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Add PyPI release (#106)
* Add PyPI release draft * Update pooch version * Disable the PyPI release for testing only * Enable PyPI release * Fix classifier in pyproject.toml * Fix the issue of "Can't have direct dependency" from git source codes * Enable multiple command runs * Add README.md * Fix math equations in README.md
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‎.github/workflows/pypi_release.yaml‎

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# This workflow is adapted from:
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# https://packaging.python.org/en/latest/guides/publishing-package-distribution-releases-using-github-actions-ci-cd-workflows/
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# Changes made:
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# - Removed emoticons
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# - Updated some actions to more recent versions
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# - Customized for the qc-AtomDB repository
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name: PyPI Release
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on:
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push:
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tags:
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# Trigger on version tags (e.g., v1.0.0)
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- "v[0-9].[0-9].[0-9]*"
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- "[0-9].[0-9].[0-9]*"
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# Trigger on pre-release tags (e.g., v1.0.0-alpha.1)
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- "v[0-9].[0-9].[0-9]*-*"
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- "[0-9].[0-9].[0-9]*-*"
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env:
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# The name of the package to be published to PyPI and TestPyPI.
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PYPI_NAME: qc-AtomDB
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jobs:
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build:
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name: Build 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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with:
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fetch-depth: 0
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: "3.11"
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- name: Install pypa/build
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run: |
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# install from github
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# TODO: change to pypi once the release of qc-grid is made
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python -m pip install git+https://github.com/theochem/grid.git@master
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python -m pip install build
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- name: Build package
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run: >-
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python -m build
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- name: Store the distribution packages
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uses: actions/upload-artifact@v4
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with:
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name: python-package-distributions
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path: dist/
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publish-to-pypi:
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name: Publish Python distribution to PyPI
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# only publish to PyPI on tag pushes
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if: startsWith(github.ref, 'refs/tags/')
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needs:
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- build
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runs-on: ubuntu-latest
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environment:
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name: PyPI-Release
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url: https://pypi.org/project/${{ env.PYPI_NAME }}
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permissions:
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id-token: write
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steps:
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- name: Download all the dists
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uses: actions/download-artifact@v4
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with:
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name: python-package-distributions
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path: dist/
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- name: Publish distribution to PyPI
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uses: pypa/gh-action-pypi-publish@release/v1
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env:
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TWINE_USERNAME: "__token__"
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TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
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github-release:
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name: Sign the Python distribution with Sigstore and upload them to GitHub Release
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needs:
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- publish-to-pypi
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runs-on: ubuntu-latest
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permissions:
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contents: write
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id-token: write
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steps:
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- name: Download all the dists
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uses: actions/download-artifact@v4
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with:
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name: python-package-distributions
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path: dist/
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- name: Sign the dists with Sigstore
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uses: sigstore/[email protected]
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with:
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inputs: >-
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./dist/*.tar.gz
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./dist/*.whl
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- name: Create GitHub Release
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env:
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GITHUB_TOKEN: ${{ github.token }}
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run: >-
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gh release create
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'${{ github.ref_name }}'
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--repo '${{ github.repository }}'
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--notes ""
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- name: Upload artifact signatures to GitHub Release
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env:
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GITHUB_TOKEN: ${{ github.token }}
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run: >-
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gh release upload
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'${{ github.ref_name }}' dist/**
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--repo '${{ github.repository }}'
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publish-to-testpypi:
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name: Publish Python distribution to TestPyPI
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# if: ${{ github.ref == 'refs/heads/master' && github.repository_owner == 'theochem' }}
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needs:
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- build
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runs-on: ubuntu-latest
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environment:
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name: TestPyPI
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url: https://test.pypi.org/project/${{ env.PYPI_NAME }}
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permissions:
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id-token: write
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steps:
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- name: Download all the dists
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uses: actions/download-artifact@v4
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with:
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name: python-package-distributions
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path: dist/
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- name: Publish distribution to TestPyPI
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uses: pypa/gh-action-pypi-publish@release/v1
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with:
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repository-url: https://test.pypi.org/legacy/
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env:
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TWINE_USERNAME: "__token__"
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TWINE_PASSWORD: ${{ secrets.TEST_PYPI_TOKEN }}

