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Refactor to support post-numpy.distutils future
This splits scikits.odes into 4 packages: * scikits-odes-core: contains DaeBase and OdeBase which all other packages use. Uses setuptools as the build system. * scikits-odes-daepack: contains the daepack fortran code plus f2py wrappers and associated python code. Uses mesonpy as the build system, as f2py really only supports mesonpy now. * scikits-odes-sundials: contains the cython sundials wrappers. Uses setuptools as the build system, as meson does not align with how we're using cython. * scikits-odes (using the correct normalised package name): contains the high-level wrapper code to switch between solvers. Also contains the compatibility code to allow old imports to work across the packages. Uses setuptools as the build backend. Each package has its own directory, though currently there are symlinks to shared files, and the docs and API docs are for all packages (there hasn't been too much change there). CI is also updated, with only scikits-odes-daepack failing due to conflicts between tox and meson. Tests haven't been moved, there is likely some cleanup to do, and to improve the code coverage of each of the packages.
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‎.github/workflows/test-core.yml‎

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name: Test scikits-odes-core
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on: [push, pull_request]
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jobs:
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tests:
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runs-on: ubuntu-latest
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strategy:
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fail-fast: false
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matrix:
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include:
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#- python-version: "3.7"
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# tox-env: py37
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#- python-version: "3.8"
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# tox-env: py38
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#- python-version: "3.9"
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# tox-env: py39
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#- python-version: "3.10"
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# tox-env: py310
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#- python-version: "3.11"
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# tox-env: py311
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#- python-version: "3.12"
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# tox-env: py312
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- python-version: "3.11"
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tox-env: check-manifest
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#- python-version: "3.11"
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# tox-env: checkreadme
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steps:
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- uses: actions/checkout@v2
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v2
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with:
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python-version: ${{ matrix.python-version }}
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- name: Get pip cache dir
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id: pip-cache
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run: |
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echo "::set-output name=dir::$(pip cache dir)"
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- name: pip cache
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uses: actions/cache@v2
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with:
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path: ${{ steps.pip-cache.outputs.dir }}
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key: ${{ runner.os }}-pip-1
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restore-keys: |
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${{ runner.os }}-pip-
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- name: Install python dependencies
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run: |
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python -m pip install --upgrade pip
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python -m pip install --upgrade tox
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- name: Run tests
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run: |
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cd packages/scikits-odes-core && tox
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env:
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TOXENV: ${{ matrix.tox-env }}

‎.github/workflows/test-daepack.yml‎

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name: Test scikits-odes-daepack
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on: [push, pull_request]
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jobs:
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tests:
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runs-on: ubuntu-latest
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strategy:
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fail-fast: false
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matrix:
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include:
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- python-version: "3.7"
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tox-env: py37
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- python-version: "3.8"
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tox-env: py38
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- python-version: "3.9"
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tox-env: py39
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- python-version: "3.10"
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tox-env: py310
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- python-version: "3.11"
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tox-env: py311
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- python-version: "3.12"
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tox-env: py312
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steps:
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- uses: actions/checkout@v2
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v2
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install build dependencies
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run: sudo apt-get install gfortran
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- name: Get pip cache dir
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id: pip-cache
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run: |
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echo "::set-output name=dir::$(pip cache dir)"
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- name: pip cache
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uses: actions/cache@v2
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with:
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path: ${{ steps.pip-cache.outputs.dir }}
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key: ${{ runner.os }}-pip-1
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restore-keys: |
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${{ runner.os }}-pip-
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- name: Install python dependencies
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run: |
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python -m pip install --upgrade pip
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python -m pip install --upgrade tox
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- name: Run tests
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run: |
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cd packages/scikits-odes-daepack && tox
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env:
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TOXENV: ${{ matrix.tox-env }}

