Bump super-linter/super-linter from 8.0.0 to 8.3.0

.github/workflows/apptainer-build-deploy.yml

@@ -22,7 +22,7 @@ jobs:
         #     artifact_name: mything
         #     asset_name: mything-macos-amd64
     permissions:
-      write-all
+      contents: write
 
     container:
       image: quay.io/singularity/singularity:v3.8.1
@@ -32,6 +32,10 @@ jobs:
 
       - name: Check out code for the container builds
         uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+        with:
+          fetch-depth: 0
+          fetch-tags: true
+          persist-credentials: false
 
       - name: Build Container
         run: |
@@ -43,7 +47,7 @@ jobs:
     #        singularity push container.sif oras://ghcr.io/${GITHUB_REPOSITORY}:${tag}
 
       - name: Upload container to release
-        uses: svenstaro/upload-release-action@v2
+        uses: svenstaro/upload-release-action@6b7fa9f267e90b50a19fef07b3596790bb941741
         with:
           repo_token: ${{ secrets.GITHUB_TOKEN }}
           file: ${{ matrix.artifact_name }}

.github/workflows/codecov.yml

@@ -10,13 +10,17 @@ jobs:
   cov:
     name: Codecov
     runs-on: ubuntu-latest
+    permissions:
+      contents: read
     steps:
     - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
       with:
         ref: ${{ github.event.pull_request.head.ref || github.ref }}
         fetch-depth: 1
+        fetch-tags: true
+        persist-credentials: false
     - name: Setup Python
-      uses: actions/setup-python@v6
+      uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405
       with:
         python-version: 3.13
     - name: Install dependencies
@@ -28,7 +32,7 @@ jobs:
       run: |
         pytest -v --cov=gaps --cov-report=html --cov-branch --cov-report=xml:coverage.xml --cov-fail-under=95
     - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v5
+      uses: codecov/codecov-action@671740ac38dd9b0130fbe1cec585b89eea48d3de
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         files: ./coverage.xml

.github/workflows/docs.yml

@@ -18,8 +18,9 @@ jobs:
         with:
           fetch-depth: 0
           fetch-tags: true
+          persist-credentials: false
 
-      - uses: prefix-dev/setup-pixi@v0.9.4
+      - uses: prefix-dev/setup-pixi@a0af7a228712d6121d37aba47adf55c1332c9c2e
         with:
           pixi-version: v0.62.2
           locked: true
@@ -33,7 +34,7 @@ jobs:
           pixi run -e dev python-docs
 
       - name: deploy
-        uses: peaceiris/actions-gh-pages@v4.0.0
+        uses: peaceiris/actions-gh-pages@4f9cc6602d3f66b9c108549d475ec49e8ef4d45e
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           publish_dir: ./docs/_build/html

.github/workflows/linter.yml

@@ -11,14 +11,20 @@ jobs:
   lint:
     name: Lint Code Base with Ruff
     runs-on: ubuntu-latest
+    permissions:
+      contents: read
     steps:
       - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
-      - uses: astral-sh/ruff-action@v3
+        with:
+          fetch-depth: 0
+          fetch-tags: true
+          persist-credentials: false
+      - uses: astral-sh/ruff-action@4919ec5cf1f49eff0871dbcea0da843445b837e6
         with:
           version: "latest"
           args: check
           src: "./gaps"
-      - uses: astral-sh/ruff-action@v3
+      - uses: astral-sh/ruff-action@4919ec5cf1f49eff0871dbcea0da843445b837e6
         with:
           version: "latest"
           args: format --check

.github/workflows/pixi_tests.yml

@@ -9,6 +9,8 @@ on:
 jobs:
   tests:
     runs-on: ${{ matrix.os }}
+    permissions:
+      contents: read
     strategy:
       fail-fast: false
       max-parallel: 8
@@ -20,8 +22,10 @@ jobs:
       uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
       with:
         fetch-depth: 0
+        fetch-tags: true
+        persist-credentials: false
 
-    - uses: prefix-dev/setup-pixi@v0.9.4
+    - uses: prefix-dev/setup-pixi@a0af7a228712d6121d37aba47adf55c1332c9c2e
       with:
         pixi-version: v0.62.2
         locked: true

.github/workflows/pr_rev_cli_tests.yml

@@ -5,21 +5,27 @@ on: pull_request
 jobs:
   rev_cli_tests:
     runs-on: ubuntu-latest
+    permissions:
+      contents: read
     steps:
     - name: checkout gaps
       uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
       with:
         ref: ${{ github.event.pull_request.head.ref }}
         fetch-depth: 1
+        fetch-tags: true
         path: gaps
+        persist-credentials: false
     - name: checkout reV
       uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
       with:
         repository: NatLabRockies/reV
         fetch-depth: 1
         path: reV
+        fetch-tags: true
+        persist-credentials: false
     - name: Set up Python
-      uses: conda-incubator/setup-miniconda@v3
+      uses: conda-incubator/setup-miniconda@fc2d68f6413eb2d87b895e92f8584b5b94a10167
       with:
         auto-update-conda: true
         python-version: 3.9

.github/workflows/publish_to_pypi.yml

@@ -20,8 +20,9 @@ jobs:
       with:
         fetch-depth: 0
         fetch-tags: true
+        persist-credentials: false
 
-    - uses: prefix-dev/setup-pixi@v0.9.4
+    - uses: prefix-dev/setup-pixi@a0af7a228712d6121d37aba47adf55c1332c9c2e
       with:
         pixi-version: v0.62.2
         locked: true
@@ -33,4 +34,4 @@ jobs:
       run: pixi run -e dev build-wheels
 
