[med-svn] [Git][med-team/python-ruffus][master] 8 commits: Add patch to fix syntaxwarnings (Closes: #1086958)
Ananthu C V (@weepingclown)
gitlab at salsa.debian.org
Thu Dec 5 14:25:03 GMT 2024
Ananthu C V pushed to branch master at Debian Med / python-ruffus
Commits:
1b627fb3 by Ananthu C V at 2024-12-05T19:17:44+05:30
Add patch to fix syntaxwarnings (Closes: #1086958)
- - - - -
bbb250d4 by Ananthu C V at 2024-12-05T19:18:38+05:30
Use newer dh-sequence-*, mark B-D with correct build-profiles and run wrap-and-sort
- - - - -
a03947b2 by Ananthu C V at 2024-12-05T19:18:51+05:30
Add patch to fix regex compilation error message check in py3.13 (Closes: #1082265)
- - - - -
c9c0188a by Ananthu C V at 2024-12-05T19:18:52+05:30
Use execute_after_* targets instead of overrides in d/rules
- - - - -
1b450f3a by Ananthu C V at 2024-12-05T19:18:53+05:30
Bump standards version to 4.7.0 (no changes needed)
- - - - -
ba30ba46 by Ananthu C V at 2024-12-05T19:20:49+05:30
Correct patch header metadata
- - - - -
efa135d8 by Ananthu C V at 2024-12-05T19:38:01+05:30
Add patch to drop distutils usage
- - - - -
f874b396 by Ananthu C V at 2024-12-05T19:39:05+05:30
Upload to unstable
- - - - -
12 changed files:
- debian/changelog
- debian/control
- + debian/patches/drop-distutils.patch
- debian/patches/ignore_test_proxy_logger.patch
- + debian/patches/py313-regex-compilation-error-check.patch
- debian/patches/series
- debian/patches/sphinx4.patch
- + debian/patches/use-raw-strings.patch
- debian/patches/use_libjs-mathjax.patch
- debian/python-ruffus-doc.docs
- debian/rules
- debian/tests/control
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,18 @@
+python-ruffus (2.8.4-6) unstable; urgency=medium
+
+ * Team upload.
+ * Add patch to fix syntaxwarnings (Closes: #1086958)
+ * Use newer dh-sequence-*, mark B-D with correct build-profiles
+ and run wrap-and-sort
+ * Add patch to fix regex compilation error message check in
+ py3.13 (Closes: #1082265)
+ * Use execute_after_* targets instead of overrides in d/rules
+ * Bump standards version to 4.7.0 (no changes needed)
+ * Correct patch header metadata
+ * Add patch to drop distutils usage
+
+ -- Ananthu C V <weepingclown at disroot.org> Thu, 05 Dec 2024 19:38:27 +0530
+
python-ruffus (2.8.4-5) unstable; urgency=medium
* d/control: add myself to uploaders.
=====================================
debian/control
=====================================
@@ -6,14 +6,15 @@ Section: python
Testsuite: autopkgtest-pkg-python
Priority: optional
Build-Depends: debhelper-compat (= 13),
- dh-python,
+ dh-sequence-python3,
+ dh-sequence-sphinxdoc <!nodoc>,
+ graphviz,
python3-all,
+ python3-pytest <!nocheck>,
python3-setuptools,
- python3-sphinx,
- python3-sphinx-rtd-theme,
- python3-pytest,
- graphviz
-Standards-Version: 4.6.1
+ python3-sphinx <!nodoc>,
+ python3-sphinx-rtd-theme <!nodoc>
+Standards-Version: 4.7.0
Vcs-Browser: https://salsa.debian.org/med-team/python-ruffus
Vcs-Git: https://salsa.debian.org/med-team/python-ruffus.git
Homepage: http://www.ruffus.org.uk/
@@ -22,9 +23,7 @@ Rules-Requires-Root: no
Package: python3-ruffus
Architecture: all
Multi-Arch: foreign
-Depends: ${misc:Depends},
- ${python3:Depends},
- graphviz
+Depends: graphviz, ${misc:Depends}, ${python3:Depends}
Description: Python3 computation pipeline library widely used in bioinformatics
Ruffus is designed to allow scientific and other analyses to be automated
with the minimum of fuss and the least effort.
