From 1c66fd157eb355a341fb4ae9261b374403792f1e Mon Sep 17 00:00:00 2001 From: Daniel Weindl Date: Thu, 16 Nov 2023 12:22:40 +0100 Subject: [PATCH] GHA: further cleanup (#2202) --- .github/workflows/deploy_release.yml | 3 +- .../test_benchmark_collection_models.yml | 4 +- .github/workflows/test_doc.yml | 16 ++++---- .github/workflows/test_install.yml | 30 +++++---------- .github/workflows/test_petab_test_suite.yml | 6 +-- .github/workflows/test_python_cplusplus.yml | 38 ++++++------------- .github/workflows/test_python_ver_matrix.yml | 6 +-- .github/workflows/test_valgrind.yml | 17 +++------ 8 files changed, 42 insertions(+), 78 deletions(-) diff --git a/.github/workflows/deploy_release.yml b/.github/workflows/deploy_release.yml index 001d0328bf..8fe931763c 100644 --- a/.github/workflows/deploy_release.yml +++ b/.github/workflows/deploy_release.yml @@ -30,8 +30,7 @@ jobs: - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV - name: sdist - run: | - scripts/buildSdist.sh + run: scripts/buildSdist.sh - name: Publish a Python distribution to PyPI uses: pypa/gh-action-pypi-publish@release/v1 diff --git a/.github/workflows/test_benchmark_collection_models.yml b/.github/workflows/test_benchmark_collection_models.yml index e5d13946e7..bf9509e5ce 100644 --- a/.github/workflows/test_benchmark_collection_models.yml +++ b/.github/workflows/test_benchmark_collection_models.yml @@ -44,8 +44,8 @@ jobs: # install AMICI - name: Create AMICI sdist - run: | - pip3 install build && cd python/sdist && python3 -m build --sdist + run: pip3 install build && cd python/sdist && python3 -m build --sdist + - name: Install AMICI sdist run: | pip3 install --user petab[vis] && \ diff --git a/.github/workflows/test_doc.yml b/.github/workflows/test_doc.yml index 717ec9cc53..07e0afdcc8 100644 --- a/.github/workflows/test_doc.yml +++ b/.github/workflows/test_doc.yml @@ -59,18 +59,18 @@ jobs: - name: Set up doxygen uses: ./.github/actions/setup-doxygen - # install amici dependencies - - name: apt + - name: Install apt dependencies + uses: ./.github/actions/install-apt-dependencies + + - name: Install further dependencies run: | sudo apt-get update \ && sudo apt-get install -y \ - g++ \ - libatlas-base-dev \ - libboost-serialization-dev \ pandoc \ - python3-venv \ + python3-venv - - uses: ./.github/actions/setup-swig + - name: Set up SWIG + uses: ./.github/actions/setup-swig - - name: sphinx + - name: Run sphinx run: scripts/run-sphinx.sh diff --git a/.github/workflows/test_install.yml b/.github/workflows/test_install.yml index 0ad1ec0a14..be74cfa4c6 100644 --- a/.github/workflows/test_install.yml +++ b/.github/workflows/test_install.yml @@ -32,20 +32,16 @@ jobs: cmake - name: Build suitesparse - run: | - scripts/buildSuiteSparse.sh + run: scripts/buildSuiteSparse.sh - name: Build sundials - run: | - scripts/buildSundials.sh + run: scripts/buildSundials.sh - name: Build AMICI - run: | - scripts/buildAmici.sh + run: scripts/buildAmici.sh - name: Install python archive - run: | - scripts/installAmiciArchive.sh + run: scripts/installAmiciArchive.sh sdist_ubuntu: name: sdist Install Ubuntu @@ -71,16 +67,13 @@ jobs: uses: ./.github/actions/install-apt-dependencies - name: Create AMICI sdist - run: | - scripts/buildSdist.sh + run: scripts/buildSdist.sh - name: Install python sdist - run: | - pip3 install -v --user $(ls -t python/sdist/dist/amici-*.tar.gz | head -1) + run: pip3 install -v --user $(ls -t python/sdist/dist/amici-*.tar.gz | head -1) - name: Test import - run: | - python -m amici + run: python -m amici sdist_macos: @@ -113,13 +106,10 @@ jobs: && echo CPPFLAGS="-I /usr/local/Cellar/boost/1.81.0_1/include/" >> $GITHUB_ENV - name: Create AMICI sdist - run: | - scripts/buildSdist.sh + run: scripts/buildSdist.sh - name: Install python sdist - run: | - pip3 install -v --user $(ls -t python/sdist/dist/amici-*.tar.gz | head -1) + run: pip3 install -v --user $(ls -t python/sdist/dist/amici-*.tar.gz | head -1) - name: Test import - run: | - python -m amici + run: python -m amici diff --git a/.github/workflows/test_petab_test_suite.yml b/.github/workflows/test_petab_test_suite.yml index 26a4ac7a26..d5c4dc4fe8 100644 --- a/.github/workflows/test_petab_test_suite.yml +++ b/.github/workflows/test_petab_test_suite.yml @@ -44,8 +44,7 @@ jobs: && sudo apt-get install -y python3-venv - name: Build BNGL - run: | - scripts/buildBNGL.sh + run: scripts/buildBNGL.sh - run: | echo "${HOME}/.local/bin/" >> $GITHUB_PATH @@ -54,8 +53,7 @@ jobs: # install AMICI - name: Install python package - run: | - scripts/installAmiciSource.sh + run: scripts/installAmiciSource.sh - name: Install petab run: | diff --git a/.github/workflows/test_python_cplusplus.yml b/.github/workflows/test_python_cplusplus.yml index 546b297712..acc8759a3c 100644 --- a/.github/workflows/test_python_cplusplus.yml +++ b/.github/workflows/test_python_cplusplus.yml @@ -47,26 +47,20 @@ jobs: sudo apt-get update \ && sudo apt-get install -y \ cmake \ - g++ \ python3-venv \ - lcov \ - libboost-math-dev + lcov - name: Build AMICI dependencies - run: | - scripts/buildDependencies.sh + run: scripts/buildDependencies.sh - name: Build AMICI - run: | - CI_SONARCLOUD=TRUE scripts/buildAmici.sh + run: CI_SONARCLOUD=TRUE scripts/buildAmici.sh - name: C++ tests - run: | - scripts/run-cpp-tests.sh + run: scripts/run-cpp-tests.sh - name: Install python package - run: | - scripts/installAmiciSource.sh + run: scripts/installAmiciSource.sh - name: Python tests run: | @@ -98,12 +92,10 @@ jobs: && pip install jax[cpu] - name: example notebooks - run: | - scripts/runNotebook.sh python/examples/example_*/ + run: scripts/runNotebook.sh python/examples/example_*/ - name: doc notebooks - run: | - scripts/runNotebook.sh documentation/GettingStarted.ipynb + run: scripts/runNotebook.sh documentation/GettingStarted.ipynb - name: Codecov Python uses: codecov/codecov-action@v3.1.0 @@ -143,7 +135,6 @@ jobs: osx: name: Tests OSX - runs-on: macos-latest steps: @@ -170,21 +161,16 @@ jobs: && echo CPPFLAGS="-I /usr/local/Cellar/boost/1.81.0_1/include/" >> $GITHUB_ENV - name: Build AMICI - run: | - scripts/buildAll.sh + run: scripts/buildAll.sh - name: Install python package - run: | - scripts/installAmiciSource.sh + run: scripts/installAmiciSource.sh - name: cppcheck - run: | - scripts/run-cppcheck.sh + run: scripts/run-cppcheck.sh - name: Python tests - run: | - scripts/run-python-tests.sh + run: scripts/run-python-tests.sh - name: C++ tests - run: | - scripts/run-cpp-tests.sh + run: scripts/run-cpp-tests.sh diff --git a/.github/workflows/test_python_ver_matrix.yml b/.github/workflows/test_python_ver_matrix.yml index 73aba014cd..866a3fc0f7 100644 --- a/.github/workflows/test_python_ver_matrix.yml +++ b/.github/workflows/test_python_ver_matrix.yml @@ -46,11 +46,9 @@ jobs: # install AMICI - name: Build BNGL - run: | - scripts/buildBNGL.sh + run: scripts/buildBNGL.sh - name: Install python package - run: | - scripts/installAmiciSource.sh + run: scripts/installAmiciSource.sh - name: Python tests run: | diff --git a/.github/workflows/test_valgrind.yml b/.github/workflows/test_valgrind.yml index 7b513f28dd..32eea2e0c0 100644 --- a/.github/workflows/test_valgrind.yml +++ b/.github/workflows/test_valgrind.yml @@ -14,8 +14,6 @@ on: jobs: valgrind_cpp: name: Valgrind C++ - - # TODO: prepare image with more deps preinstalled runs-on: ubuntu-22.04 strategy: @@ -47,12 +45,10 @@ jobs: valgrind - name: Build AMICI - run: | - scripts/buildAll.sh + run: scripts/buildAll.sh - name: C++ tests / Valgrind - run: | - scripts/run-valgrind-cpp.sh + run: scripts/run-valgrind-cpp.sh valgrind_python: name: Valgrind Python @@ -88,13 +84,10 @@ jobs: valgrind - name: Build AMICI - run: | - scripts/buildAll.sh + run: scripts/buildAll.sh - name: Install python package - run: | - scripts/installAmiciSource.sh + run: scripts/installAmiciSource.sh - name: Python tests / Valgrind - run: | - scripts/run-valgrind-py.sh + run: scripts/run-valgrind-py.sh