[med-svn] [Git][med-team/bedops][master] 2 commits: Use 2to3 to port python files from python2 to python3
Shayan Doust
gitlab at salsa.debian.org
Sat Sep 14 14:59:04 BST 2019
Shayan Doust pushed to branch master at Debian Med / bedops
Commits:
938664d6 by Shayan Doust at 2019-09-13T14:09:48Z
Use 2to3 to port python files from python2 to python3
- - - - -
c78dee76 by Shayan Doust at 2019-09-13T14:21:42Z
Write to changelog. We still need a form of test / autopkgtest
- - - - -
3 changed files:
- debian/changelog
- + debian/patches/2to3.patch
- debian/patches/series
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+bedops (2.4.36+dfsg-2) UNRELEASED; urgency=medium
+
+ * Team upload.
+ * Use 2to3 to port python files from python2 to python3
+ Closes: #936197
+
+ -- Shayan Doust <hello at shayandoust.me> Fri, 13 Sep 2019 15:10:57 +0100
+
bedops (2.4.36+dfsg-1) unstable; urgency=medium
* Team upload.
=====================================
debian/patches/2to3.patch
=====================================
@@ -0,0 +1,234 @@
+Description: port python files using python2 to python3
+Author: Shayan Doust <hello at shayandoust.me>
+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 2019-09-13 15:06:08.879696791 +0100
++++ bedops/applications/bed/sort-bed/src/update-sort-bed-migrate-candidates.py 2019-09-13 15:06:08.871696823 +0100
+@@ -19,7 +19,7 @@
+ # 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ #
+
+-from __future__ import absolute_import, division, print_function, unicode_literals
++
+
+ 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 2019-09-13 15:06:08.879696791 +0100
++++ bedops/applications/bed/sort-bed/src/update-sort-bed-slurm.py 2019-09-13 15:06:08.871696823 +0100
+@@ -19,7 +19,7 @@
+ # 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ #
+
+-from __future__ import absolute_import, division, print_function, unicode_literals
++
+
+ 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 2019-09-13 15:06:08.879696791 +0100
++++ bedops/applications/bed/sort-bed/src/update-sort-bed-starch-slurm.py 2019-09-13 15:06:08.871696823 +0100
+@@ -19,7 +19,7 @@
+ # 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ #
+
+-from __future__ import absolute_import, division, print_function, unicode_literals
++
+
+ import sys
+ import os
+Index: bedops/applications/bed/starch/src/starch-diff.py
+===================================================================
+--- bedops.orig/applications/bed/starch/src/starch-diff.py 2019-09-13 15:06:08.879696791 +0100
++++ bedops/applications/bed/starch/src/starch-diff.py 2019-09-13 15:06:08.871696823 +0100
+@@ -19,7 +19,7 @@
+ # 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ #
+
+-from __future__ import absolute_import, division, print_function, unicode_literals
++
+
+ import sys
+ import os
+@@ -77,7 +77,7 @@
+
+ all_tests_pass = True
+
+- selected_chromosome = unicode(args.chr)
++ selected_chromosome = str(args.chr)
+ if args.debug: logger.info('Selected chromosome [%s]' % (selected_chromosome))
+
+ archive_paths = list()
+@@ -132,11 +132,11 @@
+ all_chromosomes[chromosome] = 0
+ all_chromosomes[chromosome] += 1
+
+- common_chromosomes = [k for k, v in all_chromosomes.iteritems() if v == num_files]
++ common_chromosomes = [k for k, v in all_chromosomes.items() if v == num_files]
+ common_chromosomes.sort()
+ if args.debug: logger.info('Common chromosomes [%s]' % (','.join(common_chromosomes)))
+
+- uncommon_chromosomes = [k for k, v in all_chromosomes.iteritems() if v != num_files]
++ uncommon_chromosomes = [k for k, v in all_chromosomes.items() if v != num_files]
+ 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 2019-09-13 15:06:08.879696791 +0100
++++ bedops/applications/bed/starch/test/nested_and_duplicate_elements/src/hasDuplicateElements.py 2019-09-13 15:06:08.871696823 +0100
+@@ -10,35 +10,35 @@
+ chr1_proc_out, chr1_proc_err = chr1_proc.communicate()
+ chr1_proc_out.strip('\n')
+ if int(chr1_proc_out) == 0:
+- print "[STARCH] ERROR: chr1 is reporting it doesn't have a duplicate element, but it does!"
++ print("[STARCH] ERROR: chr1 is reporting it doesn't have a duplicate element, but it does!")
