[med-svn] [Git][med-team/python-loompy][master] 14 commits: Simplify watch file

Andreas Tille gitlab at salsa.debian.org
Sun Mar 29 10:41:31 BST 2020 


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 <moeller at debian.org>  Mon, 12 Aug 2019 13:14:47 +0200
+ -- Andreas Tille <tille at debian.org>  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 <debian-med-packaging at lists.alioth.debian.org>
 Uploaders: Steffen Moeller <moeller at debian.org>
-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
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