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Merge pull request #164 from ReactionMechanismGenerator/migration
T3 Migration
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‎.github/dependabot.yml‎

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version: 2
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updates:
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- package-ecosystem: "github-actions"
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directory: "/"
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schedule:
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interval: "weekly"
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groups:
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actions:
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patterns:
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- "*"

‎.github/labeler.yml‎

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‎.github/workflows/ci.yml‎

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

‎.github/workflows/codeql.yml‎

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

‎.github/workflows/cont_int.yml‎

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