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‎.github/workflows/cancel.yml.off

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name: cancel
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on:
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workflow_run:
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workflows: ["tests"]
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types:
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- requested
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jobs:
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cancel:
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runs-on: ubuntu-latest
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steps:
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- uses: styfle/[email protected]
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with:
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all_but_latest: true
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workflow_id: ${{ github.event.workflow.id }}

‎.github/workflows/codecov.yml.off

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name: codecov
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on:
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push:
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branches: [ main ]
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pull_request:
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branches: [ main ]
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jobs:
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codecov:
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runs-on: ubuntu-22.04
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steps:
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- uses: actions/[email protected]
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with:
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submodules: recursive
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fetch-depth: 0
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- run: sudo apt install -y lcov
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- run: |
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set -xe
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pip install "pip<23" setuptools==65.2
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CMAKE_ARGS="-DCMAKE_CXX_FLAGS=--coverage -DCMAKE_C_FLAGS=--coverage -DCMAKE_Fortran_FLAGS=--coverage" pip install -e .[tests]
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pytest -We tests
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lcov --capture --directory ./build/*/_PyPartMC/CMakeFiles/_PyPartMC.dir/ --output-file coverage.info --no-external
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- run: find -name \*.gcno | grep -v pypartmc.cpp | grep -v _PyPartMC.dir | xargs rm
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- uses: codecov/[email protected]
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with:
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token: ${{ secrets.CODECOV_TOKEN }}
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fail_ci_if_error: true

‎.github/workflows/conda.yml.off

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name: conda
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on:
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push:
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branches: [ main ]
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pull_request:
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branches: [ main ]
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jobs:
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build:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: ["3.7", "3.8", "3.9"]
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steps:
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- uses: actions/checkout@v3
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with:
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submodules: recursive
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fetch-depth: 0 # https://github.com/pypa/setuptools_scm/issues/480
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- uses: conda-incubator/setup-miniconda@v2
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with:
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auto-update-conda: true
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python-version: ${{ matrix.python-version }}
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- run: python -m pip install --upgrade pip
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- run: pip install -e .[tests]
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- run: |
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cd tests
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pytest -v -s -We -p no:unraisableexception -k 'not test_todos_annotated' .

‎.github/workflows/forlint.yml.off

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name: forlint
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on:
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pull_request:
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branches: [ main ]
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push:
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branches: [ main ]
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jobs:
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lint:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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- uses: NOAA-GFDL/simple_lint@v3
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with:
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failure: true
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ftn_line_len: 101

‎.github/workflows/pdoc.yml.off

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name: pdoc
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defaults:
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run:
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shell: bash
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on:
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push:
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branches: [ main ]
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pull_request:
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branches: [ main ]
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jobs:
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deploy:
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strategy:
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matrix:
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platform: [ubuntu-latest]
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runs-on: ${{ matrix.platform }}
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steps:
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- uses: actions/checkout@v2
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with:
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submodules: recursive
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persist-credentials: false
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- uses: actions/setup-python@v2
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with:
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python-version: 3.12
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- name: Build
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run: |
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pip install pdoc
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pip install -e .
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PDOC_ALLOW_EXEC=1 python -We -m pdoc -o html PyPartMC
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- name: Deploy
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if: ${{ github.ref == 'refs/heads/main' && matrix.platform == 'ubuntu-latest' }}
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uses: JamesIves/[email protected]
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with:
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BRANCH: pdoc
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FOLDER: html
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CLEAN: true

‎.github/workflows/pre-commit.yml.off

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name: pre-commit-hooks
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on: [pull_request]
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jobs:
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build:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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- name: Set up Python 3.10
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uses: actions/setup-python@v1
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with:
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python-version: "3.10"
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- name: Linting
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run: |
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pip install pre-commit
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pre-commit clean
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pre-commit autoupdate
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pre-commit run --all-files

‎.github/workflows/pylint.yml.off

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name: pylint
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on:
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push:
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branches: [ main ]
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pull_request:
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branches: [ main ]
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jobs:
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build:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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with:
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submodules: recursive
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- uses: actions/setup-python@v2
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with:
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python-version: 3.9
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- run: |
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python -m pip install --upgrade pip
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pip install pylint nbqa
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pip install -e .[tests]
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pip install -r .binder/requirements.txt
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- run: pylint --unsafe-load-any-extension=y --disable=fixme,no-member,trailing-newlines,missing-module-docstring,missing-class-docstring,missing-function-docstring,unnecessary-pass $(git ls-files '*.py')
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- run: nbqa pylint --unsafe-load-any-extension=y --disable=fixme,no-member,duplicate-code,wrong-import-position,ungrouped-imports,trailing-whitespace,missing-function-docstring,missing-module-docstring,unsubscriptable-object,invalid-name $(git ls-files '*.ipynb')

