security: pin third-party GitHub Actions to commit SHAs + least-privilege permissions (#177)

* security: pin third-party GitHub Actions to commit SHAs + least-privilege permissions

Pin all third-party actions to full 40-char commit SHAs (version comments retained) and add a top-level least-privilege 'permissions: contents: read' block to pure-CI workflows. dtolnay/rust-toolchain gains an explicit 'toolchain: stable' input so the SHA pin preserves channel selection. From the 2026-06-22 workspace GitHub Actions security audit.

Assisted-With: Claude Opus 4.8 <noreply@anthropic.com>

* security: bump msgpack-python to clear pip-audit

Pin msgpack-python>=1.2.1 (GHSA-6v7p-g79w-8964) in the pip-audit security
block and regenerate pixi.lock. pip-audit now reports no known
vulnerabilities.

Assisted-With: Claude Opus 4.8 <noreply@anthropic.com>

Author: KedoKudo

.github/workflows/copilot-setup-steps.yml

@@ -11,6 +11,9 @@ on:
     paths:
       - .github/workflows/copilot-setup-steps.yml
 
+permissions:
+  contents: read
+
 jobs:
   # The job MUST be called `copilot-setup-steps` or it will not be picked up by Copilot.
   copilot-setup-steps:

.github/workflows/test_and_deploy.yaml

@@ -28,7 +28,7 @@ jobs:
           fetch-tags: true
 
       - name: Setup pixi
-        uses: prefix-dev/setup-pixi@v0.9.6
+        uses: prefix-dev/setup-pixi@5185adfbffb4bd703da3010310260805d89ebb11 # v0.9.6
         with:
           manifest-path: pyproject.toml
           # Workaround: Dynamic versioning (versioningit) causes lock file version mismatch.
@@ -46,7 +46,7 @@ jobs:
         run: pixi run test
 
       - name: Upload coverage to codecov
-        uses: codecov/codecov-action@v7
+        uses: codecov/codecov-action@fb8b3582c8e4def4969c97caa2f19720cb33a72f # v7
         if: github.actor != 'dependabot[bot]'
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
@@ -70,7 +70,7 @@ jobs:
           fetch-tags: true
 
       - name: Setup pixi
-        uses: prefix-dev/setup-pixi@v0.9.6
+        uses: prefix-dev/setup-pixi@5185adfbffb4bd703da3010310260805d89ebb11 # v0.9.6
         with:
           manifest-path: pyproject.toml
           # Workaround: Dynamic versioning (versioningit) causes lock file version mismatch.
@@ -94,13 +94,13 @@ jobs:
       # installed (and micromamba on PATH); pkg-install sets both up.
       - name: Install built conda package
         id: install
-        uses: neutrons/conda-actions/pkg-install@v2
+        uses: neutrons/conda-actions/pkg-install@bba9ca89d48d9ae846db9650cc63fde736340b3d # v2
         with:
           package-name: ${{ env.PKG_NAME }}
           local-channel: /tmp/local-channel
 
       - name: Verify conda package
-        uses: neutrons/conda-actions/pkg-verify@v2
+        uses: neutrons/conda-actions/pkg-verify@bba9ca89d48d9ae846db9650cc63fde736340b3d # v2
         with:
           package-name: ${{ env.PKG_NAME }}
           module-name: ${{ env.MODULE_NAME }}
@@ -109,7 +109,7 @@ jobs:
       # Audit the dependencies of the conda package we just installed. SARIF
       # results are uploaded to GitHub code scanning by the grype action.
       - name: Scan installed environment with Grype
-        uses: neutrons/conda-actions/grype@v2
+        uses: neutrons/conda-actions/grype@bba9ca89d48d9ae846db9650cc63fde736340b3d # v2
         with:
           path: ${{ steps.install.outputs.conda_install_dir }}
 
@@ -132,7 +132,7 @@ jobs:
           fetch-tags: true
 
       - name: Setup Pixi
-        uses: prefix-dev/setup-pixi@v0.9.6
+        uses: prefix-dev/setup-pixi@5185adfbffb4bd703da3010310260805d89ebb11 # v0.9.6
         with:
           manifest-path: pyproject.toml
           # Workaround: Dynamic versioning (versioningit) causes lock file version mismatch.
@@ -149,15 +149,15 @@ jobs:
           name: artifact-conda-package
 
       - name: Upload package to anaconda
-        uses: neutrons/conda-actions/publish@v2
+        uses: neutrons/conda-actions/publish@bba9ca89d48d9ae846db9650cc63fde736340b3d # v2
         with:
           anaconda-token: ${{ secrets.ANACONDA_TOKEN }}
           organization: neutrons
           package-path: ${{ env.PKG_NAME }}-*.conda
 
       - name: Remove old packages
         if: github.ref == 'refs/heads/next'
-        uses: neutrons/conda-actions/pkg-remove@v2
+        uses: neutrons/conda-actions/pkg-remove@bba9ca89d48d9ae846db9650cc63fde736340b3d # v2
         with:
           anaconda_token: ${{ secrets.ANACONDA_TOKEN }}
           organization: neutrons
@@ -180,7 +180,7 @@ jobs:
           fetch-tags: true
 
       - name: Setup pixi
-        uses: prefix-dev/setup-pixi@v0.9.6
+        uses: prefix-dev/setup-pixi@5185adfbffb4bd703da3010310260805d89ebb11 # v0.9.6
         with:
           manifest-path: pyproject.toml
           # Workaround: Dynamic versioning (versioningit) causes lock file version mismatch.
@@ -202,4 +202,4 @@ jobs:
       # publish your distributions here (need to setup on PyPI first)
       - name: Publish package distributions to PyPI
         if: startsWith(github.ref, 'refs/tags/v')
-        uses: pypa/gh-action-pypi-publish@release/v1
+        uses: pypa/gh-action-pypi-publish@cef221092ed1bacb1cc03d23a2d87d1d172e277b # v1.14.0

.github/workflows/update-lockfiles.yml

@@ -18,7 +18,7 @@ jobs:
         # checks out refspec that triggered or the default branch
 
       - name: Setup pixi
-        uses: prefix-dev/setup-pixi@v0.9.6
+        uses: prefix-dev/setup-pixi@5185adfbffb4bd703da3010310260805d89ebb11 # v0.9.6
         with:
           run-install: false
 
@@ -28,7 +28,7 @@ jobs:
           pixi update --json | pixi exec pixi-diff-to-markdown >> diff.md
 
       - name: Create pull request
-        uses: peter-evans/create-pull-request@v8
+        uses: peter-evans/create-pull-request@5f6978faf089d4d20b00c7766989d076bb2fc7f1 # v8
         # PR will target the branch checked out in the workflow
         with:
           token: ${{ secrets.GITHUB_TOKEN }}

pixi.lock

@@ -116,6 +116,7 @@ virtualenv = ">=20.36.1,<21" # Known vulnerability in <20.36.1; capped due to ht
 cryptography = ">=48.0.1"    # CVE-2026-26007, CVE-2026-39892, GHSA-537c-gmf6-5ccf
 requests = ">=2.33.0"        # CVE-2026-25645
 pillow = ">=12.2.0"          # CVE-2026-25990, CVE-2026-40192
+msgpack-python = ">=1.2.1"   # GHSA-6v7p-g79w-8964
 
 [tool.pixi.pypi-dependencies]
 # PyPI dependencies, including this package to allow local editable installs