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Catch FileNotFoundError when looking for TODO comments #804

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Dec 3, 2020
Merged

Catch FileNotFoundError when looking for TODO comments #804

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Catch FileNotFoundError when looking for TODO comments
ewels Dec 3, 2020
80e6fdd
Changelog
ewels Dec 3, 2020
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,8 @@

### Linting

* Fix linting crash when a file deleted but not yet staged in git [[#796](https://github.com/nf-core/tools/issues/796)]

### Other

## [v1.12 - Mercury Weasel](https://github.com/nf-core/tools/releases/tag/1.12) - [2020-11-19]
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32 changes: 20 additions & 12 deletions nf_core/lint.py
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Expand Up @@ -239,7 +239,7 @@ def lint_pipeline(self, release_mode=False):
log.debug("Running lint test: {}".format(fun_name))
getattr(self, fun_name)()
if len(self.failed) > 0:
log.error("Found test failures in `{}`, halting lint run.".format(fun_name))
log.critical("Found test failures in `{}`, halting lint run.".format(fun_name))
break

def check_files_exist(self):
Expand Down Expand Up @@ -1241,17 +1241,25 @@ def check_cookiecutter_strings(self):
num_files = 0
for fn in list_of_files:
num_files += 1
with io.open(fn, "r", encoding="latin1") as fh:
lnum = 0
for l in fh:
lnum += 1
cc_matches = re.findall(r"{{\s*cookiecutter[^}]*}}", l)
if len(cc_matches) > 0:
for cc_match in cc_matches:
self.failed.append(
(13, "Found a cookiecutter template string in `{}` L{}: {}".format(fn, lnum, cc_match))
)
num_matches += 1
try:
with io.open(fn, "r", encoding="latin1") as fh:
lnum = 0
for l in fh:
lnum += 1
cc_matches = re.findall(r"{{\s*cookiecutter[^}]*}}", l)
if len(cc_matches) > 0:
for cc_match in cc_matches:
self.failed.append(
(
13,
"Found a cookiecutter template string in `{}` L{}: {}".format(
fn, lnum, cc_match
),
)
)
num_matches += 1
except FileNotFoundError as e:
log.warn("`git ls-files` returned '{}' but could not open it!".format(fn))
if num_matches == 0:
self.passed.append((13, "Did not find any cookiecutter template strings ({} files)".format(num_files)))

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