Release v0.5.4 #4694
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name: CI | |
# trigger | |
on: | |
push: | |
branches: | |
- main | |
- develop | |
pull_request: | |
workflow_dispatch: | |
merge_group: | |
schedule: | |
# run Monday and Thursday at 03:42 UTC | |
- cron: '42 3 * * MON,THU' | |
env: | |
# use all available cores for compiling amici models | |
AMICI_PARALLEL_COMPILE: "" | |
# non-interactive backend for matplotlib | |
MPLBACKEND: "agg" | |
# jobs | |
jobs: | |
base: | |
runs-on: ubuntu-latest | |
strategy: | |
matrix: | |
python-version: ['3.10', '3.12'] | |
steps: | |
- name: Check out repository | |
uses: actions/checkout@v4 | |
- name: Prepare python ${{ matrix.python-version }} | |
uses: actions/setup-python@v5 | |
with: | |
python-version: ${{ matrix.python-version }} | |
- name: Cache | |
uses: actions/cache@v4 | |
with: | |
path: | | |
~/.cache/pip | |
.tox/ | |
key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}" | |
- name: Install dependencies | |
run: .github/workflows/install_deps.sh amici | |
- name: Run tests | |
timeout-minutes: 30 | |
run: tox -e base | |
env: | |
CC: clang | |
CXX: clang++ | |
- name: Coverage | |
uses: codecov/codecov-action@v4 | |
with: | |
token: ${{ secrets.CODECOV_TOKEN }} | |
file: ./coverage.xml | |
mac: | |
runs-on: macos-13 # TODO: change to macos-latest after the next release | |
strategy: | |
matrix: | |
python-version: ['3.12'] | |
steps: | |
- name: Check out repository | |
uses: actions/checkout@v4 | |
- name: Prepare python ${{ matrix.python-version }} | |
uses: actions/setup-python@v5 | |
with: | |
python-version: ${{ matrix.python-version }} | |
- name: Cache | |
uses: actions/cache@v4 | |
with: | |
path: | | |
~/.cache/pip | |
.tox/ | |
key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}" | |
- name: Install dependencies | |
run: .github/workflows/install_deps.sh amici | |
- name: Run tests | |
timeout-minutes: 30 | |
run: ulimit -n 65536 65536 && tox -e base | |
- name: Coverage | |
uses: codecov/codecov-action@v4 | |
with: | |
token: ${{ secrets.CODECOV_TOKEN }} | |
file: ./coverage.xml | |
windows: | |
runs-on: windows-latest | |
strategy: | |
matrix: | |
python-version: ['3.12'] | |
steps: | |
- name: Check out repository | |
uses: actions/checkout@v4 | |
- name: Prepare python ${{ matrix.python-version }} | |
uses: actions/setup-python@v5 | |
with: | |
python-version: ${{ matrix.python-version }} | |
- name: Cache | |
uses: actions/cache@v4 | |
with: | |
path: | | |
~\AppData\Local\pip\Cache | |
.tox | |
key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}" | |
- name: Install dependencies | |
run: | | |
pip install --upgrade pip | |
pip install tox | |
- name: Run tests | |
shell: bash | |
timeout-minutes: 10 | |
run: tox -e windows | |
petab: | |
runs-on: ubuntu-latest | |
strategy: | |
matrix: | |
python-version: ['3.10', '3.12'] | |
steps: | |
- name: Check out repository | |
uses: actions/checkout@v4 | |
- name: Prepare python ${{ matrix.python-version }} | |
uses: actions/setup-python@v5 | |
with: | |
python-version: ${{ matrix.python-version }} | |
- name: Cache | |
uses: actions/cache@v4 | |
with: | |
path: | | |
~/.cache/pip | |
.tox/ | |
key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}" | |
- name: Install dependencies | |
run: .github/workflows/install_deps.sh amici pysb | |
- name: Run tests | |
timeout-minutes: 35 | |
run: tox -e petab | |
env: | |
CC: clang | |
CXX: clang++ | |
- name: Coverage | |
uses: codecov/codecov-action@v4 | |
with: | |
token: ${{ secrets.CODECOV_TOKEN }} | |
file: ./coverage.xml | |
julia: | |
runs-on: ubuntu-latest | |
strategy: | |
matrix: | |
python-version: ['3.10', '3.12'] | |
# needed to allow julia-actions/cache to delete old caches that it has created | |
permissions: | |
actions: write | |
contents: read | |
steps: | |
- name: Check out repository | |
uses: actions/checkout@v4 | |
- name: Prepare python ${{ matrix.python-version }} | |
uses: actions/setup-python@v5 | |
with: | |
python-version: ${{ matrix.python-version }} | |
- name: Cache tox and cache | |
uses: actions/cache@v4 | |
with: | |
path: | | |
~/.cache/pip | |
.tox/ | |
key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}" | |
- name: Install julia | |
uses: julia-actions/setup-julia@v2 | |
with: | |
version: 1.9 | |
- name: Cache Julia | |
uses: julia-actions/cache@v2 | |
- name: Install dependencies | |
run: .github/workflows/install_deps.sh | |
- name: Install PEtabJL dependencies | |
run: > | |
julia -e 'using Pkg; Pkg.add(Pkg.PackageSpec(;name="PEtab", version="2.5.0")); | |
Pkg.add("OrdinaryDiffEq"); Pkg.add("Sundials")' | |
- name: Run tests | |
timeout-minutes: 25 | |
run: tox -e julia | |
- name: Coverage | |
uses: codecov/codecov-action@v4 | |
with: | |
token: ${{ secrets.CODECOV_TOKEN }} | |
file: ./coverage.xml | |
optimize: | |
runs-on: ubuntu-latest | |
strategy: | |
matrix: | |
