[Bug 2093383] [NEW] kineticstools fails autopkgtest due to argparse changes in python 3.13

[Vladimir Petko]

Public bug reported:

The autopkgtest fails with the following error:

32s ======================== 7 passed, 12 skipped in 1.07s =========================
132s cram3 --verbose --xunit-file=cramtests.xml `ls test/cram/*.t | grep -v detection_bam`
134s test/cram/version.t: failed
134s --- test/cram/version.t
134s +++ test/cram/version.t.err
134s @@ -5,8 +5,8 @@
134s  
134s    $ ipdSummary
134s    usage: ipdSummary [-h] [--version] [--log-file LOG_FILE]
134s -                    [--log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL} | --debug | --quiet | -v]
134s -                    --reference REFERENCE [--gff GFF] [--csv CSV]
134s +                    [--log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL} | --debug |
134s +                    --quiet | -v] --reference REFERENCE [--gff GFF] [--csv CSV]
134s                      [--bigwig BIGWIG] [--numWorkers NUMWORKERS]
134s                      [--pvalue PVALUE] [--maxLength MAXLENGTH]
134s                      [--identify IDENTIFY] [--methylFraction] [--outfile OUTFILE]
134s # Ran 1 tests, 0 skipped, 1 failed.
134s make: *** [Makefile:32: cram-tests] Error 1
134s autopkgtest [11:37:13]: test command1: -----------------------]
134s autopkgtest [11:37:13]: test command1:  - - - - - - - - - - results - - - - - - - - - -
134s command1             FAIL non-zero exit status 2
135s autopkgtest [11:37:14]: @@@@@@@@@@@@@@@@@@@@ summary
135s command1             FAIL non-zero exit status 2
140s nova [W] Skipping flock for amd64


[1] https://autopkgtest.ubuntu.com/results/autopkgtest-
plucky/plucky/amd64/k/kineticstools/20250105_113719_ea200@/log.gz

** Affects: kineticstools (Ubuntu)
     Importance: Undecided
         Status: New

** Affects: python3.13 (Ubuntu)
     Importance: Undecided
         Status: New

** Also affects: python3.13 (Ubuntu)
   Importance: Undecided
       Status: New

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https://bugs.launchpad.net/bugs/2093383

Title:
  kineticstools fails autopkgtest due to argparse changes in python 3.13

Status in kineticstools package in Ubuntu:
  New
Status in python3.13 package in Ubuntu:
  New

Bug description:
  The autopkgtest fails with the following error:

  32s ======================== 7 passed, 12 skipped in 1.07s =========================
  132s cram3 --verbose --xunit-file=cramtests.xml `ls test/cram/*.t | grep -v detection_bam`
  134s test/cram/version.t: failed
  134s --- test/cram/version.t
  134s +++ test/cram/version.t.err
  134s @@ -5,8 +5,8 @@
  134s  
  134s    $ ipdSummary
  134s    usage: ipdSummary [-h] [--version] [--log-file LOG_FILE]
  134s -                    [--log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL} | --debug | --quiet | -v]
  134s -                    --reference REFERENCE [--gff GFF] [--csv CSV]
  134s +                    [--log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL} | --debug |
  134s +                    --quiet | -v] --reference REFERENCE [--gff GFF] [--csv CSV]
  134s                      [--bigwig BIGWIG] [--numWorkers NUMWORKERS]
  134s                      [--pvalue PVALUE] [--maxLength MAXLENGTH]
  134s                      [--identify IDENTIFY] [--methylFraction] [--outfile OUTFILE]
  134s # Ran 1 tests, 0 skipped, 1 failed.
  134s make: *** [Makefile:32: cram-tests] Error 1
  134s autopkgtest [11:37:13]: test command1: -----------------------]
  134s autopkgtest [11:37:13]: test command1:  - - - - - - - - - - results - - - - - - - - - -
  134s command1             FAIL non-zero exit status 2
  135s autopkgtest [11:37:14]: @@@@@@@@@@@@@@@@@@@@ summary
  135s command1             FAIL non-zero exit status 2
  140s nova [W] Skipping flock for amd64


  [1] https://autopkgtest.ubuntu.com/results/autopkgtest-
  plucky/plucky/amd64/k/kineticstools/20250105_113719_ea200@/log.gz

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