@@ -41,9 +40,7 @@ Description: Python3 computation pipeline library widely used in bioinformatics
Package: python-ruffus-doc
Architecture: all
Section: doc
-Depends: ${misc:Depends},
- ${sphinxdoc:Depends},
- libjs-mathjax
+Depends: libjs-mathjax, ${misc:Depends}, ${sphinxdoc:Depends}
Multi-Arch: foreign
Description: documentation for python-ruffus computation pipeline library
Ruffus is designed to allow scientific and other analyses to be automated
=====================================
debian/patches/drop-distutils.patch
=====================================
@@ -0,0 +1,11 @@
+Description: drop usage of deprecated distuils module
+Author: Ananthu C V <weepingclown at debian.org>
+Last-Update: 2024-12-05
+--- a/ez_setup.py
++++ b/ez_setup.py
+@@ -19,4 +19,3 @@
+ import warnings
+-
+-from distutils import log
++import logging as log
+
=====================================
debian/patches/ignore_test_proxy_logger.patch
=====================================
@@ -10,7 +10,7 @@ Description: Ignore test test_proxy_logger.py (fails to write on /tmp)
open("/tmp/lg.log", "w").close()
PermissionError: [Errno 13] Permission denied: '/tmp/lg.log'
Author: Andreas Tille <tille at debian.org>
-Last-Update: Thu, 30 Sep 2021 14:18:35 +0200
+Last-Update: 2021-09-30
--- a/ruffus/test/run_all_unit_tests3.cmd
+++ b/ruffus/test/run_all_unit_tests3.cmd
=====================================
debian/patches/py313-regex-compilation-error-check.patch
=====================================
@@ -0,0 +1,11 @@
+Description: Fix regex compilation error assertion for python3.13
+Author: Ananthu C V <weepingclown at debian.org>
+Last-Update: 2024-12-05
+--- a/ruffus/test/test_ruffus_utility.py
++++ b/ruffus/test/test_ruffus_utility.py
+@@ -280,3 +280,4 @@
+ e.args == ('Dummy Task', "test1: regular expression regex('.*)') is malformed\n[sre_constants.error: (unbalanced parenthesis)]") or
+- e.args == ('Dummy Task', "test1: regular expression regex('.*)') is malformed\n[re.error: (unbalanced parenthesis at position 2)]"))
++ e.args == ('Dummy Task', "test1: regular expression regex('.*)') is malformed\n[re.error: (unbalanced parenthesis at position 2)]") or
++ e.args == ('Dummy Task', "test1: regular expression regex('.*)') is malformed\n[re.PatternError: (unbalanced parenthesis at position 2)]"))
+
=====================================
debian/patches/series
=====================================
@@ -2,3 +2,6 @@ use_libjs-mathjax.patch
sphinx4.patch
ignore_test_proxy_logger.patch
reasonable-multiprocessing.patch
+use-raw-strings.patch
+py313-regex-compilation-error-check.patch
+drop-distutils.patch
=====================================
debian/patches/sphinx4.patch
=====================================
@@ -1,5 +1,5 @@
Author: Andreas Tille <tille at debian.org>
-Last-Update: Thu, 30 Sep 2021 14:18:35 +0200
+Last-Update: 2021-09-30
Forwarded: https://github.com/cgat-developers/ruffus/issues/127
Description: Adapt to sphinx 4.x API
=====================================
debian/patches/use-raw-strings.patch
=====================================
