[med-svn] [Git][med-team/htsjdk][master] 9 commits: New upstream builds now thanks to Olivier Sallou

Andreas Tille gitlab at salsa.debian.org
Tue Apr 17 14:43:12 BST 2018 

Andreas Tille pushed to branch master at Debian Med / htsjdk


Commits:
7cd41d98 by Andreas Tille at 2018-04-17T14:31:13+02:00
New upstream builds now thanks to Olivier Sallou

- - - - -
fc28e38c by Andreas Tille at 2018-04-17T14:32:09+02:00
Point Vcs-fields to salsa.d.o

- - - - -
911c73a5 by Andreas Tille at 2018-04-17T14:42:43+02:00
Spelling

- - - - -
93990028 by Andreas Tille at 2018-04-17T14:45:35+02:00
Updated copyright

- - - - -
39c638c8 by Andreas Tille at 2018-04-17T14:54:19+02:00
Formatting

- - - - -
88e55f31 by Andreas Tille at 2018-04-17T14:54:52+02:00
Remove further non-existing file from d/copyright

- - - - -
a8423563 by Andreas Tille at 2018-04-17T15:14:26+02:00
Add key "Louis Bergelson (sonatype release key) <louisb at broadinstitute.org>" since the poms are signed with this key, fix get-poms target

- - - - -
a070906d by Andreas Tille at 2018-04-17T15:24:08+02:00
DEP3

- - - - -
3b837ed4 by Andreas Tille at 2018-04-17T15:34:17+02:00
Use 2to3 to convert Python script to Python3; Upload to experimental

- - - - -


9 changed files:

- debian/broadinstitute-keyring.gpg
- debian/changelog
- debian/control
- debian/copyright
- debian/libhtsjdk-java.README.Debian
- debian/patches/60-enable-tests
- + debian/patches/80-2to3.patch
- debian/patches/series
- debian/rules


Changes:

=====================================
debian/broadinstitute-keyring.gpg
=====================================
Binary files a/debian/broadinstitute-keyring.gpg and b/debian/broadinstitute-keyring.gpg differ


=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,10 +1,14 @@
-htsjdk (2.14.3+dfsg-1) UNRELEASED-targeting-experimental; urgency=medium
+htsjdk (2.14.3+dfsg-1) experimental; urgency=medium
 
   [ Andreas Tille ]
   * New upstream version
-    Closes: #894289 (FIXME: check this!)
+    Closes: #894289
   * cme fix dpkg-control
-  * Standards-Version: 4.1.3
+  * Standards-Version: 4.1.4
+  * Point Vcs-fields to salsa.d.o
+  * Update d/copyright
+  * d/rules: fix get-poms target
+  * Use 2to3 to convert Python script to Python3
  
   [ Olivier Sallou ]
   * d/patches/30-disable-scalatest.patch
@@ -16,11 +20,13 @@ htsjdk (2.14.3+dfsg-1) UNRELEASED-targeting-experimental; urgency=medium
   [TODO - O. Sallou in progress]
   * Reintroduce unit tests now that gradle 3.4 is available in sid
     - [done] new patch added for latest upstream, referencing junit classes
-    - [done] added testng() call in build.gradle with a patch and set test call in d/rules back
-    - testng fails now with jcommander classnotfound exception, this is a testng bug
-      (#895886: testng: jcommander classes not found), wait to be fixed to enable tests in d/rules
+    - [done] added testng() call in build.gradle with a patch and set test
+             call in d/rules back
+    - testng fails now with jcommander classnotfound exception, this is a
+      testng bug (#895886: testng: jcommander classes not found), wait to
+      be fixed to enable tests in d/rules
 
- -- Andreas Tille <tille at debian.org>  Wed, 28 Mar 2018 14:19:04 +0200
+ -- Andreas Tille <tille at debian.org>  Tue, 17 Apr 2018 15:14:40 +0200
 
 htsjdk (2.8.1+dfsg-2) unstable; urgency=medium
 


=====================================
debian/control
=====================================
--- a/debian/control
+++ b/debian/control
@@ -24,9 +24,9 @@ Build-Depends: default-jdk (>= 2:1.8),
                junit4,
                libjimfs-java,
                scala-library
-Standards-Version: 4.1.3
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/htsjdk.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/htsjdk.git
+Standards-Version: 4.1.4
+Vcs-Browser: https://salsa.debian.org/med-team/htsjdk
+Vcs-Git: https://salsa.debian.org/med-team/htsjdk.git
 Homepage: http://samtools.github.io/htsjdk/
 
