improve build annotation by read --ddg_dir in place instead of copying it#95
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…ad ddG input directly
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Pull request overview
This PR refactors the stability-change (ΔΔG) annotation pipeline to avoid copying user-provided RaSP prediction directories, and simplifies shared globals by removing an unused directory-copy helper.
Changes:
- Stop deleting the ΔΔG input directory inside
parse_ddg_rasp(leaving cleanup to the caller). - Update
build_annotations.get_annotations()to parse ΔΔG directly from a user-supplied directory, and only clean up when the ΔΔG data was downloaded by the tool. - Remove the
copy_dirhelper fromscripts/globals.pyand update imports accordingly.
Reviewed changes
Copilot reviewed 3 out of 3 changed files in this pull request and generated 1 comment.
| File | Description |
|---|---|
scripts/plotting/stability_change.py |
Removes internal cleanup of the input directory after parsing ΔΔG. |
scripts/plotting/build_annotations.py |
Switches from copying ΔΔG inputs to reading in-place; adds conditional cleanup for downloaded inputs. |
scripts/globals.py |
Removes the now-unused copy_dir helper function. |
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May 26, 2026
fix: clearer logs in build-annotations ΔΔG step (follow-up to #95)
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Summary
build-annotations --ddg_dir <path>used to copy the entire ΔΔG bundle into a temp directory, parse it, then delete the copy. For multi-GB bundles on networked storage this added ~10 minutes (silently, the copy progress log was DEBUG-only). The copy was pure overhead — nothing in the workflow modifies the input directory.Changes
build_annotations.py:--ddg_diris read in place. Caller now controls cleanup via acleanup_inputflag —Trueonly for the download path.stability_change.py:rm_dir(input_path)lifted out ofparse_ddg_rasp(lifecycle is the caller's concern). Unusedrm_dirimport removed.globals.py:copy_dirdeleted (now dead code)."Completed!"after input-prep replaced with branch-specific messages; duplicate"Parsing completed!"line dropped; trailing newline added tostability_change.py.