[med-svn] [Git][med-team/python-biom-format][master] 4 commits: cme fix dpkg-control
Andreas Tille (@tille)
gitlab at salsa.debian.org
Mon May 18 18:09:02 BST 2026
Andreas Tille pushed to branch master at Debian Med / python-biom-format
Commits:
e369b9cd by Andreas Tille at 2026-05-18T18:14:59+02:00
cme fix dpkg-control
- - - - -
b29ae916 by Andreas Tille at 2026-05-18T18:54:19+02:00
in1d was replaced by isin in numpy 2.4 Closes: #1131071
- - - - -
b9bcda8e by Andreas Tille at 2026-05-18T19:04:06+02:00
Remove useless dist-info dir from python3.14 space
- - - - -
b9d91225 by Andreas Tille at 2026-05-18T19:07:52+02:00
Upload to unstable
- - - - -
11 changed files:
- biom/assets/exercise_cli.sh
- biom/table.py
- debian/changelog
- debian/control
- + debian/patches/numpy-2.4.patch
- debian/patches/series
- debian/rules
- − doc/_templates/layout.html
- doc/sphinxext/numpydoc/numpydoc/__init__.py
- doc/sphinxext/numpydoc/numpydoc/linkcode.py
- doc/sphinxext/numpydoc/numpydoc/numpydoc.py
Changes:
=====================================
biom/assets/exercise_cli.sh
=====================================
@@ -3,7 +3,7 @@ set -xe
table=examples/min_sparse_otu_table_hdf5.biom
obsmd=examples/obs_md.txt
-if [[ ! -f ${table} ]];
+if [ ! -f ${table} ] ;
then
echo "This script expects to operate in the base repository directory"
exit 1
=====================================
biom/table.py
=====================================
@@ -4234,7 +4234,7 @@ html
else:
desired_ids = np.asarray(desired_ids)
# Get the index of the source ids to include
- idx = np.in1d(source_ids, desired_ids)
+ idx = np.isin(source_ids, desired_ids)
# Retrieve only the ids that we are interested on
ids = source_ids[idx]
# Check that all desired ids have been found on source ids
=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+python-biom-format (2.1.17-2) unstable; urgency=medium
+
+ * cme fix dpkg-control
+ * in1d was replaced by isin in numpy 2.4
+ Closes: #1131071
+ * Remove useless dist-info dir from python3.14 space
+
+ -- Andreas Tille <tille at debian.org> Mon, 18 May 2026 19:04:28 +0200
+
python-biom-format (2.1.17-1) unstable; urgency=medium
[ Étienne Mollier ]
=====================================
debian/control
=====================================
@@ -1,42 +1,46 @@
Source: python-biom-format
+Standards-Version: 4.7.4
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille at debian.org>,
- Étienne Mollier <emollier at debian.org>
+Uploaders:
+ Andreas Tille <tille at debian.org>,
+ Étienne Mollier <emollier at debian.org>,
Section: python
Testsuite: autopkgtest-pkg-python
-Priority: optional
-Build-Depends: debhelper-compat (= 13),
- dh-sequence-python3,
- pybuild-plugin-pyproject,
- help2man,
- bash-completion,
- cython3,
- python3-all-dev,
- python3-click,
- python3-h5py,
- python3-numpy,
- python3-numpy-dev,
- python3-numpydoc,
- python3-pandas,
- python3-setuptools,
- python3-scipy,
- python3-sphinx,
- python3-matplotlib,
- python3-pytest <!nocheck>,
- python3-pytest-cov <!nocheck>
-Standards-Version: 4.7.2
+Build-Depends:
+ debhelper-compat (= 13),
+ dh-sequence-python3,
+ pybuild-plugin-pyproject,
+ help2man,
+ bash-completion,
+ cython3,
+ python3-all-dev,
+ python3-click,
+ python3-h5py,
+ python3-numpy,
+ python3-numpy-dev,
+ python3-numpydoc,
+ python3-pandas,
+ python3-setuptools,
+ python3-scipy,
+ python3-sphinx,
+ python3-matplotlib,
+ python3-pytest <!nocheck>,
+ python3-pytest-cov <!nocheck>,
Vcs-Browser: https://salsa.debian.org/med-team/python-biom-format
Vcs-Git: https://salsa.debian.org/med-team/python-biom-format.git
Homepage: https://biom-format.org/
Package: python3-biom-format
Architecture: any
-Depends: python3-h5py,
- ${misc:Depends},
- ${python3:Depends},
- ${shlibs:Depends}
-Suggests: python-biom-format-doc
-Provides: biom-format-tools
+Depends:
+ python3-h5py,
+ ${misc:Depends},
+ ${python3:Depends},
+ ${shlibs:Depends},
+Suggests:
+ python-biom-format-doc,
+Provides:
+ biom-format-tools,
Description: Biological Observation Matrix (BIOM) format (Python 3)
The BIOM file format (canonically pronounced biome) is designed to be a
