diff options
| -rw-r--r-- | debian/changelog | 12 | ||||
| -rw-r--r-- | debian/clean | 4 | ||||
| -rw-r--r-- | debian/control | 3 | ||||
| -rw-r--r-- | debian/patches/healthcheck-all.patch | 27 | ||||
| -rw-r--r-- | debian/patches/series | 1 | ||||
| -rwxr-xr-x | debian/rules | 6 | ||||
| -rw-r--r-- | tests/test_unary.py | 2 |
7 files changed, 49 insertions, 6 deletions
diff --git a/debian/changelog b/debian/changelog index 81007e2..9ba27bb 100644 --- a/debian/changelog +++ b/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@debian.org> Wed, 23 Aug 2023 19:54:31 +0200 + pyranges (0.0.111+ds-4) unstable; urgency=medium * Team upload. diff --git a/debian/clean b/debian/clean new file mode 100644 index 0000000..8efb1c7 --- /dev/null +++ b/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 diff --git a/debian/control b/debian/control index d5b99ea..92193c1 100644 --- a/debian/control +++ b/debian/control @@ -1,6 +1,7 @@ Source: pyranges Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org> -Uploaders: Steffen Moeller <moeller@debian.org> +Uploaders: Steffen Moeller <moeller@debian.org>, + Étienne Mollier <emollier@debian.org> Section: python Testsuite: autopkgtest-pkg-python Priority: optional diff --git a/debian/patches/healthcheck-all.patch b/debian/patches/healthcheck-all.patch new file mode 100644 index 0000000..b49296e --- /dev/null +++ b/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@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): + diff --git a/debian/patches/series b/debian/patches/series index b9467fc..0a042cc 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1,3 +1,4 @@ fix_dtype.patch reorder.patch numpy_1.24.patch +healthcheck-all.patch diff --git a/debian/rules b/debian/rules index 50fbe09..e3b8a81 100755 --- a/debian/rules +++ b/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 diff --git a/tests/test_unary.py b/tests/test_unary.py index 06548c2..8d922cd 100644 --- a/tests/test_unary.py +++ b/tests/test_unary.py @@ -289,7 +289,7 @@ chipseq = pr.data.chipseq() @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): |