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cdienercdiener
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modernize packaging
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‎.github/workflows/docs.yml

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name: Build and release docs
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name: Build and deploy docs
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on:
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push:
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pip install sphinx nbsphinx sphinx-book-theme sphinx-autoapi
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- name: Build docs
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run: |
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cp NEWS.md docs/source
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cd docs && make html
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- name: Deploy
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uses: peaceiris/actions-gh-pages@v3

‎.github/workflows/pythonpackage.yml

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# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
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# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
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name: Python package
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name: Test and deploy
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on:
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push:

‎MANIFEST.in

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This file was deleted.

‎NEWS.md

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@@ -5,6 +5,17 @@ This includes a list of major changes for each minor version starting from 0.19.
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For information on how to use `micom` please read the docs at
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https://micom-dev.github.io/micom.
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### 0.22.3
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Fixed a bug where incorrectly labeled biomass demand reactions were treated like an
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exchange.
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### 0.22.2
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Lowered the required version for pandas to re-enable compatibility with Python 3.6.
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Docs are now built on all pushes.
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### 0.22.1
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`atol` and `rtol` are now consistently exposed.

‎docs/source/index.rst

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Knockouts <taxa_knockouts>
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Intervention studies <elasticities>
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Writing your own workflows <workflows>
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Release Notes <NEWS>
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Indices and tables

‎pyproject.toml

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[build-system]
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requires = [
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'setuptools>=40.6.0',
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'wheel'
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]
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build-backend = "setuptools.build_meta"
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[tool.black]
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line-length = 88
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target-version = ['py38']
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include = '\.pyi?$'
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exclude = '''
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(
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/(
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\.eggs # exclude a few common directories in the
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| \.git # root of the project
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| \.hg
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| \.mypy_cache
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| \.tox
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| \.venv
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| _build
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| buck-out
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| build
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| dist
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)/
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)
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'''

‎setup.cfg

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[metadata]
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name = micom
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description = Microbial community modeling based on cobrapy.
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long_description = file: README.rst
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long_description_content_type = text/x-rst
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url = https://github.com/micom-dev/micom
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author = Christian Diener
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author_email = mail@cdiener.com
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license = Apache License 2.0
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classifiers =
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Development Status :: 5 - Production/Stable
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Intended Audience :: Science/Research
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Topic :: Scientific/Engineering :: Bio-Informatics
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License :: OSI Approved :: Apache Software License
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Programming Language :: Python :: 3
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Programming Language :: Python :: 3.6
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Programming Language :: Python :: 3.7
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Programming Language :: Python :: 3.8
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Programming Language :: Python :: 3.9
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keywords =
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microbiome
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microbiota
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modeling
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metabolism
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community
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[options]
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packages = find:
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zip_safe = True
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python_requires = >=3.6
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install_requires =
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cobra>=0.17.1
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depinfo>=1.7.0
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optlang>=1.4.7
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pandas>=1.0.0
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rich>=9.10.0
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jinja2>=2.10.0
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scikit-learn>=0.22.0
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scipy>=1.0.0
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symengine>=0.6.1
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tests_require =
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coverage
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pytest
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pytest-cov
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[options.packages.find]
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exclude =
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docs
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tests
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[option.package_data]
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micom =
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data/*.csv
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data/*.gz
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data/templates/*.*
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data/artifacts/*.*
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[bumpversion]
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current_version = 0.22.3
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commit = True
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replace = __version__ = "{new_version}"
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[tool:pytest]
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filterwarnings = ignore::DeprecationWarning
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ignore::FutureWarning
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filterwarnings =
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ignore::DeprecationWarning
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ignore::FutureWarning
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[bdist_wheel]
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universal = 1
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[coverage:run]
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source = micom
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branch = True
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omit = micom/_version.py
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[coverage:report]
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exclude_lines =
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pragma: no cover
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def __repr__
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if self\.debug
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raise AssertionError
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raise NotImplementedError
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if 0:
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if __name__ == .__main__.:
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exclude_lines =
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pragma: no cover
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def __repr__
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if self\.debug
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raise AssertionError
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raise NotImplementedError
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if 0:
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if __name__ == .__main__.:
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ignore_errors = True
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[flake8]
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exclude = tests/*, docs/*, versioneer.py, _version.py
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max-line-length = 88
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ignore =
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E203
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D202
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ignore =
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E203
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[pydocstyle]
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convention = numpy

‎setup.py

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"""setup.py for micom."""
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"""setup.py for micom.
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from setuptools import setup, find_packages
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This is a shim left here for compatibility reasons.
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"""
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# To use a consistent encoding
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from codecs import open
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from os import path
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from setuptools import setup
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here = path.abspath(path.dirname(__file__))
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# Get the long description from the README file
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with open(path.join(here, "README.rst"), encoding="utf-8") as f:
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long_description = f.read()
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setup(
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name="micom",
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# Versions should comply with PEP440. For a discussion on single-sourcing
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# the version across setup.py and the project code, see
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# https://packaging.python.org/en/latest/single_source_version.html
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version="0.22.3",
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description="Microbial community modeling based on cobrapy.",
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long_description=long_description,
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# The project's main homepage.
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url="https://github.com/micom-dev/micom",
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# Author details
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author="Christian Diener",
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author_email="mail@cdiener.com",
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# Choose your license
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license="Apache License 2.0",
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# See https://pypi.python.org/pypi?%3Aaction=list_classifiers
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classifiers=[
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# How mature is this project? Common values are
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# 3 - Alpha
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# 4 - Beta
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# 5 - Production/Stable
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"Development Status :: 5 - Production/Stable",
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# Indicate who your project is intended for
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"Intended Audience :: Science/Research",
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"Topic :: Scientific/Engineering :: Bio-Informatics",
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# Pick your license as you wish (should match "license" above)
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"License :: OSI Approved :: Apache Software License",
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# Specify the Python versions you support here. In particular, ensure
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# that you indicate whether you support Python 2, Python 3 or both.
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"Programming Language :: Python :: 3",
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"Programming Language :: Python :: 3.6",
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"Programming Language :: Python :: 3.7",
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"Programming Language :: Python :: 3.8",
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"Programming Language :: Python :: 3.9",
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],
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# What does your project relate to?
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keywords="microbiota modeling metabolism community",
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# You can just specify the packages manually here if your project is
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# simple. Or you can use find_packages().
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packages=find_packages(exclude=["docs", "tests"]),
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package_data={
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"micom": [
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path.join("data", "*.csv"),
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path.join("data", "*.gz"),
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path.join("data", "templates", "*.*"),
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path.join("data", "artifacts", "*.*")
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]
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},
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# Alternatively, if you want to distribute just a my_module.py, uncomment
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# this:
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# py_modules=["my_module"],
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# List run-time dependencies here. These will be installed by pip when
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# your project is installed. For an analysis of "install_requires" vs pip's
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# requirements files see:
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# https://packaging.python.org/en/latest/requirements.html
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python_requires=">=3.6",
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install_requires=[
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"cobra>=0.17.1",
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"depinfo>=1.7.0",
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"optlang>=1.4.7",
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"pandas>=1.0.0",
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"rich>=9.10.0",
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"jinja2>=2.10.0",
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"scikit-learn>=0.22.0",
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"scipy>=1.0.0",
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"symengine>=0.6.1"
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],
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# List additional groups of dependencies here (e.g. development
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# dependencies). You can install these using the following syntax,
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# for example:
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# $ pip install -e .[dev,test]
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extras_require={
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"dev": [""],
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"test": ["coverage", "pytest", "pytest-cov"],
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},
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)
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setup(version="0.22.3")

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