[med-svn] [Git][med-team/obitools][master] 9 commits: cython3.patch: fix build failure with cython3.
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Tue Nov 4 22:21:54 GMT 2025
Étienne Mollier pushed to branch master at Debian Med / obitools
Commits:
2f9c4e79 by Étienne Mollier at 2025-11-04T22:33:00+01:00
cython3.patch: fix build failure with cython3.
Closes: #1119752
- - - - -
f05b1b4f by Étienne Mollier at 2025-11-04T22:40:44+01:00
no_cython_in_binary_package.patch: dep3 header.
- - - - -
85021ed5 by Étienne Mollier at 2025-11-04T22:44:35+01:00
d/watch: convert to v5 PyPI project scanner.
- - - - -
65899a37 by Étienne Mollier at 2025-11-04T22:54:38+01:00
cflags.patch: new: propagate missing CFLAGS.
Closes: #1119509
- - - - -
de9cc70d by Étienne Mollier at 2025-11-04T23:07:51+01:00
d/{clean,rules}: repair the "clean" target.
Closes: #1047870
- - - - -
df56f323 by Étienne Mollier at 2025-11-04T23:08:26+01:00
d/control: drop redundant Rules-Requires-Root: no.
- - - - -
5e9b7cb8 by Étienne Mollier at 2025-11-04T23:08:43+01:00
d/control: declare compliance to standards version 4.7.2.
- - - - -
eae9ab29 by Étienne Mollier at 2025-11-04T23:19:51+01:00
d/triggers: new: ensure ldconfig execution after install.
- - - - -
d547a30b by Étienne Mollier at 2025-11-04T23:21:13+01:00
d/changelog: ready for upload to unstable.
- - - - -
10 changed files:
- debian/changelog
- + debian/clean
- debian/control
- + debian/patches/cflags.patch
- + debian/patches/cython3.patch
- debian/patches/no_cython_in_binary_package.patch
- debian/patches/series
- debian/rules
- + debian/triggers
- debian/watch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,17 @@
+obitools (3.0.1~b26+dfsg-5) unstable; urgency=medium
+
+ * Team upload.
+ * cython3.patch: fix build failure with cython3. (Closes: #1119752)
+ * cflags.patch: new: propagate missing CFLAGS. (Closes: #1119509)
+ * d/{clean,rules}: repair the "clean" target. (Closes: #1047870)
+ * d/triggers: new: ensure ldconfig execution after install.
+ * no_cython_in_binary_package.patch: dep3 header.
+ * d/watch: convert to v5 PyPI project scanner.
+ * d/control: drop redundant Rules-Requires-Root: no.
+ * d/control: declare compliance to standards version 4.7.2.
+
+ -- Étienne Mollier <emollier at debian.org> Tue, 04 Nov 2025 23:20:25 +0100
+
obitools (3.0.1~b26+dfsg-4) unstable; urgency=medium
* Team upload.
=====================================
debian/clean
=====================================
@@ -0,0 +1 @@
+libcobitools3.so
=====================================
debian/control
=====================================
@@ -11,11 +11,10 @@ Build-Depends: debhelper-compat (= 13),
python3-setuptools,
cython3,
cmake
-Standards-Version: 4.7.0
+Standards-Version: 4.7.2
Vcs-Browser: https://salsa.debian.org/med-team/obitools
Vcs-Git: https://salsa.debian.org/med-team/obitools.git
Homepage: https://metabarcoding.org/obitools3
-Rules-Requires-Root: no
Testsuite: autopkgtest-pkg-python
Package: obitools
=====================================
debian/patches/cflags.patch
=====================================
@@ -0,0 +1,19 @@
+Description: complement CFLAGS instead of erasing them.
+ This change allows forwarding Debian's build flags for hardening.
+Author: Étienne Mollier <emollier at debian.org>
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1119509
+Forwarded: no
+Last-Update: 2025-11-04
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- obitools.orig/setup.py
++++ obitools/setup.py
+@@ -111,7 +111,7 @@
+ 'breathe>=4.0.0'
+ ]
+
+-os.environ['CFLAGS'] = '-O3 -w -I "src" -I "src/libecoPCR" -I "src/libjson"'
++os.environ['CFLAGS'] += ' -O3 -w -I "src" -I "src/libecoPCR" -I "src/libjson"'
+
+
+ from Cython.Build import cythonize
=====================================
debian/patches/cython3.patch
=====================================
@@ -0,0 +1,57 @@
+Description: fix build failure with cython3.
