[med-svn] [Git][med-team/ragout][master] 4 commits: More stable clean. Another Python3 issue.

[Steffen Möller]

Steffen Möller pushed to branch master at Debian Med / ragout


Commits:
6a1d3049 by Steffen Möller at 2020-01-04T19:23:02+01:00
More stable clean. Another Python3 issue.

- - - - -
b49f7374 by Steffen Möller at 2020-01-04T19:27:42+01:00
dfsg -> ds

- - - - -
f8d2ee67 by Steffen Möller at 2020-01-04T19:37:56+01:00
Added d/gbp.conf

- - - - -
9c222fd0 by Steffen Möller at 2020-01-04T19:38:10+01:00
It is a team-upload

- - - - -


5 changed files:

- debian/changelog
- + debian/gbp.conf
- debian/patches/2to3.patch
- debian/rules
- debian/watch


Changes:

=====================================
debian/changelog
=====================================
@@ -1,4 +1,6 @@
-ragout (2.2-1) unstable; urgency=medium
+ragout (2.2+ds-1) unstable; urgency=medium
+
+  * Team upload
 
   [Andreas Tille]
   * New upstream version
@@ -10,12 +12,15 @@ ragout (2.2-1) unstable; urgency=medium
   * Not having Python install binaries in setup.py, chaning
     d/ragout.install accordingly
   * bin/ragout was still about to invoke python2
+  * maketrans is now a static function of str
   * not allowing bin/ragout to change $PATH 
   * demoted sibelia to recommends runtime dependency as there are
     modules that don't use it.
     TODO: Find out what happened to
       https://salsa.debian.org/med-team/sibelia
     which is not in new or main.
+  * use "ds" not "dfsg" as version suffix since files were removed
+    but no functional changes have been performed.
 
  -- Steffen Moeller <moeller at debian.org>  Sat, 04 Jan 2020 19:07:58 +0100
 


=====================================
debian/gbp.conf
=====================================
@@ -0,0 +1,3 @@
+[import-orig]
+pristine-tar = True
+


=====================================
debian/patches/2to3.patch
=====================================
@@ -422,10 +422,10 @@ Index: ragout/ragout/main.py
 -#import synteny_backend.cactus
 -import synteny_backend.maf
 -import synteny_backend.hal
-+from synteny_backend import sibelia
++from ragout.synteny_backend import sibelia
 +#from synteny_backend import cactus
-+from synteny_backend import maf
-+from synteny_backend import hal
++from ragout.synteny_backend import maf
++from ragout.synteny_backend import hal
  
  logger = logging.getLogger()
  debugger = DebugConfig.get_instance()
@@ -1269,3 +1269,27 @@ Index: ragout/bin/ragout
  #Ragout entry point
  from ragout.main import main
  sys.exit(main())
+Index: ragout/ragout/parsers/fasta_parser.py
+===================================================================
+--- ragout.orig/ragout/parsers/fasta_parser.py
++++ ragout/ragout/parsers/fasta_parser.py
+@@ -8,8 +8,6 @@ This module provides some basic FASTA I/
+ 
+ import logging
+ 
+-from string import maketrans
+-
+ logger = logging.getLogger()
+ 
+ class FastaError(Exception):
+@@ -61,8 +59,8 @@ def write_fasta_dict(fasta_dict, filenam
+                 f.write(fasta_dict[header][i:i + 60] + "\n")
+ 
+ 
+-COMPL = maketrans("ATGCURYKMSWBVDHNXatgcurykmswbvdhnx",
+-                  "TACGAYRMKSWVBHDNXtacgayrmkswvbhdnx")
++COMPL = str.maketrans("ATGCURYKMSWBVDHNXatgcurykmswbvdhnx",
++                      "TACGAYRMKSWVBHDNXtacgayrmkswvbhdnx")
+ def reverse_complement(string):
+     return string[::-1].translate(COMPL)
+ 


=====================================
debian/rules
=====================================
@@ -15,7 +15,7 @@ override_dh_install:
 	find debian -name LICENSE -delete
 
 override_dh_auto_clean:
-	dh_auto_clean
+	dh_auto_clean || true
 	rm -f bin/ragout-maf2synteny bin/ragout-overlap
 	rm -rf .pybuild
 	find . -name "*.o" -delete


=====================================
debian/watch
=====================================
@@ -1,4 +1,4 @@
 version=4
 
-opts="repacksuffix=+dfsg,dversionmangle=auto,repack,compression=xz" \
+opts="repacksuffix=+ds,dversionmangle=auto,repack,compression=xz" \
   https://github.com/fenderglass/Ragout/releases/latest .*/archive/v?@ANY_VERSION@@ARCHIVE_EXT@



View it on GitLab: https://salsa.debian.org/med-team/ragout/compare/c8991daa17bb287539836c822f77dfe48368fe61...9c222fd000295dbf25fb2756261a7dfcd3bdfa2b

-- 
View it on GitLab: https://salsa.debian.org/med-team/ragout/compare/c8991daa17bb287539836c822f77dfe48368fe61...9c222fd000295dbf25fb2756261a7dfcd3bdfa2b
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