From 6d0db1bf80dfac9683c66843458522bca74fa197 Mon Sep 17 00:00:00 2001 From: Giordon Stark Date: Thu, 13 Aug 2026 13:12:23 -0500 Subject: [PATCH 1/7] ci: pin GitHub Actions to SHAs and harden workflow permissions Pin all actions to full-length commit SHAs with version comments (actions-up), add explicit least-privilege permissions blocks, set persist-credentials: false on checkout, add a concurrency group to deploy.yml, and name previously-anonymous jobs to clear zizmor findings. Assisted-by: Claude (Anthropic) --- .github/workflows/deploy.yml | 10 +++++++++- .github/workflows/docs.yml | 15 +++++++++++---- .github/workflows/semantic-pr-check.yml | 5 ++++- 3 files changed, 24 insertions(+), 6 deletions(-) diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml index 829148d..422fd35 100644 --- a/.github/workflows/deploy.yml +++ b/.github/workflows/deploy.yml @@ -6,12 +6,20 @@ on: - main workflow_dispatch: +concurrency: + group: ${{ github.workflow }}-${{ github.ref }} + cancel-in-progress: true + +# Dispatch uses a dedicated PAT (secrets.MANIACLAB_AI_FACTORY_DEPLOY_TOKEN), not GITHUB_TOKEN +permissions: {} + jobs: trigger-gitops: + name: Trigger AI Factory GitOps runs-on: ubuntu-latest steps: - name: Send Repository Dispatch to maniaclab/ai_factory - uses: peter-evans/repository-dispatch@v4 + uses: peter-evans/repository-dispatch@28959ce8df70de7be546dd1250a005dd32156697 # v4.0.1 with: token: ${{ secrets.MANIACLAB_AI_FACTORY_DEPLOY_TOKEN }} repository: maniaclab/ai_factory diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 6e8572b..105d5aa 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -12,15 +12,21 @@ concurrency: group: ${{ github.workflow }}-${{ github.ref }} cancel-in-progress: true +permissions: {} + jobs: build: + name: Build docs runs-on: ubuntu-latest + permissions: + contents: read # to checkout the repo steps: - - uses: actions/checkout@v7 + - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1 with: fetch-depth: 0 + persist-credentials: false - - uses: prefix-dev/setup-pixi@v0.10.1 + - uses: prefix-dev/setup-pixi@f00437f565399d418b0acc85936d12c1fb668347 # v0.10.1 with: pixi-version: v0.49.0 @@ -32,11 +38,12 @@ jobs: - name: Upload static files as artifact id: deployment - uses: actions/upload-pages-artifact@v5 + uses: actions/upload-pages-artifact@fc324d3547104276b827a68afc52ff2a11cc49c9 # v5.0.0 with: path: site/ deploy: + name: Deploy docs if: github.event_name == 'push' && github.ref == 'refs/heads/main' && github.repository == 'usatlas/af-docs' @@ -58,4 +65,4 @@ jobs: steps: - name: Deploy to GitHub Pages id: deployment - uses: actions/deploy-pages@v5 + uses: actions/deploy-pages@cd2ce8fcbc39b97be8ca5fce6e763baed58fa128 # v5.0.0 diff --git a/.github/workflows/semantic-pr-check.yml b/.github/workflows/semantic-pr-check.yml index e551b30..0f93957 100644 --- a/.github/workflows/semantic-pr-check.yml +++ b/.github/workflows/semantic-pr-check.yml @@ -1,6 +1,9 @@ name: Semantic Pull Request on: + # zizmor: ignore[dangerous-triggers] no PR head is checked out and only the PR + # title is read via the GitHub API; pull_request_target is required so + # statuses: write works for PRs opened from forks. pull_request_target: types: - opened @@ -24,6 +27,6 @@ jobs: steps: - name: Check PR title matches Conventional Commits spec - uses: amannn/action-semantic-pull-request@v6 + uses: amannn/action-semantic-pull-request@48f256284bd46cdaab1048c3721360e808335d50 # v6.1.1 env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} From c31cf536019b32e4214a83442f2d3041ae30ccf6 Mon Sep 17 00:00:00 2001 From: Giordon Stark Date: Thu, 13 Aug 2026 13:12:33 -0500 Subject: [PATCH 2/7] ci: add zizmor pre-commit hook and tighten dependabot cooldown Add the zizmor pre-commit hook to catch GitHub Actions security issues locally, switch Dependabot to monthly grouped updates under