[med-svn] [Git][med-team/python-bcbio-gff][master] 4 commits: python-syntax-warning.patch: new: fix SyntaxWarning.
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Tue Nov 5 22:00:31 GMT 2024
Étienne Mollier pushed to branch master at Debian Med / python-bcbio-gff
Commits:
0e219a4e by Étienne Mollier at 2024-11-05T22:39:04+01:00
python-syntax-warning.patch: new: fix SyntaxWarning.
Closes: #1085892
- - - - -
2622e8bd by Étienne Mollier at 2024-11-05T22:40:01+01:00
d/control: declare compliance to standards version 4.7.0.
- - - - -
c9e97ef3 by Étienne Mollier at 2024-11-05T22:59:30+01:00
distutils-deprecation.patch: new: remove use of deprecated distutils.
- - - - -
e3de0f7f by Étienne Mollier at 2024-11-05T23:00:04+01:00
d/changelog: ready for upload to unstable.
- - - - -
5 changed files:
- debian/changelog
- debian/control
- + debian/patches/distutils-deprecation.patch
- + debian/patches/python-syntax-warning.patch
- + debian/patches/series
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+python-bcbio-gff (0.7.1-2) unstable; urgency=medium
+
+ * python-syntax-warning.patch: new: fix SyntaxWarning. (Closes: #1085892)
+ * d/control: declare compliance to standards version 4.7.0.
+ * distutils-deprecation.patch: new: remove use of deprecated distutils.
+
+ -- Étienne Mollier <emollier at debian.org> Tue, 05 Nov 2024 22:59:55 +0100
+
python-bcbio-gff (0.7.1-1) unstable; urgency=medium
* New upstream version
=====================================
debian/control
=====================================
@@ -12,7 +12,7 @@ Build-Depends: debhelper-compat (= 13),
python3-biopython,
python3-six,
debhelper
-Standards-Version: 4.6.2
+Standards-Version: 4.7.0
Vcs-Browser: https://salsa.debian.org/med-team/python-bcbio-gff
Vcs-Git: https://salsa.debian.org/med-team/python-bcbio-gff.git
Homepage: https://github.com/chapmanb/bcbb/tree/master/gff
=====================================
debian/patches/distutils-deprecation.patch
=====================================
@@ -0,0 +1,292 @@
+Description: migrate away from distutils.
+ Following [PEP 632], the distutils module is deprecated. In bcbio.gff,
+ this module is still in use for it's logging facility, so a
+ contemporary approach would be to use the "logging" module instead of
+ distutils. logging.warning behaves essentially the same way as
+ distutils.log.warn; there was also a logging.warn function but it is
+ deprecated in favor of warning, thus this patch does not attempt to do
+ something smart with things allowed by the import semantics.
+ .
+ [PEP 632]: https://peps.python.org/pep-0632/
+
+Author: Étienne Mollier <emollier at debian.org>
+Forwarded: https://github.com/chapmanb/bcbb/pull/146
+Last-Update: 2024-11-05
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- python-bcbio-gff.orig/distribute_setup.py
++++ python-bcbio-gff/distribute_setup.py
+@@ -21,8 +21,7 @@
+ import tempfile
+ import tarfile
+ import optparse
+-
+-from distutils import log
++import logging
+
+ try:
+ from site import USER_SITE
+@@ -69,7 +68,7 @@
+ def _install(tarball, install_args=()):
+ # extracting the tarball
+ tmpdir = tempfile.mkdtemp()
+- log.warn('Extracting in %s', tmpdir)
++ logging.warning('Extracting in %s', tmpdir)
+ old_wd = os.getcwd()
+ try:
+ os.chdir(tmpdir)
+@@ -80,13 +79,13 @@
+ # going in the directory
+ subdir = os.path.join(tmpdir, os.listdir(tmpdir)[0])
+ os.chdir(subdir)
+- log.warn('Now working in %s', subdir)
++ logging.warning('Now working in %s', subdir)
+
+ # installing
+- log.warn('Installing Distribute')
++ logging.warning('Installing Distribute')
+ if not _python_cmd('setup.py', 'install', *install_args):
+- log.warn('Something went wrong during the installation.')
+- log.warn('See the error message above.')
++ logging.warning('Something went wrong during the installation.')
++ logging.warning('See the error message above.')
+ # exitcode will be 2
+ return 2
+ finally:
+@@ -97,7 +96,7 @@
+ def _build_egg(egg, tarball, to_dir):
+ # extracting the tarball
+ tmpdir = tempfile.mkdtemp()
+- log.warn('Extracting in %s', tmpdir)
++ logging.warning('Extracting in %s', tmpdir)
+ old_wd = os.getcwd()
+ try:
+ os.chdir(tmpdir)
+@@ -108,17 +107,17 @@
+ # going in the directory
+ subdir = os.path.join(tmpdir, os.listdir(tmpdir)[0])
+ os.chdir(subdir)
+- log.warn('Now working in %s', subdir)
++ logging.warning('Now working in %s', subdir)
+
+ # building an egg
+- log.warn('Building a Distribute egg in %s', to_dir)
++ logging.warning('Building a Distribute egg in %s', to_dir)
+ _python_cmd('setup.py', '-q', 'bdist_egg', '--dist-dir', to_dir)
+
+ finally:
+ os.chdir(old_wd)
+ shutil.rmtree(tmpdir)
+ # returning the result
+- log.warn(egg)
++ logging.warning(egg)
+ if not os.path.exists(egg):
+ raise IOError('Could not build the egg.')