‎.github/workflows/test-namespace.yml‎

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name: Test scikits-odes
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on: [push, pull_request]
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jobs:
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tests:
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runs-on: ubuntu-latest
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strategy:
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fail-fast: false
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matrix:
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include:
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#- python-version: "3.7"
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# sundials-version: "6.5.0"
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# tox-env: py37
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# sundials-precision: double
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# sundials-index-size: 64
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- python-version: "3.8"
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sundials-version: "6.5.0"
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tox-env: py38
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sundials-precision: double
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sundials-index-size: 64
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- python-version: "3.9"
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sundials-version: "6.5.0"
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tox-env: py39
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sundials-precision: double
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sundials-index-size: 64
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- python-version: "3.10"
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sundials-version: "6.5.0"
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tox-env: py310
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sundials-precision: double
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sundials-index-size: 64
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- python-version: "3.11"
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sundials-version: "6.5.0"
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tox-env: py311
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sundials-precision: double
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sundials-index-size: 64
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- python-version: "3.12"
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sundials-version: "6.5.0"
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tox-env: py312
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sundials-precision: double
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sundials-index-size: 64
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- python-version: "3.11"
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sundials-version: "6.5.0"
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tox-env: check-manifest
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sundials-precision: double
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sundials-index-size: 64
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#- python-version: "3.11"
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# sundials-version: "6.5.0"
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# tox-env: checkreadme
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# sundials-precision: double
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# sundials-index-size: 64
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- python-version: "3.11"
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sundials-version: "6.5.0"
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tox-env: py311
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sundials-precision: double
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sundials-index-size: 32
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#- python-version: "3.11"
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# sundials-version: "6.5.0"
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# tox-env: py311
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# sundials-precision: single
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# sundials-index-size: 64
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- python-version: "3.11"
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sundials-version: "6.5.0"
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tox-env: py311
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sundials-precision: extended
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sundials-index-size: 64
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steps:
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- uses: actions/checkout@v2
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v2
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install build dependencies
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run: sudo apt-get install gfortran liblapack-dev
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- name: Sundials cache
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uses: actions/cache@v2
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with:
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path: ~/sundials
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key: ${{ runner.os }}-sundials-${{ matrix.sundials-version }}
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restore-keys: |
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${{ runner.os }}-sundials-
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- name: Install sundials
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run: |
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source ci_support/ensure_sundials_installed.sh &&
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printf "export LD_LIBRARY_PATH=$LD_LIBRARY_PATH\n export LIBRARY_PATH=$LIBRARY_PATH\n export CPATH=$CPATH" > sundials_env.sh
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env:
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SUNDIALS_VERSION: ${{ matrix.sundials-version }}
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SUNDIALS_PRECISION: ${{ matrix.sundials-precision }}
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SUNDIALS_INDEX_SIZE: ${{ matrix.sundials-index-size }}
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- name: Get pip cache dir
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id: pip-cache
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run: |
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echo "::set-output name=dir::$(pip cache dir)"
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- name: pip cache
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uses: actions/cache@v2
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with:
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path: ${{ steps.pip-cache.outputs.dir }}
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key: ${{ runner.os }}-pip-1
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restore-keys: |
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${{ runner.os }}-pip-
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- name: Install python dependencies
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run: |
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python -m pip install --upgrade pip
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python -m pip install --upgrade tox
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- name: Run tests
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run: |
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cat sundials_env.sh
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source sundials_env.sh &&
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env &&
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cd packages/scikits-odes &&
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tox
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env:
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TOXENV: ${{ matrix.tox-env }}

‎.github/workflows/test-overall.yml‎

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name: Python package
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on: [push, pull_request]
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jobs:
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tests:
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runs-on: ubuntu-latest
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strategy:
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fail-fast: false
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matrix:
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include:
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#- python-version: "3.7"
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# sundials-version: "6.5.0"
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# tox-env: py37-test
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# sundials-precision: double
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# sundials-index-size: 64
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- python-version: "3.8"
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sundials-version: "6.5.0"
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tox-env: py38-test
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sundials-precision: double
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sundials-index-size: 64
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- python-version: "3.9"
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sundials-version: "6.5.0"
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tox-env: py39-test
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sundials-precision: double
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sundials-index-size: 64
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- python-version: "3.10"
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sundials-version: "6.5.0"
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tox-env: py310-test
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sundials-precision: double
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sundials-index-size: 64
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- python-version: "3.11"
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sundials-version: "6.5.0"
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tox-env: py311-test
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sundials-precision: double
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sundials-index-size: 64
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- python-version: "3.12"
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sundials-version: "6.5.0"
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tox-env: py312-test
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sundials-precision: double
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sundials-index-size: 64
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- python-version: "3.11"
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sundials-version: "6.5.0"
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tox-env: doctr
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sundials-precision: double
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sundials-index-size: 64
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- python-version: "3.11"
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sundials-version: "6.5.0"
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tox-env: docs
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sundials-precision: double
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sundials-index-size: 64
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- python-version: "3.11"
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sundials-version: "6.5.0"
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tox-env: py311-test
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sundials-precision: double
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sundials-index-size: 32
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#- python-version: "3.11"
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# sundials-version: "6.5.0"
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# tox-env: py311-test
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# sundials-precision: single
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# sundials-index-size: 64
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- python-version: "3.11"
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sundials-version: "6.5.0"
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tox-env: py311-test
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sundials-precision: extended
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sundials-index-size: 64
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#- python-version: "3.12"
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# sundials-version: "6.5.0"
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# tox-env: py312-notebooks
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# sundials-precision: double
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# sundials-index-size: 64
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steps:
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- uses: actions/checkout@v2
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v2
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install build dependencies
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run: sudo apt-get install gfortran liblapack-dev
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- name: Sundials cache
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uses: actions/cache@v2
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with:
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path: ~/sundials
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key: ${{ runner.os }}-sundials-${{ matrix.sundials-version }}
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restore-keys: |
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${{ runner.os }}-sundials-
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- name: Install sundials
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run: |
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source ci_support/ensure_sundials_installed.sh &&
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printf "export LD_LIBRARY_PATH=$LD_LIBRARY_PATH\n export LIBRARY_PATH=$LIBRARY_PATH\n export CPATH=$CPATH" > sundials_env.sh
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env:
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SUNDIALS_VERSION: ${{ matrix.sundials-version }}
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SUNDIALS_PRECISION: ${{ matrix.sundials-precision }}
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SUNDIALS_INDEX_SIZE: ${{ matrix.sundials-index-size }}
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- name: Get pip cache dir
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id: pip-cache
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run: |
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echo "::set-output name=dir::$(pip cache dir)"
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- name: pip cache
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uses: actions/cache@v2
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with:
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path: ${{ steps.pip-cache.outputs.dir }}
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key: ${{ runner.os }}-pip-1
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restore-keys: |
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${{ runner.os }}-pip-
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- name: Install python dependencies
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run: |
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python -m pip install --upgrade pip
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python -m pip install "setuptools<=64.0.0"
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python -m pip install --upgrade tox
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- name: Run tests
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run: |
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cat sundials_env.sh
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source sundials_env.sh &&
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env &&
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tox
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env:
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TOXENV: ${{ matrix.tox-env }}

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