[med-svn] [Git][med-team/bedops][master] 7 commits: Depends: s/python/python3/
Andreas Tille
gitlab at salsa.debian.org
Sat Jan 11 06:36:19 GMT 2020
Andreas Tille pushed to branch master at Debian Med / bedops
Commits:
2ab59170 by Andreas Tille at 2020-01-11T06:27:36+01:00
Depends: s/python/python3/
- - - - -
ac60215c by Andreas Tille at 2020-01-11T06:28:00+01:00
R-U: Trailing whitespace in debian/changelog
- - - - -
18ec6d66 by Andreas Tille at 2020-01-11T06:28:06+01:00
Set upstream metadata fields: Bug-Database, Bug-Submit.
- - - - -
70a9f9ca by Andreas Tille at 2020-01-11T06:28:07+01:00
Remove obsolete field Name from debian/upstream/metadata (already present in machine-readable debian/copyright).
- - - - -
cf988253 by Andreas Tille at 2020-01-11T07:16:44+01:00
Close bug
- - - - -
a19b30fc by Andreas Tille at 2020-01-11T07:23:59+01:00
fix shebang lines in Python scripts
- - - - -
0ceb0cf9 by Andreas Tille at 2020-01-11T07:35:38+01:00
Upload to unstable
- - - - -
4 changed files:
- debian/changelog
- debian/control
- debian/patches/2to3.patch
- debian/upstream/metadata
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,15 @@
+bedops (2.4.37+dfsg-2) unstable; urgency=medium
+
+ * Team upload.
+ * Depends: s/python/python3/ + fix shebang lines in Python scripts
+ Closes: #948590
+ * Remove trailing whitespace in debian/changelog
+ * Set upstream metadata fields: Bug-Database, Bug-Submit.
+ * Remove obsolete field Name from debian/upstream/metadata (already
+ present in machine-readable debian/copyright).
+
+ -- Andreas Tille <tille at debian.org> Sat, 11 Jan 2020 07:24:20 +0100
+
bedops (2.4.37+dfsg-1) unstable; urgency=medium
* Team upload.
@@ -7,7 +19,7 @@ bedops (2.4.37+dfsg-1) unstable; urgency=medium
-- Steffen Moeller <moeller at debian.org> Wed, 23 Oct 2019 16:44:58 +0200
bedops (2.4.36+dfsg-2) unstable; urgency=medium
-
+
* Team upload.
* Use 2to3 to port python files from python2 to python3
Closes: #936197
=====================================
debian/control
=====================================
@@ -20,7 +20,7 @@ Package: bedops
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends},
- python,
+ python3,
tcsh
Description: high-performance genomic feature operations
BEDOPS is a suite of tools to address common questions raised in genomic
=====================================
debian/patches/2to3.patch
=====================================
@@ -4,10 +4,14 @@ Bug-Debian: https://bugs.debian.org/936197
Last-Update: 2019-09-13
---
-Index: bedops/applications/bed/sort-bed/src/update-sort-bed-migrate-candidates.py
-===================================================================
---- bedops.orig/applications/bed/sort-bed/src/update-sort-bed-migrate-candidates.py
-+++ bedops/applications/bed/sort-bed/src/update-sort-bed-migrate-candidates.py
+--- a/applications/bed/sort-bed/src/update-sort-bed-migrate-candidates.py
++++ b/applications/bed/sort-bed/src/update-sort-bed-migrate-candidates.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+
+ #
+ # BEDOPS
@@ -19,7 +19,7 @@
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
#
@@ -17,10 +21,14 @@ Index: bedops/applications/bed/sort-bed/src/update-sort-bed-migrate-candidates.p
import sys
import os
-Index: bedops/applications/bed/sort-bed/src/update-sort-bed-slurm.py
-===================================================================
---- bedops.orig/applications/bed/sort-bed/src/update-sort-bed-slurm.py
-+++ bedops/applications/bed/sort-bed/src/update-sort-bed-slurm.py
+--- a/applications/bed/sort-bed/src/update-sort-bed-slurm.py
++++ b/applications/bed/sort-bed/src/update-sort-bed-slurm.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+
