Adding nf-core modules lint command
#842
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@@ Coverage Diff @@
## dev #842 +/- ##
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- Coverage 70.51% 69.79% -0.72%
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Files 33 34 +1
Lines 3680 4129 +449
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+ Hits 2595 2882 +287
- Misses 1085 1247 +162
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By the way I've added the file comparison code as a function of the Or did you plan to have that code within this function: |
Co-authored-by: Harshil Patel <[email protected]>
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Awesome work! Made a few changes but generally fairly happy now. I'm sure it'll need a lot more work still but I think it's fine to merge.
- Changed how lint tests are reported
- Gave everything a test id, so that we can add in the ability to ignore tests in the future with a config, and link to docs.
- Print results in a table with a column for file path, much easier to read
- Added
--alland if neither that nor tool name is given, run prompts to ask what to lint - Other stuff probably. It's late.
PR checklist
CHANGELOG.mdis updateddocsis updatedThis PR adds the command
nf-core modules lint <directory> <module>to nf-core.There are still some things to do, like adding tests, updating the docs and integrating with
nf-core lint, but I felt now is the right time to do at least a draft PR in case a different structure is desired :)Description
I have added a
ModuleLintclass in themodules.pyfile, which takes care of the linting. Given a directory, it checks whether it is a clone ofnf-core/modulesor a pipeline directory. In the former cases, it makes some checks for every module and also looks for the necessary test files. When additionally given a module name in the forsoftware/toolorsoftware(depending on the module), it only lints this module.When using on a nf-core pipeline directory, it performs the same checks for all modules installed from nf-core (except for the tests) and also runs some quick checks on the local modules (only issuing warnings here).
The
ModuleLint.lint()function returns a dict of{passed, warned, failed}which can be used to integrate the results directly intonf-core lint. When used on it's own it can also print similar results asnf-core lint(I basically copied the_print_resultscode :) )Alright, that's the current status. What's left to do:
nf-core lintI would be glad to get some feedback on further checks that could be implemented (or left-out) and of course let me if I should change something in the overall structure.