[med-svn] [Git][med-team/sepp][master] Further refinement

[Steffen Möller]

Steffen Möller pushed to branch master at Debian Med / sepp


Commits:
5fd4cab3 by Steffen Moeller at 2020-12-12T23:29:25+01:00
Further refinement

- - - - -


4 changed files:

- debian/changelog
- debian/control
- debian/patches/using_python3_interpreter.patch
- debian/rules


Changes:

=====================================
debian/changelog
=====================================
@@ -1,7 +1,8 @@
-sepp (4.3.10+dfsg-4) UNRELEASED; urgency=medium
+sepp (4.3.10+dfsg-4) unstable; urgency=medium
 
   * Team upload.
   * Now truly also bringing d/sepp.install to salsa
+  * d/rules clean: Allowing for repeated builds cleaning *.jar *.class
 
  -- Steffen Moeller <moeller at debian.org>  Sat, 12 Dec 2020 19:39:54 +0100
   


=====================================
debian/control
=====================================
@@ -9,12 +9,12 @@ Build-Depends: debhelper-compat (= 13),
                python3,
                python3-setuptools,
                python3-dendropy,
-               pplacer,
-               hmmer,
                ant,
                libjenkins-json-java,
                libgoogle-gson-java,
-               ncbi-blast+
+               ncbi-blast+ <!nocheck>,
+               pplacer <!nocheck>,
+               hmmer <!nocheck>
 Standards-Version: 4.5.1
 Vcs-Browser: https://salsa.debian.org/med-team/sepp
 Vcs-Git: https://salsa.debian.org/med-team/sepp.git


=====================================
debian/patches/using_python3_interpreter.patch
=====================================
@@ -5,43 +5,73 @@ Origin: https://www.debian.org/doc/packaging-manuals/python-policy/programs.html
 Forwarded: https://github.com/smirarab/sepp/issues/88
 Last-Update: 2020-10-07
 
---- a/run_abundance.py
-+++ b/run_abundance.py
+Index: sepp/run_abundance.py
+===================================================================
+--- sepp.orig/run_abundance.py
++++ sepp/run_abundance.py
 @@ -1,4 +1,4 @@
 -#!/usr/bin/env python
 +#!/usr/bin/env python3
  # -*- coding: utf-8 -*-
  from sepp.metagenomics import main
  
---- a/run_sepp.py
-+++ b/run_sepp.py
+Index: sepp/run_sepp.py
+===================================================================
+--- sepp.orig/run_sepp.py
++++ sepp/run_sepp.py
 @@ -1,4 +1,4 @@
 -#!/usr/bin/env python
 +#!/usr/bin/env python3
  # -*- coding: utf-8 -*-
  from sepp.exhaustive import ExhaustiveAlgorithm
  
---- a/run_tipp.py
-+++ b/run_tipp.py
+Index: sepp/run_tipp.py
+===================================================================
+--- sepp.orig/run_tipp.py
++++ sepp/run_tipp.py
 @@ -1,4 +1,4 @@
 -#!/usr/bin/env python
 +#!/usr/bin/env python3
  # -*- coding: utf-8 -*-
  from sepp.exhaustive_tipp import main
  
---- a/run_tipp_tool.py
-+++ b/run_tipp_tool.py
+Index: sepp/run_tipp_tool.py
+===================================================================
+--- sepp.orig/run_tipp_tool.py
++++ sepp/run_tipp_tool.py
 @@ -1,4 +1,4 @@
 -#!/usr/bin/env python
 +#!/usr/bin/env python3
  # -*- coding: utf-8 -*-
  
  
---- a/run_upp.py
-+++ b/run_upp.py
+Index: sepp/run_upp.py
+===================================================================
+--- sepp.orig/run_upp.py
++++ sepp/run_upp.py
 @@ -1,4 +1,4 @@
 -#!/usr/bin/env python
 +#!/usr/bin/env python3
  # -*- coding: utf-8 -*-
  from sepp.exhaustive_upp import main
  
+Index: sepp/sepp-package/run-sepp.sh
+===================================================================
+--- sepp.orig/sepp-package/run-sepp.sh
++++ sepp/sepp-package/run-sepp.sh
+@@ -134,7 +134,14 @@ set -e
+ if [ ! -z "$printDebug" ]; then
+ 	export SEPP_DEBUG=True
+ fi;
+-python $DIR/sepp/run_sepp.py -P $p -A $a -t $t -a $alg -r $rxi -f $f -o $name $opts -d $tmp/ -p $tmpssd 1>sepp-$name-out.log 2>sepp-$name-err.log
++
++runMe=/usr/bin/run_sepp.py
++if [ -e $DIR/sepp/run_sepp.py ]; then
++	runMe=$DIR/sepp/run_sepp.py
++fi
++
++echo "I: Invoking python3 $runMe -P $p -A $a -t $t -a $alg -r $rxi -f $f -o $name $opts -d $tmp/ -p $tmpssd 1>sepp-$name-out.log 2>sepp-$name-err.log"
++python3 $runMe -P $p -A $a -t $t -a $alg -r $rxi -f $f -o $name $opts -d $tmp/ -p $tmpssd 1>sepp-$name-out.log 2>sepp-$name-err.log
+ 
+ tail sepp-$name-*
+ 


=====================================
debian/rules
=====================================
@@ -38,6 +38,10 @@ override_dh_auto_clean:
 	$(RM) -rf tools/bundled
 	$(RM) -rf tools/merge/build
 	$(RM) sepp.config tipp.config upp.config
+	find . -name "*.class" -delete
+	find . -name "*.jar" -delete
+	rm -f  home.path sepp.egg-info/PKG-INFO sepp.egg-info/SOURCES.txt sepp.egg-info/dependency_links.txt sepp.egg-info/requires.txt sepp.egg-info/top_level.txt
+
 
 override_dh_auto_install:
 	dh_auto_install



View it on GitLab: https://salsa.debian.org/med-team/sepp/-/commit/5fd4cab3e7c8a096cb4b631b60916b75eddc0503

-- 
View it on GitLab: https://salsa.debian.org/med-team/sepp/-/commit/5fd4cab3e7c8a096cb4b631b60916b75eddc0503
You're receiving this email because of your account on salsa.debian.org.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20201212/373876eb/attachment-0001.html>