Michael R. Crusoe pushed to branch master at Debian Med / q2-diversity-lib
Commits:
24c518a2 by Michael R. Crusoe at 2024-06-26T01:10:01+02:00
Only build for Python 3.11 until upstream catches up with Python 3.12.
- - - - -
2639f551 by Michael R. Crusoe at 2024-06-26T11:30:58+02:00
d/control: require newer python3-skbio version
to fix "AttributeError: module 'skbio.diversity.alpha' has no
attribute 'sobs'"
- - - - -
9852ba15 by Michael R. Crusoe at 2024-06-26T11:35:20+02:00
copy fixes to d/control.in
- - - - -
5 changed files:
- debian/changelog
- debian/control
- debian/control.in
- debian/rules
- debian/tests/run-unit-test
Changes:
=====================================
debian/changelog
=====================================
@@ -4,6 +4,10 @@ q2-diversity-lib (2024.5.0-1) UNRELEASED; urgency=medium
* New upstream version
* Regenerate debian/control from debian/control.in (routine-update)
* d/patches/configparser.patch: copy from qiime packaging
+ * Only build for Python 3.11 until upstream catches up with Python
+ 3.12.
+ * d/control: require newer python3-skbio version to fix
+ "AttributeError: module 'skbio.diversity.alpha' has no attribute 'sobs'"
-- Michael R. Crusoe <cru...@debian.org> Tue, 25 Jun 2024 03:35:06 +0200
=====================================
debian/control
=====================================
@@ -6,7 +6,7 @@ Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
dh-sequence-python3,
- python3,
+ python3-all,
python3-setuptools,
python3-pytest <!nocheck>,
python3-statsmodels <!nocheck>,
@@ -32,7 +32,8 @@ Depends: ${shlibs:Depends},
r-cran-vegan,
python3-statsmodels,
python3-unifrac,
- unifrac-tools
+ unifrac-tools,
+ python3-skbio (>= 0.6)
Description: QIIME2 plugin to expose diversity metrics/measures as actions
QIIME 2 is a powerful, extensible, and decentralized microbiome analysis
package with a focus on data and analysis transparency. QIIME 2 enables
=====================================
debian/control.in
=====================================
@@ -5,7 +5,7 @@ Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
dh-sequence-python3,
- python3,
+ python3-all,
python3-setuptools,
python3-pytest <!nocheck>,
python3-statsmodels <!nocheck>,
@@ -31,7 +31,8 @@ Depends: ${shlibs:Depends},
r-cran-vegan,
python3-statsmodels,
python3-unifrac,
- unifrac-tools
+ unifrac-tools,
+ python3-skbio (>= 0.6)
Description: QIIME2 plugin to expose diversity metrics/measures as actions
QIIME 2 is a powerful, extensible, and decentralized microbiome analysis
package with a focus on data and analysis transparency. QIIME 2 enables
=====================================
debian/rules
=====================================
@@ -3,6 +3,8 @@
DH_VERBOSE := 1
export LC_ALL=C.UTF-8
+export PYBUILD_DISABLE=python3.12
+
# For testing, we need .egg-info so the entry points are available.
export PYBUILD_BEFORE_TEST=python{version} setup.py develop --install-dir
{build_dir}
# Delete .egg-info and other files that were generated along with .egg-info
=====================================
debian/tests/run-unit-test
=====================================
@@ -18,7 +18,10 @@ if [ ! -e /usr/bin/py.test-3 ] ; then
fi
# Run build-time tests
-for py in $(py3versions -s 2> /dev/null)
-do
- ${py} -m pytest -v --cov=${pkg}
-done
+#for py in $(py3versions -s 2> /dev/null)
+# do
+# ${py} -m pytest -v --cov=${pkg}
+# done
+#
+
+python3.11 -m pytest -v --cov=${pkg}
View it on GitLab:
https://salsa.debian.org/med-team/q2-diversity-lib/-/compare/168f4089abeb656040e19e85ab771232f03b076d...9852ba15d5d8569e85d2ecc8ba547a02fcef1d0c
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View it on GitLab:
https://salsa.debian.org/med-team/q2-diversity-lib/-/compare/168f4089abeb656040e19e85ab771232f03b076d...9852ba15d5d8569e85d2ecc8ba547a02fcef1d0c
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