Fix linting multiple remotes

[mashehu]

Addresses #2052.

[awgymer]

From the error logs:

LookupError: Could not find branch information for component
'custom/custom/dumpsoftwareversions'.Please remove the 'modules.json' and rerun
the command to recreate it

That path looks wrong, like it's derived custom as the org path?

[mirpedrol]

LGTM! I also tested it and seems to work nicely 👌

[awgymer]

There is another error because ModulesJson.get_all_components returns None if it would return {}.
There is only one place in the codebase that this is expected:

tools/nf_core/components/info.py

Lines 107 to 117 in 53ccaef

	else:
	components = self.modules_json.get_all_components(self.component_type).get(
	self.modules_repo.remote_url
	)
	components = [
	component if dir == "nf-core" else f"{dir}/{component}" for dir, component in components
	]
	if components is None:
	raise UserWarning(
	f"No {self.component_type[:-1]} installed from '{self.modules_repo.remote_url}'"
	)

But actually if it ever returned None the list comprehension would error and if components is None would never be reached

This is wrong too. That actually uses .get so would fail! I don't think anywhere in the codebase expects or can handle a return value of None. (The list comp point still stands though - that will fail if .get returns None)

[awgymer]

Error from test_modules_lint_patched_modules:

╭─ [!] 4 Module Test Warnings ─────────────────────────────────────────────────╮
│                                           ╷                ╷                 │
│ Module name                               │ File path      │ Test message    │
│╶──────────────────────────────────────────┼────────────────┼────────────────╴│
│ bismark/align                             │ modules/nf-co… │ Conda update:   │
│                                           │                │ bioconda::bism… │
│                                           │                │ 0.23.0 ->       │
│                                           │                │ 0.24.0          │
│ custom/dumpsoftwareversions               │ modules/nf-co… │ New version     │
│                                           │                │ available       │
│ fastqc                                    │ modules/nf-co… │ New version     │
│                                           │                │ available       │
│ custom/dumpsoftwareversions               │ modules/nf-co… │ Process name    │
│                                           │                │ not used for    │
│                                           │                │ versions.yml    │
│                                           ╵                ╵                 │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ [✗] 1 Module Test Failed ───────────────────────────────────────────────────╮
│                                           ╷                ╷                 │
│ Module name                               │ File path      │ Test message    │
│╶──────────────────────────────────────────┼────────────────┼────────────────╴│
│ bismark/align                             │ modules/nf-co… │ Local copy of   │
│                                           │                │ module does not │
│                                           │                │ match remote    │
│                                           ╵                ╵                 │
╰──────────────────────────────────────────────────────────────────────────────╯

And the difference:

input:                                                                    
 -    tuple val(meta), path(reads)                                              
 -    path index                                                                
 +    tuple val(meta), path(reads), path(index)      

[awgymer]

test_modules_lint_no_gitlab fails because it sees modules:

custom/dumpsoftwareversions | /var/folders/q2/785gjdb95c952rl7m18rzmww0000gp/T/tmp7lru83qs/mypipeline/modules/nf-core/custom/dumpsoftwareversions
fastqc | /var/folders/q2/785gjdb95c952rl7m18rzmww0000gp/T/tmp7lru83qs/mypipeline/modules/nf-core/fastqc
multiqc | /var/folders/q2/785gjdb95c952rl7m18rzmww0000gp/T/tmp7lru83qs/mypipeline/modules/nf-core/multiqc

It seems that it is fetching all modules regardless of the org?
This makes sense since you are in self.pipeline_dir.
self.all_remote_modules is collated as a list of all modules from all remotes.

[codecov]

Codecov Report

Merging #2071 (0a33a77) into dev (8fadd99) will increase coverage by 0.13%.
The diff coverage is 96.29%.

@@            Coverage Diff             @@
##              dev    #2071      +/-   ##
==========================================
+ Coverage   67.84%   67.98%   +0.13%     
==========================================
  Files          43       43              
  Lines        5592     5597       +5     
==========================================
+ Hits         3794     3805      +11     
+ Misses       1798     1792       -6     

Impacted Files	Coverage Δ
nf_core/components/info.py	80.00% <0.00%> (ø)
nf_core/components/remove.py	84.81% <100.00%> (+1.26%)	⬆️
nf_core/components/update.py	81.51% <100.00%> (ø)
nf_core/modules/lint/__init__.py	83.51% <100.00%> (+0.62%)	⬆️
nf_core/modules/lint/module_changes.py	87.50% <100.00%> (+1.78%)	⬆️
nf_core/modules/lint/module_version.py	82.60% <100.00%> (+0.79%)	⬆️
nf_core/modules/modules_repo.py	83.49% <100.00%> (ø)
nf_core/modules/nfcore_module.py	100.00% <100.00%> (ø)
nf_core/modules/lint/main_nf.py	66.15% <0.00%> (+1.52%)	⬆️

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