[med-svn] [Git][med-team/maffilter][master] 14 commits: Install examples in the main package
Pranav Ballaney
gitlab at salsa.debian.org
Sun Aug 23 13:59:32 BST 2020
Pranav Ballaney pushed to branch master at Debian Med / maffilter
Commits:
93fb42bd by Pranav Ballaney at 2020-08-23T17:52:51+05:30
Install examples in the main package
- - - - -
6d44b62f by Pranav Ballaney at 2020-08-23T17:52:56+05:30
Add autopkgtests
- - - - -
56f84904 by Pranav Ballaney at 2020-08-23T17:53:55+05:30
Install docs
- - - - -
e13c05df by Pranav Ballaney at 2020-08-23T17:54:22+05:30
Add Pranav Ballaney to Uploaders
- - - - -
1bb00071 by Pranav Ballaney at 2020-08-23T18:16:54+05:30
Update changelog
- - - - -
8143e501 by Pranav Ballaney at 2020-08-23T18:17:03+05:30
routine-update: Standards-Version: 4.5.0
- - - - -
85a7d3f1 by Pranav Ballaney at 2020-08-23T18:17:03+05:30
routine-update: debhelper-compat 13
- - - - -
15d7fc53 by Pranav Ballaney at 2020-08-23T18:17:04+05:30
routine-update: Secure URI in copyright format
- - - - -
39651e7d by Pranav Ballaney at 2020-08-23T18:17:04+05:30
routine-update: Remove trailing whitespace in debian/copyright
- - - - -
aaf98e33 by Pranav Ballaney at 2020-08-23T18:17:04+05:30
routine-update: Add salsa-ci file
- - - - -
48467608 by Pranav Ballaney at 2020-08-23T18:17:05+05:30
routine-update: Rules-Requires-Root: no
- - - - -
ba5558b2 by Pranav Ballaney at 2020-08-23T18:17:15+05:30
Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse.
- - - - -
e9d6797e by Pranav Ballaney at 2020-08-23T18:17:16+05:30
Remove obsolete field Name from debian/upstream/metadata (already present in machine-readable debian/copyright).
- - - - -
676ba7a6 by Pranav Ballaney at 2020-08-23T18:19:26+05:30
routine-update: Ready to upload to unstable
- - - - -
12 changed files:
- + debian/README.test
- debian/changelog
- − debian/compat
- debian/control
- debian/copyright
- − debian/maffilter-examples.examples
- + debian/maffilter-examples.install
- debian/maffilter.docs
- + debian/salsa-ci.yml
- + debian/tests/control
- + debian/tests/run-unit-test
- debian/upstream/metadata
Changes:
=====================================
debian/README.test
=====================================
@@ -0,0 +1,8 @@
+Notes on how this package can be tested.
+────────────────────────────────────────
+
+This package can be tested by running the provided test:
+
+ sh run-unit-test
+
+in order to confirm its integrity.
=====================================
debian/changelog
=====================================
@@ -1,3 +1,22 @@
+maffilter (1.3.1+dfsg-2) unstable; urgency=medium
+
+ * Install examples in the main package
+ * Add autopkgtests
+ * Install docs
+ * Add Pranav Ballaney to Uploaders
+ * Standards-Version: 4.5.0 (routine-update)
+ * debhelper-compat 13 (routine-update)
+ * Secure URI in copyright format (routine-update)
+ * Remove trailing whitespace in debian/copyright (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.
+ * Remove obsolete field Name from debian/upstream/metadata (already
+ present in machine-readable debian/copyright).
+
+ -- Pranav Ballaney <ballaneypranav at gmail.com> Sun, 23 Aug 2020 18:17:16 +0530
+
maffilter (1.3.1+dfsg-1) unstable; urgency=medium
[ Julien Dutheil ]
=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-10
=====================================
debian/control
=====================================
@@ -1,20 +1,22 @@
Source: maffilter
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Andreas Tille <tille at debian.org>,
- Julien Dutheil <julien.dutheil at univ-montp2.fr>
+ Julien Dutheil <julien.dutheil at univ-montp2.fr>,
+ Pranav Ballaney <ballaneypranav at gmail.com>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 13),
cmake,
texinfo,
libbpp-phyl-omics-dev (>= 2.4.1),
- libboost-iostreams-dev (>= 1.54.0),
+ libboost-iostreams-dev,
zlib1g-dev,
libbz2-dev
-Standards-Version: 4.2.0
+Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/maffilter
Vcs-Git: https://salsa.debian.org/med-team/maffilter.git
-Homepage: https://jydu.github.io/maffilter/
+Homepage: https://jydu.github.io/maffilter/
+Rules-Requires-Root: no
Package: maffilter
Architecture: any
=====================================
debian/copyright
=====================================
@@ -1,4 +1,4 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: MafFilter
Upstream-Contact: Julien Dutheil <julien.dutheil at univ-montp2.fr>
Source: http://biopp.univ-montp2.fr/repos/sources/maffilter/
@@ -33,16 +33,16 @@ License: CeCILL
The provided software is distributed under the CeCILL license:
.