@@ -0,0 +1,330 @@
+Description: use raw strings to avoid syntax warnings
+Author: Ananthu C V <weepingclown at debian.org>
+Last-Update: 2024-12-05
+--- a/ruffus/cmdline.py
++++ b/ruffus/cmdline.py
+@@ -667,3 +667,3 @@
+ def handle_verbose(options):
+- """
++ r"""
+ raw options.verbose is a list of specifiers
+@@ -706,4 +706,4 @@
+ # '+' : i.e. --verbose. This just increases the current verbosity value by 1
+- # '\d+' : e.g. --verbose 6. This (re)sets the verbosity value
+- # '\d+:\d+' : e.g. --verbose 7:-5 The second number is the verbose_abbreviated_path
++ # r'\d+' : e.g. --verbose 6. This (re)sets the verbosity value
++ # r'\d+:\d+' : e.g. --verbose 7:-5 The second number is the verbose_abbreviated_path
+ #
+--- a/ruffus/combinatorics.py
++++ b/ruffus/combinatorics.py
+@@ -25,3 +25,3 @@
+ #################################################################################
+-"""
++r"""
+
+--- a/ruffus/proxy_logger.py
++++ b/ruffus/proxy_logger.py
+@@ -25,3 +25,3 @@
+ #################################################################################
+-"""
++r"""
+ ****************************************************************************
+@@ -322,3 +322,3 @@
+ def make_shared_logger_and_proxy(logger_factory, logger_name, args):
+- """
++ r"""
+ Make a `logging <http://docs.python.org/library/logging.html>`_ object
+--- a/ruffus/ruffus_utility.py
++++ b/ruffus/ruffus_utility.py
+@@ -501,3 +501,3 @@
+ def path_decomposition_regex_match(test_str, compiled_regex):
+- """
++ r"""
+ Returns a dictionary identifying the components of a file path.
+--- a/ruffus/test/test_combinatorics.py
++++ b/ruffus/test/test_combinatorics.py
+@@ -387,6 +387,6 @@
+ self.assertTrue(re.search('Job needs update:.*Missing files.*'
+- '\[.*{tempdir}/a_name.tmp1, '
++ r'\[.*{tempdir}/a_name.tmp1, '
+ '.*{tempdir}/e_name.tmp1, '
+ '.*{tempdir}/h_name.tmp1, '
+- '.*{tempdir}/a_name.e_name.h_name.tmp2\]'.format(tempdir=tempdir), s.getvalue(), re.DOTALL))
++ r'.*{tempdir}/a_name.e_name.h_name.tmp2\]'.format(tempdir=tempdir), s.getvalue(), re.DOTALL))
+
+@@ -462,5 +462,5 @@
+ self.assertTrue(re.search('Job needs update:.*Missing files.*'
+- '\[.*{tempdir}/a_name.tmp1, '
++ r'\[.*{tempdir}/a_name.tmp1, '
+ '.*{tempdir}/b_name.tmp1, '
+- '.*{tempdir}/a_name.b_name.tmp2\]'.format(tempdir=tempdir), s.getvalue(), re.DOTALL))
++ r'.*{tempdir}/a_name.b_name.tmp2\]'.format(tempdir=tempdir), s.getvalue(), re.DOTALL))
+
+@@ -488,6 +488,6 @@
+ self.assertTrue(re.search(
+- '\[.*{tempdir}/a_name.tmp1, '
++ r'\[.*{tempdir}/a_name.tmp1, '
+ '.*{tempdir}/b_name.tmp1, '
+ '.*{tempdir}/c_name.tmp1, '
+- '.*{tempdir}/a_name.b_name.c_name.tmp2\]'.format(tempdir=tempdir), s.getvalue()))
++ r'.*{tempdir}/a_name.b_name.c_name.tmp2\]'.format(tempdir=tempdir), s.getvalue()))
+
+@@ -515,5 +515,5 @@
+ verbose=5, wrap_width=10000, pipeline="main")
+- self.assertTrue(re.search('\[.*{tempdir}/a_name.tmp1, '
++ self.assertTrue(re.search(r'\[.*{tempdir}/a_name.tmp1, '
+ '.*{tempdir}/b_name.tmp1, '
+- '.*{tempdir}/a_name.b_name.tmp2\]'.format(tempdir=tempdir), s.getvalue()))
