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thalassemiathalassemia
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Merge pull request #53 from CovertLab/numpy2
Update Build Toolchain
2 parents fabb713 + 5fc79db commit d93454f

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‎.github/workflows/release.yml‎

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name: Build and upload to PyPI
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on:
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push:
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release:
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types:
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- published
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jobs:
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# Build the wheels for Linux, Windows and macOS for Python 3.9 and newer
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build_wheels:
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name: Build wheel for cp${{ matrix.python }}-${{ matrix.platform_id }}
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runs-on: ${{ matrix.os }}
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strategy:
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# Ensure that a wheel builder finishes even if another fails
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fail-fast: false
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matrix:
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include:
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# Window 64 bit
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- os: windows-latest
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python: 39
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platform_id: win_amd64
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- os: windows-latest
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python: 310
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platform_id: win_amd64
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- os: windows-latest
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python: 311
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platform_id: win_amd64
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- os: windows-latest
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python: 312
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platform_id: win_amd64
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- os: windows-latest
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python: 313
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platform_id: win_amd64
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- os: windows-latest
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python: 313t
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platform_id: win_amd64
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free_threaded_support: True
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# Linux 64 bit manylinux2014
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- os: ubuntu-latest
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python: 39
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platform_id: manylinux_x86_64
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- os: ubuntu-latest
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python: 310
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platform_id: manylinux_x86_64
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- os: ubuntu-latest
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python: 311
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platform_id: manylinux_x86_64
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- os: ubuntu-latest
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python: 312
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platform_id: manylinux_x86_64
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- os: ubuntu-latest
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python: 313
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platform_id: manylinux_x86_64
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- os: ubuntu-latest
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python: 313t
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platform_id: manylinux_x86_64
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free_threaded_support: True
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# MacOS x86_64
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- os: macos-13
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python: 39
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platform_id: macosx_x86_64
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- os: macos-13
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python: 310
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platform_id: macosx_x86_64
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- os: macos-13
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python: 311
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platform_id: macosx_x86_64
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- os: macos-13
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python: 312
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platform_id: macosx_x86_64
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- os: macos-13
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python: 313
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platform_id: macosx_x86_64
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- os: macos-13
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python: 313t
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platform_id: macosx_x86_64
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free_threaded_support: True
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# MacOS arm64
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- os: macos-14
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python: 39
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platform_id: macosx_arm64
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- os: macos-14
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python: 310
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platform_id: macosx_arm64
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- os: macos-14
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python: 311
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platform_id: macosx_arm64
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- os: macos-14
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python: 312
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platform_id: macosx_arm64
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- os: macos-14
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python: 313
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platform_id: macosx_arm64
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- os: macos-14
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python: 313t
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platform_id: macosx_arm64
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free_threaded_support: True
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steps:
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- uses: actions/checkout@v4
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- name: Build wheels
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env:
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CIBW_FREE_THREADED_SUPPORT: ${{ matrix.free_threaded_support }}
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CIBW_BUILD: cp${{ matrix.python }}-${{ matrix.platform_id }}
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CIBW_TEST_REQUIRES: pytest psutil
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CIBW_TEST_COMMAND: pytest -v {project}/test
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CIBW_ENVIRONMENT: USE_CYTHON=1
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uses: pypa/cibuildwheel@v2.22.0
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- uses: actions/upload-artifact@v4
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with:
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name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
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path: ./wheelhouse/*.whl
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build_sdist:
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name: Build source distribution
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- name: Build sdist
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run: pipx run build --sdist
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- uses: actions/upload-artifact@v4
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with:
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name: cibw-sdist
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path: dist/*.tar.gz
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upload_pypi:
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needs: [build_wheels, build_sdist]
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runs-on: ubuntu-latest
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environment:
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name: pypi
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url: https://pypi.org/p/stochastic-arrow
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permissions:
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id-token: write
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if: github.event_name == 'release' && github.event.action == 'published'
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steps:
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- uses: actions/download-artifact@v4
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with:
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# unpacks all CIBW artifacts into dist/
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pattern: cibw-*
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path: dist
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merge-multiple: true
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- uses: pypa/gh-action-pypi-publish@release/v1

