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22 changes: 22 additions & 0 deletions .github/workflows/audit-orphans.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,22 @@
name: Audit orphaned benchmark data

on:
pull_request:
branches: [main]
schedule:
- cron: "0 9 * * 1"
workflow_dispatch:

jobs:
audit:
runs-on: ubuntu-latest
permissions:
contents: read
steps:
- uses: actions/checkout@v4
- uses: actions/checkout@v4
with:
repository: ericchansen/q2mm
ref: master
path: q2mm-sibling
- run: bash scripts/audit-orphans.sh "${GITHUB_WORKSPACE}/q2mm-sibling"
7 changes: 6 additions & 1 deletion README.md
Original file line number Diff line number Diff line change
Expand Up @@ -71,7 +71,8 @@ For this repo specifically:
(documentation, paper figure, regression test) belong here.

Run `scripts/audit-orphans.sh` (see below) periodically to catch any
directories that have lost their references.
directories that have lost their references. The same audit now runs
automatically on every pull request and weekly on Mondays.

## Auditing for orphaned data

Expand All @@ -80,6 +81,10 @@ directories that have lost their references.
scripts/audit-orphans.sh ../q2mm
```

The audit also runs automatically in
[Audit orphaned benchmark data](.github/workflows/audit-orphans.yml) on every
pull request, weekly on Mondays at 09:00 UTC, and on manual dispatch.

The script walks every `benchmarks/<system>/<subdir>/` and searches the
q2mm checkout (`docs/`, `test/`, `q2mm/`, `scripts/`, `examples/`) for
references to that path. Any subdirectory without a reference is
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