add a function to check if patch files contain outdated paths #1878
Conversation
This file contains 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
Codecov Report
@@ Coverage Diff @@
## dev #1878 +/- ##
==========================================
- Coverage 60.06% 59.96% -0.11%
==========================================
Files 37 37
Lines 4640 4663 +23
==========================================
+ Hits 2787 2796 +9
- Misses 1853 1867 +14
Help us with your feedback. Take ten seconds to tell us how you rate us. Have a feature suggestion? Share it here. |
ewels
reviewed
Oct 5, 2022
Co-authored-by: Phil Ewels <phil.ewels@scilifelab.se>
adamrtalbot
approved these changes
Oct 5, 2022
Comment on lines
+192
to
+221
| def check_patch_paths(self, patch_path, module_name): | ||
| """ | ||
| Check that paths in patch files are updated to the new modules path | ||
| """ | ||
| if patch_path.exists(): | ||
| log.info(f"Modules {module_name} contains a patch file.") | ||
| rewrite = False | ||
| with open(patch_path, "r") as fh: | ||
| lines = fh.readlines() | ||
| for index, line in enumerate(lines): | ||
| # Check if there are old paths in the patch file and replace | ||
| if f"modules/{self.modules_repo.repo_path}/modules/{module_name}/" in line: | ||
| rewrite = True | ||
| lines[index] = line.replace( | ||
| f"modules/{self.modules_repo.repo_path}/modules/{module_name}/", | ||
| f"modules/{self.modules_repo.repo_path}/{module_name}/", | ||
| ) | ||
| if rewrite: | ||
| log.info(f"Updating paths in {patch_path}") | ||
| with open(patch_path, "w") as fh: | ||
| for line in lines: | ||
| fh.write(line) | ||
| # Update path in modules.json if the file is in the correct format | ||
| modules_json = ModulesJson(self.dir) | ||
| modules_json.load() | ||
| if modules_json.has_git_url_and_modules(): | ||
| modules_json.modules_json["repos"][self.modules_repo.remote_url]["modules"][ | ||
| self.modules_repo.repo_path | ||
| ][module_name]["patch"] = str(patch_path.relative_to(Path(self.dir).resolve())) | ||
| modules_json.dump() |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
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.
Closes #1868
The new function runs in every
nf-core modulescommand, when we check if themodulesdirectory structure is outdated and try to fix it.It updates paths from patch files.
PR checklist
CHANGELOG.mdis updateddocsis updated