Lance Lin pushed to branch master at Debian Med / pyensembl
Commits: 125f35aa by Lance Lin at 2023-08-17T21:36:25+07:00 Run source unittests during build and autopkgtest - - - - - 5 changed files: - debian/changelog - debian/control - debian/rules - + debian/tests/control - + debian/tests/run-unit-test Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,12 @@ +pyensembl (2.2.8+ds-2) UNRELEASED; urgency=medium + + * d/rules: Run source unittests during build + * d/tests/*: Add autopkgtest for source unittests + * d/control: Add python3-pytest and python3-nose to Build-Depends + Remove Testsuite: autopkgtest-pkg-python + + -- Lance Lin <[email protected]> Wed, 16 Aug 2023 20:37:38 +0700 + pyensembl (2.2.8+ds-1) unstable; urgency=medium * Team upload. ===================================== debian/control ===================================== @@ -13,14 +13,15 @@ Build-Depends: debhelper-compat (= 13), python3-datacache, python3-serializable, python3-memoized-property, - python3-gtfparse + python3-gtfparse, + python3-nose <!nocheck>, + python3-pytest <!nocheck>, # python3-tinytimer # only run during tests that are not run because of # demand for internet access Standards-Version: 4.6.2 Homepage: https://github.com/openvax/pyensembl Vcs-Browser: https://salsa.debian.org/med-team/pyensembl Vcs-Git: https://salsa.debian.org/med-team/pyensembl.git -Testsuite: autopkgtest-pkg-python Rules-Requires-Root: no Package: pyensembl ===================================== debian/rules ===================================== @@ -2,6 +2,19 @@ export DH_VERBOSE = 1 export PYBUILD_NAME=pyensembl +# See d/tests/control for why the following tests are ignored: +export PYBUILD_TEST_ARGS=--ignore=test/test_download_cache.py --ignore=test/test_ensembl_gtf.py \ + --ignore=test/test_gene_ids.py --ignore=test/test_gene_names.py \ + --ignore=test/test_gene_objects.py --ignore=test/test_id_length.py \ + --ignore=test/test_missing_genome_sources.py --ignore=test/test_mouse.py \ + --ignore=test/test_search.py --ignore=test/test_sequence_data.py \ + --ignore=test/test_serialization.py --ignore=test/test_transcript_ids.py \ + --ignore=test/test_transcript_objects.py --ignore=test/test_ucsc_gtf.py \ + --ignore=test/test_contigs.py --ignore=test/test_exon_id.py \ + --ignore=test/test_exon_object.py --ignore=test/test_string_representation.py \ + --ignore=test/test_timings.py --ignore=test/test_transcript_sequences.py \ + --ignore=test/test_transcript_support_level.py + %: dh $@ --with python3 --buildsystem=pybuild ===================================== debian/tests/control ===================================== @@ -0,0 +1,3 @@ +Tests: run-unit-test +Depends: python3-all, python3-nose, python3-pytest, pyensembl +Restrictions: needs-internet ===================================== debian/tests/run-unit-test ===================================== @@ -0,0 +1,46 @@ +#!/bin/bash +set -e + +pkg=pyensembl +if [ "$AUTOPKGTEST_TMP" = "" ] ; then + AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX` + trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM +fi + +cp -a test/ $AUTOPKGTEST_TMP + +cd $AUTOPKGTEST_TMP + +# common.py and data.py are missing from the source tarball in Pypi, but these +# files are present in the Github source code. These files are required to run +# the following tests: +rm test/test_download_cache.py +rm test/test_ensembl_gtf.py +rm test/test_gene_ids.py +rm test/test_gene_names.py +rm test/test_gene_objects.py +rm test/test_id_length.py +rm test/test_missing_genome_sources.py +rm test/test_mouse.py +rm test/test_search.py +rm test/test_sequence_data.py +rm test/test_serialization.py +rm test/test_transcript_ids.py +rm test/test_transcript_objects.py +rm test/test_ucsc_gtf.py + +# pyensembl is missing a dependency needed to import test data. The test data +# could be added to debian/tests/data or in a multi-source tarball depending +# on the size of data being added. The following tests are affected: +rm test/test_contigs.py +rm test/test_exon_id.py +rm test/test_exon_object.py +rm test/test_string_representation.py +rm test/test_timings.py +rm test/test_transcript_sequences.py +rm test/test_transcript_support_level.py + +for py in $(py3versions -s) +do + $py -m pytest test +done View it on GitLab: https://salsa.debian.org/med-team/pyensembl/-/commit/125f35aa707b49e8e73387c960bbefcc0ef624f0 -- View it on GitLab: https://salsa.debian.org/med-team/pyensembl/-/commit/125f35aa707b49e8e73387c960bbefcc0ef624f0 You're receiving this email because of your account on salsa.debian.org.
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