+ #
+ # BEDOPS
@@ -19,7 +19,7 @@
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
#
@@ -30,10 +38,14 @@ Index: bedops/applications/bed/sort-bed/src/update-sort-bed-slurm.py
import sys
import os
-Index: bedops/applications/bed/sort-bed/src/update-sort-bed-starch-slurm.py
-===================================================================
---- bedops.orig/applications/bed/sort-bed/src/update-sort-bed-starch-slurm.py
-+++ bedops/applications/bed/sort-bed/src/update-sort-bed-starch-slurm.py
+--- a/applications/bed/sort-bed/src/update-sort-bed-starch-slurm.py
++++ b/applications/bed/sort-bed/src/update-sort-bed-starch-slurm.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+
+ #
+ # BEDOPS
@@ -19,7 +19,7 @@
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
#
@@ -43,10 +55,14 @@ Index: bedops/applications/bed/sort-bed/src/update-sort-bed-starch-slurm.py
import sys
import os
-Index: bedops/applications/bed/starch/src/starch-diff.py
-===================================================================
---- bedops.orig/applications/bed/starch/src/starch-diff.py
-+++ bedops/applications/bed/starch/src/starch-diff.py
+--- a/applications/bed/starch/src/starch-diff.py
++++ b/applications/bed/starch/src/starch-diff.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+
+ #
+ # BEDOPS
@@ -19,7 +19,7 @@
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
#
@@ -79,10 +95,14 @@ Index: bedops/applications/bed/starch/src/starch-diff.py
uncommon_chromosomes.sort()
if args.debug: logger.info('Uncommon chromosomes [%s]' % (','.join(uncommon_chromosomes)))
-Index: bedops/applications/bed/starch/test/nested_and_duplicate_elements/src/hasDuplicateElements.py
-===================================================================
---- bedops.orig/applications/bed/starch/test/nested_and_duplicate_elements/src/hasDuplicateElements.py
-+++ bedops/applications/bed/starch/test/nested_and_duplicate_elements/src/hasDuplicateElements.py
+--- a/applications/bed/starch/test/nested_and_duplicate_elements/src/hasDuplicateElements.py
++++ b/applications/bed/starch/test/nested_and_duplicate_elements/src/hasDuplicateElements.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+
+ import os, sys, subprocess
+
@@ -10,35 +10,35 @@ chr1_proc = subprocess.Popen([unstarch,
chr1_proc_out, chr1_proc_err = chr1_proc.communicate()
chr1_proc_out.strip('\n')
@@ -124,10 +144,14 @@ Index: bedops/applications/bed/starch/test/nested_and_duplicate_elements/src/has
sys.exit(os.EX_USAGE)
sys.exit(os.EX_OK)
-Index: bedops/applications/bed/starch/test/nested_and_duplicate_elements/src/hasNestedElements.py
-===================================================================
---- bedops.orig/applications/bed/starch/test/nested_and_duplicate_elements/src/hasNestedElements.py
-+++ bedops/applications/bed/starch/test/nested_and_duplicate_elements/src/hasNestedElements.py
+--- a/applications/bed/starch/test/nested_and_duplicate_elements/src/hasNestedElements.py
++++ b/applications/bed/starch/test/nested_and_duplicate_elements/src/hasNestedElements.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+
+ import os, sys, subprocess
+
@@ -10,35 +10,35 @@ chr1_proc = subprocess.Popen([unstarch,
chr1_proc_out, chr1_proc_err = chr1_proc.communicate()
chr1_proc_out.strip('\n')
@@ -169,10 +193,8 @@ Index: bedops/applications/bed/starch/test/nested_and_duplicate_elements/src/has
sys.exit(os.EX_USAGE)
sys.exit(os.EX_OK)
-Index: bedops/docs/conf.py
-===================================================================
---- bedops.orig/docs/conf.py
-+++ bedops/docs/conf.py
+--- a/docs/conf.py
++++ b/docs/conf.py
@@ -42,8 +42,8 @@ source_suffix = '.rst'
master_doc = 'index'
