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Modules restructure #1859

Merged
merged 29 commits into from
Oct 4, 2022
Merged

Modules restructure #1859

merged 29 commits into from
Oct 4, 2022

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mirpedrol
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Apply the changes needed for the restructure of the nf-core/modules repository.

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

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codecov bot commented Oct 3, 2022

Codecov Report

Merging #1859 (ee8459a) into dev (aca662e) will decrease coverage by 0.15%.
The diff coverage is 59.37%.

@@            Coverage Diff             @@
##              dev    #1859      +/-   ##
==========================================
- Coverage   64.64%   64.49%   -0.16%     
==========================================
  Files          34       34              
  Lines        4115     4137      +22     
==========================================
+ Hits         2660     2668       +8     
- Misses       1455     1469      +14     
Impacted Files Coverage Δ
nf_core/__main__.py 53.50% <0.00%> (ø)
nf_core/modules/info.py 16.66% <0.00%> (-0.38%) ⬇️
nf_core/modules/lint/main_nf.py 65.76% <ø> (ø)
nf_core/modules/lint/meta_yml.py 67.39% <ø> (ø)
nf_core/modules/lint/module_changes.py 85.71% <ø> (ø)
nf_core/modules/lint/module_patch.py 58.66% <ø> (ø)
nf_core/modules/lint/module_version.py 82.60% <ø> (ø)
nf_core/modules/module_utils.py 49.10% <56.25%> (+0.10%) ⬆️
nf_core/modules/modules_command.py 84.21% <66.66%> (+0.42%) ⬆️
nf_core/modules/modules_repo.py 81.31% <69.23%> (+0.20%) ⬆️
... and 6 more

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@ewels ewels left a comment

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This is a huge amount of work! 🙇🏻

Only made it a couple of files in but thought I'd submit now to get my questions in. Will try to read more but likely won't have time for a full review.

nf_core/__main__.py Outdated Show resolved Hide resolved
@@ -93,7 +93,8 @@ def init_mod_name(self, module):
if self.repo_type == "modules":
modules = self.get_modules_clone_modules()
else:
modules = self.modules_json.get_all_modules().get(self.modules_repo.fullname)
modules = self.modules_json.get_all_modules().get(self.modules_repo.remote_url)
modules = [module if dir == "nf-core" else f"{dir}/{module}" for dir, module in modules]
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Reading quickly so can't see the full context, but why do we need special treatment for nf-core here?

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This is to get the module name suggestions, it will usually be nf-core, so we don't need to have nf-core/TOOL, but in case you have modules from other repos I thought it would be nice to differentiate and have the other directory listed.

@@ -153,7 +156,7 @@ def get_local_yaml(self):

log.debug(f"Module '{self.module}' meta.yml not found locally")
else:
module_base_path = os.path.join(self.dir, "modules")
module_base_path = os.path.join(self.dir, "modules", "nf-core")
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As above, hardcoded nf-core strings make me nervous 😅

nf_core/__main__.py Outdated Show resolved Hide resolved
nf_core/__main__.py Outdated Show resolved Hide resolved
@maxulysse
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checks are all green, that's good enough for me

@mirpedrol mirpedrol merged commit 3e52b75 into dev Oct 4, 2022
@mirpedrol mirpedrol deleted the modules-restructure branch October 4, 2022 09:49
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3 participants