deps: bump gitpython 3.1.50 -> 3.1.52 in the production lockfile (clears 3 GHSA advisories)#151
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environments/requirements.lock still pinned gitpython 3.1.50 (transitive via snakemake) while environments/requirements-ci.txt was already at 3.1.52, so the production lock lagged the fix. 3.1.50 carries GHSA-2f96-g7mh-g2hx, GHSA-956x-8gvw-wg5v and GHSA-v396-v7q4-x2qj (command injection via long-option prefix abbreviation), all resolved in 3.1.51 and later. The wheel and sdist hashes match PyPI and the existing ci manifest. Found by auditing the installed lockfile with pip-audit.
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What
Bumps
gitpython3.1.50 -> 3.1.52 inenvironments/requirements.lock(transitive via snakemake).Why
The production lockfile still pinned the vulnerable
gitpython==3.1.50even thoughenvironments/requirements-ci.txtwas already bumped to3.1.52(#136 only touched the CI manifest; the production lock lagged). 3.1.50 carries three advisories:GHSA-2f96-g7mh-g2hx- command injection via long-option prefix abbreviationGHSA-956x-8gvw-wg5vGHSA-v396-v7q4-x2qjAll are resolved in 3.1.51+. Actual runtime risk is low (gitpython is not on the peptide-scoring path), but a fix exists, so per project policy we bump rather than dismiss.
Verification
sha256hashes match PyPI for 3.1.52 and the existingrequirements-ci.txtpins exactly (same version, same two hashes).grep gitpython==3.1.5-> only 3.1.52).Note on end-to-end proof
This was surfaced by auditing the installed lockfile with pip-audit (PR #148). Because this branch is off
main(which does not yet carry that pip-audit fix), this branch's advisory scan is still the old lock-resolve form. The definitive "0 gitpython findings" proof lands once both this PR and #148 are onmain; recommended order is to merge #148 first, then update this branch.