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 <[email protected]> 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 <[email protected]. Uploaders: Kevin Murray <[email protected]> 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 <[email protected]> +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.
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