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Post-merge Tests

Fix SolutionArray.read_csv when using Pandas 3.x #384

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Fix SolutionArray.read_csv when using Pandas 3.x

Fix SolutionArray.read_csv when using Pandas 3.x #384

Workflow file for this run

.github/workflows/post-merge-tests.yml at fea039d
name: Post-merge Tests
on:
workflow_dispatch: # allow manual triggering of this workflow
inputs:
outgoing_ref:
description: "The ref to be built. Can be a tag, commit hash, or branch name"
required: true
default: "main"
push:
# Run when the main branch is pushed to
branches:
- main
# Run on pull requests when this file is modified
pull_request:
branches:
- main
paths:
- .github/workflows/post-merge-tests.yml
permissions:
contents: read
env:
UV_INDEX: https://pypi.anaconda.org/scientific-python-nightly-wheels/simple
REQUIREMENTS_TXT_FILE: "platform/ci_support/post_merge_reqs.txt"
jobs:
prerelease-cython:
name: Pre-release Cython
runs-on: ubuntu-22.04
timeout-minutes: 60
steps:
- uses: actions/checkout@v4
name: Checkout the repository
with:
submodules: recursive
persist-credentials: false
- name: Setup Python
uses: actions/setup-python@v5
with:
python-version: 3.13
- name: Install uv
uses: astral-sh/setup-uv@e92bafb6253dcd438e0484186d7669ea7a8ca1cc # v6.4.3
with:
python-version: 3.13
cache-dependency-glob: |
${{ env.REQUIREMENTS_TXT_FILE }}
enable-cache: true
- name: Install Apt dependencies
run: |
sudo apt update
sudo apt install libboost-dev libopenblas-dev libhdf5-dev doxygen
- name: Install Python dependencies
run: |
uv venv --python 3.13 --seed
sed -i 's/cython.*//g' "${REQUIREMENTS_TXT_FILE}"
uv pip install -r "${REQUIREMENTS_TXT_FILE}"
uv pip install --prerelease=allow --only-binary=":all:" cython
- name: Build Cantera
run: uv run scons build env_vars=all
CXX=clang++-14 CC=clang-14 f90_interface=n extra_lib_dirs=/usr/lib/llvm/lib
-j4 debug=n --debug=time logging=debug python_package=y
- name: Build Tests
run: uv run scons -j4 build-tests
- name: Run compiled tests
run: uv run scons test-gtest test-legacy --debug=time
- name: Run Python tests
run: uv run pytest -raP -v -n auto --durations=50 test/python
env:
LD_LIBRARY_PATH: "${LD_LIBRARY_PATH}:build/lib"
PYTHONPATH: build/python
ubuntu-docker:
name: Docker 'ubuntu:${{ matrix.image }}' image with Sundials MPI ${{ matrix.mpi }}
strategy:
matrix:
include:
- image: "devel"
options: ""
mpi: override # fall back to bundled Sundials (system_sundials=default)
- image: "rolling"
options: "system_sundials=y CC=mpicc CXX=mpicxx FORTRAN=mpifort"
mpi: enabled # use MPI compiler wrappers
fail-fast: false
runs-on: ubuntu-latest
timeout-minutes: 60
container:
image: ubuntu:${{ matrix.image }}
steps:
- name: Install git on ubuntu:${{ matrix.image }}
run: |
apt update -y
apt install -y --no-install-recommends git ca-certificates
git config --global init.defaultBranch main
git config --global --add safe.directory /__w/cantera/cantera
- uses: actions/checkout@v4
name: Checkout the repository
with:
submodules: recursive
persist-credentials: false
- name: Install Apt dependencies
# Use packages from ubuntu image when possible
run: |
apt install -y --no-install-recommends python3 python3-pip pipenv scons \
build-essential libboost-dev gfortran libopenmpi-dev libpython3-dev \
libblas-dev liblapack-dev libhdf5-dev libfmt-dev libyaml-cpp-dev \
libgtest-dev libgmock-dev libeigen3-dev libsundials-dev \
openmpi-bin libopenmpi-dev \
cython3 python3-numpy python3-pandas python3-pint python3-graphviz \
python3-ruamel.yaml python3-setuptools python3-wheel python3-pytest \
python3-pytest-xdist doxygen python3-jinja2
gcc --version
- name: Install Python dependencies
run: |
pipenv install pytest-github-actions-annotate-failures
- name: Build Cantera
run: |
scons build env_vars=all -j4 debug=n --debug=time logging=debug \
