🩹 added patch command for subworkflows #2861
Conversation
This comment was marked as outdated.
This comment was marked as outdated.
This comment was marked as resolved.
This comment was marked as resolved.
|
for testing you can do similar things to https://github.com/nf-core/tools/blob/master/tests/modules/patch.py |
|
Hello! @ctuni are you planning to work on this PR, otherwise I would like to take over and finish it up :) |
|
Hello! Thank you for reviving this, please go ahead and let me know if I can help with anything! |
|
@ctuni this might help your future development work 😉 pip install pre-commit
pre-commit installIt'll run |
| if subworkflow.is_patched: | ||
| # If the subworkflow is patched, we need to apply | ||
| # the patch in reverse before comparing with the remote | ||
| tempdir_parent = Path(tempfile.mkdtemp()) | ||
| tempdir = tempdir_parent / "tmp_subworkflow_dir" | ||
| shutil.copytree(subworkflow.component_dir, tempdir) | ||
| try: | ||
| new_lines = ComponentsDiffer.try_apply_patch( | ||
| subworkflow.component_type, | ||
| subworkflow.component_name, | ||
| subworkflow.org, | ||
| subworkflow.patch_path, | ||
| tempdir, | ||
| reverse=True, | ||
| ) | ||
| for file, lines in new_lines.items(): | ||
| with open(tempdir / file, "w") as fh: | ||
| fh.writelines(lines) | ||
| except LookupError: | ||
| # This error is already reported by subworkflow_patch, so just return |
There was a problem hiding this comment.
wtihout checking, this feels like we would also use the same logic inn modules_changes. can we make a components_changes superfunction?
There was a problem hiding this comment.
I think this is part of a bigger restructure where we have a components lint instead of splitting modules and subworkflows
Related to issue: #1891
Is there a straightforward way to test this?