[med-svn] [Git][med-team/drop-seq][master] 4 commits: libla4j-java is now packaged
Andreas Tille
gitlab at salsa.debian.org
Thu May 21 06:38:08 BST 2020
Andreas Tille pushed to branch master at Debian Med / drop-seq
Commits:
6ebd16c3 by Andreas Tille at 2020-05-21T07:02:13+02:00
libla4j-java is now packaged
- - - - -
2023c522 by Andreas Tille at 2020-05-21T07:07:21+02:00
New upstream version 2.3.0+dfsg
- - - - -
87ceae9c by Andreas Tille at 2020-05-21T07:08:38+02:00
Update upstream source from tag 'upstream/2.3.0+dfsg'
Update to upstream version '2.3.0+dfsg'
with Debian dir fa2c7fb247a32d722663c55b2c54802f8a834d21
- - - - -
aa0fdd79 by Andreas Tille at 2020-05-21T07:37:38+02:00
Remove jacoco from tests since its not packaged for Debian
- - - - -
9 changed files:
- − .github/ISSUE_TEMPLATE/bug_report.md
- − .github/ISSUE_TEMPLATE/documentation-request.md
- − .github/ISSUE_TEMPLATE/feature_request.md
- − .gitignore
- debian/control
- debian/copyright
- debian/patches/debian_packaged_libs.patch
- − lib/la4j-0.5.5.jar
- − lib/test/jacocoant.jar
Changes:
=====================================
.github/ISSUE_TEMPLATE/bug_report.md deleted
=====================================
@@ -1,31 +0,0 @@
----
-name: Bug report
-about: Create a report to help us improve
-title: ''
-labels: ''
-assignees: ''
-
----
-
-### Instructions
-
-- Use a **concise** yet **descriptive** title
-
-### Affected tool(s)
-_Tool name(s), special parameters?_
-
-### Affected version(s)
-- [ ] Latest public release version [version?]
-- [ ] Latest development/master branch as of [date of test?]
-
-### Description
-_Describe the problem below. Provide **screenshots** , **stacktrace** , **logs** where appropriate._
-
-#### Steps to reproduce
-_Tell us how to reproduce this issue. If possible, include command lines that reproduce the problem and provide a minimal test case._
-
-#### Expected behavior
-_Tell us what should happen_
-
-#### Actual behavior
-_Tell us what happens instead_
=====================================
.github/ISSUE_TEMPLATE/documentation-request.md deleted
=====================================
@@ -1,18 +0,0 @@
----
-name: Documentation request
-about: Submit a request for additions, corrections or improvements to documentation.
-title: ''
-labels: ''
-assignees: ''
-
----
-
-### Instructions
-
-- Use a **concise** yet **descriptive** title;
-
-### Tool(s) involved
-_Tool name(s), parameters?_
-
-### Description
-_Describe what needs to be added or modified._
=====================================
.github/ISSUE_TEMPLATE/feature_request.md deleted
=====================================
@@ -1,19 +0,0 @@
----
-name: Feature request
-about: Suggest an idea for this project
-title: ''
-labels: ''
-assignees: ''
-
----
-
-### Instructions
-
-- Use a **concise** yet **descriptive** title;
-
-### Tool(s) involved
-_Tool name(s), special parameters?_
-
-### Description
-_Specify whether you want a modification of an existing behavior or addition of a new capability._
-_Provide **examples**, **screenshots**, where appropriate._
=====================================
.gitignore deleted
=====================================
@@ -1,4 +0,0 @@
-classes
-testclasses
-dist
-jacoco_reports
=====================================
debian/control
=====================================
@@ -11,6 +11,7 @@ Build-Depends: debhelper-compat (= 12),
libcommons-lang-java,
libguava-java,
libyaml-snake-java,
+ libla4j-java,
libjcommander-java <!nocheck>,
junit4 <!nocheck>,
testng <!nocheck>
@@ -28,7 +29,8 @@ Depends: ${java:Depends},
libcommons-collections4-java,
libcommons-lang-java,
libguava-java,
- libyaml-snake-java
+ libyaml-snake-java,
+ libla4j-java,
Description: analyzing Drop-seq data
This software provide for core computational analysis of Drop-seq data,
which shows you how to transform raw sequence data into an expression
=====================================
debian/copyright
=====================================
@@ -1,15 +1,9 @@
Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: drop-seq
Source: https://github.com/broadinstitute/Drop-seq/releases
-Files-Excluded: */picard-*.jar
- */commons-collections*.jar
- */commons-lang*.jar
- */guava*.jar
- */snakeyaml*.jar
- */jcommander*.jar
- */junit*.jar
- */testng*.jar
+Files-Excluded: lib
*/Drop-seq_Alignment_Cookbook.pdf
+ */.git*
Files: *
Copyright: 2018-2020 Broad Institute
=====================================
debian/patches/debian_packaged_libs.patch
=====================================
@@ -1,6 +1,6 @@
--- a/build.xml
+++ b/build.xml
-@@ -35,12 +35,12 @@
+@@ -35,19 +35,19 @@
<property name="classes.test" location="testclasses"/>
<property name="test.output" location="dist/test"/>
<property name="javadoc" location="javadoc"/>
@@ -15,3 +15,36 @@
<include name="*.jar"/>
</fileset>
</path>
+ <path id="test.classpath">
+ <pathelement location="${classes}"/>
+ <path refid="classpath"/>
+- <fileset dir="${lib}/test">
++ <fileset dir="/usr/share/java">
+ <include name="*.jar"/>
+ </fileset>
+ </path>
+--- a/src/ant/defs.xml
++++ b/src/ant/defs.xml
+@@ -122,12 +122,14 @@
+ xmlns:jacoco="antlib:org.jacoco.ant"
+ to the <project> element in the file where this file is included.
+ -->
++<!-- jacoco is not packaged for Debianso we can not run this test
+ <property name="jacoco.dir" location="jacoco_reports"/>
+ <property name="jacoco.binary" location="${jacoco.dir}/jacoco.exec"/>
+
+ <taskdef uri="antlib:org.jacoco.ant" resource="org/jacoco/ant/antlib.xml">
+ <classpath path="${public.dir}/lib/test/jacocoant.jar"/>
+ </taskdef>
++-->
+
+ <!-- Unfortunately can't invoke a macro from inside <jacoco:coverage>, so testng invocation is duplicated -->
+ <target name="coverage" depends="compile-tests">
+@@ -169,5 +171,7 @@
+ </jacoco:report>
+ </target>
+
++<!-- jacoco is not packaged for Debianso we can not run this test
+ <target name="coverage-and-report" depends="coverage, coverage-report"
+ description="Run unit test suite with coverage and generate report"/>
++-->
=====================================
lib/la4j-0.5.5.jar deleted
=====================================
Binary files a/lib/la4j-0.5.5.jar and /dev/null differ
=====================================
lib/test/jacocoant.jar deleted
=====================================
Binary files a/lib/test/jacocoant.jar and /dev/null differ
View it on GitLab: https://salsa.debian.org/med-team/drop-seq/-/compare/f04c4ecbb3971c37819dccbd624b95e345153f02...aa0fdd797e8b7043e82028a7fe9926a326cef4aa
--
View it on GitLab: https://salsa.debian.org/med-team/drop-seq/-/compare/f04c4ecbb3971c37819dccbd624b95e345153f02...aa0fdd797e8b7043e82028a7fe9926a326cef4aa
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