++ r'.*{tempdir}/a_name.b_name.tmp2\]'.format(tempdir=tempdir), s.getvalue()))
+
+@@ -540,6 +540,6 @@
+ verbose=5, wrap_width=10000, pipeline="main")
+- self.assertTrue(re.search('\[.*{tempdir}/a_name.tmp1, '
++ self.assertTrue(re.search(r'\[.*{tempdir}/a_name.tmp1, '
+ '.*{tempdir}/b_name.tmp1, '
+ '.*{tempdir}/c_name.tmp1, '
+- '.*{tempdir}/a_name.b_name.c_name.tmp2\]'.format(tempdir=tempdir), s.getvalue()))
++ r'.*{tempdir}/a_name.b_name.c_name.tmp2\]'.format(tempdir=tempdir), s.getvalue()))
+
+@@ -567,5 +567,5 @@
+ verbose=5, wrap_width=10000, pipeline="main")
+- self.assertTrue(re.search('\[.*{tempdir}/a_name.tmp1, '
++ self.assertTrue(re.search(r'\[.*{tempdir}/a_name.tmp1, '
+ '.*{tempdir}/b_name.tmp1, '
+- '.*{tempdir}/a_name.b_name.tmp2\]'.format(tempdir=tempdir), s.getvalue()))
++ r'.*{tempdir}/a_name.b_name.tmp2\]'.format(tempdir=tempdir), s.getvalue()))
+
+@@ -592,6 +592,6 @@
+ verbose=5, wrap_width=10000, pipeline="main")
+- self.assertTrue(re.search('\[.*{tempdir}/a_name.tmp1, '
++ self.assertTrue(re.search(r'\[.*{tempdir}/a_name.tmp1, '
+ '.*{tempdir}/b_name.tmp1, '
+ '.*{tempdir}/c_name.tmp1, '
+- '.*{tempdir}/a_name.b_name.c_name.tmp2\]'.format(tempdir=tempdir), s.getvalue()))
++ r'.*{tempdir}/a_name.b_name.c_name.tmp2\]'.format(tempdir=tempdir), s.getvalue()))
+
+--- a/ruffus/test/test_newstyle_regex_error_messages.py
++++ b/ruffus/test/test_newstyle_regex_error_messages.py
+@@ -309,3 +309,3 @@
+ self.assertTrue(re.search(
+- 'Missing files.*\[{tempdir}/a_name.tmp1, {tempdir}/a_name.tmp2'.format(tempdir=tempdir), s.getvalue(), re.DOTALL))
++ r'Missing files.*\[{tempdir}/a_name.tmp1, {tempdir}/a_name.tmp2'.format(tempdir=tempdir), s.getvalue(), re.DOTALL))
+
+@@ -351,3 +351,3 @@
+ self.assertTrue(re.search(
+- 'Missing files.*\[{tempdir}/a_name.tmp1, {tempdir}/a_name.tmp2'.format(tempdir=tempdir), s.getvalue(), re.DOTALL))
++ r'Missing files.*\[{tempdir}/a_name.tmp1, {tempdir}/a_name.tmp2'.format(tempdir=tempdir), s.getvalue(), re.DOTALL))
+
+@@ -369,3 +369,3 @@
+ self.assertRaisesRegex(fatal_error_input_file_does_not_match,
+- "File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*invalid group reference",
++ r"File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*invalid group reference",
+ pipeline_printout,
+@@ -374,3 +374,3 @@
+ self.assertRaisesRegex(RethrownJobError,
+- "File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*invalid group reference",
++ r"File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*invalid group reference",
+ test_pipeline.run,
+@@ -408,3 +408,3 @@
+ self.assertRaisesRegex(fatal_error_input_file_does_not_match,
+- "File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*unknown group name",
++ r"File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*unknown group name",
+ test_pipeline.printout,
+@@ -413,3 +413,3 @@
+ self.assertRaisesRegex(RethrownJobError,
+- "File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*unknown group name",
++ r"File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*unknown group name",
+ test_pipeline.run,