 Package: libhtsjdk-java
@@ -36,7 +36,7 @@ Depends: ${misc:Depends},
          ${java:Depends}
 Recommends: ${java:Recommends}
 Suggests: picard-tools,
-          python
+          python3
 Description: Java API for high-throughput sequencing data (HTS) formats
  HTSJDK is an implementation of a unified Java library for accessing common
  file formats, such as SAM (Sequence Alignment/Map) and VCF, used for


=====================================
debian/copyright
=====================================
--- a/debian/copyright
+++ b/debian/copyright
@@ -1,15 +1,15 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Source: https://github.com/samtools/htsjdk/releases
 Comment: Convenience binary jar files are removed.
 Files-Excluded: gradle/wrapper/gradle-wrapper.jar
 
 Files: *
-Copyright: 2009-2015, The Broad Institute
+Copyright: 2009-2018, The Broad Institute
 License: MIT
 
 Files: debian/*
 Copyright: 2010 Shaun Jackman <sjackman at debian.org>
-           2013 Olivier Sallou <osallou at debian.org>
+           2013-2018 Olivier Sallou <osallou at debian.org>
            2015 Vincent Danjean <vdanjean at debian.org>
 License: ISC
  Permission to use, copy, modify, and/or distribute this software for any
@@ -18,7 +18,7 @@ License: ISC
 
 Files: scripts/*
   src/main/*
-Copyright: 2009-2016, The Broad Institute
+Copyright: 2009-2018, The Broad Institute
 License: Expat
 
 Files: src/main/java/htsjdk/samtools/AsyncSAMFileWriter.java
@@ -190,7 +190,6 @@ License: LGPL-2.1
 Files: src/main/java/htsjdk/tribble/readers/AsciiLineReaderIterator.java
   src/main/java/htsjdk/tribble/readers/LineIterator.java
   src/main/java/htsjdk/tribble/readers/LineIteratorImpl.java
-  src/main/java/htsjdk/tribble/readers/LineReaderUtil.java
 Copyright: 2009-2015, The Broad Institute
 License: MIT
 
@@ -276,10 +275,6 @@ Files: src/test/java/htsjdk/samtools/fastq/*
 Copyright: 2009-2015, The Broad Institute
 License: MIT
 
-Files: src/test/java/htsjdk/samtools/fastq/FastqWriterTest.java
-Copyright: 2009-2015, The Broad Institute
-License: Expat
-
 Files: src/test/java/htsjdk/samtools/filter/InsertSizeFilterTest.java
   src/test/java/htsjdk/samtools/filter/MappingQualityFilterTest.java
 Copyright: 2009-2015, The Broad Institute
@@ -498,8 +493,8 @@ License: W3C-Software
       date changes were made. (We recommend you provide URIs to the location
       from which the code is derived).
  .
- In addition, creators of derivitive works must include the full text of this
- NOTICE in a location viewable to users of the derivitive work.
+ In addition, creators of derivative works must include the full text of this
+ NOTICE in a location viewable to users of the derivative work.
  .
  THIS SOFTWARE AND DOCUMENTATION IS PROVIDED "AS IS," AND COPYRIGHT HOLDERS
  MAKE NO REPRESENTATIONS OR WARRANTIES, EXPRESS OR IMPLIED, INCLUDING BUT NOT


=====================================
debian/libhtsjdk-java.README.Debian
=====================================
--- a/debian/libhtsjdk-java.README.Debian
+++ b/debian/libhtsjdk-java.README.Debian
@@ -8,10 +8,10 @@ reverse dependencies.
 
