diff -Nru dwgsim-0.1.12/debian/changelog dwgsim-0.1.12/debian/changelog --- dwgsim-0.1.12/debian/changelog 2019-01-08 12:03:23.000000000 +0000 +++ dwgsim-0.1.12/debian/changelog 2019-12-15 15:37:09.000000000 +0000 @@ -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 Sun, 15 Dec 2019 16:37:09 +0100 + dwgsim (0.1.12-2) unstable; urgency=medium * Team upload. diff -Nru dwgsim-0.1.12/debian/compat dwgsim-0.1.12/debian/compat --- dwgsim-0.1.12/debian/compat 2019-01-08 12:03:23.000000000 +0000 +++ dwgsim-0.1.12/debian/compat 1970-01-01 00:00:00.000000000 +0000 @@ -1 +0,0 @@ -11 \ No newline at end of file diff -Nru dwgsim-0.1.12/debian/control dwgsim-0.1.12/debian/control --- dwgsim-0.1.12/debian/control 2019-01-08 12:03:23.000000000 +0000 +++ dwgsim-0.1.12/debian/control 2019-12-15 15:37:09.000000000 +0000 @@ -3,11 +3,11 @@ Uploaders: Kevin Murray 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/ diff -Nru dwgsim-0.1.12/debian/patches/2to3.patch dwgsim-0.1.12/debian/patches/2to3.patch --- dwgsim-0.1.12/debian/patches/2to3.patch 1970-01-01 00:00:00.000000000 +0000 +++ dwgsim-0.1.12/debian/patches/2to3.patch 2019-12-15 15:37:09.000000000 +0000 @@ -0,0 +1,105 @@ +Description: Use 2to3 to port from Python2 to Python3 +Bug-Debian: https://bugs.debian.org/943001 +Author: Andreas Tille +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 diff -Nru dwgsim-0.1.12/debian/patches/series dwgsim-0.1.12/debian/patches/series --- dwgsim-0.1.12/debian/patches/series 2019-01-08 12:03:23.000000000 +0000 +++ dwgsim-0.1.12/debian/patches/series 2019-12-15 15:37:09.000000000 +0000 @@ -1 +1,2 @@ 0001-Debian-ise-makefile.patch +2to3.patch diff -Nru dwgsim-0.1.12/debian/rules dwgsim-0.1.12/debian/rules --- dwgsim-0.1.12/debian/rules 2019-01-08 12:03:23.000000000 +0000 +++ dwgsim-0.1.12/debian/rules 2019-12-15 15:37:09.000000000 +0000 @@ -11,7 +11,7 @@ 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))) diff -Nru dwgsim-0.1.12/debian/upstream/metadata dwgsim-0.1.12/debian/upstream/metadata --- dwgsim-0.1.12/debian/upstream/metadata 2019-01-08 12:03:23.000000000 +0000 +++ dwgsim-0.1.12/debian/upstream/metadata 2019-12-15 15:37:09.000000000 +0000 @@ -1,7 +1,10 @@ Registry: - - Name: OMICtools - Entry: OMICS_00249 - - Name: bio.tools - Entry: NA - - Name: SciCrunch - Entry: SCR_002342 \ No newline at end of file +- 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