ci: simplify workflow setup and labels

.github/actions/setup-reeds-env/action.yml

@@ -0,0 +1,61 @@
+name: Setup ReEDS Environment
+description: Setup cached micromamba Python and/or Julia environment for ReEDS CI.
+
+inputs:
+  setup-python:
+    description: Setup micromamba environment from environment.yml.
+    required: false
+    default: "true"
+  setup-julia:
+    description: Setup Julia toolchain.
+    required: false
+    default: "true"
+  julia-version:
+    description: Julia version to install.
+    required: false
+    default: "1.12.1"
+  instantiate-julia:
+    description: Run julia --project=. instantiate.jl.
+    required: false
+    default: "true"
+
+outputs:
+  mamba-env-path:
+    description: Micromamba environment path.
+    value: ${{ steps.mamba.outputs.environment-path }}
+  julia-bindir:
+    description: Julia binary directory.
+    value: ${{ steps.setup-julia.outputs.julia-bindir }}
+
+runs:
+  using: composite
+  steps:
+    - name: Setup micromamba env
+      if: ${{ fromJSON(inputs.setup-python) }}
+      id: mamba
+      uses: mamba-org/setup-micromamba@add3a49764cedee8ee24e82dfde87f5bc2914462 # v2
+      with:
+        environment-file: environment.yml
+        cache-environment: true
+        post-cleanup: "all"
+        cache-environment-key: ${{ runner.os }}-conda-${{ hashFiles('environment.yml') }}
+
+    - name: Restore Julia cache
+      if: ${{ fromJSON(inputs.setup-julia) }}
+      uses: actions/cache@5a3ec84eff668545956fd18022155c47e93e2684 # v4
+      with:
+        path: ~/.julia
+        key: julia-${{ runner.os }}-${{ hashFiles('Project.toml') }}
+        restore-keys: julia-${{ runner.os }}-
+
+    - name: Setup Julia
+      if: ${{ fromJSON(inputs.setup-julia) }}
+      id: setup-julia
+      uses: julia-actions/setup-julia@5c9647d97b78a5debe5164e9eec09d653d29bd71 # v2
+      with:
+        version: ${{ inputs.julia-version }}
+
+    - name: Instantiate Julia project
+      if: ${{ fromJSON(inputs.setup-julia) && fromJSON(inputs.instantiate-julia) }}
+      shell: bash -le {0}
+      run: julia --project=. instantiate.jl

.github/dependabot.yml

@@ -0,0 +1,65 @@
+version: 2
+
+updates:
+  - package-ecosystem: "conda"
+    directory: /
+    schedule:
+      interval: "weekly"
+    cooldown:
+      default-days: 7
+    open-pull-requests-limit: 2
+    labels:
+      - "dependencies"
+    reviewers:
+      - "kennedy-mindermann"
+    commit-message:
+      prefix: "build"
+      include: "scope"
+    rebase-strategy: "auto"
+
+  - package-ecosystem: "pip"
+    directory: /
+    schedule:
+      interval: "weekly"
+    cooldown:
+      default-days: 7
+    open-pull-requests-limit: 2
+    labels:
+      - "dependencies"
+    reviewers:
+      - "kennedy-mindermann"
+    commit-message:
+      prefix: "build"
+      include: "scope"
+    rebase-strategy: "auto"
+
+  - package-ecosystem: "julia"
+    directory: /
+    schedule:
+      interval: "weekly"
+    cooldown:
+      default-days: 7
+    open-pull-requests-limit: 2
+    labels:
+      - "dependencies"
+    reviewers:
+      - "kennedy-mindermann"
+    commit-message:
+      prefix: "build"
+      include: "scope"
+    rebase-strategy: "auto"
+
+  - package-ecosystem: "github-actions"
+    directory: /
+    schedule:
+      interval: "weekly"
+    cooldown:
+      default-days: 7
+    labels:
+      - "dependencies"
+    reviewers:
+      - "kennedy-mindermann"
+    commit-message:
+      prefix: "build"
+      include: "scope"
+    rebase-strategy: "auto"