general-use format for representing biological sample by observation
@@ -64,8 +68,9 @@ Package: python-biom-format-doc
Architecture: all
Multi-Arch: foreign
Section: doc
-Depends: ${misc:Depends},
- ${sphinxdoc:Depends}
+Depends:
+ ${misc:Depends},
+ ${sphinxdoc:Depends},
Description: documentation for BIOM format
The BIOM file format (canonically pronounced biome) is designed to be a
general-use format for representing biological sample by observation
=====================================
debian/patches/numpy-2.4.patch
=====================================
@@ -0,0 +1,16 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: 2018-05-18
+Bug-Debian: https://bugs.debian.org/1131071
+Description: in1d was replaced by isin in numpy 2.4
+
+--- a/biom/table.py
++++ b/biom/table.py
+@@ -4234,7 +4234,7 @@ html
+ else:
+ desired_ids = np.asarray(desired_ids)
+ # Get the index of the source ids to include
+- idx = np.in1d(source_ids, desired_ids)
++ idx = np.isin(source_ids, desired_ids)
+ # Retrieve only the ids that we are interested on
+ ids = source_ids[idx]
+ # Check that all desired ids have been found on source ids
=====================================
debian/patches/series
=====================================
@@ -3,3 +3,4 @@ no-web-adds.patch
fix_future_import.patch
sphinx_1.6.patch
posix_shell.patch
+numpy-2.4.patch
=====================================
debian/rules
=====================================
@@ -42,3 +42,8 @@ execute_after_dh_installexamples:
execute_after_dh_auto_install:
find $(PYBUILD_DESTDIR) -name .coverage -delete
+
+execute_after_dh_python3:
+ rm -rf debian/*/usr/lib/python3.14/dist-packages/biom_format-2.1.17.dist-info
+ rmdir debian/*/usr/lib/python3.14/dist-packages
+ rmdir debian/*/usr/lib/python3.14
=====================================
doc/_templates/layout.html deleted
=====================================
@@ -1,28 +0,0 @@
-{% extends "!layout.html" %}
-
-{# Add github banner (from: https://github.com/blog/273-github-ribbons). #}
-{% block header %}
- {{ super() }}
- <a href="https://github.com/biocore/biom-format"><img
- style="position: absolute; top: 0; right: 0; border: 0;"
- src="https://s3.amazonaws.com/github/ribbons/forkme_right_red_aa0000.png"
- alt="Fork me on GitHub"></a>
-{% endblock %}
-
-{# include the Google Analytics Tracker #}
-{% block footer %}
-{{ super() }}
-<script type="text/javascript">
-
- var _gaq = _gaq || [];
- _gaq.push(['_setAccount', 'UA-6636235-6']);
- _gaq.push(['_trackPageview']);
-
- (function() {
- var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
- ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
- var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
- })();
-
-</script>
-{% endblock %}
=====================================
doc/sphinxext/numpydoc/numpydoc/__init__.py
=====================================
@@ -1,3 +1 @@
-from __future__ import division, absolute_import, print_function
-
from .numpydoc import setup
=====================================
doc/sphinxext/numpydoc/numpydoc/linkcode.py
=====================================
@@ -9,7 +9,6 @@
:license: BSD, see LICENSE for details.
"""
-from __future__ import division, absolute_import, print_function
import warnings
import collections
=====================================
doc/sphinxext/numpydoc/numpydoc/numpydoc.py
=====================================
@@ -26,7 +26,7 @@ if sphinx.__version__ < '1.0.1':
raise RuntimeError("Sphinx 1.0.1 or newer is required")
from .docscrape_sphinx import get_doc_object, SphinxDocString
-from sphinx.util.compat import Directive
+from docutils.parsers.rst import Directive
if sys.version_info[0] >= 3:
sixu = lambda s: s
View it on GitLab: https://salsa.debian.org/med-team/python-biom-format/-/compare/6e686b62f0c764ff66ef5d2e9a905bf4fabe0688...b9d91225d437f638b359ae0c6043edb70eb8bda3
--
View it on GitLab: https://salsa.debian.org/med-team/python-biom-format/-/compare/6e686b62f0c764ff66ef5d2e9a905bf4fabe0688...b9d91225d437f638b359ae0c6043edb70eb8bda3
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