T3 Migration

.github/dependabot.yml

@@ -0,0 +1,10 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    groups:
+      actions:
+        patterns:
+          - "*"

.github/workflows/ci.yml

@@ -0,0 +1,150 @@
+name: T3 CI
+
+on:
+  workflow_dispatch:
+  pull_request:
+    branches: [main]
+    types: [opened, synchronize, reopened]
+  schedule:
+    - cron: '0 0 * * *'
+
+jobs:
+  lint:
+    name: Lint (ruff)
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: astral-sh/ruff-action@v3
+        with:
+          args: "check ."
+
+  build-and-test:
+    name: Build and Test T3
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -el {0}
+
+    steps:
+      # 1. Checkout T3 (The repo running this CI)
+      - name: Checkout T3
+        uses: actions/checkout@v4
+        with:
+          path: T3
+
+      # 2. Checkout ARC (Dependency)
+      - name: Checkout ARC
+        uses: actions/checkout@v4
+        with:
+          repository: ReactionMechanismGenerator/ARC
+          ref: linear_ts
+          path: ARC
+
+      # 3. Checkout RMG Database
+      - name: Checkout RMG Database
+        uses: actions/checkout@v4
+        with:
+          repository: ReactionMechanismGenerator/RMG-database
+          path: RMG-database
+          ref: main
+          fetch-depth: 1
+
+      # 4. Checkout RMG-Py (needed at runtime for the rmg_env subprocess)
+      - name: Checkout RMG-Py
+        uses: actions/checkout@v4
+        with:
+          repository: ReactionMechanismGenerator/RMG-Py
+          path: RMG-Py
+          ref: xTB
+          fetch-depth: 1
+
+      # 5. Clean Disk (Important for heavy conda envs)
+      - name: Clean Ubuntu Image
+        uses: jlumbroso/free-disk-space@main
+        with:
+          tool-cache: true
+          android: true
+          dotnet: true
+          haskell: true
+          large-packages: true
+          swap-storage: true
+
+      # 6. Setup T3 Environment
+      - name: Set up micromamba (t3_env)
+        uses: mamba-org/setup-micromamba@v2
+        with:
+          environment-name: t3_env
+          environment-file: T3/environment.yml
+          cache-environment: true
+          generate-run-shell: true
+
+      # 7. Setup RMG Environment (rmg_env) — required by all T3 tests that
+      - name: Set up micromamba (rmg_env)
+        uses: mamba-org/setup-micromamba@v2
+        with:
+          environment-name: rmg_env
+          environment-file: RMG-Py/environment.yml
+          cache-environment: true
+          generate-run-shell: false
+          create-args: >-
+            --channel-priority flexible
+
+      # 8. Compile RMG-Py (Cython extensions, in rmg_env)
+      - name: Compile RMG-Py
+        shell: bash -el {0}
+        working-directory: RMG-Py
+        run: |
+          micromamba run -n rmg_env make
+          echo "PYTHONPATH=${{ github.workspace }}/RMG-Py" >> $GITHUB_ENV
+
+      # 9. Install & Compile ARC (Dependency, into t3_env)
+      - name: Install and Compile ARC
+        shell: micromamba-shell {0}
+        working-directory: ARC
+        run: |
+          echo "::group::Install PyRDL (The ARC Way)"
+          bash devtools/install_pyrdl.sh t3_env
+          echo "::endgroup::"
+
+          echo "::group::Compile ARC extensions"
+          make compile
+          echo "::endgroup::"
+
+          echo "::group::Install ARC in editable mode"
+          pip install -e .
+          echo "::endgroup::"
+
+      # 9b. Install xTB into its own xtb_env (used by ARC for gfn2 jobs)
+      - name: Install xTB
+        shell: bash -el {0}
+        working-directory: ARC
+        run: bash devtools/install_xtb.sh
+
+      # 10. Install T3 (Self)
+      - name: Install T3
+        shell: micromamba-shell {0}
+        working-directory: T3
+        run: |
+          pip install -e .
+
+      # 11. Run T3 Tests
+      - name: Run Tests
+        shell: micromamba-shell {0}
+        working-directory: T3
+        run: |
+          echo "Running T3 Tests..."
+          export PYTHONPATH="$PYTHONPATH:$(pwd):${{ github.workspace }}/ARC:${{ github.workspace }}/RMG-Py"
+          export RMG_DB_PATH="${{ github.workspace }}/RMG-database"
+
+          # Run pytest on the T3 tests directory
+          pytest tests/ --cov=t3 --cov-report=xml -ra -vv
+
+      # 9. Upload Coverage
+      - name: Upload coverage data
+        uses: codecov/codecov-action@v5
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          file: T3/coverage.xml
+          flags: unittests
+          name: codecov-t3
+          fail_ci_if_error: false

.github/workflows/codeql.yml

@@ -25,18 +25,18 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@v2
+      uses: github/codeql-action/init@v3
       with:
         languages: ${{ matrix.language }}
         queries: security-and-quality
 
     - name: Autobuild
-      uses: github/codeql-action/autobuild@v2
+      uses: github/codeql-action/autobuild@v3
 
     - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v2
+      uses: github/codeql-action/analyze@v3
       with:
         category: "/language:${{matrix.language}}"