This software is governed by the CeCILL license under French law and
- abiding by the rules of distribution of free software. You can use,
+ abiding by the rules of distribution of free software. You can use,
modify and/ or redistribute the software under the terms of the CeCILL
license as circulated by CEA, CNRS and INRIA at the following URL
- "http://www.cecill.info".
+ "http://www.cecill.info".
.
As a counterpart to the access to the source code and rights to copy,
modify and redistribute granted by the license, users are provided only
with a limited warranty and the software's author, the holder of the
economic rights, and the successive licensors have only limited
- liability.
+ liability.
.
In this respect, the user's attention is drawn to the risks associated
with loading, using, modifying and/or developing or reproducing the
@@ -51,12 +51,12 @@ License: CeCILL
therefore means that it is reserved for developers and experienced
professionals having in-depth computer knowledge. Users are therefore
encouraged to load and test the software's suitability as regards their
- requirements in conditions enabling the security of their systems and/or
- data to be ensured and, more generally, to use and operate it in the
- same conditions as regards security.
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
.
The fact that you are presently reading this means that you have had
knowledge of the CeCILL license and that you accept its terms.
- .
+ .
The complete text of the license may be found here:
http://www.cecill.info/licences/Licence_CeCILL_V2-en.html
=====================================
debian/maffilter-examples.examples deleted
=====================================
@@ -1 +0,0 @@
-examples/*
=====================================
debian/maffilter-examples.install
=====================================
@@ -0,0 +1 @@
+examples/* /usr/share/doc/maffilter/examples
=====================================
debian/maffilter.docs
=====================================
@@ -1 +1,4 @@
AUTHORS*
+docs/*
+debian/README*
+debian/tests/run-unit-test
\ No newline at end of file
=====================================
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/tests/control
=====================================
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr
=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,44 @@
+#!/bin/bash
+set -e
+
+pkg=maffilter
+
+export LC_ALL=C.UTF-8
+if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
+ AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+ # Double quote below to expand the temporary directory variable now versus
+ # later is on purpose.
+ # shellcheck disable=SC2064
+ trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
+
+cd "${AUTOPKGTEST_TMP}"
+
+echo -e "\e[93m\e[1mTest 1\e[0m"
+cd Gorilla
+maffilter param=MafFilter.bpp
+
+echo "9c51b6fdc2e80984ddf6ee35952c0d6c Compara.epo_5_catarrhini_hsap-projected.chr22.subset.nogap.cleaned_aln.dnd" >> checksums
+echo "714f5fded274bee99dd226185a27dfb5 Compara.epo_5_catarrhini_hsap-projected.chr22.subset.nogap.cleaned_aln_ingroup.dnd" >> checksums
+echo "d067203b8f652e4f47c4a58ce12d1815 Compara.epo_5_catarrhini_hsap-projected.chr22.subset.nogap.cleaned_aln.maffilter.log" >> checksums
+echo "232c69cbdc5b73263d573b21859549cc Compara.epo_5_catarrhini_hsap-projected.chr22.subset.nogap.cleaned_aln.statistics.csv" >> checksums
+
+md5sum --check checksums
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 2\e[0m"
+cd ../Ztritici
+maffilter param=MafFilter.bpp
+
+echo "afa5a0fd088462771515f3e944997c54 tba_refIPO323.maffilter.log" >> checksums
+echo "2925897d64377830e46bdea80e1683c1 tba_refIPO323.statistics.csv" >> checksums
+echo "0de0fe49364e19c880665d62a611cc38 Zt12g_CDS.aln" >> checksums
+echo "baa191046d49a17f0bbbb206aafec478 Zt12g_CDS.statistics.csv" >> checksums
+
+md5sum --check checksums
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
=====================================
debian/upstream/metadata
=====================================
@@ -1,4 +1,5 @@
-Name: MafFilter
+Bug-Database: https://github.com/jydu/maffilter/issues
+Bug-Submit: https://github.com/jydu/maffilter/issues/new
Reference:
Author: Julien Y Dutheil and Sylvain Gaillard and Eva H Stukenbrock
Title: >
@@ -16,3 +17,5 @@ Reference:
Registry:
- Name: OMICtools
Entry: OMICS_06743
+Repository: https://github.com/jydu/maffilter.git
+Repository-Browse: https://github.com/jydu/maffilter
View it on GitLab: https://salsa.debian.org/med-team/maffilter/-/compare/7b58176021267b4e7860e377d89844a2e4ccdb29...676ba7a6c700c14580bdbc12498d7b14912e4582
--
View it on GitLab: https://salsa.debian.org/med-team/maffilter/-/compare/7b58176021267b4e7860e377d89844a2e4ccdb29...676ba7a6c700c14580bdbc12498d7b14912e4582
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