‎.github/workflows/readme_listings.yml.off

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name: readme_listings
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defaults:
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run:
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shell: bash
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on:
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push:
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branches: [ main ]
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pull_request:
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branches: [ main ]
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schedule:
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- cron: '0 13 * * 4'
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jobs:
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julia:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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with:
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submodules: recursive
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- uses: actions/setup-python@v1
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with:
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python-version: 3.9
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- uses: jwlawson/[email protected]
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with:
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cmake-version: '3.26.x'
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- run: pip install -e .
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- run: pip install pytest-codeblocks pytest
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- run: python -c "import pytest_codeblocks; code=pytest_codeblocks.extract_from_file('README.md'); f=open('readme.jl', 'w'); f.writelines(block.code for block in code if block.syntax=='Julia'); f.close()"
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- run: cat -n readme.jl
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- uses: julia-actions/setup-julia@v1
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- run: mkdir readme_output
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- run: julia readme.jl > readme_output/julia.txt
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- uses: actions/upload-artifact@v4
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with:
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name: readme_output-julia
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path: readme_output
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python:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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with:
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submodules: recursive
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- uses: actions/setup-python@v1
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with:
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python-version: 3.9
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- uses: jwlawson/[email protected]
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with:
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cmake-version: '3.26.x'
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- run: pip install -e .
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- run: pip install pytest-codeblocks pytest
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- run: python -c "import pytest_codeblocks; code=pytest_codeblocks.extract_from_file('README.md'); f=open('readme.py', 'w'); f.writelines(block.code for block in code if block.syntax=='Python'); f.close()"
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- run: cat -n readme.py
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- run: mkdir readme_output
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- run: python -We readme.py > readme_output/python.txt
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- uses: actions/upload-artifact@v4
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with:
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name: readme_output-python
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path: readme_output
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fortran:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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with:
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submodules: recursive
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- run: |
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sudo apt-get update
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sudo apt-get install libnetcdff-dev
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- run: |
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cd readme_fortran
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mkdir build
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cd build
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PARTMC_HOME=../../gitmodules/partmc cmake ..
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make
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- run: |
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mkdir readme_output
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cd readme_fortran
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./build/main > ../readme_output/fortran.txt
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- uses: actions/upload-artifact@v4
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with:
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name: readme_output-fortran
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path: readme_output
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assert:
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runs-on: ubuntu-latest
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needs: [julia, python, matlab, fortran]
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steps:
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- uses: actions/setup-python@v2
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- run: pip install numpy
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- uses: actions/download-artifact@v4
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with:
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pattern: readme_output-*
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merge-multiple: true
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path: readme_output
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- run : python -c 'import numpy as np; import os; dir="readme_output/"; data=[float(np.loadtxt(dir+file)) for file in os.listdir(dir)]; print("data:", data); similar_as_first = np.array([abs(data[0]-k)/data[0] for k in data[1:]]); print("similar_as_first", similar_as_first); assert((similar_as_first < .5).all())'
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matlab:
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runs-on: ubuntu-20.04
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steps:
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- uses: actions/checkout@v2
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with:
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submodules: recursive
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- uses: actions/setup-python@v1
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with:
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python-version: 3.8
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- uses: jwlawson/[email protected]
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with:
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cmake-version: '3.26.x'
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- run: |
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echo "CC=gcc-9" >> $GITHUB_ENV
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echo "CXX=g++-9" >> $GITHUB_ENV
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VERBOSE=1 pip install --verbose -e .
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- run: pip install pytest-codeblocks pytest
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- run: python -c "import pytest_codeblocks; code=pytest_codeblocks.extract_from_file('README.md'); f=open('readme.m', 'w'); f.writelines(block.code for block in code if block.syntax=='Matlab'); f.close()"
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- run: cat -n readme.m
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# see https://github.com/pybind/cmake_example/pull/164
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- run: |
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echo "pybind11_type=type" > pybind11_builtins.py
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echo "PYTHONPATH=." >> $GITHUB_ENV
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- uses: matlab-actions/setup-matlab@v0
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with:
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release: R2022a
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- run: mkdir readme_output
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- uses: matlab-actions/run-command@v0
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with:
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startup-options: -nojvm
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command: diary('readme_output/matlab.txt'), readme
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- uses: actions/upload-artifact@v4
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with:
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name: readme_output-matlab
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path: readme_output
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‎.github/workflows/stale.yml.off

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# This workflow warns and then closes issues and PRs that have had no activity for a specified amount of time.
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#
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# You can adjust the behavior by modifying this file.
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# For more information, see:
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# https://github.com/actions/stale
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name: Mark stale issues and pull requests
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on:
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schedule:
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- cron: '45 15 * * *'
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jobs:
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stale:
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runs-on: ubuntu-latest
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permissions:
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issues: write
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pull-requests: write
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steps:
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- uses: actions/stale@v9
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with:
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repo-token: ${{ secrets.GITHUB_TOKEN }}
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stale-issue-message: 'Stale issue message'
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stale-pr-message: 'Stale pull request message'
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stale-issue-label: 'no-activity'
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stale-pr-label: 'no-activity'
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operations-per-run: 3
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days-before-stale: 90
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days-before-close: 30

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