Andreas Tille pushed to branch master at Debian Med / python-pybedtools
Commits: bcecf9a3 by Andreas Tille at 2020-05-13T08:55:50+02:00 Rebuild against available architectures - - - - - 18297b49 by Andreas Tille at 2020-05-13T08:56:33+02:00 routine-update: Standards-Version: 4.5.0 - - - - - c233707f by Andreas Tille at 2020-05-13T08:56:40+02:00 R-U: Trailing whitespace in debian/rules - - - - - b1f37009 by Andreas Tille at 2020-05-13T08:56:40+02:00 routine-update: Add salsa-ci file - - - - - 93d78f9a by Andreas Tille at 2020-05-13T08:56:40+02:00 routine-update: Rules-Requires-Root: no - - - - - 8084054a by Andreas Tille at 2020-05-13T08:56:48+02:00 Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse. Fixes: lintian: upstream-metadata-missing-bug-tracking See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html Fixes: lintian: upstream-metadata-missing-repository See-also: https://lintian.debian.org/tags/upstream-metadata-missing-repository.html - - - - - e85142bc by Andreas Tille at 2020-05-13T09:08:07+02:00 Add missing shebang lines - - - - - d860ae79 by Andreas Tille at 2020-05-13T09:12:05+02:00 Move example script to examples - - - - - ebc34a08 by Andreas Tille at 2020-05-13T09:13:35+02:00 Fix permission of script - - - - - 9c707c14 by Andreas Tille at 2020-05-13T09:14:30+02:00 There is obviously some reason to do manual cleaning - - - - - 6e694bb0 by Andreas Tille at 2020-05-13T09:18:35+02:00 Upload to unstable - - - - - 8 changed files: - debian/changelog - debian/control - + debian/patches/add_missing_shebang.patch - debian/patches/series - debian/pybedtools-bin.lintian-overrides - debian/rules - + debian/salsa-ci.yml - debian/upstream/metadata Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,20 @@ +python-pybedtools (0.8.0-4) unstable; urgency=medium + + * Team upload. + * Rebuild against available architectures + Closes: #960411 + * Standards-Version: 4.5.0 (routine-update) + * Remove trailing whitespace in debian/rules (routine-update) + * Add salsa-ci file (routine-update) + * Rules-Requires-Root: no (routine-update) + * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, + Repository-Browse. + * Add missing shebang lines in scripts + * Move example script to examples + * Fix permission of script + + -- Andreas Tille <[email protected]> Wed, 13 May 2020 09:14:53 +0200 + python-pybedtools (0.8.0-3) unstable; urgency=medium * Mark the -doc package Multi-Arch: foreign ===================================== debian/control ===================================== @@ -24,10 +24,11 @@ Build-Depends: debhelper-compat (= 12), python3-sphinx, r-base-core, zlib1g-dev -Standards-Version: 4.4.0 +Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/python-pybedtools Vcs-Git: https://salsa.debian.org/med-team/python-pybedtools.git Homepage: https://daler.github.io/pybedtools/ +Rules-Requires-Root: no Package: pybedtools-bin Architecture: all ===================================== debian/patches/add_missing_shebang.patch ===================================== @@ -0,0 +1,21 @@ +Author: Andreas Tille <[email protected]> +Last-Update: Wed, 13 May 2020 08:56:48 +0200 +Description: Add missing shebang lines + +--- a/pybedtools/scripts/annotate.py ++++ b/pybedtools/scripts/annotate.py +@@ -1,3 +1,4 @@ ++#!/usr/bin/python3 + """ + annotate a file with the neearest features in another. + +--- a/pybedtools/scripts/examples/pbt_plotting_example.py ++++ b/pybedtools/scripts/examples/pbt_plotting_example.py +@@ -1,4 +1,6 @@ +-from __future__ import print_function ++#!