+
+@@ -207,7 +206,7 @@
+ src = dst = None
+ if not os.path.exists(saveto): # Avoid repeated downloads
+ try:
+- log.warn("Downloading %s", url)
++ logging.warning("Downloading %s", url)
+ src = urlopen(url)
+ # Read/write all in one block, so we don't create a corrupt file
+ # if the download is interrupted.
+@@ -254,9 +253,9 @@
+ f.close()
+ if existing_content == content:
+ # already patched
+- log.warn('Already patched.')
++ logging.warning('Already patched.')
+ return False
+- log.warn('Patching...')
++ logging.warning('Patching...')
+ _rename_path(path)
+ f = open(path, 'w')
+ try:
+@@ -277,14 +276,14 @@
+
+ def _rename_path(path):
+ new_name = path + '.OLD.%s' % time.time()
+- log.warn('Renaming %s to %s', path, new_name)
++ logging.warning('Renaming %s to %s', path, new_name)
+ os.rename(path, new_name)
+ return new_name
+
+
+ def _remove_flat_installation(placeholder):
+ if not os.path.isdir(placeholder):
+- log.warn('Unkown installation at %s', placeholder)
++ logging.warning('Unkown installation at %s', placeholder)
+ return False
+ found = False
+ for file in os.listdir(placeholder):
+@@ -292,10 +291,10 @@
+ found = True
+ break
+ if not found:
+- log.warn('Could not locate setuptools*.egg-info')
++ logging.warning('Could not locate setuptools*.egg-info')
+ return
+
+- log.warn('Moving elements out of the way...')
++ logging.warning('Moving elements out of the way...')
+ pkg_info = os.path.join(placeholder, file)
+ if os.path.isdir(pkg_info):
+ patched = _patch_egg_dir(pkg_info)
+@@ -303,7 +302,7 @@
+ patched = _patch_file(pkg_info, SETUPTOOLS_PKG_INFO)
+
+ if not patched:
+- log.warn('%s already patched.', pkg_info)
++ logging.warning('%s already patched.', pkg_info)
+ return False
+ # now let's move the files out of the way
+ for element in ('setuptools', 'pkg_resources.py', 'site.py'):
+@@ -311,7 +310,7 @@
+ if os.path.exists(element):
+ _rename_path(element)
+ else:
+- log.warn('Could not find the %s element of the '
++ logging.warning('Could not find the %s element of the '
+ 'Setuptools distribution', element)
+ return True
+
+@@ -319,28 +318,28 @@
+
+
+ def _after_install(dist):
+- log.warn('After install bootstrap.')
++ logging.warning('After install bootstrap.')
+ placeholder = dist.get_command_obj('install').install_purelib
+ _create_fake_setuptools_pkg_info(placeholder)
+
+
+ def _create_fake_setuptools_pkg_info(placeholder):
+ if not placeholder or not os.path.exists(placeholder):
+- log.warn('Could not find the install location')
++ logging.warning('Could not find the install location')
+ return
+ pyver = '%s.%s' % (sys.version_info[0], sys.version_info[1])
+ setuptools_file = 'setuptools-%s-py%s.egg-info' % \
+ (SETUPTOOLS_FAKED_VERSION, pyver)
+ pkg_info = os.path.join(placeholder, setuptools_file)
+ if os.path.exists(pkg_info):
+- log.warn('%s already exists', pkg_info)
++ logging.warning('%s already exists', pkg_info)
+ return
+
+- log.warn('Creating %s', pkg_info)
++ logging.warning('Creating %s', pkg_info)
+ try:
+ f = open(pkg_info, 'w')
+ except EnvironmentError:
+- log.warn("Don't have permissions to write %s, skipping", pkg_info)
++ logging.warning("Don't have permissions to write %s, skipping", pkg_info)
+ return
+ try:
+ f.write(SETUPTOOLS_PKG_INFO)
+@@ -348,7 +347,7 @@
+ f.close()
+
+ pth_file = os.path.join(placeholder, 'setuptools.pth')
+- log.warn('Creating %s', pth_file)
++ logging.warning('Creating %s', pth_file)
+ f = open(pth_file, 'w')
+ try:
+ f.write(os.path.join(os.curdir, setuptools_file))
+@@ -365,7 +364,7 @@
+ pkg_info = os.path.join(path, 'EGG-INFO', 'PKG-INFO')
+ if os.path.exists(pkg_info):
+ if _same_content(pkg_info, SETUPTOOLS_PKG_INFO):
+- log.warn('%s already patched.', pkg_info)
++ logging.warning('%s already patched.', pkg_info)
+ return False
+ _rename_path(path)
+ os.mkdir(path)
+@@ -382,7 +381,7 @@
+
+
+ def _before_install():
+- log.warn('Before install bootstrap.')
