[med-svn] [Git][med-team/alter-sequence-alignment][master] 8 commits: Add autopkgtests
Nilesh Patra
gitlab at salsa.debian.org
Mon Nov 16 11:47:46 GMT 2020
Nilesh Patra pushed to branch master at Debian Med / alter-sequence-alignment
Commits:
cb6b5e03 by Nilesh Patra at 2020-11-16T16:34:49+05:30
Add autopkgtests
- - - - -
74542cab by Nilesh Patra at 2020-11-16T16:35:12+05:30
routine-update: Standards-Version: 4.5.0
- - - - -
a409cf3d by Nilesh Patra at 2020-11-16T16:35:12+05:30
routine-update: debhelper-compat 13
- - - - -
e2d16f13 by Nilesh Patra at 2020-11-16T16:35:22+05:30
routine-update: Add salsa-ci file
- - - - -
6c81a9fb by Nilesh Patra at 2020-11-16T16:35:22+05:30
routine-update: Rules-Requires-Root: no
- - - - -
cfe0b324 by Nilesh Patra at 2020-11-16T16:35:34+05:30
Set upstream metadata fields: Bug-Submit.
Changes-By: lintian-brush
Fixes: lintian: upstream-metadata-missing-bug-tracking
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html
- - - - -
22073afa by Nilesh Patra at 2020-11-16T11:42:28+00:00
Set CLASSPATH
- - - - -
f4e1fb17 by Nilesh Patra at 2020-11-16T11:42:56+00:00
Upload to unstable
- - - - -
6 changed files:
- debian/changelog
- debian/control
- + debian/salsa-ci.yml
- + debian/tests/control
- + debian/tests/run-unit-test
- debian/upstream/metadata
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,19 @@
+alter-sequence-alignment (1.3.4-4) unstable; urgency=medium
+
+ * Team Upload.
+ [ Andreas Tille ]
+ * Remove substvars
+
+ [ Nilesh Patra ]
+ * Add autopkgtests
+ * Standards-Version: 4.5.0 (routine-update)
+ * debhelper-compat 13 (routine-update)
+ * Add salsa-ci file (routine-update)
+ * Rules-Requires-Root: no (routine-update)
+ * Set upstream metadata fields: Bug-Submit.
+
+ -- Nilesh Patra <npatra974 at gmail.com> Mon, 16 Nov 2020 16:35:35 +0530
+
alter-sequence-alignment (1.3.4-3) unstable; urgency=medium
* Replace python-markdown by markdown
=====================================
debian/control
=====================================
@@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Andreas Tille <tille at debian.org>
Section: java
Priority: optional
-Build-Depends: debhelper-compat (= 12),
+Build-Depends: debhelper-compat (= 13),
javahelper,
maven-debian-helper,
libproperties-maven-plugin-java,
@@ -13,10 +13,11 @@ Build-Depends: debhelper-compat (= 12),
libargs4j-java,
rename,
markdown
-Standards-Version: 4.4.1
+Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/alter-sequence-alignment
Vcs-Git: https://salsa.debian.org/med-team/alter-sequence-alignment.git
Homepage: http://sing.ei.uvigo.es/ALTER/
+Rules-Requires-Root: no
Package: alter-sequence-alignment
Architecture: all
=====================================
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: @, default-jdk
+Restrictions: allow-stderr
=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,88 @@
+#!/bin/bash
+set -e
+
+pkg="alter-sequence-alignment"
+CUR_DIR=`pwd`
+
+if [ "$AUTOPKGTEST_TMP" = "" ] ; then
+ AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
+ trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cp -a ${CUR_DIR}/alter-lib/src/main/java/* $AUTOPKGTEST_TMP
+cp -a ${CUR_DIR}/alter-web/src/main/resources/* $AUTOPKGTEST_TMP
+
+cd $AUTOPKGTEST_TMP
+gunzip -r *
+
+echo "Test 1"
+alter-sequence-alignment -i muscle.aln -ia -of FASTA -oo Linux -op MUSCLE -o test1
+[ -s test1 ] || exit 1
+rm -f ./test1
+echo "PASS"
+
+echo "Test 2"
+alter-sequence-alignment -i tcoffee.aln -ia -of MSF -oo Linux -op TCoffee -o test2
+[ -s test2 ] || exit 1
+rm -f ./test2
+echo "PASS"
+
+echo "Test converter"
+cat >TestAlter.java <<HERE
+import es.uvigo.ei.sing.alter.converter.Converter;
+import es.uvigo.ei.sing.alter.converter.DefaultFactory;
+import es.uvigo.ei.sing.alter.parser.ParseException;
+
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Paths;
+
+public class TestAlter {
+
+ public static void main(String[] args) throws IOException {
+ Converter converter = new DefaultFactory().getConverter(
+ "Linux", // Input operating system (Linux, MacOS or Windows)
+ "clustal", // Input program (Clustal, MAFFT, MUSCLE, PROBCONS or TCoffee)
+ "NEXUS", // Input format (ALN, FASTA, GDE, MEGA, MSF, NEXUS, PHYLIP or PIR)
+ false, // Autodetect format (other input options are omitted)
+ false, // Collapse sequences to haplotypes
+ true, // Treat gaps as missing data when collapsing
+ false, // Count missing data as differences when collapsing
+ 0, // Connection limit (sequences differing at <= l sites will be collapsed) (default is l=0)
+ "windows", // Output operating system (Linux, MacOS or Windows)
+ "general", // Output program (jModelTest, MrBayes, PAML, PAUP, PhyML,
+ // ProtTest, RAxML, TCS, CodABC,
+ // BioEdit, MEGA, dnaSP, Se-Al, Mesquite, SplitsTree, Clustal, MAFFT,
+ // MUSCLE, PROBCONS, TCoffee, Gblocks, SeaView, trimAl or GENERAL)
+ "aln", // Output format (ALN, FASTA, GDE, MEGA, MSF, NEXUS, PHYLIP or PIR)
+ false, // Low case output
+ false, // Output residue numbers (only ALN format)
+ false, // Sequential output (only NEXUS and PHYLIP formats)
+ false, // Output match characters
+ "MyConverterApp" // identifier for log messages
+ );
+
+
+ try {
+ String inputSequence = new String(Files.readAllBytes(Paths.get("clustal.nex")));
+
+ String converted = converter.convert(inputSequence);
+
+ System.out.println("converted file:");
+ System.out.println(converted);
+
+ } catch (ParseException e) {
+ System.err.println("the input file seems to contain errors");
+ e.printStackTrace();
+ }
+
+ }
+}
+
+HERE
+
+CLASSPATH=".:/usr/share/java/alter-lib.jar:/usr/share/java/alter.jar"
+javac TestAlter.java
+java TestAlter
+rm -f ./TestAlter*
+echo "PASS"
=====================================
debian/upstream/metadata
=====================================
@@ -1,3 +1,4 @@
+Bug-Submit: https://github.com/sing-group/ALTER/issues/new
Reference:
Author: >
Daniel Glez-Peña and Daniel Gómez-Blanco and Miguel Reboiro-Jato and
View it on GitLab: https://salsa.debian.org/med-team/alter-sequence-alignment/-/compare/784dd949b12436812afb9d12c1bb8d093476f855...f4e1fb17243f50d690365bc4d51ee067131d5b08
--
View it on GitLab: https://salsa.debian.org/med-team/alter-sequence-alignment/-/compare/784dd949b12436812afb9d12c1bb8d093476f855...f4e1fb17243f50d690365bc4d51ee067131d5b08
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