the modern "github-actions" ecosystem alias with a 7-day cooldown, and freeze all existing pre-commit hook revs to their commit SHAs. Assisted-by: Claude (Anthropic) --- .github/dependabot.yml | 6 ++++-- .pre-commit-config.yaml | 25 ++++++++++++++++--------- 2 files changed, 20 insertions(+), 11 deletions(-) diff --git a/.github/dependabot.yml b/.github/dependabot.yml index 6c4b369..1974bcd 100644 --- a/.github/dependabot.yml +++ b/.github/dependabot.yml @@ -4,8 +4,10 @@ updates: - package-ecosystem: "github-actions" directory: "/" schedule: - interval: "weekly" + interval: "monthly" groups: - actions: + github-actions: patterns: - "*" + cooldown: + default-days: 7 diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 9eb6a1e..2aab45a 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -7,13 +7,13 @@ exclude: ^(\.cruft\.json|\.copier-answers\.yml|pixi\.lock)$ repos: - repo: https://github.com/adamchainz/blacken-docs - rev: "1.20.0" + rev: "fda77690955e9b63c6687d8806bafd56a526e45f" # frozen: 1.20.0 hooks: - id: blacken-docs additional_dependencies: [black==26.*] - repo: https://github.com/pre-commit/pre-commit-hooks - rev: "v6.0.0" + rev: "3e8a8703264a2f4a69428a0aa4dcb512790b2c8c" # frozen: v6.0.0 hooks: - id: check-added-large-files - id: check-case-conflict @@ -29,35 +29,35 @@ repos: - id: trailing-whitespace - repo: https://github.com/pre-commit/pygrep-hooks - rev: "v1.10.0" + rev: "3a6eb0fadf60b3cccfd80bad9dbb6fae7e47b316" # frozen: v1.10.0 hooks: - id: rst-backticks - id: rst-directive-colons - id: rst-inline-touching-normal - repo: https://github.com/rbubley/mirrors-prettier - rev: "v3.9.6" + rev: "0ee178619d696787ca73d210cc191d720868c631" # frozen: v3.9.6 hooks: - id: prettier types_or: [yaml, markdown, html, css, scss, javascript, json] args: [--prose-wrap=always] - repo: https://github.com/astral-sh/ruff-pre-commit - rev: "v0.16.1" + rev: "39d9ac5938dadb73df0564a45f163e25ff9fa6e2" # frozen: v0.16.1 hooks: - id: ruff-check args: ["--fix", "--show-fixes"] - id: ruff-format - repo: https://github.com/codespell-project/codespell - rev: "v2.4.3" + rev: "57b21406f092110c18776e39b0bda50d37c945c8" # frozen: v2.4.3 hooks: - id: codespell exclude: ".+.ipynb" args: ["-w", "-L", "SLAC,checkin,slac,thq"] - repo: https://github.com/shellcheck-py/shellcheck-py - rev: "v0.11.0.1" + rev: "745eface02aef23e168a8afb6b5737818efbea95" # frozen: v0.11.0.1 hooks: - id: shellcheck @@ -70,14 +70,21 @@ repos: exclude: ^\.pre-commit-config\.yaml$ - repo: https://github.com/python-jsonschema/check-jsonschema - rev: "0.37.4" + rev: "6b63472e72e1a91ed8a2f6d483790dfb644fa1d3" # frozen: 0.37.4 hooks: - id: check-dependabot - id: check-github-workflows - id: check-readthedocs + - repo: https://github.com/zizmorcore/zizmor-pre-commit + rev: 451b56af716f9f0d0c2b816503a3fd0cf8b036fa # frozen: v1.29.0 + hooks: + - id: zizmor + files: "^\\.github" + args: [--persona=pedantic] + - repo: https://github.com/rstcheck/rstcheck - rev: "v6.3.0" + rev: "d8774e96810795967ed9603f445b4e751e7b313f" # frozen: v6.3.0 hooks: - id: rstcheck additional_dependencies: ["rstcheck[sphinx,toml]"] From 19125c72f4712ccdbfe535e1df45a653047e16ff Mon Sep 17 00:00:00 2001 From: Giordon Stark Date: Thu, 13 Aug 2026 13:12:43 -0500 Subject: [PATCH 3/7] ci: add 7-day exclude-newer cooldown to pixi workspace Delay pulling brand-new conda-forge/PyPI releases into the pixi environment for 7 days, matching the Dependabot/actions-up cooldown used elsewhere in this change set. Assisted-by: Claude (Anthropic) --- pixi.toml | 1 + 1 file changed, 1 insertion(+) diff --git a/pixi.toml b/pixi.toml index 20d1f30..3cedccf 100644 --- a/pixi.toml +++ b/pixi.toml @@ -4,6 +4,7 @@ channels = ["conda-forge"] name = "af-docs" platforms = ["linux-64", "linux-aarch64", "osx-64", "osx-arm64", "win-64"] version = "0.1.0" +exclude-newer = "7d" [dependencies] python = ">=3.14.0,<3.15" From 84ba862686684c239578a9303aede8723433b746 Mon Sep 17 00:00:00 2001 From: Giordon Stark Date: Thu, 13 Aug 2026 14:03:37 -0500 Subject: [PATCH 4/7] pixi v7 lock --- pixi.lock | 2816 +++++++++++++++++++++++++++-------------------------- 1 file changed, 1410 insertions(+), 1406 deletions(-) diff --git a/pixi.lock b/pixi.lock index e6f5e37..9dbc559 100644 --- a/pixi.lock +++ b/pixi.lock @@ -1,27 +1,20 @@ -version: 6 +version: 7 +platforms: +- name: linux-64 +- name: linux-aarch64 +- name: osx-64 +- name: osx-arm64 +- name: win-64 environments: default: channels: - url: https://conda.anaconda.org/conda-forge/ - 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- conda: https://conda.anaconda.org/conda-forge/noarch/distlib-0.4.0-pyhd8ed1ab_0.conda - - conda: https://conda.anaconda.org/conda-forge/noarch/filelock-3.29.0-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/icu-78.3-h33c6efd_0.conda - - conda: https://conda.anaconda.org/conda-forge/noarch/identify-2.6.19-pyhd8ed1ab_0.conda - - conda: https://conda.anaconda.org/conda-forge/noarch/importlib-metadata-8.8.0-pyhcf101f3_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.45.1-default_hbd61a6d_102.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.7.5-hecca717_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/libffi-3.5.2-h3435931_0.conda @@ -34,51 +27,51 @@ environments: - conda: https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.42-h5347b49_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.2-h25fd6f3_2.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/lychee-0.23.0-he64ecbb_0.conda - 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uses: prefix-dev/setup-pixi@f00437f565399d418b0acc85936d12c1fb668347 # v0.10.1 - with: - pixi-version: v0.49.0 - name: Check documentation run: pixi run build-check From 9da2d9e600c6538fac8b70a8306058287f3cc602 Mon Sep 17 00:00:00 2001 From: Giordon Stark Date: Thu, 13 Aug 2026 14:09:14 -0500 Subject: [PATCH 6/7] url changes --- docs/slac/jupyter_extra.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/slac/jupyter_extra.md b/docs/slac/jupyter_extra.md index 99033a0..36260d4 100644 --- a/docs/slac/jupyter_extra.md +++ b/docs/slac/jupyter_extra.md @@ -75,7 +75,7 @@ After this and restart the Jupyter environment, you will see a new kernel call ## Using built-in Conda environments Some images, such as `atlas/20210403` has Andconda3 built-in to support Conda -environments such as ["rapids-0.18"](https://rapids.ai/start.html) and +environments such as ["rapids-0.18"](https://rapids.ai) and "tf-keras-gpu". You can use these Conda environments by `source /opt/anaconda3/etc/profile.d/conda.sh`. Alternatively, you can also mix them with your own Conda installation and environments by creating a file From 30eb774772882b91432d197606b9bf10e298929e Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Thu, 13 Aug 2026 19:09:30 +0000 Subject: [PATCH 7/7] style: pre-commit fixes --- docs/slac/jupyter_extra.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/slac/jupyter_extra.md b/docs/slac/jupyter_extra.md index 36260d4..da4dc02 100644 --- a/docs/slac/jupyter_extra.md +++ b/docs/slac/jupyter_extra.md @@ -75,8 +75,8 @@ After this and restart the Jupyter environment, you will see a new kernel call ## Using built-in Conda environments Some images, such as `atlas/20210403` has Andconda3 built-in to support Conda -environments such as ["rapids-0.18"](https://rapids.ai) and -"tf-keras-gpu". You can use these Conda environments by +environments such as ["rapids-0.18"](https://rapids.ai) and "tf-keras-gpu". You +can use these Conda environments by `source /opt/anaconda3/etc/profile.d/conda.sh`. Alternatively, you can also mix them with your own Conda installation and environments by creating a file `~/.condarc` and put the following lines inside