[med-svn] [Git][med-team/alter-sequence-alignment][master] 7 commits: cme fix dpkg-control
Andreas Tille
gitlab at salsa.debian.org
Wed Jul 4 13:31:27 BST 2018
Andreas Tille pushed to branch master at Debian Med / alter-sequence-alignment
Commits:
bdd39f6d by Andreas Tille at 2018-07-04T13:15:41+02:00
cme fix dpkg-control
- - - - -
884adc99 by Andreas Tille at 2018-07-04T13:16:22+02:00
debhelper 11
- - - - -
fd40fefb by Andreas Tille at 2018-07-04T13:53:07+02:00
Leave out web app from build
- - - - -
8b5af30d by Andreas Tille at 2018-07-04T14:09:52+02:00
Sort out JAR name, drop now unneeded patches
- - - - -
e078fa53 by Andreas Tille at 2018-07-04T14:19:06+02:00
Remove non-applicable parts of the doc, adapt doc to Debian installation
- - - - -
261bb22b by Andreas Tille at 2018-07-04T14:24:58+02:00
Install basic doc
- - - - -
a3644dc3 by Andreas Tille at 2018-07-04T14:29:37+02:00
Upload to unstable
- - - - -
15 changed files:
- debian/alter-sequence-alignment.jlibs
- debian/alter-sequence-alignment.poms
- debian/changelog
- debian/compat
- debian/control
- debian/copyright
- + debian/docs
- debian/maven.rules
- − debian/patches/fix_unmappable_characters.patch
- − debian/patches/lower_case_jar.patch
- debian/patches/series
- debian/patches/suppress_build_web_interface.patch
- + debian/patches/update_doc.patch
- − debian/patches/use_debian_packaged_jar.patch
- debian/rules
Changes:
=====================================
debian/alter-sequence-alignment.jlibs
=====================================
--- a/debian/alter-sequence-alignment.jlibs
+++ b/debian/alter-sequence-alignment.jlibs
@@ -1 +1 @@
-alter-lib/dist/*
+alter-lib/target/alter-*.jar
=====================================
debian/alter-sequence-alignment.poms
=====================================
--- a/debian/alter-sequence-alignment.poms
+++ b/debian/alter-sequence-alignment.poms
@@ -27,4 +27,3 @@
#
pom.xml --has-package-version
alter-lib/pom.xml --has-package-version
-alter-web/pom.xml --has-package-version
=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,10 +1,13 @@
-alter-sequence-alignment (1.3.4-1) UNRELEASED; urgency=medium
+alter-sequence-alignment (1.3.4-1) unstable; urgency=medium
* New upstream version
* d/watch: Source moved to Github
* Update copyright
+ * Standards-Version: 4.1.4
+ * Point VCS fields to Salsa
+ * debhelper 11
- -- Andreas Tille <tille at debian.org> Wed, 04 Jul 2018 09:05:14 +0200
+ -- Andreas Tille <tille at debian.org> Wed, 04 Jul 2018 14:25:09 +0200
alter-sequence-alignment (1.3.3+dfsg-1) unstable; urgency=low
=====================================
debian/compat
=====================================
--- a/debian/compat
+++ b/debian/compat
@@ -1 +1 @@
-9
+11
=====================================
debian/control
=====================================
--- a/debian/control
+++ b/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 (>= 9),
+Build-Depends: debhelper (>= 11~),
javahelper,
maven-debian-helper,
libproperties-maven-plugin-java,
@@ -11,10 +11,11 @@ Build-Depends: debhelper (>= 9),
libjavacc-maven-plugin-java,
libmaven-assembly-plugin-java,
libargs4j-java,
- libmaven-war-plugin-java
-Standards-Version: 3.9.6
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/alter-sequence-alignment.git
-Vcs-Git: git://anonscm.debian.org/debian-med/alter-sequence-alignment.git
+ rename,
+ python-markdown
+Standards-Version: 4.1.4
+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/
Package: alter-sequence-alignment
=====================================
debian/copyright
=====================================
--- a/debian/copyright
+++ b/debian/copyright
@@ -8,12 +8,12 @@ Copyright: 2009-2016 David Posada <dposada at uvigo.es>,
Florentino Fdez-Riverola <riverola at uvigo.es>
License: LGPL-3+
-Files: alter-lib/src/cmdLine/*.java
- alter-lib/src/converter/*.java
- alter-lib/src/gui/*.java
- alter-lib/src/reader/*
- alter-lib/src/types/*
- alter-lib/src/writer/*
+Files: alter-lib/src/main/java/es/uvigo/ei/sing/alter/cmdLine/*.java
+ alter-lib/src/main/java/es/uvigo/ei/sing/alter/converter/*.java
+ alter-lib/src/main/java/es/uvigo/ei/sing/alter/gui/*.java
+ alter-lib/src/main/java/es/uvigo/ei/sing/alter/reader/*
+ alter-lib/src/main/java/es/uvigo/ei/sing/alter/types/*
+ alter-lib/src/main/java/es/uvigo/ei/sing/alter/writer/*
Copyright: 2009-2016 David Posada <dposada at uvigo.es>,
Florentino Fdez-Riverola <riverola at uvigo.es>
License: GPL-3+
=====================================
debian/docs
=====================================
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1 @@
+README*
=====================================
debian/maven.rules
=====================================
--- a/debian/maven.rules
+++ b/debian/maven.rules
@@ -1,4 +1,2 @@
-
es.uvigo.ei.sing alter-lib jar s/.*/debian/ * *
es.uvigo.ei.sing alter-project pom s/.*/debian/ * *
-es.uvigo.ei.sing alter-web war s/.*/debian/ * *
=====================================
debian/patches/fix_unmappable_characters.patch deleted
=====================================
--- a/debian/patches/fix_unmappable_characters.patch
+++ /dev/null
@@ -1,105 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Sat, 05 Sep 2015 07:13:34 +0200
-Description: Build has problems with non-ASCII characters in comments
-
---- a/alter-lib/src/converter/ProgramOptions.java
-+++ b/alter-lib/src/converter/ProgramOptions.java
-@@ -22,7 +22,7 @@ import java.util.*;
- /**
- * Provides methods to check the supported programs and formats, as well as
- * the possible options for each one of them.
-- * @author Daniel Gonzalez Peña
-+ * @author Daniel Gonzalez Pena
- */
- public class ProgramOptions{
-
---- a/alter-lib/src/reader/ReaderUtils.java
-+++ b/alter-lib/src/reader/ReaderUtils.java
-@@ -38,7 +38,7 @@ public class ReaderUtils
- public static void replaceMatch(Sequence seq, Sequence first) throws ParseException
- {
- if (seq.getData().contains("."))
-- //Lanzar excepción si el caracter está en la primera secuencia
-+ //Lanzar excepcion si el caracter esta en la primera secuencia
- if (seq == first)
- throw new ParseException("Match character \".\" in first sequence of MSA.");
- else
---- a/alter-lib/src/writer/Writer.java
-+++ b/alter-lib/src/writer/Writer.java
-@@ -20,7 +20,7 @@ package writer;
- import types.MSA;
-
- /**
-- * Define los métodos que deben implementar todos los escritores.
-+ * Define los metodos que deben implementar todos los escritores.
- * @author Daniel Gomez Blanco
- * @version 1.1
- */
---- a/alter-lib/src/writer/FastaWriter.java
-+++ b/alter-lib/src/writer/FastaWriter.java
-@@ -145,7 +145,7 @@ public class FastaWriter implements Writ
- //Mientras queden caracteres por escribir
- while(!data.isEmpty())
- {
-- //Si hay caracteres para hacer una línea
-+ //Si hay caracteres para hacer una linea
- if (data.length() > 60)
- {
- outb.append(data.substring(0, 60));
---- a/alter-lib/src/writer/NexusWriter.java
-+++ b/alter-lib/src/writer/NexusWriter.java
-@@ -343,7 +343,7 @@ public class NexusWriter implements Writ
- outb.append(id + WriterUtils.align(id.length(),longestId)
- + WriterUtils.align(longestId, 10) + " ");
-
-- //Escribir una línea si es posible
-+ //Escribir una linea si es posible
- if (data[index].length() > 50)
- {
- outb.append(data[index].substring(0, 50));
---- a/alter-lib/src/writer/PhylipCodABCWriter.java
-+++ b/alter-lib/src/writer/PhylipCodABCWriter.java
-@@ -25,7 +25,7 @@ import types.Typeable;
-
- /**
- * Extends class PhylipWriter to adapt the output to CodABC.
-- * @author Daniel Glez-Peña
-+ * @author Daniel Glez-Pena
- * @version 1.0
- */
-
---- a/alter-lib/src/writer/PirDnaSPWriter.java
-+++ b/alter-lib/src/writer/PirDnaSPWriter.java
-@@ -34,7 +34,7 @@ public class PirDnaSPWriter extends PirW
- /**
- * Constructor de la clase. Llama al constructor de la superclase.
- * @param os Sistema operativo de salida.
-- * @param lowerCase Salida en letras minúsculas.
-+ * @param lowerCase Salida en letras minusculas.
- * @param match Salida codificada con caracteres match.
- * @param logger Nombre del logger a instanciar.
- */
-@@ -45,7 +45,7 @@ public class PirDnaSPWriter extends PirW
-
- /**
- * Escribe un MSA en formato PIR adaptado a dnaSP. Para ello
-- * comprueba que el MSA no sea de proteínas. Luego llama al método de la superclase.
-+ * comprueba que el MSA no sea de proteinas. Luego llama al metodo de la superclase.
- * @param msa MSA de entrada.
- * @return Cadena con la el MSA en formato PIR.
- */
---- a/alter-lib/src/writer/PirWriter.java
-+++ b/alter-lib/src/writer/PirWriter.java
-@@ -114,10 +114,10 @@ public class PirWriter implements Writer
-
- /**
- * Devuelve una cadena con el identificador de la secuencia. En caso de
-- * que el identificador de secuencia esté repetido se renombra.
-+ * que el identificador de secuencia este repetido se renombra.
- * @param seq Secuencia de la cual se desea obtener el identificador.
- * @param ids Secuencias copiadas hasta el momento.
-- * @return Identificador de secuencia único.
-+ * @return Identificador de secuencia unico.
- */
- protected String getId(Sequence seq, LinkedHashSet<String> ids)
- {
=====================================
debian/patches/lower_case_jar.patch deleted
=====================================
--- a/debian/patches/lower_case_jar.patch
+++ /dev/null
@@ -1,15 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Sat, 05 Sep 2015 07:13:34 +0200
-Description: Resulting JAR should have lower case name
-
---- a/alter-lib/build.xml
-+++ b/alter-lib/build.xml
-@@ -49,7 +49,7 @@
- </target>
- <target name="buildjar" depends="clean, build">
- <mkdir dir="${dist}"/>
-- <jar destfile="${dist}/ALTER.jar"
-+ <jar destfile="${dist}/alter.jar"
- basedir="${build}" manifest="${ALTERLIB.basedir}/MANIFEST.MF"/>
- </target>
- </project>
=====================================
debian/patches/series
=====================================
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,4 +1,2 @@
-#suppress_build_web_interface.patch
-#use_debian_packaged_jar.patch
-#fix_unmappable_characters.patch
-#lower_case_jar.patch
+suppress_build_web_interface.patch
+update_doc.patch
=====================================
debian/patches/suppress_build_web_interface.patch
=====================================
--- a/debian/patches/suppress_build_web_interface.patch
+++ b/debian/patches/suppress_build_web_interface.patch
@@ -1,30 +1,18 @@
Author: Andreas Tille <tille at debian.org>
-Last-Update: Sat, 05 Sep 2015 07:13:34 +0200
+Last-Update: Wed, 04 Jul 2018 09:05:14 +0200
Description: Currently only the library is packaged while the web interface is ignored
The rationale is that libalter-java is packaged as a dependency for
- other packages. There was no explicite request to package the
+ other packages. There was no explicit request to package the
web interface which involves a lot of third party JARs and thus
makes it complex to package.
---- a/build.xml
-+++ b/build.xml
-@@ -1,9 +1,8 @@
- <?xml version="1.0" encoding="UTF-8"?>
--<project name="ALTER" default="buildall" basedir=".">
-+<project name="ALTER" default="buildlib" basedir=".">
+--- a/pom.xml
++++ b/pom.xml
+@@ -32,7 +32,6 @@
- <target name="buildlib">
- <ant antfile="build.xml" dir="./alter-lib" inheritAll="false"/>
-- <copy file="./alter-lib/dist/ALTER.jar" tofile="./web/ALTER.jar"/>
- </target>
-
- <target name="buildall" depends="clean, buildlib">
-@@ -11,8 +10,6 @@
- </target>
- <target name="clean">
- <ant antfile="build.xml" dir="./alter-lib" target="clean" inheritAll="false"/>
-- <ant antfile="build.xml" dir="./web" target="clean" inheritAll="false"/>
-- <delete file="./web/ALTER.jar"/>
- </target>
-
- </project>
+ <modules>
+ <module>alter-lib</module>
+- <module>alter-web</module>
+ </modules>
+
+ <build>
=====================================
debian/patches/update_doc.patch
=====================================
--- /dev/null
+++ b/debian/patches/update_doc.patch
@@ -0,0 +1,59 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Wed, 04 Jul 2018 09:05:14 +0200
+Description: Remove non-applicable parts of the doc, adapt doc to Debian installation
+
+--- a/README.md
++++ b/README.md
+@@ -14,41 +14,16 @@ ALTER contains a set of components:
+ 3. A desktop graphical user interface (GUI).