system_eigen=y system_fmt=y ${{ matrix.options }} \
system_yamlcpp=y system_blas_lapack=y hdf_support=y \
cc_flags=-D_GLIBCXX_ASSERTIONS python_package=y f90_interface=y
- name: Build Tests
run: scons -j4 build-tests
- name: Run compiled tests
run: scons test-gtest test-legacy --debug=time
- name: Run Python tests
run: python3 -m pytest -raP -v -n auto --durations=50 test/python
env:
LD_LIBRARY_PATH: "${LD_LIBRARY_PATH}:build/lib"
PYTHONPATH: build/python
fedora-docker:
name: Docker 'fedora:${{ matrix.image }}' image
strategy:
matrix:
image: [rawhide, latest]
fail-fast: false
runs-on: ubuntu-latest
timeout-minutes: 60
container:
image: fedora:${{ matrix.image }}
steps:
- name: Install git on fedora:${{ matrix.image }}
run: |
dnf install -y git
git config --global init.defaultBranch main
git config --global --add safe.directory /__w/cantera/cantera
- uses: actions/checkout@v4
name: Checkout the repository
with:
persist-credentials: false
- name: Install dependencies
# Use packages from Fedora
run: |
dnf install -y boost-devel eigen3-devel fmt-devel gcc gcc-c++ \
gcc-fortran gmock-devel gtest-devel python3 python3-cython \
python3-devel python3-numpy python3-pandas python3-pint python3-pip \
python3-pytest python3-pytest-xdist python3-ruamel-yaml python3-scipy \
python3-scons python3-wheel sundials-devel yaml-cpp-devel hdf5-devel \
highfive-devel python3-graphviz python3-packaging python3-setuptools \
python3-jinja2 doxygen
- name: Build Cantera
run: |
scons build -j4 debug=n --debug=time logging=debug python_package=y \
f90_interface=y extra_inc_dirs=/usr/include/eigen3 libdirname=/usr/lib64 \
system_eigen=y system_fmt=y system_blas_lapack=y system_sundials=y \
system_yamlcpp=y system_blas_lapack=y hdf_support=y
# note: 'system_highfive=y' is omitted as the current packaged version is too old;
# once newer version is available in 'latest', this should be tested as well
- name: Build Tests
run: scons -j4 build-tests
- name: Run compiled tests
run: scons test-gtest test-legacy --debug=time
- name: Run Python tests
run: python3 -m pytest -raP -v -n auto --durations=50 test/python
env:
LD_LIBRARY_PATH: build/lib
PYTHONPATH: build/python
ubuntu-python-prerelease:
name: ${{ matrix.os }} with Python ${{ matrix.python-version }}
runs-on: ${{ matrix.os }}
timeout-minutes: 60
strategy:
matrix:
python-version: ['3.14']
os: ['ubuntu-22.04', 'ubuntu-24.04']
fail-fast: false
steps:
- uses: actions/checkout@v4
name: Checkout the repository
with:
submodules: recursive
persist-credentials: false
- name: Setup Python
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
allow-prereleases: true
- name: Install uv
uses: astral-sh/setup-uv@e92bafb6253dcd438e0484186d7669ea7a8ca1cc # v6.4.3
with:
python-version: ${{ matrix.python-version }}
enable-cache: true
cache-dependency-glob: |
${{ env.REQUIREMENTS_TXT_FILE }}
- name: Install Apt dependencies
run: |
sudo apt update
sudo apt install libboost-dev gfortran libopenmpi-dev \
libblas-dev liblapack-dev libhdf5-dev libfmt-dev doxygen \
libopenblas-dev
gcc --version
- name: Install Python dependencies
run: |
uv venv --python ${{ matrix.python-version }} --seed
sed -i 's/cython.*\|pandas\|numpy\|scipy//g' "${REQUIREMENTS_TXT_FILE}"
uv pip install -r "${REQUIREMENTS_TXT_FILE}"
uv pip install --prerelease=allow numpy cython pandas scipy
- name: Build Cantera
run: |
uv run scons build env_vars=all -j4 debug=n --debug=time logging=debug \
system_fmt=y system_blas_lapack=y hdf_support=y cc_flags=-D_GLIBCXX_ASSERTIONS \
python_package=y
- name: Build Tests
run: uv run scons -j4 build-tests
- name: Run compiled tests
run: uv run scons test-gtest test-legacy --debug=time
- name: Run Python tests
run: uv run pytest -raP -v -n auto --durations=50 test/python
env:
LD_LIBRARY_PATH: "${LD_LIBRARY_PATH}:build/lib"
PYTHONPATH: build/python
macos-homebrew:
