[med-svn] [Git][med-team/pyranges][master] 5 commits: healthcheck-all.patch: new: fix test failure.

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch master at Debian Med / pyranges


Commits:
051023b6 by Étienne Mollier at 2023-08-23T19:29:32+02:00
healthcheck-all.patch: new: fix test failure.

The test failure seems to be caused by a call to an obsoleted method
in a decorator describing the properties of the affected test.

Closes: #1042046

- - - - -
eb1ca22f by Étienne Mollier at 2023-08-23T19:47:51+02:00
d/control: add myself to uploaders.

- - - - -
d20e89f3 by Étienne Mollier at 2023-08-23T19:52:33+02:00
d/rules: use execute_after_dh_* targets in place of overrides.

- - - - -
ce89fca3 by Étienne Mollier at 2023-08-23T19:53:03+02:00
d/clean: remove remnants of *.bam* test data.

- - - - -
e47fd1e3 by Étienne Mollier at 2023-08-23T19:55:01+02:00
ready to upload to unstable.

- - - - -


6 changed files:

- debian/changelog
- + debian/clean
- debian/control
- + debian/patches/healthcheck-all.patch
- debian/patches/series
- debian/rules


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,15 @@
+pyranges (0.0.111+ds-5) unstable; urgency=medium
+
+  * healthcheck-all.patch: new: fix test failure.
+    The test failure seems to be caused by a call to an obsoleted method
+    in a decorator describing the properties of the affected test.
+    (Closes: #1042046)
+  * d/control: add myself to uploaders.
+  * d/rules: use execute_after_dh_* targets in place of overrides.
+  * d/clean: remove remnants of *.bam* test data.
+
+ -- Étienne Mollier <emollier at debian.org>  Wed, 23 Aug 2023 19:54:31 +0200
+
 pyranges (0.0.111+ds-4) unstable; urgency=medium
 
   * Team upload.


=====================================
debian/clean
=====================================
@@ -0,0 +1,4 @@
+pyranges/example_data/control.bam
+pyranges/example_data/control.bam.bai
+tests/test_data/test_sorted.bam
+tests/test_data/test_sorted.bam.bai


=====================================
debian/control
=====================================
@@ -1,6 +1,7 @@
 Source: pyranges
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Steffen Moeller <moeller at debian.org>
+Uploaders: Steffen Moeller <moeller at debian.org>,
+           Étienne Mollier <emollier at debian.org>
 Section: python
 Testsuite: autopkgtest-pkg-python
 Priority: optional


=====================================
debian/patches/healthcheck-all.patch
=====================================
@@ -0,0 +1,27 @@
+Description: fix deprecated HealthCheck.all() decorator parameter.
+ The HealthCheck.all() method has been deprecated in favor of specifying in a
+ list which checks to ignore in a subsequent test function.  The error message
+ suggests use of HealthCheck.return_value.  Other options are documented on
+ Python hypothesis module documentation[1].  It is worth noting the attribute
+ return_value itself is marked as deprecated, so we might as well just buy us
+ some time until a possibly more appropriate fix.
+ .
+ [1]: https://hypothesis.readthedocs.io/en/latest/settings.html#health-checks
+
+Author: Étienne Mollier <emollier at debian.org>
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1042046
+Forwarded: no
+Last-Update: 2023-08-23
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- pyranges.orig/tests/test_unary.py
++++ pyranges/tests/test_unary.py
+@@ -289,7 +289,7 @@
+ @settings(
+     max_examples=max_examples,
+     deadline=deadline,
+-    suppress_health_check=HealthCheck.all())
++    suppress_health_check=[HealthCheck.return_value])
+ @given(selector=selector())  # pylint: disable=no-value-for-parameter
+ def test_getitem(selector):
+ 


=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
 fix_dtype.patch
 reorder.patch
 numpy_1.24.patch
+healthcheck-all.patch


=====================================
debian/rules
=====================================
@@ -13,16 +13,14 @@ export PYBUILD_TEST_ARGS=-n $(shell nproc)
 %:
 	dh $@ --with python3 --buildsystem=pybuild
 
-override_dh_auto_build:
-	dh_auto_build
+execute_after_dh_auto_build:
 	echo 'Generating corresponding files ...'
 	cat debian/missing-sources/test_sorted.sam| samtools view -Sb - > tests/test_data/test_sorted.bam
 	cat debian/missing-sources/control.sam| samtools view -Sb - > pyranges/example_data/control.bam
 	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
 
-override_dh_install:
-	dh_install
+execute_after_dh_install:
 	find debian/ -name *.bam* | xargs rm -rf
 	find debian/ -name 'hi' | xargs rm -rf
 	find debian/ -name '.hypothesis' | xargs rm -rf



View it on GitLab: https://salsa.debian.org/med-team/pyranges/-/compare/5f31038b23defd2a58d0901fcab3a29f1e3f5d32...e47fd1e3b19c858115e54a5a56f9e6193cb36bed

-- 
View it on GitLab: https://salsa.debian.org/med-team/pyranges/-/compare/5f31038b23defd2a58d0901fcab3a29f1e3f5d32...e47fd1e3b19c858115e54a5a56f9e6193cb36bed
You're receiving this email because of your account on salsa.debian.org.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20230823/230dc666/attachment-0001.htm>