Andreas Tille pushed to branch master at Debian Med / python-loompy
Commits: 34e1724d by Andreas Tille at 2020-03-29T11:16:36+02:00 Simplify watch file - - - - - 5d565003 by Andreas Tille at 2020-03-29T11:16:57+02:00 routine-update: Standards-Version: 4.5.0 - - - - - f0629e18 by Andreas Tille at 2020-03-29T11:16:57+02:00 routine-update: debhelper-compat 12 - - - - - c182c240 by Andreas Tille at 2020-03-29T11:17:03+02:00 routine-update: Add salsa-ci file - - - - - 58381f89 by Andreas Tille at 2020-03-29T11:17:03+02:00 routine-update: Rules-Requires-Root: no - - - - - e326c79f by Andreas Tille at 2020-03-29T11:17:05+02:00 Trim trailing whitespace. Fixes: lintian: file-contains-trailing-whitespace See-also: https://lintian.debian.org/tags/file-contains-trailing-whitespace.html - - - - - 0f678465 by Andreas Tille at 2020-03-29T11:17:07+02:00 Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse. - - - - - fd186ffa by Andreas Tille at 2020-03-29T11:20:47+02:00 cme fix dpkg-control - - - - - e6776569 by Andreas Tille at 2020-03-29T11:22:45+02:00 Build-Depends: python3-scipy, use nocheck - - - - - 2a483a36 by Andreas Tille at 2020-03-29T11:32:31+02:00 Section: python - - - - - cf233cff by Andreas Tille at 2020-03-29T11:33:11+02:00 Enhance description - - - - - 1f236cd0 by Andreas Tille at 2020-03-29T11:34:15+02:00 Remove ineffective file which is not needed anyway - - - - - 9ff59a57 by Andreas Tille at 2020-03-29T11:38:26+02:00 Create manpage - - - - - 0539abb6 by Andreas Tille at 2020-03-29T11:39:14+02:00 Team upload to new - - - - - 11 changed files: - debian/changelog - − debian/compat - debian/control - + debian/createmanpages - + debian/loompy.1 - + debian/manpages - − debian/python-loompy.docs - debian/rules - + debian/salsa-ci.yml - debian/upstream/metadata - debian/watch Changes: ===================================== debian/changelog ===================================== @@ -1,9 +1,6 @@ -python-loompy (3.0.6+dfsg-1) UNRELEASED; urgency=medium +python-loompy (3.0.6+dfsg-1) unstable; urgency=medium + * Team upload. * Initial release (Closes: #934597) - Resubmitted with improved copyright. Thanks go to Thorsten. - The new version (up from 2.x) has a build-dep on a Python module "numpy_groupies". - This still needs to be packaged. - - -- Steffen Moeller <[email protected]> Mon, 12 Aug 2019 13:14:47 +0200 + -- Andreas Tille <[email protected]> Sun, 29 Mar 2020 11:39:05 +0200 ===================================== debian/compat deleted ===================================== @@ -1 +0,0 @@ -11 ===================================== debian/control ===================================== @@ -1,33 +1,40 @@ Source: python-loompy -Section: science -Priority: optional Maintainer: Debian Med Packaging Team <[email protected]> Uploaders: Steffen Moeller <[email protected]> -Build-Depends: debhelper (>= 11), dh-python, - python3-all, python3-setuptools, - python3-h5py, - python3-numba, - python3-click -Standards-Version: 4.4.0 -Homepage: https://github.com/linnarsson-lab/loompy +Section: science +Priority: optional +Testsuite: autopkgtest-pkg-python +Build-Depends: debhelper-compat (= 12), + dh-python, + python3-all, + python3-setuptools, + python3-h5py <!nocheck>, + python3-numba <!nocheck>, + python3-click <!nocheck>, + python3-scipy <!nocheck>, + python3-numpy-groupies <!nocheck> +Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/python-loompy Vcs-Git: https://salsa.debian.org/med-team/python-loompy.git -#Testsuite: autopkgtest-pkg-python +Homepage: https://github.com/linnarsson-lab/loompy +Rules-Requires-Root: no -#install_requires=['h5py', 'numpy', 'scipy', 'setuptools', 'numba', 'click', "numpy-groupies"], Package: python3-loompy Architecture: all -Depends: ${python3:Depends}, ${misc:Depends}, - python3-h5py, - python3-numpy, - python3-scipy, - python3-pandas, - python3-click +Section: python +Depends: ${python3:Depends}, + ${misc:Depends}, + python3-h5py, + python3-numpy, + python3-scipy, + python3-pandas, + python3-click, + python3-numpy-groupies Description: access loom formatted files for bioinformatics Loom is an efficient file format for very large omics datasets, consisting of a main matrix, optional additional layers, a variable number of row and column annotations. Loom also supports sparse - graphs. We use loom files to store single-cell gene expression data: + graphs. Loom files are used to store single-cell gene expression data: the main matrix contains the actual expression values (one column per cell, one row per gene); row and column annotations contain metadata for genes and cells, such as Name, Chromosome, Position (for genes), ===================================== debian/createmanpages ===================================== @@ -0,0 +1,28 @@ +#!