name: Install Latest Python with Homebrew on ${{ matrix.os }}
runs-on: ${{ matrix.os }}
timeout-minutes: 90
strategy:
matrix:
os: ['macos-14', 'macos-15']
fail-fast: false
steps:
- uses: actions/checkout@v4
name: Checkout the repository
with:
submodules: recursive
persist-credentials: false
- name: Setup uv
uses: astral-sh/setup-uv@e92bafb6253dcd438e0484186d7669ea7a8ca1cc # v6.4.3
with:
enable-cache: true
cache-dependency-glob: |
${{ env.REQUIREMENTS_TXT_FILE }}
# NumPy is installed here for the Python custom rate tests
- name: Install Brew dependencies
run: |
brew install --display-times boost libomp hdf5 python numpy doxygen
- name: Set Include folder
run: echo "BOOST_INC_DIR=$(brew --prefix)/include" >> $GITHUB_ENV
# This is necessary because of PEP 668 https://peps.python.org/pep-0668/
# PEP 668 prohibits installation to system Python packages via pip
- name: Create a virtualenv for dependencies
run: |
uv venv --python "$(brew --prefix)/bin/python3" --seed
- name: Install Python dependencies
# SCons must be installed into the virtualenv because packaging is a dependency
# and we can't install packaging for the homebrew Python
run: |
uv pip install -r "${REQUIREMENTS_TXT_FILE}"
- name: Build Cantera
run: |
uv run scons build env_vars=all -j3 debug=n --debug=time logging=debug \
boost_inc_dir=${BOOST_INC_DIR} python_package=y
- name: Build Tests
run: uv run scons -j3 build-tests
- name: Run compiled tests
run: uv run scons test-gtest test-legacy --debug=time
- name: Run Python tests
run: uv run pytest -raP -v -n auto --durations=50 test/python
env:
DYLD_LIBRARY_PATH: "${DYLD_LIBRARY_PATH}:build/lib"
PYTHONPATH: build/python
macos-sporadic-failures:
# exact clone of 'macos-multiple-pythons' runner on main.yml
# used to test status of GH issue Cantera/cantera#1916
name: ${{ matrix.macos-version }} with Python ${{ matrix.python-version }}
runs-on: ${{ matrix.macos-version }}
timeout-minutes: 90
strategy:
matrix:
macos-version: ['macos-13'] # 'macos-13-large', 'macos-13-xlarge' require paid plans
python-version: ['3.13'] # previously failed for 3.13.4 and 3.13.5 on macos-13
fail-fast: false
steps:
- uses: actions/checkout@v4
name: Checkout the repository
with:
submodules: recursive
persist-credentials: false
- name: Write dependencies to a file for caching
run: |
echo "scons ruamel.yaml numpy cython!=3.1.2 pandas pytest pytest-xdist pytest-github-actions-annotate-failures pint graphviz Jinja2" | tr " " "\n" > requirements.txt
- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
cache: pip
cache-dependency-path: requirements.txt
- name: Install Brew dependencies
run: brew install --display-times boost libomp hdf5 doxygen
- name: Set Include folder
run:
echo "BOOST_INC_DIR=$(brew --prefix)/include" >> $GITHUB_ENV
- name: Upgrade pip
run: python -m pip install -U pip setuptools wheel
- name: Install Python dependencies
run: python -m pip install -r requirements.txt
- name: Build Cantera with legacy CLib
run: scons build env_vars=all -j3 debug=n --debug=time
boost_inc_dir=${BOOST_INC_DIR} ${{ matrix.extra-build-args }} clib_legacy=y
- name: Build Tests
run: scons -j3 build-tests --debug=time
- name: Run compiled tests
run: scons test-gtest test-legacy --debug=time
- name: Run Python tests
run: |
export DYLD_LIBRARY_PATH=build/lib
python3 -m pytest -raP -v -n auto --durations=50 test/python
- name: Rebuild Cantera with generated CLib
run: |
scons build clib_legacy=n -j3
if: matrix.python-version == '3.12' && matrix.macos-version == 'macos-13'
- name: Run googletests for generated CLib
run: scons test-clib --debug=time
if: matrix.python-version == '3.12' && matrix.macos-version == 'macos-13'
- name: Upload shared library
uses: actions/upload-artifact@v4
if: matrix.python-version == '3.12' && matrix.macos-version == 'macos-13'
with:
path: build/lib/libcantera_shared.dylib
name: libcantera_shared.dylib
retention-days: 2