[med-svn] [Git][med-team/dwgsim][master] 6 commits: Use 2to3 to port from Python2 to Python3
Andreas Tille
gitlab at salsa.debian.org
Sun Dec 15 16:03:38 GMT 2019
Andreas Tille pushed to branch master at Debian Med / dwgsim
Commits:
875e540a by Andreas Tille at 2019-12-15T15:35:28Z
Use 2to3 to port from Python2 to Python3
- - - - -
125ba162 by Andreas Tille at 2019-12-15T15:36:37Z
Replace python-markdown by markdown
- - - - -
e06469ba by Andreas Tille at 2019-12-15T15:37:01Z
routine-update: debhelper-compat 12
- - - - -
7946f246 by Andreas Tille at 2019-12-15T15:37:03Z
routine-update: Standards-Version: 4.4.1
- - - - -
a7216f5d by Andreas Tille at 2019-12-15T15:37:09Z
Set upstream metadata fields: Bug-Database.
- - - - -
60ccf2b2 by Andreas Tille at 2019-12-15T15:58:38Z
routine-update: Ready to upload to unstable
- - - - -
7 changed files:
- debian/changelog
- − debian/compat
- debian/control
- + debian/patches/2to3.patch
- debian/patches/series
- debian/rules
- debian/upstream/metadata
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,15 @@
+dwgsim (0.1.12-3) unstable; urgency=medium
+
+ * Team upload.
+ * Use 2to3 to port from Python2 to Python3
+ Closes: #943001
+ * Replace python-markdown by markdown
+ * debhelper-compat 12
+ * Standards-Version: 4.4.1
+ * Set upstream metadata fields: Bug-Database.
+
+ -- Andreas Tille <tille at debian.org> Sun, 15 Dec 2019 16:37:09 +0100
+
dwgsim (0.1.12-2) unstable; urgency=medium
* Team upload.
=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-11
\ No newline at end of file
=====================================
debian/control
=====================================
@@ -3,11 +3,11 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Kevin Murray <spam at kdmurray.id.au>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 12),
samtools (>= 1.7-2),
- python-markdown,
+ markdown,
zlib1g-dev
-Standards-Version: 4.3.0
+Standards-Version: 4.4.1
Vcs-Browser: https://salsa.debian.org/med-team/dwgsim
Vcs-Git: https://salsa.debian.org/med-team/dwgsim.git
Homepage: https://github.com/nh13/DWGSIM/
=====================================
debian/patches/2to3.patch
=====================================
@@ -0,0 +1,105 @@
+Description: Use 2to3 to port from Python2 to Python3
+Bug-Debian: https://bugs.debian.org/943001
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Sun, 15 Dec 2019 16:33:53 +0100
+
+--- a/scripts/dwgsim_eval_plot.py
++++ b/scripts/dwgsim_eval_plot.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+
+ import os
+ import sys
+@@ -34,7 +34,7 @@ class Table:
+ fh.close()
+
+ # re-arrange the data
+- self.matrix = [[data[i][j] for j in xrange(ncol)] for i in xrange(len(data))]
++ self.matrix = [[data[i][j] for j in range(ncol)] for i in range(len(data))]
+
+ # NB: assumes sorted descending
+ def __parse(self, line):
+--- a/scripts/galaxy/dwgsim_eval_wrapper.py
++++ b/scripts/galaxy/dwgsim_eval_wrapper.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+
+ """
+ Runs DWGSIM_EVAL
+@@ -46,15 +46,15 @@ def run_process ( cmd, name, tmp_dir, bu
+ pass
+ tmp_stderr.close()
+ if returncode != 0:
+- raise Exception, stderr
+- except Exception, e:
+- raise Exception, 'Error in \'' + name + '\'. \n' + str( e )
++ raise Exception(stderr)
++ except Exception as e:
++ raise Exception('Error in \'' + name + '\'. \n' + str( e ))
+
+ def check_output ( output, canBeEmpty ):
+ if 0 < os.path.getsize( output ):