+ This patch fixes failures to make use of the python2 specific type
+ converter PyInt_FromLong by replacing it by PyLong_FromLong, from a
+ file shipped by the final versions of cython3.
+Author: Étienne Mollier <emollier at debian.org>
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1119752
+Forwarded: no
+Last-Update: 2025-11-04
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- obitools.orig/python/obitools3/dms/column/typed_column/int.pyx
++++ obitools/python/obitools3/dms/column/typed_column/int.pyx
+@@ -24,7 +24,7 @@
+ OBITuple_NA, \
+ obiint_t
+
+-from cpython.int cimport PyInt_FromLong
++from cpython.long cimport PyLong_FromLong
+
+ from libc.stdint cimport int32_t
+
+@@ -59,7 +59,7 @@
+ if value == OBIInt_NA :
+ result = None
+ else :
+- result = PyInt_FromLong(value)
++ result = PyLong_FromLong(value)
+ return result
+
+
+@@ -87,7 +87,7 @@
+ if value == OBIInt_NA :
+ result = None
+ else :
+- result = PyInt_FromLong(value)
++ result = PyLong_FromLong(value)
+ return result
+
+ cpdef object get_line(self, index_t line_nb) :
+@@ -109,7 +109,7 @@
+ value = obi_get_int_with_elt_idx_and_col_p_in_view(view_p, column_p, line_nb, i)
+ obi_errno_to_exception(line_nb=line_nb, elt_id=i, error_message="Problem getting a value from a column")
+ if value != OBIInt_NA :
+- value_in_result = PyInt_FromLong(value)
++ value_in_result = PyLong_FromLong(value)
+ result[elements_names[i]] = value_in_result
+ if all_NA :
+ all_NA = False
+@@ -152,7 +152,7 @@
+
+ for i in range(value_length) :
+ value = array[i]
+- value_in_result = PyInt_FromLong(value)
++ value_in_result = PyLong_FromLong(value)
+ result.append(value_in_result)
+
+ return tuple(result)
=====================================
debian/patches/no_cython_in_binary_package.patch
=====================================
@@ -1,7 +1,7 @@
Description: Drop cython3 dependency from binary package
Bug-Debian: https://bugs.debian.org/1057995
Author: Andreas Tille <tille at debian.org>
-Last-Update: Sun, 17 Dec 2023 20:49:16 +0100
+Last-Update: 2023-12-17
--- obitools.orig/requirements.txt
+++ obitools/requirements.txt
=====================================
debian/patches/series
=====================================
@@ -4,3 +4,5 @@ any_arch
no-rpath
python3.12
python3.13
+cython3.patch
+cflags.patch
=====================================
debian/rules
=====================================
@@ -14,9 +14,6 @@ export PYBUILD_DISABLE=test
%:
dh $@ --buildsystem=pybuild
-override_dh_auto_clean:
- # skip it
-
override_dh_clean:
dh_clean
rm -rf build
=====================================
debian/triggers
=====================================
@@ -0,0 +1 @@
+activate-noawait ldconfig
=====================================
debian/watch
=====================================
@@ -1,3 +1,7 @@
-version=4
-opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//,uversionmangle=s/(rc|a|b|c)/~$1/,repack,compression=xz" \
-https://pypi.debian.net/OBITools3/OBITools3-(.+)\.(?:zip|tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz)))
+Version: 5
+
+Source: https://pypi.python.org/packages/source/O/OBITools3/
+Matching-Pattern: OBITools3- at ANY_VERSION@@ARCHIVE_EXT@
+UVersion-Mangle: s/(rc|a|b|c)/~$1/
+Repack-Suffix: +dfsg
+DVersion-Mangle: auto
View it on GitLab: https://salsa.debian.org/med-team/obitools/-/compare/74c4d1f747a6aee6809b579dd2cdd37d65d9ca38...d547a30b4e57c65bb6c551ecb19e925eba0d8abb
--
View it on GitLab: https://salsa.debian.org/med-team/obitools/-/compare/74c4d1f747a6aee6809b579dd2cdd37d65d9ca38...d547a30b4e57c65bb6c551ecb19e925eba0d8abb
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