+@@ -425,3 +425,3 @@
+ self.assertRaisesRegex(fatal_error_input_file_does_not_match,
+- "File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*unknown group name",
++ r"File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*unknown group name",
+ test_pipeline.printout,
+@@ -430,3 +430,3 @@
+ self.assertRaisesRegex(RethrownJobError,
+- "File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*unknown group name",
++ r"File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*unknown group name",
+ test_pipeline.run,
+@@ -443,3 +443,3 @@
+ self.assertRaisesRegex(fatal_error_input_file_does_not_match,
+- "File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*invalid group reference",
++ r"File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*invalid group reference",
+ test_pipeline.printout,
+@@ -448,3 +448,3 @@
+ self.assertRaisesRegex(RethrownJobError,
+- "File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*invalid group reference",
++ r"File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*invalid group reference",
+ test_pipeline.run,
+--- a/ruffus/test/test_file_name_parameters.py
++++ b/ruffus/test/test_file_name_parameters.py
+@@ -799,3 +799,3 @@
+ unnamed_args = [tempdir + "/*.test",
+- task.formatter("/(?P<name>\w+).test$"),
++ task.formatter(r"/(?P<name>\w+).test$"),
+ ["{path[0]}/{name[0]}.output1{ext[0]}", "{path[0]}/{name[0]}.output2"], "{path[0]}/{name[0]}.output3"]
+@@ -1591,5 +1591,5 @@
+ args = [[tempdir + "/a.test1", tempdir + "/b.test1"],
+- task.formatter("(?:.+/)?(?P<ID>\w+)\.(.+)"),
++ task.formatter(r"(?:.+/)?(?P<ID>\w+)\.(.+)"),
+ [tempdir + "/c.test2", tempdir + "/d.test2", tempdir + "/e.ignore"],
+- task.formatter("(?:.+/)?(?P<ID>\w+)\.(test2)"),
++ task.formatter(r"(?:.+/)?(?P<ID>\w+)\.(test2)"),
+ r"{path[0][0]}/{ID[0][0]}.{1[1][0]}.output"]
+@@ -1632,5 +1632,5 @@
+ #
+- paths = self.do_task_product([tempdir + "/a.test1", tempdir + "/b.test1"], task.formatter("(?:.+/)?(?P<ID>\w+)\.(.+)"),
++ paths = self.do_task_product([tempdir + "/a.test1", tempdir + "/b.test1"], task.formatter(r"(?:.+/)?(?P<ID>\w+)\.(.+)"),
+ [tempdir + "/c.test2", tempdir + "/d.test2", tempdir +
+- "/e.ignore"], task.formatter("(?:.+/)?(?P<ID>\w+)\.(test2)"),
++ "/e.ignore"], task.formatter(r"(?:.+/)?(?P<ID>\w+)\.(test2)"),
+ task.inputs(
+@@ -1651,5 +1651,5 @@
+ #
+- paths = self.do_task_product([tempdir + "/a.test1", tempdir + "/b.test1"], task.formatter("(?:.+/)?(?P<ID>\w+)\.(.+)"),
++ paths = self.do_task_product([tempdir + "/a.test1", tempdir + "/b.test1"], task.formatter(r"(?:.+/)?(?P<ID>\w+)\.(.+)"),
+ [tempdir + "/c.test2", tempdir + "/d.test2", tempdir +
+- "/e.ignore"], task.formatter("(?:.+/)?(?P<ID>\w+)\.(test2)"),
++ "/e.ignore"], task.formatter(r"(?:.+/)?(?P<ID>\w+)\.(test2)"),
+ add_inputs(
+--- a/ruffus/test/test_ruffus_utility.py
++++ b/ruffus/test/test_ruffus_utility.py
+@@ -510,3 +510,3 @@
+ def helper(self, data, result):
+- regex_str = "([a-z]+)\.([a-z]+)\.([a-z]+)\.([a-z]+)"
++ regex_str = r"([a-z]+)\.([a-z]+)\.([a-z]+)\.([a-z]+)"
