[med-svn] [Git][med-team/pyranges][master] 5 commits: d/rules: greatly simplify parallel argument handling.

Fri May 2 22:08:34 BST 2025


Étienne Mollier pushed to branch master at Debian Med / pyranges


Commits:
35fefe45 by Étienne Mollier at 2025-05-02T22:36:47+02:00
d/rules: greatly simplify parallel argument handling.

- - - - -
bdc64988 by Étienne Mollier at 2025-05-02T23:03:07+02:00
reorder.patch: filled dep3 header.

- - - - -
0f769af7 by Étienne Mollier at 2025-05-02T23:03:31+02:00
d/patches/*: normalize Last-Update timestamps.

- - - - -
0a9c4e8a by Étienne Mollier at 2025-05-02T23:06:39+02:00
d/rules: skip tests outside 64-bit platforms.

The test suite is both of heavy weight for 32-bit cpu, and
structurally not written to target anything else than 64-bit cpu.
Since the package is arch-all, removal from specific architectures
also happens to be not feasible.

Closes: #1103074

- - - - -
af83d682 by Étienne Mollier at 2025-05-02T23:08:13+02:00
d/changelog: ready for upload to unstable.

- - - - -


6 changed files:

- debian/changelog
- debian/patches/no_install_depends_cython.patch
- debian/patches/numpy_1.24.patch
- debian/patches/pandas2.0.patch
- debian/patches/reorder.patch
- debian/rules


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,16 @@
+pyranges (0.0.111+ds-9) unstable; urgency=medium
+
+  * d/rules: skip tests outside 64-bit platforms.
+    The test suite is both of heavy weight for 32-bit cpu, and
+    structurally not written to target anything else than 64-bit cpu.
+    Since the package is arch-all, removal from specific architectures
+    also happens to be not feasible. (Closes: #1103074)
+  * d/rules: greatly simplify parallel argument handling.
+  * reorder.patch: filled dep3 header.
+  * d/patches/*: normalize Last-Update timestamps.
+
+ -- Étienne Mollier <emollier at debian.org>  Fri, 02 May 2025 23:07:29 +0200
+
 pyranges (0.0.111+ds-8) unstable; urgency=medium
 
   [ Johannes Schauer Marin Rodrigues ]


=====================================
debian/patches/no_install_depends_cython.patch
=====================================
@@ -1,7 +1,7 @@
 Description: No runtime dependency from cython
 Bug-Debian: https://bugs.debian.org/1058012
 Author: Andreas Tille <tille at debian.org>
-Last-Update: Mon, 11 Dec 2023 10:10:25 +0100
+Last-Update: 2023-12-11
 
 --- a/setup.py
 +++ b/setup.py


=====================================
debian/patches/numpy_1.24.patch
=====================================
@@ -1,7 +1,7 @@
 Description: Adapt to numpy 1.24
 Bug-Debian: https://bugs.debian.org/1028852
 Author: Andreas Tille <tille at debian.org>
-Last-Update: Sat, 14 Jan 2023 16:30:10 +0100
+Last-Update: 2023-01-14
 
 --- a/tests/test_binary.py
 +++ b/tests/test_binary.py


=====================================
debian/patches/pandas2.0.patch
=====================================
@@ -1,7 +1,7 @@
 Description: Fix for Pandas 2.0
 Bug-Debian: https://bugs.debian.org/1044064
 Author: Andreas Tille <tille at debian.org>
-Last-Update: Sun, 18 Feb 2024 07:02:12 +0100
+Last-Update: 2024-02-18
 
 --- a/tests/test_binary.py
 +++ b/tests/test_binary.py


=====================================
debian/patches/reorder.patch
=====================================
@@ -1,3 +1,9 @@
+Description: Add patch to fix FTBFS
+Author: Nilesh Patra <nilesh at debian.org>
+Bug-Debian: https://bugs.debian.org/1022476
+Last-Update: 2022-10-24
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
 --- a/setup.py
 +++ b/setup.py
 @@ -1,6 +1,6 @@


=====================================
debian/rules
=====================================
@@ -2,7 +2,8 @@
 # See debhelper(7) (uncomment to enable)
 # output every command that modifies files on the build system.
 #export DH_VERBOSE = 1
-
+include /usr/share/dpkg/buildopts.mk
+include /usr/share/dpkg/architecture.mk
 export PYBUILD_NAME=pyranges
 export PYBUILD_BEFORE_TEST=\
 	mkdir -pv {build_dir}/tests {build_dir}/pyranges \
@@ -10,13 +11,7 @@ export PYBUILD_BEFORE_TEST=\
 	&& cp -av {dir}/tests/test_data {build_dir}/tests \
 	&& cp -av {dir}/tests/data {build_dir}/tests \
 	&& cp -av {dir}/pyranges/example_data {build_dir}/pyranges
-
-ifneq (,$(filter parallel=%,$(DEB_BUILD_OPTIONS)))
-       NUMJOBS = $(patsubst parallel=%,%,$(filter parallel=%,$(DEB_BUILD_OPTIONS)))
-else
-       NUMJOBS = $(shell nproc)
-endif
-export PYBUILD_TEST_ARGS=-v -n $(NUMJOBS)
+export PYBUILD_TEST_ARGS=-v -n $(DEB_BUILD_OPTION_PARALLEL)
 
 %:
 	dh $@ --buildsystem=pybuild
@@ -28,6 +23,13 @@ execute_after_dh_auto_build:
 	samtools index tests/test_data/test_sorted.bam tests/test_data/test_sorted.bam.bai
 	samtools index pyranges/example_data/control.bam pyranges/example_data/control.bam.bai
 
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
+ifneq ($(DEB_BUILD_ARCH_BITS),64)
+override_dh_auto_test:
+	@echo "W: tests skipped on non-64-bit due to #1103074."
+endif
+endif
+
 execute_after_dh_install:
 	find debian/ -name *.bam* | xargs rm -rf
 	find debian/ -name 'hi' | xargs rm -rf



View it on GitLab: https://salsa.debian.org/med-team/pyranges/-/compare/d297b8cfa0eb3a0086500167e8248b4eca3c4399...af83d68248edd326ac6be64af28023414196e49d

-- 
View it on GitLab: https://salsa.debian.org/med-team/pyranges/-/compare/d297b8cfa0eb3a0086500167e8248b4eca3c4399...af83d68248edd326ac6be64af28023414196e49d
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