[med-svn] [Git][med-team/python-biopython][master] 5 commits: Packaging update (routine-update)

[Karsten Schöke (@karso)]

Karsten Schöke pushed to branch master at Debian Med / python-biopython


Commits:
e6d20714 by Karsten Schöke at 2026-08-21T11:39:34+02:00
Packaging update (routine-update)

- - - - -
fafcf933 by Karsten Schöke at 2026-08-21T15:12:24+02:00
fix routine-update issue.

- - - - -
84a20cc2 by Karsten Schöke at 2026-08-21T15:13:16+02:00
lintian-overrides are no longer needed.

- - - - -
cd23df90 by Karsten Schöke at 2026-08-21T15:17:02+02:00
d/rules: Fix FTBR: The second build is invoked with the `nocheck` option again.

- - - - -
5ac6e41b by Karsten Schöke at 2026-08-21T19:17:56+02:00
Update changelog for 1.88+dfsg-2 release

- - - - -


4 changed files:

- debian/changelog
- − debian/python-biopython-doc.lintian-overrides
- debian/rules
- debian/upstream/metadata


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+python-biopython (1.88+dfsg-2) unstable; urgency=medium
+
+  * Team upload.
+  * lintian-overrides are no longer needed.
+  * fix routine-update issue.
+  * d/rules: Fix FTBR: The second build is invoked with 
+    the `nocheck` option again. (Closes: #1144126)
+
+ -- Karsten Schöke <karsten.schoeke at geobasis-bb.de>  Fri, 21 Aug 2026 19:17:36 +0200
+
 python-biopython (1.88+dfsg-1) unstable; urgency=medium
 
   * Team upload.


=====================================
debian/python-biopython-doc.lintian-overrides deleted
=====================================
@@ -1,5 +0,0 @@
-# We really need these zero byte files for running the test suite and
-# there was actually work done to keep it, since dh_installdocs ignores
-# the file
-python-biopython-doc: zero-byte-file-in-doc-directory [usr/share/doc/python-biopython-doc/Tests/Blast/tab_2226_tblastn_002.txt]
-python-biopython-doc: zero-byte-file-in-doc-directory [usr/share/doc/python-biopython-doc/Tests/Blat/psl_34_002.chain]


=====================================
debian/rules
=====================================
@@ -93,18 +93,6 @@ override_dh_auto_install:
 	dh_numpy3 -ppython3-biopython
 
 override_dh_auto_test:
-ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
-	#set -e \
-	#; for avoid in \
-	#	$(EXCLUDENONFREE) \
-	#	$(EXCLUDENOTPACKAGED) \
-	#	$(EXCLUDEARCH) \
-	#	$(EXCLUDEDATABASE) \
-	#; do mkdir -p Tests_avoid \
-	#;    mv Tests/test_$${avoid}.py Tests_avoid \
-	#; done
-	# For the doc package we need a clean testsuite without all the
-	# remaining files.  So keep a clean copy here
 	mkdir -p debian/tmp_tests
 	cp -a Tests debian/tmp_tests
 	# remove duplicated file
@@ -143,7 +131,6 @@ ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
 			    rmdir {build_dir}/Tests_avoid; \
 			fi'
 	rm -r $(LIBCIFPP_DATA_DIR)
-endif
 
 DOCPKG = python-biopython-doc
 DOCDIR = $(CURDIR)/debian/$(DOCPKG)/usr/share/doc/$(DOCPKG)
@@ -154,6 +141,10 @@ ifeq (,$(filter nodoc,$(DEB_BUILD_OPTIONS)))
 	# dh_installdocs seems to refuse copying zero length files (for
 	# instance Tests/Blast/tab_2226_tblastn_002.txt) but these are
 	# needed for the tests as well
+	mkdir -p debian/tmp_tests
+	cp -a Tests debian/tmp_tests
+	# remove duplicated file
+	rm -f debian/tmp_tests/Tests/Quality/example.fastq.gz
 	cp -a debian/tmp_tests/* $(DOCDIR)
 
 	find debian -name __pycache__ -type d | xargs rm -rf


=====================================
debian/upstream/metadata
=====================================
@@ -31,6 +31,3 @@ Registry:
 Repository: https://github.com/biopython/biopython.git
 Repository-Browse: https://github.com/biopython/biopython
 Security-Contact: https://github.com/biopython/biopython/tree/HEAD/.github/SECURITY.md
-Repository: https://github.com/biopython/biopython.git
-Repository-Browse: https://github.com/biopython/biopython/
-Security-Contact: https://github.com/biopython/biopython//tree/HEAD/.github/SECURITY.md



View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/compare/e358b5dc59b531d993cfef868e4617233456a4e5...5ac6e41bbc90814802a908a5d17aaf0526f87c91

-- 
View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/compare/e358b5dc59b531d993cfef868e4617233456a4e5...5ac6e41bbc90814802a908a5d17aaf0526f87c91
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