+ try_result = regex_replace("aaa.bbb.ccc.aaa",
+--- a/ruffus/test/test_newstyle_combinatorics.py
++++ b/ruffus/test/test_newstyle_combinatorics.py
+@@ -399,6 +399,6 @@
+ self.assertTrue(re.search('Job needs update:.*Missing files.*'
+- '\[.*{tempdir}/a_name.tmp1, '
++ r'\[.*{tempdir}/a_name.tmp1, '
+ '.*{tempdir}/e_name.tmp1, '
+ '.*{tempdir}/h_name.tmp1, '
+- '.*{tempdir}/a_name.e_name.h_name.tmp2\]'.format(tempdir=tempdir), s.getvalue(), re.DOTALL))
++ r'.*{tempdir}/a_name.e_name.h_name.tmp2\]'.format(tempdir=tempdir), s.getvalue(), re.DOTALL))
+
+@@ -473,5 +473,5 @@
+ self.assertTrue(re.search('Job needs update:.*Missing files.*'
+- '\[.*{tempdir}/a_name.tmp1, '
++ r'\[.*{tempdir}/a_name.tmp1, '
+ '.*{tempdir}/b_name.tmp1, '
+- '.*{tempdir}/a_name.b_name.tmp2\]'.format(tempdir=tempdir), s.getvalue(), re.DOTALL))
++ r'.*{tempdir}/a_name.b_name.tmp2\]'.format(tempdir=tempdir), s.getvalue(), re.DOTALL))
+
+@@ -499,6 +499,6 @@
+ self.assertTrue(re.search(
+- '\[.*{tempdir}/a_name.tmp1, '
++ r'\[.*{tempdir}/a_name.tmp1, '
+ '.*{tempdir}/b_name.tmp1, '
+ '.*{tempdir}/c_name.tmp1, '
+- '.*{tempdir}/a_name.b_name.c_name.tmp2\]'.format(tempdir=tempdir), s.getvalue()))
++ r'.*{tempdir}/a_name.b_name.c_name.tmp2\]'.format(tempdir=tempdir), s.getvalue()))
+
+@@ -526,5 +526,5 @@
+ s, [check_permutations2_merged_task], verbose=5, wrap_width=10000)
+- self.assertTrue(re.search('\[.*{tempdir}/a_name.tmp1, '
++ self.assertTrue(re.search(r'\[.*{tempdir}/a_name.tmp1, '
+ '.*{tempdir}/b_name.tmp1, '
+- '.*{tempdir}/a_name.b_name.tmp2\]'.format(tempdir=tempdir), s.getvalue()))
++ r'.*{tempdir}/a_name.b_name.tmp2\]'.format(tempdir=tempdir), s.getvalue()))
+
+@@ -551,6 +551,6 @@
+ s, [check_permutations3_merged_task], verbose=5, wrap_width=10000)
+- self.assertTrue(re.search('\[.*{tempdir}/a_name.tmp1, '
++ self.assertTrue(re.search(r'\[.*{tempdir}/a_name.tmp1, '
+ '.*{tempdir}/b_name.tmp1, '
+ '.*{tempdir}/c_name.tmp1, '
+- '.*{tempdir}/a_name.b_name.c_name.tmp2\]'.format(tempdir=tempdir), s.getvalue()))
++ r'.*{tempdir}/a_name.b_name.c_name.tmp2\]'.format(tempdir=tempdir), s.getvalue()))
+
+@@ -578,5 +578,5 @@
+ s, [check_combinations_with_replacement2_merged_task], verbose=5, wrap_width=10000)
+- self.assertTrue(re.search('\[.*{tempdir}/a_name.tmp1, '
++ self.assertTrue(re.search(r'\[.*{tempdir}/a_name.tmp1, '
+ '.*{tempdir}/b_name.tmp1, '
+- '.*{tempdir}/a_name.b_name.tmp2\]'.format(tempdir=tempdir), s.getvalue()))
++ r'.*{tempdir}/a_name.b_name.tmp2\]'.format(tempdir=tempdir), s.getvalue()))
+
+@@ -603,6 +603,6 @@
+ s, [check_combinations_with_replacement3_merged_task], verbose=5, wrap_width=10000)
+- self.assertTrue(re.search('\[.*{tempdir}/a_name.tmp1, '
++ self.assertTrue(re.search(r'\[.*{tempdir}/a_name.tmp1, '
+ '.*{tempdir}/b_name.tmp1, '
+ '.*{tempdir}/c_name.tmp1, '
+- '.*{tempdir}/a_name.b_name.c_name.tmp2\]'.format(tempdir=tempdir), s.getvalue()))
++ r'.*{tempdir}/a_name.b_name.c_name.tmp2\]'.format(tempdir=tempdir), s.getvalue()))
+
+--- a/ruffus/test/test_regex_error_messages.py
++++ b/ruffus/test/test_regex_error_messages.py
