan Dale <dalerr at niddk.nih.gov>
+Date: Wed, 8 Nov 2017 15:35:02 -0500
+Subject: [PATCH] address #227
+
+---
+ pybedtools/contrib/bigwig.py | 62 +++++++++++++++++++++++++++++++++++++-------
+ pybedtools/test/test1.py | 36 ++++++++++++++-----------
+ 2 files changed, 73 insertions(+), 25 deletions(-)
+
+--- a/pybedtools/contrib/bigwig.py
++++ b/pybedtools/contrib/bigwig.py
+@@ -48,8 +48,17 @@ def bedgraph_to_bigwig(bedgraph, genome,
+ bedgraph.fn,
+ genome_file,
+ output]
+- p = subprocess.Popen(cmds, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+- stdout, stderr = p.communicate()
++ try:
++ p = subprocess.Popen(cmds, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
++ stdout, stderr = p.communicate()
++ except FileNotFoundError:
++ raise FileNotFoundError(
++ "bedGraphToBigWig was not found on the path. This is an external "
++ "tool from UCSC which can be downloaded from "
++ "http://hgdownload.soe.ucsc.edu/admin/exe/. Alternatatively, use "
++ "`conda install ucsc-bedgraphtobigwig`"
++ )
++
+ if p.returncode:
+ raise ValueError("cmds: %s\nstderr:%s\nstdout:%s"
+ % (" ".join(cmds), stderr, stdout))
+@@ -72,8 +81,16 @@ def bigwig_to_bedgraph(fn, chrom=None, s
+ outfn = pybedtools.BedTool._tmp()
+ cmds.append(outfn)
+
+- p = subprocess.Popen(cmds, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+- stdout, stderr = p.communicate()
++ try:
++ p = subprocess.Popen(cmds, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
++ stdout, stderr = p.communicate()
++ except FileNotFoundError:
++ raise FileNotFoundError(
++ "bigWigToBedGraph was not found on the path. This is an external "
++ "tool from UCSC which can be downloaded from "
++ "http://hgdownload.soe.ucsc.edu/admin/exe/. Alternatatively, use "
++ "`conda install ucsc-bedgraphtobigwig`"
++ )
+ if p.returncode:
+ raise ValueError("cmds: %s\nstderr:%s\nstdout:%s"
+ % (" ".join(cmds), stderr, stdout))
+@@ -87,8 +104,17 @@ def wig_to_bigwig(wig, genome, output):
+ wig.fn,
+ genome_file,
+ output]
+- subprocess.Popen(cmds, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+- stdout, stderr = p.communicate()
++
++ try:
++ p = subprocess.Popen(cmds, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
++ stdout, stderr = p.communicate()
++ except FileNotFoundError:
++ raise FileNotFoundError(
++ "bigWigToBedGraph was not found on the path. This is an external "
++ "tool from UCSC which can be downloaded from "
++ "http://hgdownload.soe.ucsc.edu/admin/exe/. Alternatatively, use "
++ "`conda install ucsc-bedgraphtobigwig`"
++ )
+ if p.returncode:
+ raise ValueError('cmds: %s\nstderr:%s\nstdout:%s'
+ % (' '.join(cmds), stderr, stdout))
+@@ -120,15 +146,31 @@ def bam_to_bigwig(bam, genome, output, s
+ x.fn,
+ genome_file,
+ output]
+- p = subprocess.Popen(cmds, stdout=subprocess.PIPE, stderr=subprocess.PIPE, universal_newlines=True)
+- stdout, stderr = p.communicate()
++ try:
++ p = subprocess.Popen(cmds, stdout=subprocess.PIPE, stderr=subprocess.PIPE, universal_newlines=True)
++ stdout, stderr = p.communicate()
++ except FileNotFoundError:
++ raise FileNotFoundError(
++ "bedGraphToBigWig was not found on the path. This is an external "
++ "tool from UCSC which can be downloaded from "
++ "http://hgdownload.soe.ucsc.edu/admin/exe/. Alternatatively, use "
++ "`conda install ucsc-bedgraphtobigwig`"
++ )
+