++ logging.warning('Before install bootstrap.')
+ _fake_setuptools()
+
+
+@@ -405,12 +404,12 @@
+
+
+ def _fake_setuptools():
+- log.warn('Scanning installed packages')
++ logging.warning('Scanning installed packages')
+ try:
+ import pkg_resources
+ except ImportError:
+ # we're cool
+- log.warn('Setuptools or Distribute does not seem to be installed.')
++ logging.warning('Setuptools or Distribute does not seem to be installed.')
+ return
+ ws = pkg_resources.working_set
+ try:
+@@ -424,43 +423,43 @@
+ )
+
+ if setuptools_dist is None:
+- log.warn('No setuptools distribution found')
++ logging.warning('No setuptools distribution found')
+ return
+ # detecting if it was already faked
+ setuptools_location = setuptools_dist.location
+- log.warn('Setuptools installation detected at %s', setuptools_location)
++ logging.warning('Setuptools installation detected at %s', setuptools_location)
+
+ # if --root or --preix was provided, and if
+ # setuptools is not located in them, we don't patch it
+ if not _under_prefix(setuptools_location):
+- log.warn('Not patching, --root or --prefix is installing Distribute'
++ logging.warning('Not patching, --root or --prefix is installing Distribute'
+ ' in another location')
+ return
+
+ # let's see if its an egg
+ if not setuptools_location.endswith('.egg'):
+- log.warn('Non-egg installation')
++ logging.warning('Non-egg installation')
+ res = _remove_flat_installation(setuptools_location)
+ if not res:
+ return
+ else:
+- log.warn('Egg installation')
++ logging.warning('Egg installation')
+ pkg_info = os.path.join(setuptools_location, 'EGG-INFO', 'PKG-INFO')
+ if (os.path.exists(pkg_info) and
+ _same_content(pkg_info, SETUPTOOLS_PKG_INFO)):
+- log.warn('Already patched.')
++ logging.warning('Already patched.')
+ return
+- log.warn('Patching...')
++ logging.warning('Patching...')
+ # let's create a fake egg replacing setuptools one
+ res = _patch_egg_dir(setuptools_location)
+ if not res:
+ return
+- log.warn('Patching complete.')
++ logging.warning('Patching complete.')
+ _relaunch()
+
+
+ def _relaunch():
+- log.warn('Relaunching...')
++ logging.warning('Relaunching...')
+ # we have to relaunch the process
+ # pip marker to avoid a relaunch bug
+ _cmd1 = ['-c', 'install', '--single-version-externally-managed']
+@@ -525,7 +524,7 @@
+ install_args = []
+ if options.user_install:
+ if sys.version_info < (2, 6):
+- log.warn("--user requires Python 2.6 or later")
++ logging.warning("--user requires Python 2.6 or later")
+ raise SystemExit(1)
+ install_args.append('--user')
+ return install_args
=====================================
debian/patches/python-syntax-warning.patch
=====================================
@@ -0,0 +1,24 @@
+Description: fix SyntaxWarning.
+ This change treats the regex passed to the compiler as a raw string.
+ This resolve the following warning:
+ .
+ /usr/lib/python3/dist-packages/BCBio/GFF/GFFParser.py:71:
+ SyntaxWarning: invalid escape sequence '\w'
+ gff3_kw_pat = re.compile("\w+=")
+Author: Étienne Mollier <emollier at debian.org>
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1085892
+Forwarded: https://github.com/chapmanb/bcbb/pull/145
+Last-Update: 2024-11-05
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- python-bcbio-gff.orig/BCBio/GFF/GFFParser.py
++++ python-bcbio-gff/BCBio/GFF/GFFParser.py
+@@ -68,7 +68,7 @@
+ out.append(p)
+ return out
+
+- gff3_kw_pat = re.compile("\w+=")
++ gff3_kw_pat = re.compile(r"\w+=")
+ def _split_keyvals(keyval_str):
+ """Split key-value pairs in a GFF2, GTF and GFF3 compatible way.
+
=====================================
debian/patches/series
=====================================
@@ -0,0 +1,2 @@
+python-syntax-warning.patch
+distutils-deprecation.patch
View it on GitLab: https://salsa.debian.org/med-team/python-bcbio-gff/-/compare/732c730d1f859c2b7ad2453d79c8cd4f14aa4b3d...e3de0f7f2f70974462cbadf48d17dd9cce8d2a4e
--
View it on GitLab: https://salsa.debian.org/med-team/python-bcbio-gff/-/compare/732c730d1f859c2b7ad2453d79c8cd4f14aa4b3d...e3de0f7f2f70974462cbadf48d17dd9cce8d2a4e
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