[med-svn] [Git][med-team/python-pyfaidx][master] 10 commits: New upstream version 0.7.2.2
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Tue Nov 28 21:19:05 GMT 2023
Étienne Mollier pushed to branch master at Debian Med / python-pyfaidx
Commits:
6b70bd6f by Étienne Mollier at 2023-09-25T20:38:16+02:00
New upstream version 0.7.2.2
- - - - -
8934ec6e by Étienne Mollier at 2023-09-25T20:38:16+02:00
routine-update: New upstream version
- - - - -
882d3642 by Étienne Mollier at 2023-09-25T20:38:17+02:00
Update upstream source from tag 'upstream/0.7.2.2'
Update to upstream version '0.7.2.2'
with Debian dir 63ee0e2763831f734f6c2dfb9da888083bfaad17
- - - - -
5f03d68a by Étienne Mollier at 2023-09-25T20:40:43+02:00
fix-pkg-resources.patch: refresh.
- - - - -
a4766340 by Étienne Mollier at 2023-09-25T20:40:56+02:00
manual-layout.patch: refresh.
- - - - -
786c5022 by Étienne Mollier at 2023-11-28T22:05:14+01:00
d/control: new test dependency.
Upstream replace pkg_resource usage by python3-import-metadata.
- - - - -
37935e54 by Étienne Mollier at 2023-11-28T22:08:16+01:00
fix-pkg-resources.patch: remove.
With upstream moving to importlib_metadata, this patch is now just
interferring with the test suite, so removed.
- - - - -
c423b4e8 by Étienne Mollier at 2023-11-28T22:10:23+01:00
d/*lintian-overrides: refer to python as python2.
This fixes a lintian pedantic notice about Python capitalization.
- - - - -
eb7ee68c by Étienne Mollier at 2023-11-28T22:13:00+01:00
d/python3-pyfaidx.lintian-overrides: new.
Fix false positive lintian information about top_level.txt dist-info
file being documentation outside /usr/share/doc.
- - - - -
6568bf61 by Étienne Mollier at 2023-11-28T22:17:54+01:00
ready to upload to unstable.
- - - - -
11 changed files:
- README.rst
- .codecov.yml → codecov.yml
- debian/changelog
- debian/control
- − debian/patches/fix-pkg-resources.patch
- debian/patches/manual-layout.patch
- debian/patches/series
- debian/python-pyfaidx-examples.lintian-overrides
- + debian/python3-pyfaidx.lintian-overrides
- pyfaidx/__init__.py
- pyproject.toml
Changes:
=====================================
README.rst
=====================================
@@ -1,4 +1,4 @@
-|CI| |Package| |PyPI| |Coverage| |Depsy|
+|CI| |Package| |PyPI| |Coverage| |Depsy| |Downloads|
Description
-----------
@@ -646,3 +646,6 @@ Comprehensive Cancer Center in the Department of Oncology.
.. |Package| image:: https://github.com/mdshw5/pyfaidx/actions/workflows/pypi.yml/badge.svg
:target: https://github.com/mdshw5/pyfaidx/actions/workflows/pypi.yml
+
+.. |Downloads| image:: https://img.shields.io/pypi/dm/pyfaidx.svg
+ :target: https://pypi.python.org/pypi/pyfaidx/
=====================================
.codecov.yml → codecov.yml
=====================================
=====================================
debian/changelog
=====================================
@@ -1,3 +1,20 @@
+python-pyfaidx (0.7.2.2-1) unstable; urgency=medium
+
+ * New upstream version 0.7.2.2
+ * manual-layout.patch: refresh.
+ * d/control: new test dependency.
+ Upstream replace pkg_resource usage by python3-import-metadata.
+ * fix-pkg-resources.patch: remove.
+ With upstream moving to importlib_metadata, this patch is now just
+ interfering with the test suite, so removed.
+ * d/*lintian-overrides: refer to python as python2.
+ This fixes a lintian pedantic notice about Python capitalization.
+ * d/python3-pyfaidx.lintian-overrides: new.
+ Fix false positive lintian information about top_level.txt dist-info
+ file being documentation outside /usr/share/doc.
+
+ -- Étienne Mollier <emollier at debian.org> Tue, 28 Nov 2023 22:14:27 +0100
+
python-pyfaidx (0.7.2.1-1) unstable; urgency=medium
* New upstream version
=====================================
debian/control
=====================================
@@ -11,6 +11,7 @@ Build-Depends: debhelper-compat (= 13),
python3-coverage,
python3-setuptools,
python3-biopython,
+ python3-importlib-metadata <!nocheck>,
python3-numpy <!nocheck>,
python3-pkg-resources <!nocheck>,
pybuild-plugin-pyproject,
=====================================
debian/patches/fix-pkg-resources.patch deleted
=====================================
@@ -1,27 +0,0 @@
-Description: pkg-resources only works once the package has been installed and breaks
- in-place testing. Workaround it by making it n/a if not found
-Author: Nilesh Patra <nilesh at debian.org>
-Forwarded: not-needed
-Last-Update: 2022-02-17
---- a/pyfaidx/__init__.py
-+++ b/pyfaidx/__init__.py
-@@ -7,6 +7,7 @@ from __future__ import division
-
- import datetime
- import os
-+import pkg_resources
- import re
- import string
- import sys
-@@ -33,7 +34,10 @@ try:
- except ImportError:
- fsspec = None
-
--__version__ = get_distribution("pyfaidx").version
-+try:
-+ __version__ = get_distribution("pyfaidx").version
-+except (ImportError, pkg_resources.DistributionNotFound):
-+ __version__ = 'n/a'
-
- if sys.version_info > (3, ):
- buffer = memoryview
=====================================
debian/patches/manual-layout.patch
=====================================
@@ -11,7 +11,7 @@ Last-Update: 2023-07-18
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
--- python-pyfaidx.orig/pyproject.toml
+++ python-pyfaidx/pyproject.toml
-@@ -41,3 +41,6 @@
+@@ -42,3 +42,6 @@
[tool.setuptools_scm]
local_scheme = "no-local-version"
=====================================
debian/patches/series
=====================================
@@ -1,4 +1,3 @@
test-locale-to-c.patch
remove-ignore-docstring.patch
-fix-pkg-resources.patch
manual-layout.patch
=====================================
debian/python-pyfaidx-examples.lintian-overrides
=====================================
@@ -1,3 +1,3 @@
-# Package name is inherited from cohabitation between python and python3, but
+# Package name is inherited from cohabitation between python2 and python3, but
# is unrelated to any interpreted files, that's just example data.
python-pyfaidx-examples: python-package-depends-on-package-from-other-python-variant Suggests: python3-pyfaidx
=====================================
debian/python3-pyfaidx.lintian-overrides
=====================================
@@ -0,0 +1,2 @@
+# top_level.txt is not particularly documentation and looks needed there.
+python3-pyfaidx: package-contains-documentation-outside-usr-share-doc [usr/lib/python3/dist-packages/pyfaidx-0.0.0.dist-info/top_level.txt]
=====================================
pyfaidx/__init__.py
=====================================
@@ -18,7 +18,11 @@ from math import ceil
from os.path import getmtime
from tempfile import TemporaryFile
from threading import Lock
-from pkg_resources import get_distribution
+
+try:
+ from importlib.metadata import version
+except ImportError: #python < 3.8
+ from importlib_metadata import version
from six import PY2, PY3, integer_types, string_types
from six.moves import zip_longest
@@ -33,7 +37,7 @@ try:
except ImportError:
fsspec = None
-__version__ = get_distribution("pyfaidx").version
+__version__ = version("pyfaidx")
if sys.version_info > (3, ):
buffer = memoryview
=====================================
pyproject.toml
=====================================
@@ -28,7 +28,8 @@ classifiers = [
]
dependencies = [
"six",
- "setuptools"
+ "setuptools",
+ "importlib_metadata"
]
dynamic = ["version"]
View it on GitLab: https://salsa.debian.org/med-team/python-pyfaidx/-/compare/8b4fee7c8564cec69df9662e6ac3a45786212181...6568bf610e9c133d7ab102caffd6508b8aed0fac
--
View it on GitLab: https://salsa.debian.org/med-team/python-pyfaidx/-/compare/8b4fee7c8564cec69df9662e6ac3a45786212181...6568bf610e9c133d7ab102caffd6508b8aed0fac
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