Testing out Reftrace for regex replacement in modules #3745
+168
−32
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
… linting Replace regex-based process label validation with structured parsing using the Reftrace library. This provides more accurate parsing of Nextflow syntax and better error handling. Key changes: - Enhanced MockModuleLint to create temporary files for Reftrace compatibility - Updated check_process_labels to use Reftrace Module objects instead of raw lines - Modified integration to parse modules with Reftrace and handle parse errors - Updated unit tests to create proper Nextflow syntax files for testing Addresses Yuxin's challenge with integrating Reftrace into the testing infrastructure while maintaining the existing linting functionality. 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <noreply@anthropic.com>
Codecov Report❌ Patch coverage is
☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
|
mashehu
reviewed
Sep 23, 2025
|
|
||
|
|
||
| def check_process_labels(self, lines): | ||
| def check_process_labels(self, mod): |
There was a problem hiding this comment.
could you please add type hints to the function?
mashehu
reviewed
Sep 23, 2025
Comment on lines
+21
to
+34
| basic_process = """process TEST_PROCESS { | ||
| label 'process_high' | ||
| input: | ||
| path input_file | ||
| output: | ||
| path "output.txt" | ||
| script: | ||
| ''' | ||
| echo "test" > output.txt | ||
| ''' | ||
| } |
There was a problem hiding this comment.
how about using modules.create here, so we have some sanity check against the template. or do we need to remove too much boilerplate code because the template skeleton is not complete enough?
mashehu
reviewed
Sep 23, 2025
Comment on lines
+107
to
+108
| if os.path.exists(temp_file.name): | ||
| os.unlink(temp_file.name) |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
5 participants
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
I've been trying testing out how to use Reftrace to replace some regex linting logic. So far I started with the process label checks using the Python API. (The previous draft PR was closed after the test restructure)
PR checklist
CHANGELOG.mdis updateddocsis updated