[med-svn] [Git][med-team/python-pbcore][master] 4 commits: d/control: restrict to 64-bit architectures due numpy changes

[Michael R. Crusoe (@crusoe)]

Michael R. Crusoe pushed to branch master at Debian Med / python-pbcore


Commits:
94d443f3 by Michael R. Crusoe at 2024-03-22T17:39:46+01:00
d/control: restrict to 64-bit architectures due numpy changes

"OverflowError: Python int too large to convert to C long"

- - - - -
8d054d0d by Michael R. Crusoe at 2024-03-22T17:46:57+01:00
d/rules: combine the two dh_auto_clean overrides into one.

- - - - -
f643f889 by Michael R. Crusoe at 2024-03-22T17:50:22+01:00
d/control: add dh-sequence dependencies for the addons.

- - - - -
c5415f13 by Michael R. Crusoe at 2024-03-22T17:59:15+01:00
routine-update: Ready to upload to unstable

- - - - -


4 changed files:

- debian/changelog
- + debian/clean
- debian/control
- debian/rules


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+python-pbcore (2.1.2+dfsg-6) unstable; urgency=medium
+
+  * Team upload.
+  * d/control: restrict to 64-bit architectures due numpy changes:
+     "OverflowError: Python int too large to convert to C long"
+  * d/rules: combine the two dh_auto_clean overrides into one
+             and use d/clean to simplify that.
+  * d/control: add dh-sequence dependencies for the addons.
+
+ -- Michael R. Crusoe <crusoe at debian.org>  Fri, 22 Mar 2024 17:59:15 +0100
+
 python-pbcore (2.1.2+dfsg-5) unstable; urgency=medium
 
   * d/control: bring back support for all python3 versions.


=====================================
debian/clean
=====================================
@@ -0,0 +1,12 @@
+_tmp/
+doc/pbcore.data.datasets.rst
+doc/pbcore.io.align.rst
+doc/pbcore.io.dataset.pyxb.rst
+coverage.xml
+.eggs/README.txt
+.pytest_cache/
+.pybuild/
+doc/_build/
+.coverage
+nosetests.xml
+pbcore.egg-info


=====================================
debian/control
=====================================
@@ -6,6 +6,8 @@ Section: python
 Priority: optional
 Build-Depends: debhelper-compat (= 13),
                dh-python,
+               dh-sequence-python3,
+               dh-sequence-sphinxdoc <!nodoc>,
                python3-sphinx <!nodoc>,
                python3-all,
                python3-setuptools,
@@ -17,7 +19,7 @@ Build-Depends: debhelper-compat (= 13),
                python3-pytest-runner <!nocheck>,
                python3-pytest-xdist <!nocheck>,
                python3-pytest-cov <!nocheck>,
-               python3-biopython (>= 1.74) <!nocheck>,
+               python3-biopython <!nocheck>,
                python3-xmlschema <!nocheck>,
                pylint,
                python3-coverage
@@ -32,12 +34,10 @@ Architecture: all
 Depends: ${misc:Depends},
          ${python3:Depends},
          python3-pkg-resources,
-         python3-biopython (>= 1.74)
+         python3-biopython
 Recommends: python3-h5py
 Suggests: python-pbcore-doc (= ${source:Version})
-Breaks: python-pbcore (<= 1.7)
 Provides: python-pbcore
-Replaces: python-pbcore
 Description: Python 3 library for processing PacBio data files
  The pbcore package provides Python modules for processing Pacific Biosciences
  data files and building PacBio bioinformatics applications. These modules
@@ -51,12 +51,12 @@ Description: Python 3 library for processing PacBio data files
 
 Package: python-pbcore-doc
 Architecture: all
+Multi-Arch: foreign
 Section: doc
 Depends: ${misc:Depends},
          ${sphinxdoc:Depends},
          libjs-jquery,
          libjs-underscore
-Multi-Arch: foreign
 Description: Python library for processing PacBio data files (documentation)
  The pbcore package provides Python modules for processing Pacific Biosciences
  data files and building PacBio bioinformatics applications. These modules


=====================================
debian/rules
=====================================
@@ -10,7 +10,7 @@ DESTDIR = $(CURDIR)/debian/python3-$(PYBUILD_NAME)
 DOCDIR = $(CURDIR)/debian/python-pbcore-doc
 export LC_ALL=C.UTF-8
 %:
-	dh $@ --with python3 --buildsystem=pybuild
+	dh $@ --buildsystem=pybuild
 
 override_dh_auto_build:
 	dh_auto_build
@@ -24,11 +24,6 @@ override_dh_install:
 override_dh_installdocs:
 	dh_installdocs -X _source
 
-override_dh_auto_clean:
-	dh_auto_clean
-	$(MAKE) clean
-	rm -rf _tmp
-
 override_dh_auto_test:
 ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
 	# we need to exclude tests requiring pbtestdata which is not packaged
@@ -51,11 +46,6 @@ endif
 override_dh_installchangelogs:
 	dh_installchangelogs CHANGELOG.org
 
-override_dh_auto_clean:
-	rm -f doc/pbcore.data.datasets.rst doc/pbcore.io.align.rst doc/pbcore.io.dataset.pyxb.rst
-	rm -fr coverage.xml .eggs/README.txt .pytest_cache
-	rm -rf .pybuild
-	rm -rf _tmp doc/_build/
+execute_after_dh_auto_clean:
+	$(MAKE) clean
 	find . -name __pycache__ | xargs -r rm -rf
-	rm -f .coverage nosetests.xml
-	rm -rf pbcore.egg-info



View it on GitLab: https://salsa.debian.org/med-team/python-pbcore/-/compare/24116efc7b98761d9518cc23aa55ea890762cade...c5415f13d79718f3ce121df3e34e2dcdf655cecd

-- 
View it on GitLab: https://salsa.debian.org/med-team/python-pbcore/-/compare/24116efc7b98761d9518cc23aa55ea890762cade...c5415f13d79718f3ce121df3e34e2dcdf655cecd
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