‎.gitignore‎

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/.idea/
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/tmp/
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stochastic_arrow/arrowhead.c
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stochastic_arrow/arrowhead.*.pyd
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stochastic_arrow/*.html
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src/stochastic_arrow/arrowhead.c
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src/stochastic_arrow/arrowhead.*.pyd
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src/stochastic_arrow/*.html
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arrow.egg-info/
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stochastic_arrow.egg-info/

‎MANIFEST.in‎

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include stochastic_arrow/obsidian.h
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include stochastic_arrow/mersenne.h
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include src/stochastic_arrow/obsidian.h
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include src/stochastic_arrow/mersenne.h

‎Makefile‎

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.DEFAULT_GOAL := compile
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clean:
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### Files for older versions of stochastic_arrow are in arrow folder
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### Files for older versions of stochastic_arrow are in arrow or stochastic_arrow folder
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rm -rf arrow/arrowhead*.so arrow/arrowhead.c arrow/arrowhead.html
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rm -rf stochastic_arrow/arrowhead*.so stochastic_arrow/arrowhead.c stochastic_arrow/arrowhead.html build/ dist/ MANIFEST .pytest_cache/ stochastic_arrow.egg-info/
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### Newer versions of stochastic_arrow are in src/stochastic_arrow folder
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rm -rf src/stochastic_arrow/arrowhead*.so src/stochastic_arrow/arrowhead.c src/stochastic_arrow/arrowhead.html src/stochastic_arrow.egg-info/
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find . -name "*.pyc" -delete
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find . -name "__pycache__" -delete
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compile:
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USE_CYTHON=1 python setup.py build_ext --inplace
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USE_CYTHON=1 python -m pip install -e .
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test: clean compile
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pytest test
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dist:
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### bdist_wheel is disabled on linux since the distribution machinery doesn't
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### yet have a way to specify compatible linux distros.
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USE_CYTHON=1 python setup.py sdist # bdist_wheel
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USE_CYTHON=1 python -m build --sdist

‎README.md‎

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history = reenact_events(stoichiometric_matrix, result['events'], state)
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```
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## Testing
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`stochastic_arrow` uses [pytest](https://docs.pytest.org/en/latest/). To test it:
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## Building
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> make clean compile
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> pytest
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This builds the extension package and installs it in editable mode.
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**NOTE:** `make compile` without an explicit `clean` might not fully build the extension.
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There are more command line features in test_arrow:
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## Testing
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`stochastic_arrow` uses [pytest](https://docs.pytest.org/en/latest/).
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To run the main tests, in the source tree:
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> python -m stochastic_arrow.test.test_arrow --complexation
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> make test
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> python -m stochastic_arrow.test.test_arrow --plot
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or
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> python -m stochastic_arrow.test.test_arrow --obsidian
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> pytest
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> python -m stochastic_arrow.test.test_arrow --memory
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There are additional command line features in test_arrow:
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> python -m stochastic_arrow.test.test_arrow --time
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> python -m test.test_arrow --help
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> python -m test.test_arrow --complexation
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> python -m test.test_arrow --complexation --runs 3
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> python -m test.test_arrow --obsidian
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> python -m test.test_arrow --memory
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> python -m test.test_arrow --time
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> python -m test.test_arrow --pickle
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> python -m test.test_arrow --test-fail-flagella
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> python -m test.test_arrow --test-fail-stdout
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> python -m test.test_hang
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More examples:
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This test requires installing a version of matplotlib that's compatible with the installed numpy:
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> python -m stochastic_arrow.test.test_hang
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> python -m test.test_arrow --plot
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> pytest -m stochastic_arrow/test/test_arrow.py
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More examples:
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> pytest -k flagella
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## Changelog
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### Version 1.1.0
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* Update build toolchain and automatically build/publish wheels for all
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major platforms and recent Python versions.
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* Build wheels with Numpy 2+ support
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### Version 1.0.0
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* Rename module to `stochastic_arrow` to avoid name conflict (Issue #51). **All users must update their import statements to use `stochastic_arrow` instead of `arrow`.**

‎optional_requirements.txt‎

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matplotlib==2.2.3
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matplotlib

‎pyproject.toml‎

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[build-system]
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requires = ["setuptools", "wheel", "cython==3.1.0a1; python_version=='3.13'", "cython; python_version!='3.13'", "numpy"]
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build-backend = "setuptools.build_meta"

‎release.sh‎

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‎requirements.txt‎

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pip
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setuptools
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build
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Cython>=0.29.34
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numpy

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