+@@ -301,3 +301,3 @@
+ self.assertTrue(re.search(
+- 'Missing files.*\[{tempdir}a_name.tmp1, {tempdir}a_name.tmp2'.format(tempdir=tempdir), s.getvalue(), re.DOTALL))
++ r'Missing files.*\[{tempdir}a_name.tmp1, {tempdir}a_name.tmp2'.format(tempdir=tempdir), s.getvalue(), re.DOTALL))
+
+@@ -343,3 +343,3 @@
+ self.assertTrue(re.search(
+- 'Missing files.*\[{tempdir}a_name.tmp1, {tempdir}a_name.tmp2'.format(tempdir=tempdir), s.getvalue(), re.DOTALL))
++ r'Missing files.*\[{tempdir}a_name.tmp1, {tempdir}a_name.tmp2'.format(tempdir=tempdir), s.getvalue(), re.DOTALL))
+
+@@ -361,3 +361,3 @@
+ self.assertRaisesRegex(fatal_error_input_file_does_not_match,
+- "File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*invalid group reference",
++ r"File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*invalid group reference",
+ pipeline_printout,
+@@ -366,3 +366,3 @@
+ self.assertRaisesRegex(RethrownJobError,
+- "File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*invalid group reference",
++ r"File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*invalid group reference",
+ pipeline_run,
+@@ -400,3 +400,3 @@
+ self.assertRaisesRegex(fatal_error_input_file_does_not_match,
+- "File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*unknown group name",
++ r"File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*unknown group name",
+ pipeline_printout,
+@@ -405,3 +405,3 @@
+ self.assertRaisesRegex(RethrownJobError,
+- "File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*unknown group name",
++ r"File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*unknown group name",
+ pipeline_run,
+@@ -417,3 +417,3 @@
+ self.assertRaisesRegex(fatal_error_input_file_does_not_match,
+- "File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*unknown group name",
++ r"File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*unknown group name",
+ pipeline_printout,
+@@ -422,3 +422,3 @@
+ self.assertRaisesRegex(RethrownJobError,
+- "File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*unknown group name",
++ r"File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*unknown group name",
+ pipeline_run,
+@@ -435,3 +435,3 @@
+ self.assertRaisesRegex(fatal_error_input_file_does_not_match,
+- "File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*invalid group reference",
++ r"File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*invalid group reference",
+ pipeline_printout,
+@@ -440,3 +440,3 @@
+ self.assertRaisesRegex(RethrownJobError,
+- "File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*invalid group reference",
++ r"File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*invalid group reference",
+ pipeline_run,
+--- a/doc/conf.py
++++ b/doc/conf.py
+@@ -67,3 +67,3 @@
+ import re
+-release = re.subn("([\d\.]+).*", r"\1", version)[0]
++release = re.subn(r"([\d\.]+).*", r"\1", version)[0]
+ print(version, release)
+--- a/ruffus/parse_old_style_ruffus.py
++++ b/ruffus/parse_old_style_ruffus.py
+@@ -177,3 +177,3 @@
+
+-func_re = re.compile("^\s*def.*\(")
++func_re = re.compile(r"^\s*def.*\(")
