Refactor nf-core modules commands
#1124
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Codecov Report
@@ Coverage Diff @@
## dev #1124 +/- ##
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+ Coverage 70.41% 70.58% +0.16%
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Files 45 48 +3
Lines 4797 4827 +30
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+ Hits 3378 3407 +29
- Misses 1419 1420 +1
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Hi @ErikDanielsson , overall I think this is a nice idea! One thing that is a bit tricky with the modules commands though is that some of them (mostly But other than that I think this is nice! But would be nice to hear what @ewels thinks about this :) |
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Thanks, I'll take a look at the lint code. |
ewels
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On my phone, didn't get very far with the review sorry. But concept sounds great! I'm happy to merge if it LGTM you guys. Especially as high risk for merge conflicts.
nf_core/modules/install.py
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| def install(self, module): | ||
| if self.repo_type == "modules": | ||
| log.error("You cannot install a module in a clone of nf-core/modules") | ||
| sys.exit(1) |
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Can we raise an exception instead and catch it in the cli code? I prefer not to have exits anywhere but there if possible.
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Other checks just return false. So that would also be fine.
Refactored
pipeline_modules.pyinto one file file pernf-core modulescommand.pipeline_modules.pyModuleCommandformodulescommands to inherit from.list,installandremovecommands.The
modulescommands are all now found in<command>.py.PR checklist
CHANGELOG.mdis updateddocsis updated