     - name: Publish package distributions to PyPI
-      uses: pypa/gh-action-pypi-publish@release/v1
+      uses: pypa/gh-action-pypi-publish@ed0c53931b1dc9bd32cbe73a98c7f6766f8a527e

.github/workflows/release_drafter.yml

@@ -7,8 +7,11 @@ on:
 jobs:
   update_release_draft:
     runs-on: ubuntu-latest
+    permissions:
+      contents: write
+      pull-requests: write
     steps:
       - name: Release Drafter
-        uses: release-drafter/release-drafter@v6.1.0
+        uses: release-drafter/release-drafter@6db134d15f3909ccc9eefd369f02bd1e9cffdf97
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/super_linter.yml

@@ -25,11 +25,15 @@ jobs:
             # super-linter needs the full git history to get the
             # list of files that changed across commits
             fetch-depth: 0
+            fetch-tags: true
+            persist-credentials: false
 
       - name: Lint Code Base
-        uses: super-linter/super-linter/slim@v8.0.0
+        uses: super-linter/super-linter/slim@61abc07d755095a68f4987d1c2c3d1d64408f1f9
         env:
           VALIDATE_ALL_CODEBASE: false
+          VALIDATE_BIOME_LINT: false
+          VALIDATE_BIOME_FORMAT: false
           VALIDATE_CHECKOV: false
           VALIDATE_CSS: false
           VALIDATE_GITHUB_ACTIONS: false
@@ -44,6 +48,7 @@ jobs:
           VALIDATE_PYTHON_PYINK: false
           VALIDATE_PYTHON_PYLINT: false
           VALIDATE_PYTHON_RUFF: false
+          VALIDATE_SPELL_CODESPELL: false
           VALIDATE_YAML: false
           VALIDATE_YAML_PRETTIER: false
           DEFAULT_BRANCH: origin/main

.github/workflows/tests_tox.yml

@@ -11,6 +11,8 @@ on:
 jobs:
   test-latest-deps:
     runs-on: ${{ matrix.os }}
+    permissions:
+      contents: read
     strategy:
       fail-fast: false
       max-parallel: 8
@@ -22,9 +24,11 @@ jobs:
     - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
       with:
         fetch-depth: 0
+        fetch-tags: true
+        persist-credentials: false
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v6
+      uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405
       with:
         python-version: ${{ matrix.python-version }}
         cache: 'pip'
@@ -35,7 +39,7 @@ jobs:
         python -m pip install tox tox-gh-actions>=2.0
 
     - name: Load tox cache
-      uses: actions/cache/restore@v5
+      uses: actions/cache/restore@cdf6c1fa76f9f475f3d7449005a359c84ca0f306
       with:
         path: .tox/
         key: ${{ runner.os }}-${{ matrix.python-version }}-tox-v1-${{ hashFiles('**/pyproject.toml') }}
@@ -49,14 +53,16 @@ jobs:
 
     - name: Save tox cache only on main
       if: github.ref == 'refs/heads/main'
-      uses: actions/cache/save@v5
+      uses: actions/cache/save@cdf6c1fa76f9f475f3d7449005a359c84ca0f306
       with:
         path: .tox/
         key: ${{ runner.os }}-${{ matrix.python-version }}-tox-v1-${{ hashFiles('**/pyproject.toml') }}
 
   test-msv:
     runs-on: ${{ matrix.os }}
     if: github.event_name == 'pull_request'
+    permissions:
+      contents: read
     strategy:
       fail-fast: false
       max-parallel: 8
@@ -67,9 +73,11 @@ jobs:
     - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
       with:
         fetch-depth: 0
+        fetch-tags: true
+        persist-credentials: false
 
     - name: Set up Python 3.9
-      uses: actions/setup-python@v6
+      uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405
       with:
         python-version: 3.9
 

.github/workflows/wildows_pytests.yml

@@ -5,6 +5,8 @@ on: pull_request
 jobs:
   pytest:
     runs-on: windows-latest
+    permissions:
+      contents: read
     strategy:
       fail-fast: false
       matrix:
@@ -15,8 +17,10 @@ jobs:
       with:
         ref: ${{ github.event.pull_request.head.ref }}
         fetch-depth: 1
+        fetch-tags: true
+        persist-credentials: false
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v6
+      uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install Dependencies

docs/source/conf.py

@@ -127,7 +127,7 @@
 
 html_context = {
     "display_github": True,
-    "github_user": "nlr",
+    "github_user": "NatLabRockies",
     "github_repo": "gaps",
     "github_version": "main",
     "conf_py_path": "/docs/source/",

examples/example_developers.rst

@@ -723,4 +723,4 @@ to render the CLI documentation for you in a visually appealing format. For an e
 Questions?
 ----------
 If you run into any issues or questions while coupling GAPs with your model, please reach out to
-Paul Pinchuk (ppinchuk@nrl.gov).
+Paul Pinchuk (ppinchuk@nlr.gov).

pyproject.toml

@@ -104,7 +104,7 @@ channels = ["conda-forge", "anaconda", "main"]
 platforms = ["osx-arm64", "osx-64", "linux-64", "win-64"]
 
 [tool.pixi.pypi-dependencies]
-NLR-gaps = { path = ".", editable = true }
+NLR-GAPs = { path = ".", editable = true }
 
 [tool.pixi.environments]
 default = { solve-group = "default" }