+ sys.exit(os.EX_USAGE)
+
+ chr2_proc = subprocess.Popen([unstarch, 'chr2', flag, archive], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+ chr2_proc_out, chr2_proc_err = chr2_proc.communicate()
+ chr2_proc_out.strip('\n')
+ if int(chr2_proc_out) == 1:
+- print "[STARCH] ERROR: chr2 is reporting it has a duplicate element, but it doesn't!"
++ print("[STARCH] ERROR: chr2 is reporting it has a duplicate element, but it doesn't!")
+ sys.exit(os.EX_USAGE)
+
+ chr3_proc = subprocess.Popen([unstarch, 'chr3', flag, archive], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+ chr3_proc_out, chr3_proc_err = chr3_proc.communicate()
+ chr3_proc_out.strip('\n')
+ if int(chr3_proc_out) == 1:
+- print "[STARCH] ERROR: chr3 is reporting it has a duplicate element, but it doesn't!"
++ print("[STARCH] ERROR: chr3 is reporting it has a duplicate element, but it doesn't!")
+ sys.exit(os.EX_USAGE)
+
+ chrAll_proc = subprocess.Popen([unstarch, 'all', flag, archive], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+ chrAll_proc_out, chrAll_proc_err = chrAll_proc.communicate()
+ chrAll_proc_out.strip('\n')
+ if int(chrAll_proc_out) == 0:
+- print "[STARCH] ERROR: 'all' chromosome usage is reporting the archive doesn't have a duplicate element, but there is a duplicate element in chr1!"
++ print("[STARCH] ERROR: 'all' chromosome usage is reporting the archive doesn't have a duplicate element, but there is a duplicate element in chr1!")
+ sys.exit(os.EX_USAGE)
+
+ chrOmit_proc = subprocess.Popen([unstarch, flag, archive], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+ chrOmit_proc_out, chrOmit_proc_err = chrOmit_proc.communicate()
+ chrOmit_proc_out.strip('\n')
+ if int(chrOmit_proc_out) == 0:
+- print "[STARCH] ERROR: omitted chromosome usage is reporting the archive doesn't have a duplicate element, but there is a duplicate element in chr1!"
++ print("[STARCH] ERROR: omitted chromosome usage is reporting the archive doesn't have a duplicate element, but there is a duplicate element in chr1!")
+ 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 2019-09-13 15:06:08.879696791 +0100
++++ bedops/applications/bed/starch/test/nested_and_duplicate_elements/src/hasNestedElements.py 2019-09-13 15:06:08.871696823 +0100
+@@ -10,35 +10,35 @@
+ chr1_proc_out, chr1_proc_err = chr1_proc.communicate()
+ chr1_proc_out.strip('\n')
+ if int(chr1_proc_out) == 1:
+- print "[STARCH] ERROR: chr1 is reporting it has a nested element, but it doesn't have one!"
++ print("[STARCH] ERROR: chr1 is reporting it has a nested element, but it doesn't have one!")
+ sys.exit(os.EX_USAGE)
+
+ chr2_proc = subprocess.Popen([unstarch, 'chr2', flag, archive], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+ chr2_proc_out, chr2_proc_err = chr2_proc.communicate()
+ chr2_proc_out.strip('\n')
+ if int(chr2_proc_out) == 0:
+- print "[STARCH] ERROR: chr2 is reporting it doesn't have a nested element, but it does!"
++ print("[STARCH] ERROR: chr2 is reporting it doesn't have a nested element, but it does!")
+ sys.exit(os.EX_USAGE)
+
+ chr3_proc = subprocess.Popen([unstarch, 'chr3', flag, archive], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+ chr3_proc_out, chr3_proc_err = chr3_proc.communicate()
+ chr3_proc_out.strip('\n')
+ if int(chr3_proc_out) == 0:
+- print "[STARCH] ERROR: chr3 is reporting it doesn't have a nested element, but it does!"
++ print("[STARCH] ERROR: chr3 is reporting it doesn't have a nested element, but it does!")
+ sys.exit(os.EX_USAGE)
+
+ chrAll_proc = subprocess.Popen([unstarch, 'all', flag, archive], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+ chrAll_proc_out, chrAll_proc_err = chrAll_proc.communicate()
+ chrAll_proc_out.strip('\n')
+ if int(chrAll_proc_out) == 0:
+- print "[STARCH] ERROR: 'all' chromosome usage is reporting the archive doesn't have a nested element, but there are nested elements in chr2 and chr3!"
++ print("[STARCH] ERROR: 'all' chromosome usage is reporting the archive doesn't have a nested element, but there are nested elements in chr2 and chr3!")
+ sys.exit(os.EX_USAGE)
+
+ chrOmit_proc = subprocess.Popen([unstarch, flag, archive], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+ chrOmit_proc_out, chrOmit_proc_err = chrOmit_proc.communicate()
+ chrOmit_proc_out.strip('\n')
+ if int(chrOmit_proc_out) == 0:
+- print "[STARCH] ERROR: omitted chromosome usage is reporting the archive doesn't have a nested element, but there are nested elements in chr2 and chr3!"
++ print("[STARCH] ERROR: omitted chromosome usage is reporting the archive doesn't have a nested element, but there are nested elements in chr2 and chr3!")
+ sys.exit(os.EX_USAGE)
+
+ sys.exit(os.EX_OK)
+Index: bedops/docs/conf.py
+===================================================================
+--- bedops.orig/docs/conf.py 2019-09-13 15:06:08.879696791 +0100
++++ bedops/docs/conf.py 2019-09-13 15:06:08.875696807 +0100
+@@ -42,8 +42,8 @@
+ master_doc = 'index'
+
+ # General information about the project.
+-project = u'BEDOPS'
+-copyright = u'2011-2019, Shane Neph, Alex Reynolds'
++project = 'BEDOPS'
++copyright = '2011-2019, Shane Neph, Alex Reynolds'
+
+ # The version info for the project you're documenting, acts as replacement for
+ # |version| and |release|, also used in various other places throughout the
+@@ -200,8 +200,8 @@
+ # Grouping the document tree into LaTeX files. List of tuples
+ # (source start file, target name, title, author, documentclass [howto/manual]).
+ latex_documents = [
+- ('index', 'BEDOPS.tex', u'BEDOPS Documentation',
+- u'Shane Neph, Alex Reynolds', 'manual'),
++ ('index', 'BEDOPS.tex', 'BEDOPS Documentation',
++ 'Shane Neph, Alex Reynolds', 'manual'),
+ ]
+
+ # The name of an image file (relative to this directory) to place at the top of
+@@ -230,8 +230,8 @@
+ # One entry per manual page. List of tuples
+ # (source start file, name, description, authors, manual section).
+ man_pages = [
+- ('index', 'bedops', u'BEDOPS Documentation',
+- [u'Shane Neph, Alex Reynolds'], 1)
++ ('index', 'bedops', 'BEDOPS Documentation',
++ ['Shane Neph, Alex Reynolds'], 1)
+ ]
+
+ # If true, show URL addresses after external links.
+@@ -244,8 +244,8 @@
+ # (source start file, target name, title, author,
+ # dir menu entry, description, category)
+ texinfo_documents = [
+- ('index', 'BEDOPS', u'BEDOPS Documentation',
+- u'Shane Neph, Alex Reynolds', 'BEDOPS', 'One line description of project.',
++ ('index', 'BEDOPS', 'BEDOPS Documentation',
++ 'Shane Neph, Alex Reynolds', 'BEDOPS', 'One line description of project.',
+ 'Miscellaneous'),
+ ]
+
+@@ -265,10 +265,10 @@
+ # -- Options for Epub output ---------------------------------------------------
+
+ # Bibliographic Dublin Core info.
+-epub_title = u'BEDOPS'
+-epub_author = u'Shane Neph, Alex Reynolds'
+-epub_publisher = u'Shane Neph, Alex Reynolds'
+-epub_copyright = u'2013, Shane Neph, Alex Reynolds'
++epub_title = 'BEDOPS'
++epub_author = 'Shane Neph, Alex Reynolds'
++epub_publisher = 'Shane Neph, Alex Reynolds'
++epub_copyright = '2013, Shane Neph, Alex Reynolds'
+
+ # The language of the text. It defaults to the language option
+ # or en if the language is not set.
=====================================
debian/patches/series
=====================================
@@ -1,2 +1,3 @@
+2to3.patch
use_debian_libs
hardening.patch
View it on GitLab: https://salsa.debian.org/med-team/bedops/compare/1e908dab998fc213ec6185917ade905f4b847b6f...c78dee766e4f1a127f7567e61d0ec3cd5e2a76e6
--
View it on GitLab: https://salsa.debian.org/med-team/bedops/compare/1e908dab998fc213ec6185917ade905f4b847b6f...c78dee766e4f1a127f7567e61d0ec3cd5e2a76e6
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