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|
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@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
|