+ if p.returncode and 'bedSort' in stderr:
+ print('BAM header was not sorted; sorting bedGraph')
+ y = x.sort()
+ cmds[1] = y.fn
+- p = subprocess.Popen(cmds, stdout=subprocess.PIPE, stderr=subprocess.PIPE, universal_newlines=True)
+- stdout, stderr = p.communicate()
++ try:
++ p = subprocess.Popen(cmds, stdout=subprocess.PIPE, stderr=subprocess.PIPE, universal_newlines=True)
++ stdout, stderr = p.communicate()
++ except FileNotFoundError:
++ raise FileNotFoundError(
++ "bedSort was not found on the path. This is an external "
++ "tool from UCSC which can be downloaded from "
++ "http://hgdownload.soe.ucsc.edu/admin/exe/. Alternatatively, use "
++ "`conda install ucsc-bedgraphtobigwig`"
++ )
+
+ if p.returncode:
+ raise ValueError('cmds: %s\nstderr: %s\nstdout: %s'
+--- a/pybedtools/test/test1.py
++++ b/pybedtools/test/test1.py
+@@ -2104,21 +2104,27 @@ def test_issue_196():
+
+
+ def test_issue_178():
+- fn = pybedtools.example_filename('gdc.othersort.bam')
+- pybedtools.contrib.bigwig.bam_to_bigwig(fn, genome='dm3', output='tmp.bw')
+- x = pybedtools.contrib.bigwig.bigwig_to_bedgraph('tmp.bw')
+- assert x == fix(
+- '''
+- chr2L 70 75 1
+- chr2L 140 145 1
+- chr2L 150 155 1
+- chr2L 160 165 1
+- chr2L 210 215 1
+- chrX 10 15 1
+- chrX 70 75 1
+- chrX 140 145 1
+- ''')
+- os.unlink('tmp.bw')
++ try:
++ fn = pybedtools.example_filename('gdc.othersort.bam')
++ pybedtools.contrib.bigwig.bam_to_bigwig(fn, genome='dm3', output='tmp.bw')
++ x = pybedtools.contrib.bigwig.bigwig_to_bedgraph('tmp.bw')
++ assert x == fix(
++ '''
++ chr2L 70 75 1
++ chr2L 140 145 1
++ chr2L 150 155 1
++ chr2L 160 165 1
++ chr2L 210 215 1
++ chrX 10 15 1
++ chrX 70 75 1
++ chrX 140 145 1
++ ''')
++ os.unlink('tmp.bw')
++
++ # If bedGraphToBigWig is not on the path, see
++ # https://github.com/daler/pybedtools/issues/227
++ except FileNotFoundError:
++ pass
+
+ def test_issue_203():
+ x = pybedtools.example_bedtool('x.bed')
=====================================
debian/patches/series
=====================================
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -3,3 +3,4 @@ enable-package-data
disable-write-version
disable-test-156
rename-scripts
+c8dff864dbc942bb7adb3e719b0702f7e3989d36.patch
=====================================
debian/rules
=====================================
--- a/debian/rules
+++ b/debian/rules
@@ -5,9 +5,8 @@ DH_VERBOSE := 1
export DEB_BUILD_MAINT_OPTIONS=hardening=+all
export PYBUILD_NAME=pybedtools
export MATPLOTLIBRC=$(CURDIR)/debian/
-# test_issue_178 fails, issue opened at upstream
-# https://github.com/daler/pybedtools/issues/227
-export PYBUILD_TEST_ARGS=--attr '!url' --exclude='(test_issue_178)'
+# Add back test_issue_178 after upstream provided a patch https://github.com/daler/pybedtools/pull/228
+export PYBUILD_TEST_ARGS=--attr '!url' # --exclude='(test_issue_178)'
export PYBUILD_BEFORE_TEST=cp {dir}/debian/mpl-expected.png {build_dir}/pybedtools/test/
export HOME=$(shell echo $$PWD"/fakehome")
View it on GitLab: https://salsa.debian.org/med-team/python-pybedtools/compare/f2ad9e590dd66dd14d811c1e5c1995062d6e2278...57355f023cf5fb0cad5ec0fefc0334b5be8dcd2c
---
View it on GitLab: https://salsa.debian.org/med-team/python-pybedtools/compare/f2ad9e590dd66dd14d811c1e5c1995062d6e2278...57355f023cf5fb0cad5ec0fefc0334b5be8dcd2c
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