 The Python script 'explain_sam_flags.py' is distributed in
 '/usr/share/libhtsjdk-java/' as a convenience for the users, but
-the package does not depend on it. You can install the default
-Python version in Debian with the following command:
+the package does not depend on it.  It was converted using 2to3
+from Python to Python3.  You can install the default
+Python3 version in Debian with the following command:
 
-apt-get install python
-
- -- Charles Plessy <plessy at debian.org>  Tue, 06 Jul 2010 16:29:56 +0900
+   sudo apt-get install python3
 
+ -- Andreas Tille <tille at debian.org>  Tue, 17 Apr 2018 15:14:40 +0200


=====================================
debian/patches/60-enable-tests
=====================================
--- a/debian/patches/60-enable-tests
+++ b/debian/patches/60-enable-tests
@@ -1,3 +1,7 @@
+Author: Olivier Sallou <osallou at debian.org>
+Last-Update: 2018-04-17
+Description: Enable tests using testng
+
 --- a/build.gradle
 +++ b/build.gradle
 @@ -86,9 +86,14 @@


=====================================
debian/patches/80-2to3.patch
=====================================
--- /dev/null
+++ b/debian/patches/80-2to3.patch
@@ -0,0 +1,34 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 17 Apr 2018 15:14:40 +0200
+Description: Use 2to3 to convert Python script to Python3
+
+--- a/scripts/explain_sam_flags.py
++++ b/scripts/explain_sam_flags.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python3
+ 
+ # The MIT License
+ #
+@@ -28,7 +28,7 @@
+ Explain each flag on the command line in plain English
+ """
+ 
+-from __future__ import division
++
+ import sys
+ 
+ lstFlags = [
+@@ -48,10 +48,10 @@ lstFlags = [
+     
+ 
+ def explain_sam_flags(iFlags):
+-    print iFlags, ":"
++    print(iFlags, ":")
+     for strFlagName, iMask in lstFlags:
+         if iFlags & iMask:
+-            print "\t" + strFlagName
++            print("\t" + strFlagName)
+ 
+ def main(argv=None):
+     if argv is None:


=====================================
debian/patches/series
=====================================
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -6,3 +6,4 @@
 50-fix-javadoc
 60-enable-tests
 70-removesometests-testng.patch
+80-2to3.patch


=====================================
debian/rules
=====================================
--- a/debian/rules
+++ b/debian/rules
@@ -21,6 +21,8 @@ override_dh_auto_test:
 override_jh_installlibs:
 	jh_installlibs --version-strip='[+]dfsg[.0-9]*'
 
+include /usr/share/dpkg/default.mk
+
 # require network, not automatically run
 # use it when the pom file must be re-downloaded from maven repo
 BASE_URL:=https://repo.maven.apache.org/maven2/com/github/samtools/htsjdk
@@ -29,7 +31,7 @@ WGET=wget --no-clobber
 get-poms:
 	$(RM) debian/$(JPKG).pom debian/$(JPKG).pom.asc
 	# extract upstream version
-	VERSION=$$(dpkg-parsechangelog -S Version | sed -e 's/\([+]dfsg[.0-9]*\)\?-[^-]\+$$//') ; \
-	$(WGET) -O debian/$(JPKG).pom $(BASE_URL)/$$VERSION/$(JPKG)-$$VERSION.pom && \
-	$(WGET) -O debian/$(JPKG).pom.asc $(BASE_URL)/$$VERSION/$(JPKG)-$$VERSION.pom.asc
+	VERSION=$$(echo $(DEB_VERSION_UPSTREAM) | sed -e 's/\([+]dfsg[.0-9]*\)$$//') ; \
+	$(WGET) -q -O debian/$(JPKG).pom $(BASE_URL)/$$VERSION/$(JPKG)-$$VERSION.pom && \
+	$(WGET) -q -O debian/$(JPKG).pom.asc $(BASE_URL)/$$VERSION/$(JPKG)-$$VERSION.pom.asc
 	gpg --trust-model=always --status-fd 1 --no-default-keyring --keyring debian/broadinstitute-keyring.gpg --verify debian/$(JPKG).pom.asc



View it on GitLab: https://salsa.debian.org/med-team/htsjdk/compare/ad71bda5d8c33061927950efedef75a94c86b5f0...3b837ed47ef5bacb55eb219f21113cc2a94cc1b3

---
View it on GitLab: https://salsa.debian.org/med-team/htsjdk/compare/ad71bda5d8c33061927950efedef75a94c86b5f0...3b837ed47ef5bacb55eb219f21113cc2a94cc1b3
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