‎README.md‎

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<!--
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This file is part of AtomDB.
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AtomDB is free software: you can redistribute it and/or modify it under
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the terms of the GNU General Public License as published by the Free
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Software Foundation, either version 3 of the License, or (at your
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option) any later version.
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AtomDB is distributed in the hope that it will be useful, but WITHOUT
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ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
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FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
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for more details.
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You should have received a copy of the GNU General Public License
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along with AtomDB. If not, see <http://www.gnu.org/licenses/>.
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-->
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[![This project supports Python 3.9+](https://img.shields.io/badge/Python-3.9+-blue.svg)](https://python.org/downloads)
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[![pytest](https://github.com/theochem/AtomDB/actions/workflows/pytest.yaml/badge.svg?branch=master)](https://github.com/theochem/AtomDB/actions/workflows/pytest.yaml)
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[![PyPI](https://img.shields.io/pypi/v/qc-AtomDB.svg)](https://pypi.python.org/pypi/qc-AtomDB/)
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![License](https://img.shields.io/github/license/theochem/AtomDB)
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[![pages-build-deployment](https://github.com/theochem/AtomDB/actions/workflows/pages/pages-build-deployment/badge.svg)](https://github.com/theochem/AtomDB/actions/workflows/pages/pages-build-deployment)
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# AtomDB
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## About
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AtomDB is a versatile, free, and open-source Python library for accessing and managing atomic and
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promolecular properties. It serves as an extended database or periodic table of neutral and charged
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atomic properties, offering accurate experimental and computational data for various atomic
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charge/multiplicity states. AtomDB is a [QC-Devs](https://qcdevs.org/) project.
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## Documentation
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AtomDB's documentation, including installation and usage instructions, as well as API documentation, is available at [atomdb.qcdevs.org](https://atomdb.qcdevs.org/).
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### Functionality
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- **Atomic scalar properties**
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AtomDB provides a wide range of atomic properties for neutral and charged atoms, including: **Atomic number**, **Atomic symbol**, **Atomic mass**, **Atomic radius**, **van der Waals radius**, **Covalent radius**, **Ionization potential**, **Electron affinity**, **Electronegativity**, **Atomic polarizability**.
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- **Point dependent properties**
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AtomDB provides functions to calculate point-dependent properties, such as:
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**Electron density** $\rho(r)$,
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**Electron density gradient** $\nabla \rho(r)$,
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**Electron density Laplacian** $\nabla^2 \rho(r)$,
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**Electron density Hessian** $\nabla^2 \rho(r)$ (for these properties, only the radial part is provided),
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and **Kinetic energy density** $ked(r)$.
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The computation of contributions per orbital, set of orbitals, or spin to these properties is also supported.
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- **Promolecular properties**
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AtomDB provides the capabilities to create promolecular models, and then estimate molecular properties from the atomic properties.
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- **Dumping and loading**
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AtomDB provides the capability to dump and load atomic properties to and from JSON files.
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For a complete list of available properties, see [this
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table](https://atomdb.qcdevs.org/api/index.html#properties).
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## Installation
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We recommend using Python 3.9 or later. The `qc-grid` is need to run `AtomDB`. You can install it
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from source for now:
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```bash
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git clone [email protected]:theochem/grid.git
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cd qc-grid
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pip install .
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```
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Then,
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`qc-AtomDB` can be installed using `pip`:
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```bash
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pip install qc-AtomDB
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```
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## Contributing
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We welcome any contributions to the AtomDB library in accordance with our [Code of Conduct](https://qcdevs.org/guidelines/qcdevs_code_of_conduct/). Please see our [Contributing Guidelines](https://qcdevs.org/guidelines/).
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Please report any issues you encounter while using AtomDB on GitHub Issues.
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For further information and inquiries, please contact us at [[email protected]](mailto:[email protected]).
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## Citing AtomDB
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Please use the following citation in any publication using AtomDB:
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```bibtex
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@article{atomdb,
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author = {S{\'a}nchez D{\'\i}az, Gabriela and Richer, Michelle and
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Mart{\'\i}nez Gonz{\'a}lez, Marco and {v}an Zyl, Maximilian and
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Pujal, Leila and Tehrani, Alireza and Bianchi, Julianna and
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Ayers, Paul W. and Heidar-Zadeh, Farnaz},
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title = {{AtomDB: A Python Library for Atomic and Promolecular Properties}},
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journal = {-},
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year = {2024},
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url = {https://atomdb.qcdevs.org/},
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}
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```

‎pyproject.toml‎

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# along with AtomDB. If not, see <http://www.gnu.org/licenses/>.
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[build-system]
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requires = ["setuptools>=65.0", "setuptools_scm[toml]>=7.1.0"]
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requires = ["setuptools>=65", "setuptools-scm>=8"]
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build-backend = "setuptools.build_meta"
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[project]
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name = "AtomDB"
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name = "qc-AtomDB"
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authors = [
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{ name="QC-Devs Community", email="[email protected]" },
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]
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license = {text = "GPL-3.0-or-later"}
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requires-python = ">=3.9"
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classifiers = [
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'Development Status :: 0 - Released',
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'Development Status :: 5 - Production/Stable',
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'Environment :: Console',
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'License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)',
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'Operating System :: POSIX :: Linux',
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"msgpack-numpy>=0.4.8",
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"h5py>=3.6.0",
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"importlib_resources>=3.0.0",
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"pooch==1.8.1",
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"pooch>=1.8.1",
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]
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dynamic = ["version"]
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[project.optional-dependencies]
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dev = [
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"pytest >=2.6",
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"pytest>=8.3.3",
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"pyscf",
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"qc-gbasis@git+https://github.com/theochem/gbasis.git@master",
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"qc-grid@git+https://github.com/theochem/grid.git@master",
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"qc-iodata@git+https://github.com/theochem/iodata.git@main",
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# "qc-gbasis@git+https://github.com/theochem/gbasis.git@master",
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"qc-gbasis",
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# "qc-grid@git+https://github.com/theochem/grid.git@master",
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# TODO: uncomment when grid is available on PyPI
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# "qc-grid",
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# "qc-iodata@git+https://github.com/theochem/iodata.git@main",
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"qc-iodata",
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]
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test_extra = [
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"pytest-md",
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markers = [
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"dev: mark a developer test, needs extra dependencies.",
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]
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