[med-svn] [Git][med-team/malt][master] 9 commits: Adding Bug and Repository fields in d/u/metadata
Pierre Gruet (@pgt)
gitlab at salsa.debian.org
Sun Jan 16 21:26:52 GMT 2022
Pierre Gruet pushed to branch master at Debian Med / malt
Commits:
6eafac8a by Pierre Gruet at 2022-01-15T21:07:08+01:00
Adding Bug and Repository fields in d/u/metadata
- - - - -
6b74b917 by Pierre Gruet at 2022-01-16T22:06:10+01:00
Updating manifest, name of built jar and dependencies
- - - - -
bd2472a7 by Pierre Gruet at 2022-01-16T22:08:55+01:00
Patches to fix build paths and classpath, like in megan-ce
- - - - -
53907eda by Pierre Gruet at 2022-01-16T22:09:21+01:00
Not caring about module-info stuff
- - - - -
ab6db2e9 by Pierre Gruet at 2022-01-16T22:09:53+01:00
Putting the pdf of the manual into the binary package
- - - - -
117a2da4 by Pierre Gruet at 2022-01-16T22:13:08+01:00
Setting DEP3 headers for patches
- - - - -
e1ddfd11 by Pierre Gruet at 2022-01-16T22:14:45+01:00
Setting Standards version to 4.6.0
- - - - -
6369a76c by Pierre Gruet at 2022-01-16T22:21:45+01:00
Renaming files in debian/ for naming scheme consistency
- - - - -
f13eb914 by Pierre Gruet at 2022-01-16T22:26:31+01:00
Adding information for doc-base registration
- - - - -
12 changed files:
- debian/control
- − debian/jlibs
- + debian/malt.doc-base
- + debian/malt.docs
- + debian/malt.jlibs
- + debian/malt.manifest
- − debian/manifest
- + debian/patches/build.patch
- debian/patches/use_debian_packaged_jloda.patch → debian/patches/fix_classpath.patch
- + debian/patches/no_module_info.patch
- debian/patches/series
- debian/upstream/metadata
Changes:
=====================================
debian/control
=====================================
@@ -9,9 +9,8 @@ Build-Depends: debhelper-compat (= 13),
default-jdk,
ant,
libjloda-java (>= 0.0+git20180523),
- libopenjfx-java,
- libcontrolsfx-java
-Standards-Version: 4.1.4
+ megan-ce
+Standards-Version: 4.6.0
Vcs-Browser: https://salsa.debian.org/med-team/malt
Vcs-Git: https://salsa.debian.org/med-team/malt.git
Homepage: https://github.com/danielhuson/malt
=====================================
debian/jlibs deleted
=====================================
@@ -1 +0,0 @@
-antbuild/MALT.jar
=====================================
debian/malt.doc-base
=====================================
@@ -0,0 +1,10 @@
+Document: male
+Title: Manual of MEGAN alignment tool (MALT)
+Author: Daniel H. Huson
+Abstract: This manual is both an introduction and a reference guide to MALT.
+ It explains how the software works and gives the comprehensive list of its
+ options.
+Section: Science/Biology
+
+Format: PDF
+Files: /usr/share/doc/malt/manual.pdf.gz
=====================================
debian/malt.docs
=====================================
@@ -0,0 +1 @@
+tex/manual/manual.pdf
=====================================
debian/malt.jlibs
=====================================
@@ -0,0 +1 @@
+antbuild/malt.jar
=====================================
debian/malt.manifest
=====================================
@@ -0,0 +1,3 @@
+/usr/share/java/malt.jar:
+ Main-Class: malt.MaltRun
+ Class-Path: /usr/share/java/jloda.jar /usr/share/java/megan.jar
=====================================
debian/manifest deleted
=====================================
@@ -1,3 +0,0 @@
-/usr/share/java/MALT.jar:
- Main-Class: malt.MaltRun
- Class-Path: /usr/share/java/jloda.jar
=====================================
debian/patches/build.patch
=====================================
@@ -0,0 +1,64 @@
+Description: fixing build paths and classpath in build.xml for a Debian build
+Author: Pierre Gruet <pgt at debian.org>
+Forwarded: not-needed
+Last-Update: 2022-01-16
+
+--- a/antbuild/build.xml
++++ b/antbuild/build.xml
+@@ -4,8 +4,8 @@
+ -->
+ <project name="MALT" default="jar" basedir=".">
+
+- <property name="ant.build.javac.source" value="13"/>
+- <property name="ant.build.javac.target" value="13"/>
++ <!--<property name="ant.build.javac.source" value="13"/>
++ <property name="ant.build.javac.target" value="13"/>-->
+
+ <property name="jfxDir" value="../../javafx/lib"/>
+ <property name="meganAntDir" value="../../megan-ce/antbuild"/>
+@@ -14,24 +14,20 @@
+
+ <path id="build.modulepath">
+ <fileset dir="../../jloda/jars" includes="*.jar"/>
+- <fileset dir="../../megan-ce/jars" includes="*.jar" excludes="data.jar"/>
+- <fileset dir="../../malt/jars" includes="*.jar" excludes="data.jar"/>
+- <fileset dir="${jfxDir}" includes="*.jar"/>
+ <fileset dir="../antbuild" includes="jloda.jar"/>
+ <fileset dir="../antbuild" includes="megan.jar"/>
+ </path>
+
+ <path id="run.modulepath">
+ <fileset dir="../../jloda/jars" includes="*.jar"/>
