Michael R. Crusoe pushed to branch master at Debian Med / seqan-raptor
Commits: 4219667e by Michael R. Crusoe at 2023-08-21T13:24:03+02:00 Fix docs only build - - - - - 04dd1015 by Michael R. Crusoe at 2023-08-21T13:30:15+02:00 d/clean: remove doc_build to fix "fails to build source after successful build". Closes: #1048716 - - - - - 01e29a30 by Michael R. Crusoe at 2023-08-21T13:30:16+02:00 r/rules: allow for existing "doc_build" directory. Fixes "Fails to build binary packages again after successful build". Closes: #1049768 - - - - - 77f6e09d by Michael R. Crusoe at 2023-08-21T13:34:56+02:00 d/rules: export and install the CWL descriptions to /usr/share/commonwl/raptor-*.cwl - - - - - 006c8eed by Michael R. Crusoe at 2023-08-21T13:35:27+02:00 d/control: suggest the virtual package cwl-runner. - - - - - 02b5b664 by Michael R. Crusoe at 2023-08-21T13:36:42+02:00 d/clean: clean up the generated manpages and CWL descriptions. - - - - - 7283ea0f by Michael R. Crusoe at 2023-08-21T14:15:56+02:00 d/tests/: add CWL-based autopkgtest. - - - - - 3e5170c6 by Michael R. Crusoe at 2023-08-21T14:17:58+02:00 routine-update: Ready to upload to unstable - - - - - 7 changed files: - debian/changelog - + debian/clean - debian/control - debian/rules - debian/seqan-raptor.install - + debian/tests/control - + debian/tests/cwl Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,19 @@ +seqan-raptor (3.0.1+ds-2) unstable; urgency=medium + + * Fix docs only build + * d/clean: remove doc_build to fix "fails to build source after + successful build". Closes: #1048716 + * r/rules: allow for existing "doc_build" directory. Fixes "Fails to + build binary packages again after successful build". Closes: + #1049768 + * d/rules: export and install the CWL descriptions to + /usr/share/commonwl/raptor-*.cwl + * d/control: suggest the virtual package cwl-runner. + * d/clean: clean up the generated manpages and CWL descriptions. + * d/tests/: add CWL-based autopkgtest. + + -- Michael R. Crusoe <[email protected]> Mon, 21 Aug 2023 14:17:58 +0200 + seqan-raptor (3.0.1+ds-1) unstable; urgency=medium * New upstream version ===================================== debian/clean ===================================== @@ -0,0 +1,3 @@ +doc_build/ +debian/*.1 +debian/*.cwl ===================================== debian/control ===================================== @@ -31,6 +31,7 @@ Rules-Requires-Root: no Package: seqan-raptor Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} +Suggests: cwl-runner Description: pre-filter for querying very large collections of nucleotide sequences Raptor is a system for approximately searching many queries such as next-generation sequencing reads or transcripts in large collections of ===================================== debian/rules ===================================== @@ -10,6 +10,9 @@ include /usr/share/dpkg/buildflags.mk %: dh $@ +override_dh_auto_configure-indep: + true + override_dh_auto_configure-arch: dh_auto_configure -- -DRAPTOR_NATIVE_BUILD=OFF -DRAPTOR_SUBMODULES_DIR=$(CURDIR)/lib -DRAPTOR_STRIP_BINARY=OFF @@ -21,10 +24,15 @@ override_dh_auto_build-arch: obj-*/bin/raptor layout --export-help man > debian/raptor-layout.1 obj-*/bin/raptor prepare --export-help man > debian/raptor-prepare.1 obj-*/bin/raptor upgrade --export-help man > debian/raptor-upgrade.1 + obj-*/bin/raptor build --export-help cwl > debian/raptor-build.cwl + obj-*/bin/raptor search --export-help cwl > debian/raptor-search.cwl + obj-*/bin/raptor layout --export-help cwl > debian/raptor-layout.cwl + obj-*/bin/raptor prepare --export-help cwl > debian/raptor-prepare.cwl + obj-*/bin/raptor upgrade --export-help cwl > debian/raptor-upgrade.cwl override_dh_auto_build-indep: ifeq (,$(filter nodoc,$(DEB_BUILD_OPTIONS) $(DEB_BUILD_PROFILES))) - mkdir doc_build && cd doc_build && cmake ../test/documentation && $(MAKE) && ctest . --output-on-failure && cd latex && $(MAKE) + mkdir -p doc_build && cd doc_build && cmake ../test/documentation && $(MAKE) && ctest . --output-on-failure && cd latex && $(MAKE) endif override_dh_auto_install-indep: ===================================== debian/seqan-raptor.install ===================================== @@ -1 +1,2 @@ usr/bin/* +debian/*.cwl /usr/share/commonwl/ ===================================== debian/tests/control ===================================== @@ -0,0 +1,3 @@ +Tests: cwl +Depends: @, cwltool, python3-setuptools, nodejs +Restrictions: allow-stderr ===================================== debian/tests/cwl ===================================== @@ -0,0 +1,17 @@ +#!/bin/bash +set -e + +pkg=seqan-raptor + +if [ "${AUTOPKGTEST_TMP}" = "" ] ; then + AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX) + trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM +fi + +cwltool --outdir "${AUTOPKGTEST_TMP}" /usr/share/commonwl/raptor-build.cwl \ + workflow/cwl/tests/raptor-build-0_bins_window_19.yml \ + | grep 098169f476fb949b0d08f2d1e05881049819b811 + +cwltool --outdir "${AUTOPKGTEST_TMP}" /usr/share/commonwl/raptor-build.cwl \ + workflow/cwl/tests/raptor-build-16_bins_window_19.yml \ + | grep 64a4328eb3dab99bf6ecd38f84f4ae45fd01a4dd View it on GitLab: https://salsa.debian.org/med-team/seqan-raptor/-/compare/ebce7114f3558873a4297c7d13b0b88e42925169...3e5170c6e52930e4422d9addc21c726e37936e2e -- View it on GitLab: https://salsa.debian.org/med-team/seqan-raptor/-/compare/ebce7114f3558873a4297c7d13b0b88e42925169...3e5170c6e52930e4422d9addc21c726e37936e2e You're receiving this email because of your account on salsa.debian.org.
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