/bin/sh +MANDIR=debian +mkdir -p $MANDIR + +VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'` +NAME=`grep "^Description:" debian/control | sed 's/^Description: *//' | head -n1` +PROGNAME=`grep "^Package:" debian/control | sed 's/^Package: *//' | head -n1` + +AUTHOR=".SH AUTHOR\n \ +This manpage was written by $DEBFULLNAME for the Debian distribution and\n \ +can be used for any other usage of the program.\ +" + +# If program name is different from package name or title should be +# different from package short description change this here +progname=loompy +help2man --no-info --no-discard-stderr --help-option=" --help" \ + --name="$NAME" \ + --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1 +echo $AUTHOR >> $MANDIR/${progname}.1 + +echo "$MANDIR/*.1" > debian/manpages + +cat <<EOT +Please enhance the help2man output. +The following web page might be helpful in doing so: + http://liw.fi/manpages/ +EOT ===================================== debian/loompy.1 ===================================== @@ -0,0 +1,21 @@ +.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.13. +.TH LOOMPY "1" "March 2020" "loompy 3.0.6" "User Commands" +.SH NAME +loompy \- access loom formatted files for bioinformatics +.SH SYNOPSIS +.B loompy +[\fI\,OPTIONS\/\fR] \fI\,COMMAND \/\fR[\fI\,ARGS\/\fR]... +.SH OPTIONS +.HP +\fB\-\-show\-message\fR / \fB\-\-hide\-message\fR +.HP +\fB\-\-verbosity\fR [error|warning|info|debug] +.TP +\fB\-\-help\fR +Show this message and exit. +.SS "Commands:" +.IP +fromfq +.SH AUTHOR + This manpage was written by Andreas Tille for the Debian distribution and + can be used for any other usage of the program. ===================================== debian/manpages ===================================== @@ -0,0 +1 @@ +debian/*.1 ===================================== debian/python-loompy.docs deleted ===================================== @@ -1,2 +0,0 @@ -README.Debian -README.source ===================================== debian/rules ===================================== @@ -5,4 +5,3 @@ export PYBUILD_NAME=loompy %: dh $@ --with python3 --buildsystem=pybuild - ===================================== debian/salsa-ci.yml ===================================== @@ -0,0 +1,4 @@ +--- +include: + - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml + - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml ===================================== debian/upstream/metadata ===================================== @@ -1,3 +1,5 @@ +Bug-Database: https://github.com/linnarsson-lab/loompy/issues +Bug-Submit: https://github.com/linnarsson-lab/loompy/issues/new Registry: - Name: OMICtools Entry: NA @@ -7,3 +9,5 @@ Registry: Entry: loompy - Name: bio.tools Entry: NA +Repository: https://github.com/linnarsson-lab/loompy.git +Repository-Browse: https://github.com/linnarsson-lab/loompy ===================================== debian/watch ===================================== @@ -1,4 +1,4 @@ version=4 -opts="dversionmangle=s/\+dfsg$//,uversionmangle=s/$/+dfsg/,repack,compression=xz,filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%python-loompy-$1.tar.gz%" \ - https://github.com/linnarsson-lab/loompy/tags \ - (?:.*?/)?v?(\d[\d.]*)\.tar\.gz debian uupdate + +opts="repacksuffix=+dfsg,dversionmangle=auto,repack,compression=xz" \ + https://github.com/linnarsson-lab/loompy/releases .*/archive/v?@ANY_VERSION@@ARCHIVE_EXT@ View it on GitLab: https://salsa.debian.org/med-team/python-loompy/-/compare/8c17601b4f658320f183017bd1e65f6064b5092e...0539abb613056f75be338c6f4f3fcb1454daf41e -- View it on GitLab: https://salsa.debian.org/med-team/python-loompy/-/compare/8c17601b4f658320f183017bd1e65f6064b5092e...0539abb613056f75be338c6f4f3fcb1454daf41e You're receiving this email because of your account on salsa.debian.org.
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