python-version: ['3.12'] | |
steps: | |
- name: Check out repository | |
uses: actions/checkout@v4 | |
- name: Prepare python ${{ matrix.python-version }} | |
uses: actions/setup-python@v5 | |
with: | |
python-version: ${{ matrix.python-version }} | |
- name: Cache | |
uses: actions/cache@v4 | |
with: | |
path: | | |
~/.cache/pip | |
.tox/ | |
key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}" | |
- name: Install dependencies | |
run: .github/workflows/install_deps.sh ipopt | |
- name: Run tests | |
timeout-minutes: 25 | |
run: tox -e optimize | |
- name: Coverage | |
uses: codecov/codecov-action@v4 | |
with: | |
token: ${{ secrets.CODECOV_TOKEN }} | |
file: ./coverage.xml | |
hierarchical: | |
runs-on: ubuntu-latest | |
strategy: | |
matrix: | |
python-version: ['3.10', '3.12'] | |
steps: | |
- name: Check out repository | |
uses: actions/checkout@v4 | |
- name: Prepare python ${{ matrix.python-version }} | |
uses: actions/setup-python@v5 | |
with: | |
python-version: ${{ matrix.python-version }} | |
- name: Cache | |
uses: actions/cache@v4 | |
with: | |
path: | | |
~/.cache/pip | |
.tox/ | |
key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}" | |
- name: Install dependencies | |
run: .github/workflows/install_deps.sh amici | |
- name: Run tests | |
timeout-minutes: 20 | |
run: tox -e hierarchical | |
- name: Coverage | |
uses: codecov/codecov-action@v4 | |
with: | |
token: ${{ secrets.CODECOV_TOKEN }} | |
file: ./coverage.xml | |
select: | |
runs-on: ubuntu-latest | |
strategy: | |
matrix: | |
python-version: ['3.10', '3.12'] | |
steps: | |
- name: Check out repository | |
uses: actions/checkout@v4 | |
- name: Prepare python ${{ matrix.python-version }} | |
uses: actions/setup-python@v5 | |
with: | |
python-version: ${{ matrix.python-version }} | |
- name: Cache | |
uses: actions/cache@v4 | |
with: | |
path: | | |
~/.cache/pip | |
.tox/ | |
key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}" | |
- name: Install dependencies | |
run: .github/workflows/install_deps.sh amici | |
- name: Run tests | |
timeout-minutes: 20 | |
run: tox -e select | |
- name: Coverage | |
uses: codecov/codecov-action@v4 | |
with: | |
token: ${{ secrets.CODECOV_TOKEN }} | |
file: ./coverage.xml | |
quality: | |
runs-on: ubuntu-latest | |
strategy: | |
matrix: | |
python-version: ['3.12'] | |
steps: | |
- name: Check out repository | |
uses: actions/checkout@v4 | |
- name: Prepare python ${{ matrix.python-version }} | |
uses: actions/setup-python@v5 | |
with: | |
python-version: ${{ matrix.python-version }} | |
- name: Cache | |
uses: actions/cache@v4 | |
with: | |
path: | | |
~/.cache/pip | |
.tox/ | |
key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}" | |
- name: Install dependencies | |
run: pip install tox pre-commit | |
- name: Check repository size | |
run: tox -e size | |
- name: Run pre-commit hooks | |
run: pre-commit run --all-files | |
docs: | |
runs-on: ubuntu-latest | |
strategy: | |
matrix: | |
python-version: ['3.11'] | |
steps: | |
- name: Check out repository | |
uses: actions/checkout@v4 | |
- name: Prepare python ${{ matrix.python-version }} | |
uses: actions/setup-python@v5 | |
with: | |
python-version: ${{ matrix.python-version }} | |
- name: Cache | |
uses: actions/cache@v4 | |
with: | |
path: | | |
~/.cache/pip | |
.tox/ | |
key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}" | |
- name: Install dependencies | |
run: .github/workflows/install_deps.sh doc amici | |
- name: Validate CITATION.cff | |
run: pip install cffconvert && cffconvert --validate | |
- name: Build doc | |
timeout-minutes: 30 | |
run: tox -e doc | |
notebooks1: | |
runs-on: ubuntu-latest | |
strategy: | |
matrix: | |
python-version: ['3.10'] | |
steps: | |
- name: Check out repository | |
uses: actions/checkout@v4 | |
- name: Prepare python ${{ matrix.python-version }} | |
uses: actions/setup-python@v5 | |
with: | |
python-version: ${{ matrix.python-version }} | |
- name: Cache | |
uses: actions/cache@v4 | |
with: | |
path: | | |
~/.cache/pip | |
.tox/ | |
key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}" | |
- name: Install dependencies | |
run: .github/workflows/install_deps.sh amici ipopt | |
- name: Run notebooks 1 | |
timeout-minutes: 20 | |
run: tox -e notebooks1 | |
notebooks2: | |
runs-on: ubuntu-latest | |
strategy: | |
matrix: | |
python-version: ['3.10'] | |
steps: | |
- name: Check out repository | |
uses: actions/checkout@v4 | |
- name: Prepare python ${{ matrix.python-version }} | |
uses: actions/setup-python@v5 | |
with: | |
python-version: ${{ matrix.python-version }} | |
- name: Cache | |
uses: actions/cache@v4 | |
with: | |
path: | | |
~/.cache/pip | |
.tox/ | |
key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}" | |
- name: Install dependencies | |
run: .github/workflows/install_deps.sh amici | |
- name: Run notebooks 2 | |
timeout-minutes: 20 | |
run: tox -e notebooks2 |