+ 4. A web interface (a running instance is here: [http://sing.ei.uvigo.es/alter](http://sing.ei.uvigo.es/alter)).
+
+-# Building ALTER and running from source
+-
+-## Build
+-Before starting, you have to download and install:
+-
+-1. Git tool for cloning the last version
+-2. A Java Compiler and tool
+-3. The Maven tool
+-
+-And now, you can download and build it by performing:
+-
+-```
+-git clone https://github.com/sing-group/ALTER.git
+-cd ALTER
+-mvn package
+-```
+
+ ## Running the desktop graphical user interface
+ ```
+-java -jar alter-lib/target/ALTER-1.3.4-jar-with-dependencies.jar
++alter-sequence-alignment
+ ```
+
+ ## Running the command line user interface
+ ```
+-java -jar alter-lib/target/ALTER-1.3.4-jar-with-dependencies.jar help
+-```
+-
+-## Running the web user interface in your own machine
+-1. Download a jetty-runner.jar, which is a server of Java Web applications. For example, download the 9.4.0RC1 version from here [here](http://central.maven.org/maven2/org/eclipse/jetty/jetty-runner/9.4.0.RC1/jetty-runner-9.4.0.RC1.jar)
+-2. Place the jetty-runner-9.4.0.RC1.jar inside your ALTER folder, and the run:
++alter-sequence-alignment help
+ ```
+-java -jar jetty-runner-9.4.0.RC1.jar alter-web/target/alter-web-1.3.4.war
+-```
+-
+-Once the server has started, surf to [http://localhost:8080](http://localhost:8080/)
+
+ # Use the core library in your projects
+
+@@ -84,7 +59,7 @@ Import our repository into your pom.xml
+
+
+ ### Include the .jar inside your classpath
+-You have to include the alter-lib/target/ALTER-1.3.4-jar-with-dependencies.jar file in your classpath
++You have to include the /usr/share/java/alter.jar file in your classpath
+
+ ## Make a sequence conversion inside your Java code
+ Here it is an example to convert a NEXUS file to ALN.
=====================================
debian/patches/use_debian_packaged_jar.patch deleted
=====================================
--- a/debian/patches/use_debian_packaged_jar.patch
+++ /dev/null
@@ -1,22 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Sat, 05 Sep 2015 07:13:34 +0200
-Description: Use Debian packaged JARs
-
---- a/alter-lib/build.xml
-+++ b/alter-lib/build.xml
-@@ -5,13 +5,13 @@
- <property name="build" location="${ALTERLIB.basedir}/build"/>
- <property name="src" location="${ALTERLIB.basedir}/src"/>
- <property name="dist" location="${ALTERLIB.basedir}/dist"/>
-- <property name="javacchome" location="${ALTERLIB.basedir}/javacc-5.0"/>
-+ <property name="javacchome" location="/usr/share/java/"/>
- <property name="grammars" location="${src}/parser"/>
- <property name="javaversion" value="1.6" />
-
- <taskdef resource="net/sf/antcontrib/antcontrib.properties">
- <classpath>
-- <pathelement location="${ALTERLIB.basedir}/ant-contrib/ant-contrib-1.0b3.jar"/>
-+ <pathelement location="/usr/share/ant/lib/ant-contrib.jar"/>
- </classpath>
- </taskdef>
-
=====================================
debian/rules
=====================================
--- a/debian/rules
+++ b/debian/rules
@@ -5,5 +5,10 @@ JAVA_HOME=/usr/lib/jvm/default-java
%:
dh $@ --with javahelper
-get-orig-source:
- uscan --verbose --force-download --repack --compression xz
+override_dh_auto_build:
+ dh_auto_build
+ markdown_py -f README.html README.md
+
+override_jh_installlibs:
+ file-rename 's/ALTER-([\d.]+)-jar-with-dependencies.jar/alter-\1.jar/' alter-lib/target/ALTER-1.3.4-jar-with-dependencies.jar
+ jh_installlibs
View it on GitLab: https://salsa.debian.org/med-team/alter-sequence-alignment/compare/4a5b42fcaec90493bed28d631b0e670d001c9c8e...a3644dc3ae1cb420d753350ed29bcbdc07db77ec
--
View it on GitLab: https://salsa.debian.org/med-team/alter-sequence-alignment/compare/4a5b42fcaec90493bed28d631b0e670d001c9c8e...a3644dc3ae1cb420d753350ed29bcbdc07db77ec
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