Add option to update modules with linting #1588
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@@ Coverage Diff @@
## dev #1588 +/- ##
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- Coverage 64.65% 64.44% -0.21%
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Files 54 54
Lines 6232 6288 +56
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+ Hits 4029 4052 +23
- Misses 2203 2236 +33
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nf_core/__main__.py
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| @@ -594,7 +594,8 @@ def create_test_yml(ctx, tool, run_tests, output, force, no_prompts): | |||
| @click.option("-a", "--all", is_flag=True, help="Run on all modules") | |||
| @click.option("--local", is_flag=True, help="Run additional lint tests for local modules") | |||
| @click.option("--passed", is_flag=True, help="Show passed tests") | |||
| def lint(ctx, tool, dir, key, all, local, passed): | |||
| @click.option("--fix", is_flag=True, help="Fix the module version if a newer version is available") | |||
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Here I'm not sure if --fix alone is a good flag name or it would be better to call it --fix_version. When running the nf-core modules lint with a --fix option, I would expect that this fixes potentially all the linting errors and not only the tool version. What do you think?
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Or maybe in a similar way that nf-core lint --fix works, by providing which kind of linting failure should be fixed. E.g. nf-core modules lint --fix versions. Not sure if it is possible to implement like this in this case
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Yes, that's true, it can also be misleading with the --fix option from the pipeline linting. I will do some refactoring to --fix_version
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I've checked the functionality of the --fix flag in the pipeline linting and I think it's different from what we have here with the version, as it allows the different lint tests, but the version fix is included in the linting of main.nf.
I changed the name of the flag to --fix-version, and we can implement the option to run specific lint tests in a different PR, do you agree?
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Apart from the comment I made, testing worked well for me:
nf-core modules lint --fix
,--./,-.
___ __ __ __ ___ /,-._.--~\
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/tools version 2.5.dev0 - https://nf-co.re
? Lint all modules or a single named module? Named module
? Tool name: kallisto/index
INFO Linting modules repo: '.' __init__.py:170
INFO Linting module: 'kallisto/index' __init__.py:174
INFO Updating package 'bioconda::kallisto' 0.46.2 -> 0.48.0
╭───────────────────────╮
│ LINT RESULTS SUMMARY │
├───────────────────────┤
│ [✔] 21 Tests Passed │
│ [!] 0 Test Warnings │
│ [✗] 0 Tests Failed │
╰───────────────────────╯
and I got these changes that I added to this PR, so all looks good to me!
Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>
Related to #1434
Add the --fix argument to linting of modules.
If --fix flag is provided, the module is updated to the latest version.
PR checklist
CHANGELOG.mdis updateddocsis updated