/usr/bin/python3 ++ ++# from __future__ import print_function + import time + import os + import pybedtools ===================================== debian/patches/series ===================================== @@ -7,3 +7,4 @@ spelling define_filenotfounderror_python2.patch remove_badges_from_documentation.patch parseDebianVersions.patch +add_missing_shebang.patch ===================================== debian/pybedtools-bin.lintian-overrides ===================================== @@ -1,9 +1,9 @@ # Better not messing with the community which expects these executables # just the ways these are. +# see https://lists.debian.org/debian-med/2018/06/msg00043.html pybedtools-bin: script-with-language-extension usr/bin/annotate.py pybedtools-bin: script-with-language-extension usr/bin/intersection_matrix.py pybedtools-bin: script-with-language-extension usr/bin/intron_exon_reads.py -pybedtools-bin: script-with-language-extension usr/bin/pbt_plotting_example.py pybedtools-bin: script-with-language-extension usr/bin/peak_pie.py pybedtools-bin: script-with-language-extension usr/bin/venn_gchart.py pybedtools-bin: script-with-language-extension usr/bin/venn_mpl.py ===================================== debian/rules ===================================== @@ -5,7 +5,7 @@ DH_VERBOSE := 1 export DEB_BUILD_MAINT_OPTIONS=hardening=+all export PYBUILD_NAME=pybedtools export MATPLOTLIBRC=$(CURDIR)/debian/ -#export PYBUILD_TEST_ARGS=--attr '!url' +#export PYBUILD_TEST_ARGS=--attr '!url' export PYBUILD_BEFORE_TEST=cp {dir}/debian/mpl-expected.png {build_dir}/pybedtools/test/ ; python3 {dir}/setup.py install --user ; export HOME=$(CURDIR)/fakehome export PYBUILD_TEST_ARGS=-v --doctest-modules export PYBUILD_AFTER_TEST=cd {dir}/docs ; make clean doctest @@ -22,12 +22,13 @@ override_dh_auto_build: python3 setup.py develop --user python3 setup.py build_sphinx -override_dh_auto_install: - dh_auto_install +override_dh_install: + dh_install rm -f debian/python3-pybedtools/usr/lib/python3*/dist-packages/pybedtools/test/prevent_open_file_regression mkdir -p debian/pybedtools-bin/usr/bin + mkdir -p debian/pybedtools-bin/usr/share/doc/pybedtools-bin/examples + mv debian/python3-pybedtools/usr/bin/*example* debian/pybedtools-bin/usr/share/doc/pybedtools-bin/examples mv debian/python3-pybedtools/usr/bin/* debian/pybedtools-bin/usr/bin/ - rm -fr debian/python-pybedtools/usr/bin rm -fr debian/python3-pybedtools/usr/bin override_dh_auto_clean: @@ -41,4 +42,8 @@ override_dh_auto_clean: rm -rf build /bin/rm -rf pybedtools/cbedtools.cpp pybedtools/featurefuncs.cpp find docs/source/autodocs/ -name "*.rst" | xargs -r /bin/rm - #dh_auto_clean + # dh_auto_clean + +override_dh_fixperms: + dh_fixperms + chmod -x debian/*/usr/lib/python3/dist-packages/pybedtools/scripts/pybedtools ===================================== debian/salsa-ci.yml ===================================== @@ -0,0 +1,4 @@ +--- +include: + - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml + - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml ===================================== debian/upstream/metadata ===================================== @@ -1,3 +1,5 @@ +Bug-Database: https://github.com/daler/pybedtools/issues +Bug-Submit: https://github.com/daler/pybedtools/issues/new Reference: - Author: R. K. Dale and B. S. Pedersen and A. R. Quinlan Title: "Pybedtools: a flexible Python library for manipulating genomic datasets\ @@ -21,4 +23,5 @@ Registry: Entry: OMICS_09508 - Name: conda:bioconda Entry: pybedtools -Repository: https://github.com/daler/pybedtools +Repository: https://github.com/daler/pybedtools.git +Repository-Browse: https://github.com/daler/pybedtools View it on GitLab: https://salsa.debian.org/med-team/python-pybedtools/-/compare/b920999b74040b9c96af14770b42e23a6a2e8b98...6e694bb007d6d21b38865304d638c49a12bf324f -- View it on GitLab: https://salsa.debian.org/med-team/python-pybedtools/-/compare/b920999b74040b9c96af14770b42e23a6a2e8b98...6e694bb007d6d21b38865304d638c49a12bf324f You're receiving this email because of your account on salsa.debian.org.
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