[med-svn] [Git][med-team/python-biopython][master] 4 commits: insert Fix-Endian-issue-with-binary-CIF.patch
Karsten Schöke (@karso)
gitlab at salsa.debian.org
Mon Jun 29 13:07:58 BST 2026
Karsten Schöke pushed to branch master at Debian Med / python-biopython
Commits:
f2fa7ce5 by Karsten Schöke at 2026-06-29T08:21:29+02:00
insert Fix-Endian-issue-with-binary-CIF.patch
- - - - -
c808f9e3 by Karsten Schöke at 2026-06-29T09:59:15+02:00
remove obsolete port_tutorial_to_muscle3.patch
- - - - -
ff75b488 by Karsten Schöke at 2026-06-29T13:09:31+02:00
d/rules: Copy test data only into {build_dir} to fix the FTBR.
- - - - -
586745a4 by Karsten Schöke at 2026-06-29T13:10:20+02:00
Update changelog for 1.87+dfsg-2 release
- - - - -
5 changed files:
- debian/changelog
- + debian/patches/Fix-Endian-issue-with-binary-CIF.patch
- − debian/patches/port_tutorial_to_muscle3.patch
- debian/patches/series
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+python-biopython (1.87+dfsg-2) unstable; urgency=medium
+
+ * Team upload.
+ * insert Fix-Endian-issue-with-binary-CIF.patch
+ * remove obsolete port_tutorial_to_muscle3.patch
+ * d/rules: Copy test data only into {build_dir} to fix the FTBR.
+
+ -- Karsten Schöke <karsten.schoeke at geobasis-bb.de> Mon, 29 Jun 2026 13:10:09 +0200
+
python-biopython (1.87+dfsg-1) unstable; urgency=medium
* Team upload.
=====================================
debian/patches/Fix-Endian-issue-with-binary-CIF.patch
=====================================
@@ -0,0 +1,31 @@
+From: =?utf-8?q?Karsten_Sch=C3=B6ke?= <karsten.schoeke at geobasis-bb.de>
+Date: Mon, 29 Jun 2026 08:14:31 +0200
+Subject: Fix Endian issue with binary CIF
+
+Forwarded: https://github.com/biopython/biopython/pull/5252
+---
+ Bio/PDB/bcifhelpermodule.c | 4 +++-
+ 1 file changed, 3 insertions(+), 1 deletion(-)
+
+diff --git a/Bio/PDB/bcifhelpermodule.c b/Bio/PDB/bcifhelpermodule.c
+index 31aa652..60680cb 100644
+--- a/Bio/PDB/bcifhelpermodule.c
++++ b/Bio/PDB/bcifhelpermodule.c
+@@ -2,6 +2,7 @@
+ #include <Python.h>
+ #include <math.h>
+ #include <stdint.h>
++#include <string.h>
+
+ static void
+ integer_unpack_u8(Py_buffer *in_view, Py_buffer *out_view)
+@@ -153,7 +154,8 @@ integer_unpack(PyObject *self, PyObject *args)
+ goto exit;
+ }
+
+- const char format = in_view.format[0];
++ const size_t l = strlen(in_view.format);
++ const char format = in_view.format[l - 1];
+
+ if (format == 'B') {
+ integer_unpack_u8(&in_view, &out_view);
=====================================
debian/patches/port_tutorial_to_muscle3.patch deleted
=====================================
@@ -1,55 +0,0 @@
-Description: adjust tutorial to document muscle3 usage.
- In addition to being up to date with the way of doing things for the upcoming
- Debian version, this fixes the doctest failures.
