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
theochem · Oct 3, 2024 · b17bdeb · b17bdeb
1 parent c625af7
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diff --git a/.github/workflows/pypi_release.yaml b/.github/workflows/pypi_release.yaml
@@ -0,0 +1,140 @@
+# This workflow is adapted from:
+# https://packaging.python.org/en/latest/guides/publishing-package-distribution-releases-using-github-actions-ci-cd-workflows/
+# Changes made:
+# - Removed emoticons
+# - Updated some actions to more recent versions
+# - Customized for the qc-AtomDB repository
+
+name: PyPI Release
+on:
+  push:
+    tags:
+      # Trigger on version tags (e.g., v1.0.0)
+      - "v[0-9].[0-9].[0-9]*"
+      - "[0-9].[0-9].[0-9]*"
+      # Trigger on pre-release tags (e.g., v1.0.0-alpha.1)
+      - "v[0-9].[0-9].[0-9]*-*"
+      - "[0-9].[0-9].[0-9]*-*"
+
+env:
+  # The name of the package to be published to PyPI and TestPyPI.
+  PYPI_NAME: qc-AtomDB
+
+jobs:
+  build:
+    name: Build distribution
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.11"
+    - name: Install pypa/build
+      run: |
+        # install from github
+        # TODO: change to pypi once the release of qc-grid is made
+        python -m pip install git+https://github.com/theochem/grid.git@master
+        python -m pip install build
+    - name: Build package
+      run: >-
+        python -m build
+    - name: Store the distribution packages
+      uses: actions/upload-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+
+  publish-to-pypi:
+    name: Publish Python distribution to PyPI
+    # only publish to PyPI on tag pushes
+    if: startsWith(github.ref, 'refs/tags/')
+    needs:
+      - build
+    runs-on: ubuntu-latest
+    environment:
+      name: PyPI-Release
+      url: https://pypi.org/project/${{ env.PYPI_NAME }}
+    permissions:
+      id-token: write
+
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Publish distribution to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      env:
+        TWINE_USERNAME: "__token__"
+        TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
+
+  github-release:
+    name: Sign the Python distribution with Sigstore and upload them to GitHub Release
+    needs:
+    - publish-to-pypi
+    runs-on: ubuntu-latest
+
+    permissions:
+      contents: write
+      id-token: write
+
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Sign the dists with Sigstore
+      uses: sigstore/[email protected]
+      with:
+        inputs: >-
+          ./dist/*.tar.gz
+          ./dist/*.whl
+    - name: Create GitHub Release
+      env:
+        GITHUB_TOKEN: ${{ github.token }}
+      run: >-
+        gh release create
+        '${{ github.ref_name }}'
+        --repo '${{ github.repository }}'
+        --notes ""
+    - name: Upload artifact signatures to GitHub Release
+      env:
+        GITHUB_TOKEN: ${{ github.token }}
+      run: >-
+        gh release upload
+        '${{ github.ref_name }}' dist/**
+        --repo '${{ github.repository }}'
+
+  publish-to-testpypi:
+    name: Publish Python distribution to TestPyPI
+    # if: ${{ github.ref == 'refs/heads/master' && github.repository_owner == 'theochem' }}
+    needs:
+    - build
+    runs-on: ubuntu-latest
+
+    environment:
+      name: TestPyPI
+      url: https://test.pypi.org/project/${{ env.PYPI_NAME }}
+
+    permissions:
+      id-token: write
+
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Publish distribution to TestPyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        repository-url: https://test.pypi.org/legacy/
+      env:
+        TWINE_USERNAME: "__token__"
+        TWINE_PASSWORD: ${{ secrets.TEST_PYPI_TOKEN }}
diff --git a/README.md b/README.md
@@ -0,0 +1,107 @@
+<!--
+This file is part of AtomDB.
+
+AtomDB is free software: you can redistribute it and/or modify it under
+the terms of the GNU General Public License as published by the Free
+Software Foundation, either version 3 of the License, or (at your
+option) any later version.
+
+AtomDB is distributed in the hope that it will be useful, but WITHOUT
+ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
+for more details.
+
+You should have received a copy of the GNU General Public License
+along with AtomDB. If not, see <http://www.gnu.org/licenses/>.
+-->
+
+[![This project supports Python 3.9+](https://img.shields.io/badge/Python-3.9+-blue.svg)](https://python.org/downloads)
+[![pytest](https://github.com/theochem/AtomDB/actions/workflows/pytest.yaml/badge.svg?branch=master)](https://github.com/theochem/AtomDB/actions/workflows/pytest.yaml)
+[![PyPI](https://img.shields.io/pypi/v/qc-AtomDB.svg)](https://pypi.python.org/pypi/qc-AtomDB/)
+![License](https://img.shields.io/github/license/theochem/AtomDB)
+[![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)
+
+# AtomDB
+
+## About
+
+AtomDB is a versatile, free, and open-source Python library for accessing and managing atomic and
+promolecular properties. It serves as an extended database or periodic table of neutral and charged
+atomic properties, offering accurate experimental and computational data for various atomic
+charge/multiplicity states. AtomDB is a [QC-Devs](https://qcdevs.org/) project.
+
+## Documentation
+
+AtomDB's documentation, including installation and usage instructions, as well as API documentation, is available at [atomdb.qcdevs.org](https://atomdb.qcdevs.org/).
+
+### Functionality
+
+- **Atomic scalar properties**
+
+  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**.
+
+- **Point dependent properties**
+
+  AtomDB provides functions to calculate point-dependent properties, such as:
+  **Electron density** $\rho(r)$,
+  **Electron density gradient** $\nabla \rho(r)$,
+  **Electron density Laplacian** $\nabla^2 \rho(r)$,
+  **Electron density Hessian** $\nabla^2 \rho(r)$ (for these properties, only the radial part is provided),
+  and **Kinetic energy density** $ked(r)$.
+
+  The computation of contributions per orbital, set of orbitals, or spin to these properties is also supported.
+
+- **Promolecular properties**
+
+  AtomDB provides the capabilities to create promolecular models, and then estimate molecular properties from the atomic properties.
+
+- **Dumping and loading**
+
+  AtomDB provides the capability to dump and load atomic properties to and from JSON files.
+
+For a complete list of available properties, see [this
+table](https://atomdb.qcdevs.org/api/index.html#properties).
+
+## Installation
+
+We recommend using Python 3.9 or later. The `qc-grid` is need to run `AtomDB`. You can install it
+from source for now:
+
+```bash
+git clone [email protected]:theochem/grid.git
+cd qc-grid
+pip install .
+```
+
+Then,
+`qc-AtomDB` can be installed using `pip`:
+
+```bash
+pip install qc-AtomDB
+
+```
+
+
+## Contributing
+
+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/).
+Please report any issues you encounter while using AtomDB on GitHub Issues.
+
+For further information and inquiries, please contact us at [[email protected]](mailto:[email protected]).
+
+## Citing AtomDB
+
+Please use the following citation in any publication using AtomDB:
+
+```bibtex
+@article{atomdb,
+        author  = {S{\'a}nchez D{\'\i}az, Gabriela and Richer, Michelle and
+                   Mart{\'\i}nez Gonz{\'a}lez, Marco and {v}an Zyl, Maximilian and
+                   Pujal, Leila and Tehrani, Alireza and Bianchi, Julianna and
+                   Ayers, Paul W. and Heidar-Zadeh, Farnaz},
+        title   = {{AtomDB: A Python Library for Atomic and Promolecular Properties}},
+        journal = {-},
+        year    = {2024},
+        url     = {https://atomdb.qcdevs.org/},
+    }
+```
diff --git a/pyproject.toml b/pyproject.toml
@@ -14,11 +14,11 @@
 # along with AtomDB. If not, see <http://www.gnu.org/licenses/>.
 
