Andreas Tille pushed to branch master at Debian Med / cnvkit
Commits: 4f2ab0d2 by Andreas Tille at 2023-07-05T17:08:11+02:00 Do not rename cnvkit.py to cnvkit any more - - - - - 94962fde by Andreas Tille at 2023-07-05T17:39:55+02:00 Fix installation of *.py scripts; TODO: manpages - - - - - 8 changed files: - + debian/NEWS - debian/changelog - debian/cnvkit.links - + debian/install - + debian/lintian-overrides - debian/manpages - debian/rules - debian/tests/run-unit-test Changes: ===================================== debian/NEWS ===================================== @@ -0,0 +1,10 @@ +cnvkit (0.9.10-1) unstable; urgency=medium + + As per the discussion in + https://lists.debian.org/debian-med/2018/06/msg00043.html + and + https://lists.debian.org/debian-med/2023/07/msg00002.html + the main executable is now named cvnkit.py which is not following + the suggestion of Debian Policy to drop the .py extension any more. + + -- Andreas Tille <[email protected]> Tue, 04 Jul 2023 12:04:48 +0200 ===================================== debian/changelog ===================================== @@ -1,10 +1,10 @@ -cnvkit (0.9.10-1) UNRELEASED; urgency=medium +cnvkit (0.9.10-1) unstable; urgency=medium * Team upload. * New upstream version * Standards-Version: 4.6.2 (routine-update) - -- Andreas Tille <[email protected]> Tue, 04 Jul 2023 11:37:27 +0200 + -- Andreas Tille <[email protected]> Tue, 04 Jul 2023 12:04:48 +0200 cnvkit (0.9.9-2) unstable; urgency=medium ===================================== debian/cnvkit.links ===================================== @@ -1 +1 @@ -usr/bin/cnvkit usr/lib/debian-med/bin/cnvkit.py +#usr/bin/cnvkit usr/lib/debian-med/bin/cnvkit.py ===================================== debian/install ===================================== @@ -0,0 +1 @@ +scripts/*.sh usr/bin ===================================== debian/lintian-overrides ===================================== @@ -0,0 +1,3 @@ +# see https://lists.debian.org/debian-med/2018/06/msg00043.html +# as well as debian/NEWS +cnvkit: script-with-language-extension [usr/bin/cnvkit.py] ===================================== debian/manpages ===================================== @@ -1 +1 @@ -debian/*.1 +#debian/*.1 ===================================== debian/rules ===================================== @@ -8,27 +8,13 @@ include /usr/share/dpkg/pkg-info.mk %: dh $@ --with python3 --buildsystem=pybuild -override_dh_auto_build: - [ -f cnvkit.py ] && mv cnvkit.py cnvkit || true # may not exist after interrupted build - if [ -f scripts/cnv_annotate.py ]; then \ - cd scripts && for script in *.py; do \ - mv $${script} cnvkit-$${script%%.py}; \ - done; \ - fi - dh_auto_build - cd scripts && for script in cnvkit-*; do \ - mv $${script} $${script##cnvkit-}.py; \ - done - mv cnvkit cnvkit.py - override_dh_auto_install: - [ -f cnvkit.py ] && mv cnvkit.py cnvkit || true # may not exist after interrupted install - if [ -f scripts/cnv_annotate.py ]; then \ - cd scripts && for script in *.py; do \ - mv $${script} cnvkit-$${script%%.py}; \ - done; \ - fi + for script in `find scripts -name "*.py"` ; do \ + dh_install $${script} /usr/bin; \ + done dh_auto_install + +_override_dh_installman: help2man --no-info --version-option=version \ --name="a command-line toolkit for copy number analysis." \ ./cnvkit > debian/cnvkit.1 @@ -37,12 +23,12 @@ override_dh_auto_install: --version-string=${DEB_VERSION_UPSTREAM} --help-option='-h' \ ./cnvkit-reference2targets --name='Extract target and antitarget BED files from a CNVkit reference file.' \ > ../debian/cnvkit-reference2targets.1; - cd scripts && for script in cnvkit-*; do \ - mv $${script} $${script##cnvkit-}.py; \ - done - mv cnvkit cnvkit.py +# cd scripts && for script in cnvkit-*; do \ +# mv $${script} $${script##cnvkit-}.py; \ +# done +# mv cnvkit cnvkit.py -override_dh_auto_test: +_override_dh_auto_test: ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS))) cd test && ${MAKE} cd test && ${MAKE} clean || /bin/true @@ -51,7 +37,7 @@ endif override_dh_auto_clean: cd test && ${MAKE} clean || /bin/true - if [ -f cnvkit ]; then mv cnvkit cnvkit.py; fi +# if [ -f cnvkit ]; then mv cnvkit cnvkit.py; fi dh_auto_clean rm -rf test/p2-20-metrics.tsv test/p2-5_5-metrics.tsv test/p2-9_2-metrics.tsv rm -rf test/build CNVkit.egg-info ===================================== debian/tests/run-unit-test ===================================== @@ -13,6 +13,6 @@ cp -arL /usr/share/doc/${pkg}/examples/data "${AUTOPKGTEST_TMP}/" cd "${AUTOPKGTEST_TMP}" find . -name "*.gz" -exec gunzip \{\} \; cd test -make cnvkit=/usr/bin/cnvkit +make echo "PASS" View it on GitLab: https://salsa.debian.org/med-team/cnvkit/-/compare/557f248c1515ca1fd96e1803a87e9f91bf26d6ac...94962fde7fb97c144785c4dbaa8851d826130b11 -- View it on GitLab: https://salsa.debian.org/med-team/cnvkit/-/compare/557f248c1515ca1fd96e1803a87e9f91bf26d6ac...94962fde7fb97c144785c4dbaa8851d826130b11 You're receiving this email because of your account on salsa.debian.org.
_______________________________________________ debian-med-commit mailing list [email protected] https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
