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Improve process label linting #2227

Merged
merged 10 commits into from
Apr 26, 2023
Merged

Improve process label linting #2227

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46fcedf
Lint all labels and check for conflicting or non-standard
awgymer Mar 29, 2023
7849dcc
Add checks for duplicated labels and warn if non-standard labels found
awgymer Apr 4, 2023
2915f2e
Fix indentation so that warning logic is outside loop and not repeate…
awgymer Apr 4, 2023
c57dbf3
Add handling and warning for labels that do not match the expected regex
awgymer Apr 4, 2023
556e100
Merge branch 'dev' into fix-lint-process-label
awgymer Apr 4, 2023
38b5603
Merge branch 'dev' into fix-lint-process-label
awgymer Apr 25, 2023
c5b3e4d
Merge branch 'dev' into fix-lint-process-label
awgymer Apr 25, 2023
ee0b95b
Move label linting code to its own method and add test for that metho…
awgymer Apr 25, 2023
d593f86
Fix test cases and ensure test is run. Make sure label linting method…
awgymer Apr 26, 2023
18b6d1a
Merge branch 'dev' into fix-lint-process-label
awgymer Apr 26, 2023
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50 changes: 39 additions & 11 deletions nf_core/modules/lint/main_nf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -236,25 +236,53 @@ def check_process_section(self, lines, fix_version, progress_bar):

# Check that process labels are correct
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correct_process_labels = ["process_single", "process_low", "process_medium", "process_high", "process_long"]
process_label = [l for l in lines if l.lstrip().startswith("label")]
if len(process_label) > 0:
try:
process_label = re.search("process_[A-Za-z]+", process_label[0]).group(0)
except AttributeError:
process_label = re.search("'([A-Za-z_-]+)'", process_label[0]).group(0)
finally:
if not process_label in correct_process_labels:
all_labels = [l for l in lines if l.lstrip().startswith("label ")]
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@fabianegli fabianegli Mar 29, 2023 •
edited
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It might be a good idea to extract this into a function. Something like get_process_label. That would make things more readable and testable. And also have tests.

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The whole method is now getting quite bloated. If the code here is accepted then I think a next step could be to split out the whole label section rather than just splitting out the list comprehension. Similarly it may be worth considering splitting out the container parsing part.

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That was then less clear than I hoped. I meant taking out the whole label selection as you propose - not just a list comprehension.

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And I think it would be ideal to do it as part of this PR.

bad_labels = []
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good_labels = []
if len(all_labels) > 0:
for label in all_labels:
try:
label = re.match("^label\s+([a-zA-Z0-9_-]+)", label).group(1)
except AttributeError:
self.warned.append(
(
"process_standard_label",
f"Process label ({process_label}) is not among standard labels: `{'`,`'.join(correct_process_labels)}`",
f"Specified label appears to contain non-alphanumerics: {label}",
self.main_nf,
)
)
continue
if label not in correct_process_labels:
bad_labels.append(label)
else:
self.passed.append(("process_standard_label", "Correct process label", self.main_nf))
good_labels.append(label)
if len(good_labels) > 1:
self.warned.append(
(
"process_standard_label",
f"Conflicting process labels found: `{'`,`'.join(good_labels)}`",
self.main_nf,
)
)
elif len(good_labels) == 1:
self.passed.append(("process_standard_label", "Correct process label", self.main_nf))
else:
self.warned.append(("process_standard_label", "Standard process label not found", self.main_nf))
if len(bad_labels) > 0:
self.warned.append(
("process_standard_label", f"Non-standard labels found: `{'`,`'.join(good_labels)}`", self.main_nf)
)
if len(all_labels) > len(set(all_labels)):
self.warned.append(
(
"process_standard_label",
f"Duplicate labels found: `{'`,`'.join(sorted(all_labels))}`",
self.main_nf,
)
)

else:
self.warned.append(("process_standard_label", "Process label unspecified", self.main_nf))
self.warned.append(("process_standard_label", "Process label not specified", self.main_nf))
for i, l in enumerate(lines):
url = None
l = l.strip(" '\"")
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