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Workflow validation #819

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wants to merge 88 commits into from
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Workflow validation #819

wants to merge 88 commits into from

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KevinMenden
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PR checklist

  • This comment contains a description of changes (with reason)
  • CHANGELOG.md is updated
  • If you've fixed a bug or added code that should be tested, add tests!
  • Documentation in docs is updated

Added the lint function actions_schema_validation which uses the GitHub workflow JSON schema to validate GitHub action workflows in .github/workflows/.

As suggested in #795

@ewels
Bump version to 1.13dev
0c81522
@ewels
Merge pull request nf-core#808 from ewels/master
27a7513 
Bump version to 1.13dev
@ewels
Rename test functions to exclude check_ prefix
993ef82
@ewels
Start playing around with improving the sphinx docs for linting
eafa914
@ewels
Fight with sphinx a bit more
70dd0d4
@ewels
Make each lint test return its results instead of updating the object
a99b7f4
@ewels
Don't use numeric test IDs
7a52fef
@ewels
Added ability to optionally load a pipeline lint config file
15d4f5e
@ewels
Config: skip test if named and is false
3b494ce
@ewels
Rename .nf-core-lint-config.yml to .nf-core-lint.yml
c01e9e4
@ewels
Log / report ignored tests
89df655
@ewels
Make module directory for linting
44ad230
@ewels
Break lint functions out into their own files
0f7f023
@ewels
Testing and tidying of the newly split linting code
0abffb4
@ewels
Add sphinx docs .rst files for all new lint test functions
f9093cb
@ewels
More bugfixes as I start working on tests
558c1d6
@ewels
Deleted lint examples, started rewriting lint tests
0a4319c
@ewels
Remove somewhat pointless lint test 'docker'
99ad455
@ewels
Spinx docs - move function reference into a subdir called 'API Refere…
abd4544 
…nce'
@ewels
Lint pytests - comment out old tests
664895e
@ewels
Lint tests - more core tests
6046bde 
* Test that loading a nf-core-lint.yml config works and properly ignores all tests
* Test the JSON results dumping (mostly the old test, fixed up)
@ewels
Lint tests - more core functions, slight simplification
094ca66
@ewels
Update lint function names in nf-core licences
3c3debd
@ewels
Clean up missing self. references in simplification of test code
02aa6dd
@ewels
Fix old references to lint_pipeline() function
1f0e4cf
@ewels
Set the pipeline name in the helper function, not a test
0eec578
@ewels
Bump versions - run all linting load functions
43cd4ba
@ewels
Try to disentangle nf_core.lint from rest of nf_core package
9603afb
@ewels
Rewrite bump-version to not using linting code.
fe268d1 
* Also made it a lot more lenient in not failing when files not found. Should fix nf-core#772
* Rewrote code to do multiple find+replace for a single file in one function call.
@ewels
Rewrite tests for bump-version
dc60c20
jfy133 and others added 28 commits December 10, 2020 13:38
@jfy133
Merge pull request nf-core#812 from nf-core/issue811
4a11490 
fix typo
@ewels
Lint test actions_lint - docs + functionality
fe9ab0a 
* Ported docs from errors.md to the docstring in rst
* Added an additional lint test to also check that yamllint is running
* Updated the nf-core lint command to match the current workflow
@ewels
Add requirements.txt for Sphinx docs generation
cb14fc7
@ewels
Docs: Small intro for tools docs homepage
6268eb8
@ewels
Ported lint error docs to docstring: conda_dockerfile
5368414
@ewels
errors to docstrings - conda_env_yaml
e8c34f0
@ewels
Fixup more lenient make_lint_rst.py helper script
364a340
@ewels
Errors to docstring - cookiecutter_strings
c4d9b59
@ewels
Files exist docs - minor tweaks
bf58a60
@ewels
Errors to docstring - licence lint test
daae3dd
@ewels
Errors to docstring - pipeline name conventions
d399079
@ewels
Errors to docstring - pipeline todos
b28eb12
@ewels
Errors to docstring - readme lint test
d2f63cd
@ewels
Errors to docstring - schema lint
117ba8f
@ewels
Errors to docstring - schema params
f9bef03
@ewels
Errors to docstring - version consistency
b6e64b4
@ewels
Errors to docstring - nextflow config
1a8b4b4
@ewels
Remove docs/lint_errors.md
135fb8b
@ewels
Merge pull request nf-core#809 from ewels/lint-refactoring
801bbf3 
Lint refactoring
@ewels
Fix sphinx api docs generation Actions workflow
fe15509
@ewels
Merge pull request nf-core#813 from ewels/fix-sphinx-docs
2571770 
Fix sphinx docs
@ewels
Ignore the gitignore for sphinx docs
6457b4d
@ewels
Merge pull request nf-core#814 from ewels/fix-sphinx-again
14f54a3 
Ignore the gitignore for sphinx docs
@KevinMenden
working schema validation of github workflows
f1235f3
@KevinMenden
added rst file
77345ee
@KevinMenden
added tests
86b4765
@KevinMenden
cosmetic changes
ec66c18
@KevinMenden
updated changelog
543e867
@github-actions
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github-actions bot commented Jan 5, 2021

Hi @KevinMenden,

It looks like this pull-request has been made against the KevinMenden/tools master branch. The master branch on nf-core repositories should always contain code from the latest release. Because of this, PRs to master are only allowed if they come from the KevinMenden/tools dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.

Thanks again for your contribution!

@KevinMenden KevinMenden closed this Jan 5, 2021
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4 participants
@KevinMenden @ewels @subwaystation @jfy133