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lint fails more gracefully in travis doesn't have before_install #113

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merged 1 commit into from
Aug 9, 2018

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HadrienG
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@HadrienG HadrienG commented Aug 9, 2018

Previous behaviour:

Traceback (most recent call last):
  File "/usr/local/bin/nf-core", line 117, in <module>
    nf_core_cli()
  File "/usr/local/lib/python3.7/site-packages/click/core.py", line 722, in __call__
    return self.main(*args, **kwargs)
  File "/usr/local/lib/python3.7/site-packages/click/core.py", line 697, in main
    rv = self.invoke(ctx)
  File "/usr/local/lib/python3.7/site-packages/click/core.py", line 1066, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/usr/local/lib/python3.7/site-packages/click/core.py", line 895, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/usr/local/lib/python3.7/site-packages/click/core.py", line 535, in invoke
    return callback(*args, **kwargs)
  File "/usr/local/bin/nf-core", line 45, in lint
    lint_obj = nf_core.lint.run_linting(pipeline_dir, release)
  File "/usr/local/lib/python3.7/site-packages/nf_core/lint.py", line 45, in run_linting
    lint_obj.lint_pipeline(release)
  File "/usr/local/lib/python3.7/site-packages/nf_core/lint.py", line 127, in lint_pipeline
    getattr(self, fname)()
  File "/usr/local/lib/python3.7/site-packages/nf_core/lint.py", line 359, in check_ci_config
    assert(docker_pull_cmd in ciconf.get('before_install'))
TypeError: argument of type 'NoneType' is not iterable

New behaviour:

ERROR: Test Failures:
  http://nf-co.re/errors#5: CI does not contain a before_install step that pulls the docker image

ERROR: Sorry, some tests failed - exiting with a non-zero error code...

@HadrienG HadrienG requested a review from ewels August 9, 2018 08:53
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codecov-io commented Aug 9, 2018

Codecov Report

Merging #113 into master will decrease coverage by 0.28%.
The diff coverage is 0%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master     #113      +/-   ##
==========================================
- Coverage   95.31%   95.02%   -0.29%     
==========================================
  Files           6        6              
  Lines         661      663       +2     
==========================================
  Hits          630      630              
- Misses         31       33       +2
Impacted Files Coverage Δ
nf_core/lint.py 97% <0%> (-0.65%) ⬇️

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@ewels
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ewels commented Aug 9, 2018

Looks great! Decreases test coverage by a line or two, but I think that's fine

@ewels ewels merged commit a6ab045 into nf-core:master Aug 9, 2018
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ewels commented Aug 10, 2018

Ah no! This one was master too. I will also revert this.

If you add a new PR against dev it should contain both this PR and also #122 and we can merge properly.

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3 participants