Refactor modules lint
#1164
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Refactor modules lint
#1164
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Codecov Report
@@ Coverage Diff @@
## dev #1164 +/- ##
==========================================
- Coverage 71.56% 70.74% -0.83%
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Files 29 49 +20
Lines 3355 5233 +1878
==========================================
+ Hits 2401 3702 +1301
- Misses 954 1531 +577
Continue to review full report at Codecov.
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KevinMenden
reviewed
Jul 9, 2021
nf_core/modules/lint/__init__.py
Outdated
| self.lint_tests = [k for k in self.lint_tests if k in self.key] | ||
| # Filter the tests by the key if one is supplied | ||
| if key: | ||
| self.filter_tests_by_key() |
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Don't we need to supply the key to the filter function here?
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You're right. Went back and forth between having key as a argument and as an attribute of the class.
KevinMenden
reviewed
Jul 9, 2021
Comment on lines
+191
to
-214
| def filter_tests_by_key(self, key): | ||
| """Filters the tests by the supplied key""" | ||
| # Check that supplied test keys exist | ||
| bad_keys = [k for k in key if k not in self.lint_tests] | ||
| if len(bad_keys) > 0: | ||
| raise AssertionError( | ||
| "Test name{} not recognised: '{}'".format( | ||
| "s" if len(bad_keys) > 1 else "", | ||
| "', '".join(bad_keys), | ||
| ) | ||
| mod_object.main_nf = mod | ||
| mod_object.module_name = os.path.basename(mod) | ||
| self.lint_module(mod_object, local=True) |
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This is only looking for bad keys right?
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ah nevermind, a bit downstream ...
KevinMenden
reviewed
Jul 9, 2021
Co-authored-by: Kevin Menden <kevin.menden@live.com>
…ls into refactor-modules-lint
KevinMenden
approved these changes
Jul 9, 2021
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Another try at refactoring
nf-core modules lintand adding module tests tonf-core lint:nf-core lintand made the general lint table and the module lint table work together.lint_utils.pyfor code used by bothmodules lintandlintcommands.On the way to resolving #1158. If these changes make sense, we should also update the markdown and json generation by
nf-core lintto also include the modules tests.PR checklist
CHANGELOG.mdis updateddocsis updated