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Merge pull request #52 from CovertLab/name_change
Rename arrow module to stochastic_arrow
2 parents fdf3db7 + 4bd8eae commit fabb713

28 files changed

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‎.github/workflows/pytest.yml‎

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# Modified from GitHub Actions template
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name: Pytest
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on:
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push:
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branches: [master]
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pull_request:
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branches: [master]
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jobs:
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test-on-ubuntu:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: ['3.9', '3.10', '3.11']
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steps:
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- uses: actions/checkout@v3
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- name: Setup Python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python-version }}
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cache: 'pip'
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install pytest
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pip install numpy
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pip install -r requirements.txt
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- name: Compile Cython
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run: |
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make clean compile
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- name: Test with pytest
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run: |
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pytest
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test-on-windows:
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runs-on: windows-latest
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strategy:
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matrix:
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python-version: ['3.9', '3.10', '3.11']
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steps:
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- uses: actions/checkout@v3
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- name: Setup Python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python-version }}
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cache: 'pip'
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install pytest
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pip install numpy
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pip install -r requirements.txt
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- name: Compile Cython
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run: |
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make clean compile
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- name: Test with pytest
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run: |
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pytest
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test-on-mac:
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runs-on: macos-latest
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strategy:
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matrix:
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python-version: ['3.9', '3.10', '3.11']
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steps:
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- uses: actions/checkout@v3
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- name: Setup Python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python-version }}
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cache: 'pip'
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install pytest
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pip install numpy
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pip install -r requirements.txt
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- name: Compile Cython
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run: |
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make clean compile
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- name: Test with pytest
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run: |
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pytest

‎.gitignore‎

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

‎MANIFEST.in‎

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include arrow/obsidian.h
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include arrow/mersenne.h
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include stochastic_arrow/obsidian.h
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include stochastic_arrow/mersenne.h

‎Makefile‎

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.DEFAULT_GOAL := compile
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clean:
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rm -rf arrow/arrowhead*.so arrow/arrowhead.c arrow/arrowhead.html build/ dist/ MANIFEST .pytest_cache/ stochastic_arrow.egg-info/
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### Files for older versions of stochastic_arrow are in 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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find . -name "*.pyc" -delete
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find . -name "__pycache__" -delete
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‎README.md‎

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stochastic-arrow
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**NOTE:** If upgrading from a version older than 1.0.0, check if the [`arrow`](https://github.com/arrow-py/arrow) datetime package is installed. If so, uninstall `arrow` before upgrading `stochastic-arrow`, then reinstall `arrow`.
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> pip show arrow
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> pip uninstall arrow
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> pip install stochastic-arrow
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> pip install arrow
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## Usage
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The `arrow` library presents a single class as an interface,
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The `stochastic_arrow` library presents a single class as an interface,
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`StochasticSystem`, which operates on a set of reactions (encoded as a `numpy`
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matrix of stoichiometrix coefficients) and associated reaction rates:
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```python
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from arrow import StochasticSystem
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from stochastic_arrow import StochasticSystem
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import numpy as np
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# Each row is a reaction and each column is a molecular species (or other
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state. `reenact_events` will do this for you:
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```python
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from arrow import reenact_events
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from stochastic_arrow import reenact_events
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history = reenact_events(stoichiometry, result['events'], state)
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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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`arrow` uses [pytest](https://docs.pytest.org/en/latest/). To test it:
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`stochastic_arrow` uses [pytest](https://docs.pytest.org/en/latest/). To test it:
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> make clean compile
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> pytest
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There are more command line features in test_arrow:
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> python -m arrow.test.test_arrow --complexation
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> python -m stochastic_arrow.test.test_arrow --complexation
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> python -m arrow.test.test_arrow --plot
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> python -m stochastic_arrow.test.test_arrow --plot
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> python -m arrow.test.test_arrow --obsidian
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> python -m stochastic_arrow.test.test_arrow --obsidian
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> python -m arrow.test.test_arrow --memory
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> python -m stochastic_arrow.test.test_arrow --memory
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> python -m arrow.test.test_arrow --time
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> python -m stochastic_arrow.test.test_arrow --time
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More examples:
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> python -m arrow.test.test_hang
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> python -m stochastic_arrow.test.test_hang
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> pytest -m arrow/test/test_arrow.py
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> pytest -m stochastic_arrow/test/test_arrow.py
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> pytest -k flagella
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## Changelog
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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`.**
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### Version 0.5.2
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* Update to Cython 0.29.34. (Cython 3.0.0 is now in beta.)

‎setup.py‎

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_ = setuptools
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with open("README.md", 'r') as readme:
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with open("README.md", 'r', encoding="utf-8") as readme:
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long_description = readme.read()
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current_dir = os.getcwd()
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arrow_dir = os.path.join(current_dir, 'arrow')
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arrow_dir = os.path.join(current_dir, 'stochastic_arrow')
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# Compile the Cython code to C for development builds:
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# USE_CYTHON=1 python setup.py build_ext --inplace
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ext = '.pyx' if USE_CYTHON else '.c'
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cython_extensions = [
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Extension('arrow.arrowhead',
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sources=['arrow/mersenne.c', 'arrow/obsidian.c', 'arrow/arrowhead'+ext,],
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include_dirs=['arrow', np.get_include()],
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Extension('stochastic_arrow.arrowhead',
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sources=[
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'stochastic_arrow/mersenne.c',
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'stochastic_arrow/obsidian.c',
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'stochastic_arrow/arrowhead'+ext,],
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include_dirs=['stochastic_arrow', np.get_include()],
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define_macros=[('NPY_NO_DEPRECATED_API', 'NPY_1_7_API_VERSION')],
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)]
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if USE_CYTHON:
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from Cython.Build import cythonize
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cython_extensions = cythonize(
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cython_extensions,
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include_path=['arrow'],
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include_path=['stochastic_arrow'],
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annotate=True, # to get an HTML code listing
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)
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setup(
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name='stochastic-arrow',
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version='0.5.2',
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packages=['arrow'],
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author='Ryan Spangler, John Mason, Jerry Morrison, Chris Skalnik, Travis Ahn-Horst',
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version='1.0.0',
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packages=['stochastic_arrow'],
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author='Ryan Spangler, John Mason, Jerry Morrison, Chris Skalnik, Travis Ahn-Horst, Sean Cheah',
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author_email='ryan.spangler@gmail.com',
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url='https://github.com/CovertLab/arrow',
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license='MIT',

arrow/__init__.py renamed to stochastic_arrow/__init__.py

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arrow/analysis/__init__.py renamed to stochastic_arrow/analysis/__init__.py

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arrow/analysis/distributions.py renamed to stochastic_arrow/analysis/distributions.py

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if __name__ == '__main__':
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import matplotlib.pyplot as plt
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from arrow.analysis.plotting import plot_full_history
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from stochastic_arrow.analysis.plotting import plot_full_history
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(fig, axes) = plt.subplots(constrained_layout = True)
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arrow/analysis/plotting.py renamed to stochastic_arrow/analysis/plotting.py

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