@@ -232,3 +254,38 @@ Index: bedops/docs/conf.py
# The language of the text. It defaults to the language option
# or en if the language is not set.
+--- a/applications/bed/starch/test/unsortable_elements/src/isUnsortable.py
++++ b/applications/bed/starch/test/unsortable_elements/src/isUnsortable.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+
+ import os, sys, subprocess
+
+--- a/tests/starch/generate_random_intervals.sh
++++ b/tests/starch/generate_random_intervals.sh
+@@ -6,7 +6,7 @@ maxLength=$3
+
+ # rand=$(od -N 4 -t uL -An /dev/urandom | tr -d " ") && rand=$(($rand % 1234))
+ # rand=$(shuf -i 0-${upperBound} -n ${samples})
+-# rand=$(python -S -c "import sys; import random; sys.stdout.write(str(random.randrange(0,${upperBound})))")
++# rand=$(python3 -S -c "import sys; import random; sys.stdout.write(str(random.randrange(0,${upperBound})))")
+
+ while IFS='' read -r line || [[ -n "$line" ]]; do
+ chr=`printf "$line" | awk '{ print $1 }'`
+@@ -18,10 +18,10 @@ while IFS='' read -r line || [[ -n "$lin
+ # length=$(od -N 4 -t uL -An /dev/urandom | tr -d " ") && length=$(($length % $maxLength))
+ # start=$(shuf -i 0-${adjustedBound} -n 1)
+ # length=$(shuf -i 0-${maxLength} -n 1)
+- # start=$(python -S -c "import sys; import random; sys.stdout.write(str(random.randrange(0,${adjustedBound})))")
+- # length=$(python -S -c "import sys; import random; sys.stdout.write(str(random.randrange(0,${maxLength})))")
++ # start=$(python3 -S -c "import sys; import random; sys.stdout.write(str(random.randrange(0,${adjustedBound})))")
++ # length=$(python3 -S -c "import sys; import random; sys.stdout.write(str(random.randrange(0,${maxLength})))")
+ # stop=$(($start + $length + 1))
+ # echo -e "$chr\t$start\t$stop\tid-$chrN-$sample"
+- echo $(python -S -c "import sys; import random; start=random.randrange(0,${adjustedBound}); length=random.randrange(0,${maxLength}); stop=start+length+1; sys.stdout.write('${chr}\t%s\t%s\tid-${chrN}-${sample}\n' % (start, stop))") | tr " " "\t"
++ echo $(python3 -S -c "import sys; import random; start=random.randrange(0,${adjustedBound}); length=random.randrange(0,${maxLength}); stop=start+length+1; sys.stdout.write('${chr}\t%s\t%s\tid-${chrN}-${sample}\n' % (start, stop))") | tr " " "\t"
+ done
+-done < "${boundsFn}"
+\ No newline at end of file
++done < "${boundsFn}"
=====================================
debian/upstream/metadata
=====================================
@@ -1,31 +1,31 @@
Cite-As: |
- Shane Neph, M. Scott Kuehn, Alex P. Reynolds, et al.
- BEDOPS: high-performance genomic feature operations
- Bioinformatics (2012) 28 (14): 1919-1920.
-Name: bedops
+ Shane Neph, M. Scott Kuehn, Alex P. Reynolds, et al.
+ BEDOPS: high-performance genomic feature operations
+ Bioinformatics (2012) 28 (14): 1919-1920.
Reference:
- - Author: >
- Shane Neph and M. Scott Kuehn and Alex P. Reynolds and Eric Haugen and
- Robert E. Thurman and Audra K. Johnson and Eric Rynes and
- Matthew T. Maurano and Jeff Vierstra and Sean Thomas and
- Richard Sandstrom and Richard Humbert and John A. Stamatoyannopoulos
- Title: "BEDOPS: high-performance genomic feature operations"
- Publisher: Bioinformatics
- Year: 2012
- Volume: 28
- Number: 14
- Pages: 1919-1920
- DOI: 10.1093/bioinformatics/bts277
- PMID: 22576172
- URL: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract
- eprint: "https://academic.oup.com/bioinformatics/article-pdf/\
- 28/14/1919/582641/bts277.pdf"
+- Author: >
+ Shane Neph and M. Scott Kuehn and Alex P. Reynolds and Eric Haugen and
+ Robert E. Thurman and Audra K. Johnson and Eric Rynes and
+ Matthew T. Maurano and Jeff Vierstra and Sean Thomas and
+ Richard Sandstrom and Richard Humbert and John A. Stamatoyannopoulos
+ Title: 'BEDOPS: high-performance genomic feature operations'
+ Publisher: Bioinformatics
+ Year: 2012
+ Volume: 28
+ Number: 14
+ Pages: 1919-1920
+ DOI: 10.1093/bioinformatics/bts277
+ PMID: 22576172
+ URL: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract
+ eprint: https://academic.oup.com/bioinformatics/article-pdf/28/14/1919/582641/bts277.pdf
Registry:
- - Name: bio.tools
- Entry: Bedops
- - Name: OMICtools
- Entry: OMICS_00949
- - Name: SciCrunch
- Entry: SCR_012865
- - Name: conda:bioconda
- Entry: bedops
+- Name: bio.tools
+ Entry: Bedops
+- Name: OMICtools
+ Entry: OMICS_00949
+- Name: SciCrunch
+ Entry: SCR_012865
+- Name: conda:bioconda
+ Entry: bedops
+Bug-Database: https://github.com/bedops/bedops/issues
+Bug-Submit: https://github.com/bedops/bedops/issues/new
View it on GitLab: https://salsa.debian.org/med-team/bedops/compare/479c48082baee8724016641cfcbd6194d5d6848e...0ceb0cf9a00a2502e100f29a23c370f1fe47f4c2
--
View it on GitLab: https://salsa.debian.org/med-team/bedops/compare/479c48082baee8724016641cfcbd6194d5d6848e...0ceb0cf9a00a2502e100f29a23c370f1fe47f4c2
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