ci: remove redundant unpinned Snakemake install (clears Scorecard Pinned-Dependencies #73)#152
Merged
Merged
Conversation
…ependencies) The DAG dry-run smoke step installed snakemake unpinned (pip install "snakemake>=8.0.0"), which OpenSSF Scorecard flagged as a Pinned-Dependencies violation (medium code-scanning alert #73). Snakemake and its full dependency set are already installed hash-pinned via environments/requirements-ci.txt in the test job "Install dependencies" step, so the separate install was redundant. Remove it; the DAG dry-run reuses the already-pinned snakemake. No functional change to the wiring check.
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
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
What
Removes the unpinned
pip install "snakemake>=8.0.0"step from thetestjob inci.yml. The DAG dry-run smoke check that follows now uses the snakemake already installed by the "Install dependencies" step.Why
OpenSSF Scorecard code-scanning alert #73 (
PinnedDependenciesID, medium):score is 8: pipCommand not pinned by hashatci.yml:152. The DAG-smoke step added in #150 installed snakemake with an unpinned version range, docking the Pinned-Dependencies score from 10 to 8.Treatment (fix, not dismiss)
Snakemake 9.23.1 and its full dependency set (pulp, 6
snakemake-interface-*plugins, configargparse, throttler, conda-inject, dpath, yte, ...) are already hash-pinned inenvironments/requirements-ci.txt, which thetestjob installs viapip install --no-deps --require-hashesbefore the DAG step. So the separate install was purely redundant. Removing it is the strongest remediation (eliminates the unpinned command entirely) and is consistent with the repo convention of dismissing a Pinned-Dependencies finding only when hash-pinning is genuinely impossible (e.g. thesestrav==<ver>self-package install, alert #52).Verification
-e .andsestrav==<ver>installs are self-package installs Scorecard does not flag / already dismissed).test (3.13)job on this PR).scorecard.ymlruns on push tomain, so alert Build(deps): bump the python-minor-patch group across 1 directory with 6 updates #73 auto-transitions to fixed once merged; no manual dismissal required.