+
+@@ -194,4 +194,4 @@
+
+-decorator_re = re.compile("^\s*@")
+-no_white_space_re = re.compile("^[^#\s]")
++decorator_re = re.compile(r"^\s*@")
++no_white_space_re = re.compile(r"^[^#\s]")
+ if __name__ == '__main__':
=====================================
debian/patches/use_libjs-mathjax.patch
=====================================
@@ -1,5 +1,5 @@
Author: Dmitry Shachnev <mitya57 at debian.org>
-Last-Update: Fri, 15 Jan 2016 15:14:14 +0300
+Last-Update: 2016-01-15
Forwarded: no
Description: Use Debian packaged mathjax
=====================================
debian/python-ruffus-doc.docs
=====================================
@@ -1,5 +1,5 @@
-ruffus/test
-doc/static_data/ruffus.pdf
+USAGE.TXT
debian/README.test
debian/tests/run-unit-test
-USAGE.TXT
+doc/static_data/ruffus.pdf
+ruffus/test
=====================================
debian/rules
=====================================
@@ -9,11 +9,12 @@ docpkg:=$(DEB_SOURCE)-doc
export PYBUILD_NAME=ruffus
%:
- dh $@ --with python3,sphinxdoc --buildsystem=pybuild
+ dh $@ --buildsystem=pybuild
-override_dh_auto_build:
- dh_auto_build
+execute_after_dh_auto_build-indep:
+ifeq (,$(filter nodoc, $(DEB_BUILD_OPTIONS)))
make --directory=doc html
+endif
override_dh_installdocs:
dh_installdocs -ppython-ruffus-doc doc/_build/html
@@ -42,8 +43,7 @@ ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
find .pybuild -name tmp | xargs rm -rf
endif
-override_dh_auto_clean:
- dh_auto_clean
+execute_after_dh_auto_clean:
rm -rf ruffus/test/temp_branching_dir \
ruffus/test/temp_filesre_combine \
ruffus/test/test_pausing_dir \
@@ -57,14 +57,12 @@ override_dh_auto_clean:
rm -f ruffus.egg-info/PKG-INFO ruffus.egg-info/SOURCES.txt ruffus.egg-info/dependency_links.txt ruffus.egg-info/top_level.txt
-override_dh_install:
- dh_install
+execute_after_dh_install:
# test files have all #!/usr/bin/python which looks wrong in python3 package
find debian/python3-$(PYBUILD_NAME)/usr/lib/python3*/dist-packages/ruffus/test -name "*.py" -exec sed -i 's+^\(#!/usr/bin/.*python\)[[:space:]]*$$+\13+' \{\} \;
# leave only the test starter that fits Python version
find debian/python3-$(PYBUILD_NAME) -name run_all_unit_tests.cmd -delete
sed -i '1s?^#! */usr/bin/env *python *$$?#!/usr/bin/python3?' `grep -Rl '^#! */usr/bin/env *python *$$' debian/python3-$(PYBUILD_NAME)`
-override_dh_fixperms:
- dh_fixperms
+execute_after_dh_fixperms:
find debian -name "run_all_unit_tests*.cmd" -executable -exec chmod -x \{\} \;
=====================================
debian/tests/control
=====================================
@@ -1,3 +1,3 @@
Tests: run-unit-test
-Depends: @, python3-pytest
+Depends: python3-pytest, @
Restrictions: allow-stderr
View it on GitLab: https://salsa.debian.org/med-team/python-ruffus/-/compare/8d11916045a7cfe766b5f53bc1853a75a7b0743b...f874b396837b28dda1efa91809e1f81b84e54001
--
View it on GitLab: https://salsa.debian.org/med-team/python-ruffus/-/compare/8d11916045a7cfe766b5f53bc1853a75a7b0743b...f874b396837b28dda1efa91809e1f81b84e54001
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