Nilesh Patra pushed to branch master at Debian Med / python-deeptoolsintervals
Commits: 7df663a7 by Nilesh Patra at 2020-07-21T18:14:00+05:30 Add a very simple autopkgtest - - - - - 28feb467 by Nilesh Patra at 2020-07-21T18:14:29+05:30 Install relevant test file - - - - - 7c020add by Nilesh Patra at 2020-07-21T18:14:55+05:30 Compat version: 13 - - - - - 3e392ed1 by Nilesh Patra at 2020-07-21T18:15:18+05:30 Add "Rules-Requires-Root:no" - - - - - d76f8699 by Nilesh Patra at 2020-07-21T18:16:17+05:30 Hardening flags - - - - - 6 changed files: - debian/control - + debian/examples - debian/rules - + debian/tests/control - + debian/tests/run-unit-test - + debian/tests/sample_test.py Changes: ===================================== debian/control ===================================== @@ -4,7 +4,7 @@ Uploaders: Steffen Moeller <[email protected]> Section: science Testsuite: autopkgtest-pkg-python Priority: optional -Build-Depends: debhelper-compat (= 12), +Build-Depends: debhelper-compat (= 13), dh-python, python3-all-dev, python3-setuptools, @@ -13,6 +13,7 @@ Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/python-deeptoolsintervals Vcs-Git: https://salsa.debian.org/med-team/python-deeptoolsintervals.git Homepage: https://github.com/deeptools/deeptools_intervals/ +Rules-Requires-Root: no Package: python3-deeptoolsintervals Architecture: any ===================================== debian/examples ===================================== @@ -0,0 +1 @@ +debian/tests/sample_test.py ===================================== debian/rules ===================================== @@ -1,6 +1,7 @@ #!/usr/bin/make -f export DH_VERBOSE = 1 +export DEB_BUILD_MAINT_OPTIONS = hardening=+all export PYBUILD_NAME=deeptoolsintervals %: ===================================== debian/tests/control ===================================== @@ -0,0 +1,4 @@ +Tests: run-unit-test +Depends: @, python3-all, python3-pytest +Restrictions: allow-stderr + ===================================== debian/tests/run-unit-test ===================================== @@ -0,0 +1,19 @@ +#!/bin/bash +set -e + +pkg=deeptoolsintervals + +if [ "${AUTOPKGTEST_TMP}" = "" ] ; then + AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX) + trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM +fi + +cp -a /usr/lib/python3/dist-packages/${pkg}/test/* -a "${AUTOPKGTEST_TMP}" +cp -a /usr/share/doc/python3-${pkg}/examples/* -a "${AUTOPKGTEST_TMP}" + +cd "${AUTOPKGTEST_TMP}" +ls + +echo 'Run sample test ....' +python3 -m pytest -v + ===================================== debian/tests/sample_test.py ===================================== @@ -0,0 +1,18 @@ +from deeptoolsintervals import GTF +from deeptoolsintervals import Enrichment + +# Very basic test to check functionality +def test_functionality(): + gtf = GTF(["GRCh38.84.2.gtf.gz", "GRCh38.84.bed", "GRCh38.84.gtf.gz"], keepExons=True) + list_labels = gtf.labels + list_labels.sort() + assert(list_labels == ['GRCh38.84.2.gtf.gz', 'GRCh38.84.bed', 'GRCh38.84.gtf.gz', 'group 1', 'group 1_r1', 'group 2', 'group 3', 'group2']) + + gtf = GTF("GRCh38.84.gtf.gz", keepExons=True) + assert(gtf.findOverlaps("chr1", 1, 20000)[0][0] >= 11800) + + gtf = Enrichment("GRCh38.84.gtf.gz", keepExons=True, attributeKey="gene_biotype") + overlap_result = list(gtf.findOverlaps("1", [(0, 2000000)])) + overlap_result.sort() + assert(overlap_result == + ['group 1', 'group 2', 'lincRNA', 'miRNA', 'processed_pseudogene', 'protein_coding', 'transcribed_unprocessed_pseudogene', 'unprocessed_pseudogene']) View it on GitLab: https://salsa.debian.org/med-team/python-deeptoolsintervals/-/compare/e36773556abf1dada9be7ff9dba173ed1e00c2cb...d76f8699db2ce639c34827b7d4ba42bf024eef0a -- View it on GitLab: https://salsa.debian.org/med-team/python-deeptoolsintervals/-/compare/e36773556abf1dada9be7ff9dba173ed1e00c2cb...d76f8699db2ce639c34827b7d4ba42bf024eef0a You're receiving this email because of your account on salsa.debian.org.
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