debian/changelog

+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@debian.org>  Sun, 15 Dec 2019 16:37:09 +0100
+
 dwgsim (0.1.12-2) unstable; urgency=medium
 
   * Team upload.

debian/compat

-11
\ No newline at end of file

debian/control

@@ -3,11 +3,11 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
 Uploaders: Kevin Murray <spam@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

+Description: Use 2to3 to port from Python2 to Python3
+Bug-Debian: https://bugs.debian.org/943001 
+Author: Andreas Tille <tille@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

 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

@@ -7,3 +7,4 @@ Registry:
   Entry: SCR_002342
 - Name: conda:bioconda
   Entry: dwgsim
+Bug-Database: https://github.com/nh13/DWGSIM/issues