-Author: Étienne Mollier <emollier at debian.org>
-Forwarded: no
-Last-Update: 2022-12-04
----
-This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
---- python-biopython.orig/Doc/Tutorial/chapter_align.tex
-+++ python-biopython/Doc/Tutorial/chapter_align.tex
-@@ -1116,7 +1116,7 @@
- >>> from Bio.Align.Applications import MuscleCommandline
- >>> cline = MuscleCommandline(input="opuntia.fasta", out="opuntia.txt")
- >>> print(cline)
--muscle -in opuntia.fasta -out opuntia.txt
-+muscle3 -in opuntia.fasta -out opuntia.txt
- \end{minted}
-
- Note that MUSCLE uses ``-in'' and ``-out'' but in Biopython we have to use
-@@ -1133,7 +1133,7 @@
- >>> from Bio.Align.Applications import MuscleCommandline
- >>> cline = MuscleCommandline(input="opuntia.fasta", out="opuntia.aln", clw=True)
- >>> print(cline)
--muscle -in opuntia.fasta -out opuntia.aln -clw
-+muscle3 -in opuntia.fasta -out opuntia.aln -clw
- \end{minted}
-
- Or, strict ClustalW output where the original ClustalW header line is
-@@ -1144,7 +1144,7 @@
- >>> from Bio.Align.Applications import MuscleCommandline
- >>> cline = MuscleCommandline(input="opuntia.fasta", out="opuntia.aln", clwstrict=True)
- >>> print(cline)
--muscle -in opuntia.fasta -out opuntia.aln -clwstrict
-+muscle3 -in opuntia.fasta -out opuntia.aln -clwstrict
- \end{minted}
-
- \noindent The \verb|Bio.AlignIO| module should be able to read these alignments
-@@ -1174,7 +1174,7 @@
- >>> from Bio.Align.Applications import MuscleCommandline
- >>> muscle_cline = MuscleCommandline(input="opuntia.fasta")
- >>> print(muscle_cline)
--muscle -in opuntia.fasta
-+muscle3 -in opuntia.fasta
- \end{minted}
-
- If we run this via the wrapper, we get back the output as a string. In order
-@@ -1254,7 +1254,7 @@
- >>> from Bio.Align.Applications import MuscleCommandline
- >>> muscle_cline = MuscleCommandline(clwstrict=True)
- >>> print(muscle_cline)
--muscle -clwstrict
-+muscle3 -clwstrict
- \end{minted}
-
- Now for the fiddly bits using the \verb|subprocess| module, stdin and stdout:
=====================================
debian/patches/series
=====================================
@@ -1,5 +1,5 @@
remove_mathml-qname.patch
privacy_breach.patch
privacy_breach_ie9.patch
-#port_tutorial_to_muscle3.patch
fix-type-cast-i386.patch
+Fix-Endian-issue-with-binary-CIF.patch
=====================================
debian/rules
=====================================
@@ -48,6 +48,15 @@ endif
# bloats the build log with irrelevant noise
EXCLUDEDATABASE=BioSQL_MySQLdb BioSQL_psycopg2
+EXCLUDED_TESTS = \
+ $(EXCLUDENONFREE) \
+ $(EXCLUDENOTPACKAGED) \
+ $(EXCLUDEARCH) \
+ $(EXCLUDEDATABASE)
+
+MOVE_EXCLUDED = \
+$(foreach t,$(EXCLUDED_TESTS),mv {build_dir}/Tests/test_$(t).py {build_dir}/Tests_avoid/; )
+
%:
dh $@ --with python3 --buildsystem=pybuild
@@ -83,15 +92,15 @@ override_dh_auto_install:
override_dh_auto_test:
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
- set -e \
- ; for avoid in \
- $(EXCLUDENONFREE) \
- $(EXCLUDENOTPACKAGED) \
- $(EXCLUDEARCH) \
- $(EXCLUDEDATABASE) \
- ; do mkdir -p Tests_avoid \
- ; mv Tests/test_$${avoid}.py Tests_avoid \
- ; done
+ #set -e \
+ #; for avoid in \
+ # $(EXCLUDENONFREE) \
+ # $(EXCLUDENOTPACKAGED) \
+ # $(EXCLUDEARCH) \
+ # $(EXCLUDEDATABASE) \
+ #; do mkdir -p Tests_avoid \
+ #; mv Tests/test_$${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
@@ -120,17 +129,17 @@ ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
cp -a Doc/Tutorial {build_dir}/Doc; \
cp -a Doc/examples {build_dir}/Doc; \
cp -a Tests {build_dir}; \
+ mkdir -p {build_dir}/Tests_avoid; \
+ $(MOVE_EXCLUDED) \
cd {build_dir}/Tests; \
env DIALIGN2_DIR=/usr/share/dialign \
EMBOSS_ROOT=/usr/lib/emboss \
HOME={build_dir}/home \
- {interpreter} run_tests.py --offline'
- # Cleanup steps after tests.
- set -e \
- ; if [ -d Tests_avoid ] \
- ; then mv Tests_avoid/* Tests \
- ; rmdir Tests_avoid \
- ; fi
+ {interpreter} run_tests.py --offline; \
+ if [ -d {build_dir}/Tests_avoid ]; then \
+ mv {build_dir}/Tests_avoid/* {build_dir}/Tests; \
+ rmdir {build_dir}/Tests_avoid; \
+ fi'
rm -r $(LIBCIFPP_DATA_DIR)
endif
View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/compare/1e8d0bad3111059aa584413f70d80a71c69abe85...586745a4b3a7b176b4ce2a3caf4bbbcee9993411
--
View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/compare/1e8d0bad3111059aa584413f70d80a71c69abe85...586745a4b3a7b176b4ce2a3caf4bbbcee9993411
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