 [build-system]
-requires = ["setuptools>=65.0", "setuptools_scm[toml]>=7.1.0"]
+requires = ["setuptools>=65", "setuptools-scm>=8"]
 build-backend = "setuptools.build_meta"
 
 [project]
-name = "AtomDB"
+name = "qc-AtomDB"
 authors = [
   { name="QC-Devs Community", email="[email protected]" },
 ]
@@ -27,7 +27,7 @@ readme = "README.rst"
 license = {text = "GPL-3.0-or-later"}
 requires-python = ">=3.9"
 classifiers = [
-   'Development Status :: 0 - Released',
+    'Development Status :: 5 - Production/Stable',
     'Environment :: Console',
     'License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)',
     'Operating System :: POSIX :: Linux',
@@ -47,7 +47,7 @@ dependencies = [
     "msgpack-numpy>=0.4.8",
     "h5py>=3.6.0",
     "importlib_resources>=3.0.0",
-    "pooch==1.8.1",
+    "pooch>=1.8.1",
 ]
 dynamic = ["version"]
 
@@ -59,11 +59,15 @@ Changelog = "https://github.com/theochem/atomdb/blob/main/CHANGELOG.md"
 
 [project.optional-dependencies]
 dev = [
-    "pytest >=2.6",
+    "pytest>=8.3.3",
     "pyscf",
-    "qc-gbasis@git+https://github.com/theochem/gbasis.git@master",
-    "qc-grid@git+https://github.com/theochem/grid.git@master",
-    "qc-iodata@git+https://github.com/theochem/iodata.git@main",
+    # "qc-gbasis@git+https://github.com/theochem/gbasis.git@master",
+    "qc-gbasis",
+    # "qc-grid@git+https://github.com/theochem/grid.git@master",
+    # TODO: uncomment when grid is available on PyPI
+    # "qc-grid",
+    # "qc-iodata@git+https://github.com/theochem/iodata.git@main",
+    "qc-iodata",
 ]
 test_extra = [
     "pytest-md",
@@ -111,5 +115,3 @@ addopts = "-m 'not dev'"
 markers = [
     "dev: mark a developer test, needs extra dependencies.",
 ]
-
-