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axelvonkampaxelvonkamp
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Pypi (#525)
* Create python-publish.yml * Update python-publish.yml * basic pyproject.toml * Update python-publish.yml * try to trigger action * fix dependencies * Update python-publish.yml * use * for Python micro version * Bump version for reupload to TestPyPI * remove pytest dependency * Update pyproject.toml * move to PyPI * Update pyproject.toml * try console script via pyproject.toml * Update python-publish.yml * cleanup * use miniforge for CI test * Update action versions * Add installation option for PyPI
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‎.github/workflows/ci-test.yml

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@@ -6,12 +6,13 @@ jobs:
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build-linux:
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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: conda-incubator/setup-miniconda@v2
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- uses: actions/checkout@v4
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- uses: conda-incubator/setup-miniconda@v3
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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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environment-file: environment.yml
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miniforge-version: latest
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activate-environment: cnapy
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- name: Test CNApy
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run: |
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build-windows:
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runs-on: "windows-latest"
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steps:
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- uses: actions/checkout@v2
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- uses: conda-incubator/setup-miniconda@v2
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- uses: actions/checkout@v4
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- uses: conda-incubator/setup-miniconda@v3
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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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environment-file: environment.yml
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miniforge-version: latest
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activate-environment: cnapy
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- name: Test CNApy
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run: |

‎.github/workflows/python-publish.yml

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# This workflow will upload a Python Package using Twine when a release is created
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# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
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# This workflow uses actions that are not certified by GitHub.
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# They are provided by a third-party and are governed by
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# separate terms of service, privacy policy, and support
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# documentation.
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name: Upload Python Package
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on:
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release:
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types: [published]
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workflow_dispatch:
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branches:
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- "pypi"
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permissions:
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contents: read
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jobs:
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deploy:
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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: Set up Python
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uses: actions/setup-python@v3
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with:
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python-version: '3.x'
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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 build
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- name: Build package
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run: python -m build
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- name: Publish package
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uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
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with:
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user: axelk1
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password: ${{ secrets.PYPI_API_TOKEN }}

‎README.md

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There are 4 alternative ways to install CNApy:
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1. If you use Windows, the easiest way is to use our Windows installer, see section [Using the Windows installer](#using-the-windows-installer).
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2. If you already have installed [Anaconda](https://www.anaconda.com/), [Miniconda](https://docs.anaconda.com/free/miniconda/index.html) or [Miniforge](https://github.com/conda-forge/miniforge) on your computer, you can directly install CNApy as a conda package as described in section [Install CNApy as conda package](#install-cnapy-as-conda-package). *Note*: If you're on MacOS and want to use CPLEX as solver, you have to use the x86 version of Anaconda as the Apple Silicon one is not supported by CPLEX yet.
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3. If you use Linux or Apple MacOS X, the easiest installation producure is our assisted installation protocol, see [Assisted installation under Linux and MacOS X](#assisted-installation-under-linux-and-macos-x).
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4. If you want to develop CNApy, follow the instruction for the cloning and setup of the CNApy repository using git and conda or mamba in section [Setup the CNApy development environment](#setup-the-cnapy-development-environment).
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2. If you have Python 3.10 on your computer you can directly install CNApy from PyPI with: ```pip install cnapy```.
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3. If you have installed [Anaconda](https://www.anaconda.com/), [Miniconda](https://docs.anaconda.com/free/miniconda/index.html) or [Miniforge](https://github.com/conda-forge/miniforge) on your computer, you can directly install CNApy as a conda package as described in section [Install CNApy as conda package](#install-cnapy-as-conda-package). *Note*: If you're on MacOS and want to use CPLEX as solver, you have to use the x86 version of Anaconda as the Apple Silicon one is not supported by CPLEX yet.
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4. If you use Linux or Apple MacOS X, the easiest installation producure is our assisted installation protocol, see [Assisted installation under Linux and MacOS X](#assisted-installation-under-linux-and-macos-x).
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5. If you want to develop CNApy, follow the instruction for the cloning and setup of the CNApy repository using git and conda or mamba in section [Setup the CNApy development environment](#setup-the-cnapy-development-environment).
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## Contribute to the CNApy development
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‎pyproject.toml

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[project]
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name = "cnapy"
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version = "1.2.1.1"
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authors = [
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{ name="Sven Thiele" },
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{ name="Axel von Kamp" },
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{ name="Pavlos Stephanos Bekiaris" },
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{ name="Philipp Schneider" }
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]
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description = "An integrated environment for metabolic network analysis."
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readme = "README.md"
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requires-python = "==3.10.*"
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classifiers = [
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"Programming Language :: Python :: 3",
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"License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)",
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"Operating System :: OS Independent",
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]
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dependencies = ["appdirs>=1.4", "matplotlib>=3.6", "requests>=2.28",
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"cobra>=0.29", "efmtool_link>=0.0.7", "optlang_enumerator>=0.0.12", "straindesign>=1.12",
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"qtpy>=2.3", "pyqtwebengine>=5.15", "qtconsole==5.4",
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"gurobipy>=11.0", "cplex>=22.1", "numpy==1.23", "scipy==1.12", "openpyxl"]
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[project.scripts]
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cnapy = "cnapy.__main__:main_cnapy"
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[project.urls]
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Homepage = "https://github.com/cnapy-org/CNApy"
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Issues = "https://github.com/cnapy-org/CNApy/issues"

‎setup.py

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setup(
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name='cnapy',
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version='1.2.1',
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url='https://github.com/cnapy-org/CNApy/',
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license='GPLv3+',
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description='An integrated environment for metabolic network analysis.',
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long_description=open('README.md', encoding="utf8").read(),
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long_description_content_type="text/asciidoc",
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author='Sven Thiele',
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author_email='sthiele78@gmail.com',
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packages=['cnapy', 'cnapy.gui_elements'],
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package_dir={'cnapy': 'cnapy'},
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package_data={'cnapy': [
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'data/*.svg', 'data/escher_cnapy.html', 'data/escher.min.js']},
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entry_points={'console_scripts': [
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'cnapy = cnapy.__main__:main_cnapy']},
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'data/*.svg', 'data/escher_cnapy.html', 'data/escher.min.js']}
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)

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