+- <fileset dir="../../megan-ce/jars" includes="*.jar"/>
+- <fileset dir="../../malt/jars" includes="*.jar"/>
+- <fileset dir="${jfxDir}" includes="*.jar"/>
+ <fileset dir="../antbuild" includes="jloda.jar"/>
+ <fileset dir="../antbuild" includes="megan.jar"/>
+ <fileset dir="../antbuild" includes="malt.jar"/>
+ </path>
+
+ <target name="init">
++ <mkdir dir="${buildSrcDir}"/>
++ <mkdir dir="${buildModulesDir}"/>
+ <mkdir dir="${buildSrcDir}/malt"/>
+ <mkdir dir="${buildModulesDir}/malt"/>
+ </target>
+@@ -40,15 +36,15 @@
+ <ant antfile="${meganAntDir}/build.xml" target="jar"/>
+ </target>
+
+- <target name="copy_sources" depends="megan">
++ <target name="copy_sources" depends="init">
+ <copy todir="${buildSrcDir}/malt">
+- <fileset dir="../../malt/src"/>
++ <fileset dir="../src"/>
+ </copy>
+ </target>
+
+ <target name="copy_resources" depends="copy_sources">
+ <copy todir="${buildModulesDir}/malt">
+- <fileset dir="../../malt/src"
++ <fileset dir="..//src"
+ includes="**/*.fxml **/*.png **/*.dtd **/*.gif **/*.css **/*.txt **/*.map **/*.info **/*.tre **/*.lvl **/*.xml"/>
+ </copy>
+ </target>
=====================================
debian/patches/use_debian_packaged_jloda.patch → debian/patches/fix_classpath.patch
=====================================
@@ -1,25 +1,41 @@
-Author: Andreas Tille <tille at debian.org>,
- Pierre Gruet <pgt at debian.org>
-Last-Update: Sat, 25 Dec 2021 21:37:16 +0100
-Description: linking to /usr/share/java/jloda.jar
+Author: Pierre Gruet <pgt at debian.org>
+Last-Update: 2022-01-15
+Description: setting paths of Debian jars used during the build
+Forwarded: not-needed
--- a/antbuild/build.xml
+++ b/antbuild/build.xml
-@@ -13,7 +13,7 @@
+@@ -12,16 +12,19 @@
+ <property name="buildSrcDir" value="../antbuild/src"/>
<property name="buildModulesDir" value="../antbuild/modules"/>
++ <path id="build.classpath">
++ <fileset dir="/usr/share/java/" includes="jloda.jar"/>
++ <fileset dir="/usr/share/java/" includes="megan.jar"/>
++ </path>
++
<path id="build.modulepath">
- <fileset dir="../../jloda/jars" includes="*.jar"/>
+- <fileset dir="../antbuild" includes="jloda.jar"/>
+- <fileset dir="../antbuild" includes="megan.jar"/>
+ <fileset dir="/usr/share/java/" includes="jloda.jar"/>
- <fileset dir="../../megan-ce/jars" includes="*.jar" excludes="data.jar"/>
- <fileset dir="../../malt/jars" includes="*.jar" excludes="data.jar"/>
- <fileset dir="${jfxDir}" includes="*.jar"/>
-@@ -22,7 +22,7 @@
++ <fileset dir="/usr/share/java/" includes="megan.jar"/>
</path>
<path id="run.modulepath">
- <fileset dir="../../jloda/jars" includes="*.jar"/>
+- <fileset dir="../antbuild" includes="jloda.jar"/>
+- <fileset dir="../antbuild" includes="megan.jar"/>
+ <fileset dir="/usr/share/java/" includes="jloda.jar"/>
- <fileset dir="../../megan-ce/jars" includes="*.jar"/>
- <fileset dir="../../malt/jars" includes="*.jar"/>
- <fileset dir="${jfxDir}" includes="*.jar"/>
++ <fileset dir="/usr/share/java/" includes="megan.jar"/>
+ <fileset dir="../antbuild" includes="malt.jar"/>
+ </path>
+
+@@ -56,6 +59,7 @@
+ debug="on"
+ modulepathref="build.modulepath"
+ >
++ <classpath refid="build.classpath" />
+ </javac>
+ </target>
+
=====================================
debian/patches/no_module_info.patch
=====================================
@@ -0,0 +1,18 @@
+Description: omitting module-path related stuff for the build
+Author: Pierre Gruet <pgt at debian.org>
+Forwarded: not-needed
+Last-Update: 2022-01-15
+
+--- a/src/module-info.java
++++ /dev/null
+@@ -1,9 +0,0 @@
+-module malt {
+- requires transitive jloda;
+- requires transitive megan;
+-
+- exports malt.tools;
+- exports malt;
+-
+- opens malt.resources.icons;
+-}
+\ No newline at end of file
=====================================
debian/patches/series
=====================================
@@ -1 +1,3 @@
-use_debian_packaged_jloda.patch
+build.patch
+fix_classpath.patch
+no_module_info.patch
=====================================
debian/upstream/metadata
=====================================
@@ -17,3 +17,7 @@ Registry:
Entry: NA
- Name: bio.tools
Entry: NA
+Bug-Database: https://github.com/danielhuson/malt/issues
+Bug-Submit: https://github.com/danielhuson/malt/issues/new
+Repository: https://github.com/danielhuson/malt.git
+Repository-Browse: https://github.com/danielhuson/malt
View it on GitLab: https://salsa.debian.org/med-team/malt/-/compare/edeb5aac742c63605c098ac979f7a4afb98e6ead...f13eb91498ec7f683b2b34c863567287dc0d172d
--
View it on GitLab: https://salsa.debian.org/med-team/malt/-/compare/edeb5aac742c63605c098ac979f7a4afb98e6ead...f13eb91498ec7f683b2b34c863567287dc0d172d
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