.github/labeler.yaml

@@ -0,0 +1,87 @@
+dependencies:
+  - head-branch:
+      - '^dependabot/.+'
+  - changed-files:
+      - any-glob-to-any-file:
+          - "environment.yml"
+          - "pyproject.toml"
+          - "requirements*.txt"
+          - "Project.toml"
+          - "Manifest.toml"
+          - ".github/dependabot.yml"
+
+github_actions:
+  - changed-files:
+      - any-glob-to-any-file:
+          - ".github/workflows/**"
+          - ".github/actions/**"
+          - ".github/scripts/**"
+
+docs:
+  - changed-files:
+      - any-glob-to-any-file:
+          - "docs/**"
+          - "**/*.md"
+          - "CITATION.cff"
+
+release:
+  - changed-files:
+      - any-glob-to-any-file:
+          - "CHANGELOG.md"
+          - "README.md"
+
+tests:
+  - changed-files:
+      - any-glob-to-any-file:
+          - "tests/**"
+          - "hourlize/tests/**"
+          - "reeds2pras/test/**"
+          - "**/test_*.py"
+          - "**/*_test.py"
+
+model_changes:
+  - changed-files:
+      - any-glob-to-any-file:
+          - "*.gms"
+          - "**/*.gms"
+          - "runbatch.py"
+          - "d_solve*.py"
+          - "reeds/**"
+          - "ReEDS_Augur/**"
+          - "Augur.py"
+          - "instantiate.jl"
+          - "reeds2pras/**"
+
+data_changes:
+  - changed-files:
+      - any-glob-to-any-file:
+          - "inputs/**"
+          - "hourlize/inputs/**"
+          - "postprocessing/**/inputs/**"
+          - "**/*.csv"
+          - "**/*.h5"
+          - "sources.csv"
+          - "sources_documentation.md"
+
+hourlize:
+  - changed-files:
+      - any-glob-to-any-file: "hourlize/**"
+
+input_processing:
+  - changed-files:
+      - any-glob-to-any-file:
+          - "input_processing/**"
+          - "preprocessing/**"
+
+postprocessing:
+  - changed-files:
+      - any-glob-to-any-file: "postprocessing/**"
+
+reeds2pras:
+  - changed-files:
+      - any-glob-to-any-file: "reeds2pras/**"
+
+switches:
+  - changed-files:
+      - any-glob-to-any-file:
+          - "cases.csv"

.github/workflows/build-docs.yaml

@@ -17,16 +17,20 @@ on:
       - main   
 
 permissions:
-  contents: write
+  contents: read
 
 jobs:
   build:
+    name: build
     runs-on: ubuntu-latest
+    permissions:
+      contents: write # Required for peaceiris/actions-gh-pages publish to gh-pages.
     steps:
       - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
         with: 
           fetch-depth: 1
           lfs: true
+          persist-credentials: false
 
       - name: Set up Python 3.12
         uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
@@ -48,11 +52,11 @@ jobs:
 
       - name: Set variables for internal github repo
         run: |
-          echo "BASE_URL=https://github.com/ReEDS-Model/ReEDS" >> $GITHUB_ENV
-          cd ${GITHUB_WORKSPACE}/docs/source/documentation_tools/
+          echo "BASE_URL=https://github.com/ReEDS-Model/ReEDS" >> "$GITHUB_ENV"
+          cd "$GITHUB_WORKSPACE/docs/source/documentation_tools/"
           sh generate_sources_md_file.sh
-          cd ${GITHUB_WORKSPACE}
-          python docs/source/documentation_tools/generate_markdown.py --githubURL "https://github.com/ReEDS-Model/ReEDS/blob/main" --reedsPath "${GITHUB_WORKSPACE}"
+          cd "$GITHUB_WORKSPACE"
+          python docs/source/documentation_tools/generate_markdown.py --githubURL "https://github.com/ReEDS-Model/ReEDS/blob/main" --reedsPath "$GITHUB_WORKSPACE"
 
       - name: Build Sphinx documentation
         env: