Update Stan to 2.36.0 #723
Workflow file for this run
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| name: bridgestan tests | |
| on: | |
| push: | |
| branches: | |
| - "main" | |
| pull_request: | |
| workflow_dispatch: {} | |
| env: | |
| CACHE_VERSION: 1 | |
| # only run one copy per PR | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }} | |
| cancel-in-progress: true | |
| jobs: | |
| build: | |
| runs-on: ${{matrix.os}} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [windows-latest, ubuntu-latest, macos-latest] | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - name: Check out github | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| - name: Stan build caching | |
| uses: actions/cache@v4 | |
| id: stan-cache | |
| with: | |
| path: ./stan/ | |
| key: ${{ runner.os }}-stan-${{ hashFiles('stan/src/stan/version.hpp') }}-v${{ env.CACHE_VERSION }} | |
| - name: Set up PATH for C example | |
| if: matrix.os == 'windows-latest' | |
| run: | | |
| Add-Content $env:GITHUB_PATH "$(pwd)/stan/lib/stan_math/lib/tbb" | |
| Add-Content $env:GITHUB_PATH "$(pwd)/test_models/full" | |
| - name: Build C example (Windows) | |
| if: matrix.os == 'windows-latest' | |
| run: | | |
| cd c-example/ | |
| make -j4 example.exe example_runtime.exe | |
| rm ../src/bridgestan.o | |
| echo "Dynamically linked example" | |
| ./example.exe | |
| echo "Runtime loading example" | |
| ./example_runtime.exe ../test_models/full/full_model.so | |
| - name: Build C example (Unix) | |
| if: matrix.os != 'windows-latest' | |
| run: | | |
| cd c-example/ | |
| make -j4 example example_static example_runtime | |
| rm ../src/bridgestan.o ../test_models/full/*.a | |
| echo "Dynamically linked example" | |
| ./example | |
| echo "Statically linked example" | |
| ./example_static | |
| echo "Runtime loading example" | |
| ./example_runtime ../test_models/full/full_model.so | |
| shell: bash | |
| # we use the cache here to build the Stan models once for multiple interfaces | |
| - name: Set up test model cache | |
| uses: actions/cache@v4 | |
| id: test-models | |
| with: | |
| path: ./test_models/ | |
| key: ${{ hashFiles('**/*.stan', 'src/*', 'stan/src/stan/version.hpp', 'Makefile') }}-${{ matrix.os }}-v${{ env.CACHE_VERSION }} | |
| - name: Build test models | |
| if: steps.test-models.outputs.cache-hit != 'true' | |
| run: | | |
| make STAN_THREADS=true O=0 test_models -j4 | |
| python: | |
| needs: [build] | |
| runs-on: ${{matrix.os}} | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest, macos-latest, windows-latest] | |
| python-version: ["3.9", "3.12"] | |
| fail-fast: false | |
| steps: | |
| - name: Check out github | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Restore Stan | |
| uses: actions/cache@v4 | |
| id: stan-cache | |
| with: | |
| path: ./stan/ | |
| key: ${{ runner.os }}-stan-${{ hashFiles('stan/src/stan/version.hpp') }}-v${{ env.CACHE_VERSION }} | |
| - name: Restore built models | |
| uses: actions/cache@v4 | |
| id: test-models | |
| with: | |
| path: ./test_models/ | |
| key: ${{ hashFiles('**/*.stan', 'src/*', 'stan/src/stan/version.hpp', 'Makefile') }}-${{ matrix.os }}-v${{ env.CACHE_VERSION }} | |
| - name: Install package | |
| run: | | |
| cd python/ | |
| pip install pytest | |
| pip install . | |
| - name: Test import | |
| run: | | |
| python -c "import bridgestan" | |
| - name: Run tests | |
| run: | | |
| pytest -v python/ | |
| cd python/ | |
| python example.py | |
| env: | |
| BRIDGESTAN: ${{ github.workspace }} | |
| - name: Run tests (Unix-specific) | |
| if: matrix.os != 'windows-latest' | |
| run: | | |
| pytest -v python/ --run-type=ad_hessian | |
| env: | |
| BRIDGESTAN: ${{ github.workspace }} | |
| julia: | |
| needs: [build] | |
| runs-on: ${{matrix.os}} | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest, macos-latest, windows-latest] | |
| julia-version: ["1"] | |
| include: | |
| - julia-version: "1.6" | |
| os: ubuntu-latest | |
| fail-fast: false | |
| steps: | |
| - name: Check out github | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| - name: Set up Julia | |
| uses: julia-actions/setup-julia@v2 | |
| with: | |
| version: ${{ matrix.julia-version }} | |
| - name: Restore Stan | |
| uses: actions/cache@v4 | |
| id: stan-cache | |
| with: | |
| path: ./stan/ | |
| key: ${{ runner.os }}-stan-${{ hashFiles('stan/src/stan/version.hpp') }}-v${{ env.CACHE_VERSION }} | |
| - name: Restore built models | |
| uses: actions/cache@v4 | |
| id: test-models | |
| with: | |
| path: ./test_models/ | |
| key: ${{ hashFiles('**/*.stan', 'src/*', 'stan/src/stan/version.hpp', 'Makefile') }}-${{ matrix.os }}-v${{ env.CACHE_VERSION }} | |
| - name: Check import | |
| run: | | |
| cd julia/ | |
| julia --project=. -e "using Pkg; Pkg.instantiate()" | |
| julia --project=. -e "using BridgeStan" | |
| - name: Run tests | |
| run: | | |
| cd julia/ | |
| julia --project=. -t 2 -e "using Pkg; Pkg.test()" | |
| julia --project=. example.jl | |
| env: | |
| BRIDGESTAN: ${{ github.workspace }} | |
| Rlang: | |
| needs: [build] | |
| runs-on: ${{matrix.os}} | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest, macos-latest, windows-latest] | |
| fail-fast: false | |
| steps: | |
| - name: Check out github | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| - name: Install R | |
| uses: r-lib/actions/setup-r@v2.11.1 | |
| - name: Install R dependencies | |
| uses: r-lib/actions/setup-r-dependencies@v2.11.1 | |
| with: | |
| packages: | | |
| any::R6 | |
| any::testthat | |
| any::devtools | |
| - name: Restore Stan | |
| uses: actions/cache@v4 | |
| with: | |
| path: ./stan/ | |
| key: ${{ runner.os }}-stan-${{ hashFiles('stan/src/stan/version.hpp') }}-v${{ env.CACHE_VERSION }} | |
| - name: Restore built models | |
| uses: actions/cache@v4 | |
| id: test-models | |
| with: | |
| path: ./test_models/ | |
| key: ${{ hashFiles('**/*.stan', 'src/*', 'stan/src/stan/version.hpp', 'Makefile') }}-${{ matrix.os }}-v${{ env.CACHE_VERSION }} | |
| - name: Run tests | |
| if: matrix.os != 'windows-latest' | |
| run: | | |
| cd R/tests/testthat | |
| gcc -fpic -shared -o test_collisions.so test_collisions.c | |
| cd ../.. | |
| Rscript -e "devtools::test(reporter = c(\"summary\", \"fail\"))" | |
| Rscript -e "install.packages(getwd(), repos=NULL, type=\"source\")" | |
| Rscript example.R | |
| env: | |
| BRIDGESTAN: ${{ github.workspace }} | |
| - name: Run tests (windows) | |
| if: matrix.os == 'windows-latest' | |
| run: | | |
| cd R/tests/testthat | |
| gcc -fpic -shared -o test_collisions.dll test_collisions.c | |
| if (!$LASTEXITCODE.Equals(0)) {exit $LASTEXITCODE} | |
| cd ../.. | |
| Rscript -e 'devtools::test(reporter = c("summary", "fail"))' | |
| if (!$LASTEXITCODE.Equals(0)) {exit $LASTEXITCODE} | |
| Rscript -e 'install.packages(getwd(), repos=NULL, type="source")' | |
| if (!$LASTEXITCODE.Equals(0)) {exit $LASTEXITCODE} | |
| Rscript example.R | |
| if (!$LASTEXITCODE.Equals(0)) {exit $LASTEXITCODE} | |
| env: | |
| BRIDGESTAN: ${{ github.workspace }} | |
| rust: | |
| needs: [build] | |
| runs-on: ${{matrix.os}} | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest, macos-latest, windows-latest] | |
| fail-fast: false | |
| steps: | |
| - name: Check out github | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| - name: Restore Stan | |
| uses: actions/cache@v4 | |
| with: | |
| path: ./stan/ | |
| key: ${{ runner.os }}-stan-${{ hashFiles('stan/src/stan/version.hpp') }}-v${{ env.CACHE_VERSION }} | |
| - name: Restore built models | |
| uses: actions/cache@v4 | |
| id: test-models | |
| with: | |
| path: ./test_models/ | |
| key: ${{ hashFiles('**/*.stan', 'src/*', 'stan/src/stan/version.hpp', 'Makefile') }}-${{ matrix.os }}-v${{ env.CACHE_VERSION }} | |
| - name: Set up TBB | |
| if: matrix.os == 'windows-latest' | |
| run: | | |
| Add-Content $env:GITHUB_PATH "$(pwd)/stan/lib/stan_math/lib/tbb" | |
| - name: Run rust tests | |
| working-directory: ./rust | |
| timeout-minutes: 60 | |
| run: | | |
| cargo clippy | |
| cargo fmt --check | |
| cargo run --example=example | |
| # run all tests with feature download-bridgestan-src | |
| cargo test --verbose --all-features | |
| cargo test --verbose model_compiling -- --ignored |