[med-svn] [Git][med-team/python-pyfaidx][master] 6 commits: biopython-1.80.patch: add; fix test failure with biopython 1.80.

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch master at Debian Med / python-pyfaidx


Commits:
f73bb6b1 by Étienne Mollier at 2022-11-25T22:29:51+01:00
biopython-1.80.patch: add; fix test failure with biopython 1.80.

- - - - -
fbe16070 by Étienne Mollier at 2022-11-25T22:31:51+01:00
d/control: add myself to uploaders.

- - - - -
25f778d4 by Étienne Mollier at 2022-11-25T22:46:36+01:00
d/t/run-unit-test: run on supported python3 versions.

- - - - -
ddc5720e by Étienne Mollier at 2022-11-25T22:46:53+01:00
d/python-pyfaidx-examples.lintian-overrides: silence warning.

The warning in question was about mixing python and python3 version in
the dependencies, but the involved python(2) file was actually
containing sample data, no scripting.

- - - - -
8377b958 by Étienne Mollier at 2022-11-25T22:50:56+01:00
d/t/control: test depends on python3-all.

- - - - -
adac4aa1 by Étienne Mollier at 2022-11-25T22:55:43+01:00
ready to upload to unstable.

- - - - -


7 changed files:

- debian/changelog
- debian/control
- + debian/patches/biopython-1.80.patch
- debian/patches/series
- + debian/python-pyfaidx-examples.lintian-overrides
- debian/tests/control
- debian/tests/run-unit-test


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+python-pyfaidx (0.7.1-2) unstable; urgency=medium
+
+  * biopython-1.80.patch: add; fix test failure with biopython 1.80.
+  * d/control: add myself to uploaders.
+  * d/t/run-unit-test: run on supported python3 versions.
+  * d/python-pyfaidx-examples.lintian-overrides: silence warning.
+  * d/t/control: test depends on python3-all.
+
+ -- Étienne Mollier <emollier at debian.org>  Fri, 25 Nov 2022 22:51:46 +0100
+
 python-pyfaidx (0.7.1-1) unstable; urgency=medium
 
   * New upstream version


=====================================
debian/control
=====================================
@@ -1,6 +1,7 @@
 Source: python-pyfaidx
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille at debian.org>
+Uploaders: Andreas Tille <tille at debian.org>,
+           Étienne Mollier <emollier at debian.org>
 Section: python
 Testsuite: autopkgtest-pkg-python
 Priority: optional


=====================================
debian/patches/biopython-1.80.patch
=====================================
@@ -0,0 +1,17 @@
+Description: fix bgzf test failure with biopython 1.80
+Author: Étienne Mollier <emollier at debian.org>
+Forwarded: https://github.com/mdshw5/pyfaidx/pull/199
+Last-Update: 2022-11-25
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- python-pyfaidx.orig/pyfaidx/__init__.py
++++ python-pyfaidx/pyfaidx/__init__.py
+@@ -409,7 +409,7 @@
+                 self._bgzf = True
+                 try:
+                     # mutable mode is not supported for bzgf anyways
+-                    self.file = bgzf.BgzfReader(fileobj=self.file, mode="b")
++                    self.file = bgzf.BgzfReader(fileobj=self.file, mode="rb")
+                 except (ValueError, IOError):
+                     raise UnsupportedCompressionFormat(
+                         "Compressed FASTA is only supported in BGZF format. Use "


=====================================
debian/patches/series
=====================================
@@ -2,3 +2,4 @@ test-locale-to-c.patch
 remove-ignore-docstring.patch
 no_setuptools-scm.patch
 fix-pkg-resources.patch
+biopython-1.80.patch


=====================================
debian/python-pyfaidx-examples.lintian-overrides
=====================================
@@ -0,0 +1,3 @@
+# Package name is inherited from cohabitation between python 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/tests/control
=====================================
@@ -1,3 +1,3 @@
 Tests: run-unit-test
-Depends: @, python3-pytest, python3-numpy, python3-biopython, tabix
+Depends: @, python3-all, python3-pytest, python3-numpy, python3-biopython, tabix
 Restrictions: allow-stderr


=====================================
debian/tests/run-unit-test
=====================================
@@ -2,7 +2,7 @@
 set -e
 
 bgzip -c tests/data/genes.fasta > tests/data/genes.fasta.gz
-for py in $(py3versions -r 2> /dev/null)
+for py in $(py3versions --supported)
 do echo "Testing with $py in $(pwd):"
     $py -m pytest -v
 done



View it on GitLab: https://salsa.debian.org/med-team/python-pyfaidx/-/compare/8e1a3a40121e5baa150e0ba5a88d476f85bd842a...adac4aa192e2f3356a73ba01c981b1ea98931ece

-- 
View it on GitLab: https://salsa.debian.org/med-team/python-pyfaidx/-/compare/8e1a3a40121e5baa150e0ba5a88d476f85bd842a...adac4aa192e2f3356a73ba01c981b1ea98931ece
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