+ return True
+ elif False == canBeEmpty:
+- raise Exception, 'The output file is empty:' + output
++ raise Exception('The output file is empty:' + output)
+
+ def __main__():
+ #Parse Command Line
+@@ -137,7 +137,7 @@ def __main__():
+ elif None != options.bam:
+ dwgsim_eval_cmd = dwgsim_eval_cmd + ' ' + options.bam
+ else:
+- raise Exception, 'Input file was neither a SAM nor BAM'
++ raise Exception('Input file was neither a SAM nor BAM')
+ dwgsim_eval_cmd = dwgsim_eval_cmd + ' > ' + options.output
+
+ # need to nest try-except in try-finally to handle 2.4
+@@ -147,7 +147,7 @@ def __main__():
+ # check that there are results in the output file
+ check_output ( options.output, False )
+ sys.stdout.write( 'DWGSIM_EVAL successful' )
+- except Exception, e:
++ except Exception as e:
+ stop_err( 'DWGSIM_EVAL failed.\n' + str( e ) )
+ finally:
+ # clean up temp dir
+--- a/scripts/galaxy/dwgsim_wrapper.py
++++ b/scripts/galaxy/dwgsim_wrapper.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+
+ """
+ Runs DWGSIM
+@@ -53,15 +53,15 @@ def run_process ( cmd, name, tmp_dir, bu
+ pass
+ tmp_stderr.close()
+ if returncode != 0:
+- raise Exception, stderr
+- except Exception, e:
+- raise Exception, 'Error in \'' + name + '\'. \n' + str( e )
++ raise Exception(stderr)
++ except Exception as e:
++ raise Exception('Error in \'' + name + '\'. \n' + str( e ))
+
+ def check_output ( output, canBeEmpty ):
+ if 0 < os.path.getsize( output ):
+ return True
+ elif False == canBeEmpty:
+- raise Exception, 'The output file is empty:' + output
++ raise Exception('The output file is empty:' + output)
+
+ def __main__():
+ #Parse Command Line
+@@ -172,7 +172,7 @@ def __main__():
+ # check that there are results in the output file
+ check_output ( options.outputBFAST, False )
+ sys.stdout.write( 'DWGSIM successful' )
+- except Exception, e:
++ except Exception as e:
+ stop_err( 'DWGSIM failed.\n' + str( e ) )
+ finally:
+ # clean up temp dir
=====================================
debian/patches/series
=====================================
@@ -1 +1,2 @@
0001-Debian-ise-makefile.patch
+2to3.patch
=====================================
debian/rules
=====================================
@@ -11,7 +11,7 @@ export DEB_BUILD_MAINT_OPTIONS=hardening=+all
override_dh_auto_build:
dh_auto_build
- markdown_py -f README.html README.md
+ markdown README.md > README.html
override_dh_auto_test:
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
=====================================
debian/upstream/metadata
=====================================
@@ -1,9 +1,10 @@
Registry:
- - Name: OMICtools
- Entry: OMICS_00249
- - Name: bio.tools
- Entry: NA
- - Name: SciCrunch
- Entry: SCR_002342
- - Name: conda:bioconda
- Entry: dwgsim
+- Name: OMICtools
+ Entry: OMICS_00249
+- Name: bio.tools
+ Entry: NA
+- Name: SciCrunch
+ Entry: SCR_002342
+- Name: conda:bioconda
+ Entry: dwgsim
+Bug-Database: https://github.com/nh13/DWGSIM/issues
View it on GitLab: https://salsa.debian.org/med-team/dwgsim/compare/13766dc5d1fc568cef00b3003267642fd244955a...60ccf2b271fb2822a89006ffb81605293ccfc8a7
--
View it on GitLab: https://salsa.debian.org/med-team/dwgsim/compare/13766dc5d1fc568cef00b3003267642fd244955a...60ccf2b271fb2822a89006ffb81605293ccfc8a7
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/20191215/4671f0c3/attachment-0001.html>
More information about the debian-med-commit
mailing list