Merge pull request #1087 from haddocking/publish

add pipeline to automatically publish package in `pypi` on every release

.github/workflows/publish.yml

@@ -0,0 +1,33 @@
+name: publish to pypi
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  pypi_release:
+    name: builds and publishes to pypi
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/haddock3
+    permissions:
+      id-token: write
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install setuptools wheel
+
+      - name: build
+        run: python -m build --sdist
+
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

README.md

@@ -1,10 +1,6 @@
 # `haddock3`
 
-<!-- <p align="center">
-
-  <img src="docs/figs/HADDOCK3-logo.png" alt="haddock3-logo" style="vertical-align: middle;">
-</p>
-<src > -->
+![haddock3-logo](https://github.com/haddocking/haddock3/blob/main/docs/figs/HADDOCK3-logo.png)
 
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10527751.svg)](https://doi.org/10.5281/zenodo.10527751)
 [![Research Software Directory](https://img.shields.io/badge/rsd-haddock3-00a3e3.svg)](https://research-software-directory.org/software/haddock3)
@@ -18,8 +14,6 @@
 [![Codacy Badge](https://app.codacy.com/project/badge/Grade/e11e7f45400f4e8589cdf5941f95233a)](https://app.codacy.com/gh/haddocking/haddock3/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_grade)
 [![Codacy Badge](https://app.codacy.com/project/badge/Coverage/e11e7f45400f4e8589cdf5941f95233a)](https://app.codacy.com/gh/haddocking/haddock3/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_coverage)
 
-![haddock3-logo](docs/figs/HADDOCK3-logo.png)
-
 ## Introduction
 
 HADDOCK, standing for **H**igh **A**mbiguity **D**riven protein-protein **DOCK**ing, is a widely used computational tool for the integrative modeling of biomolecular interactions. Developed by researchers at [Utrecht University](https://uu.nl) in the [BonvinLab](https://bonvinlab.org) for more than 20 years, it integrates various types of experimental data, biochemical, biophysical, bioinformatic prediction and knowledge to guide the docking process.
@@ -29,9 +23,7 @@ HADDOCK, standing for **H**igh **A**mbiguity **D**riven protein-protein **DOCK**
 Clone the repository and run `pip install .`;
 
 ```bash
-git clone https://github.com/haddocking/haddock3
-cd haddock3
-pip install .
+pip install haddock3
 ```
 
 Execute:
@@ -69,7 +61,7 @@ The most basic usage is:
 haddock3 <configuration-file.toml>
 ```
 
-Check the [EXAMPLES](examples/README.md) page for more some usage examples and the [MANUAL]() (_coming soon!_) for a more detailed explanation of the configuration file.
+Check the [EXAMPLES](https://github.com/haddocking/haddock3/blob/main/examples/README.md) page for more some usage examples and the [MANUAL]() (_coming soon!_) for a more detailed explanation of the configuration file.
 
 ## Support
 
@@ -94,7 +86,7 @@ If you used `haddock3` for your research, please cite us:
 
 ## Development
 
-🚧 _Coming soon! We are currently working on the development guide_ 🚧
+Please check [DEVELOPMENT](https://github.com/haddocking/haddock3/blob/main/DEVELOPMENT.md) for instructions on how to develop `haddock3`
 
 ### Code Documentation
 

pyproject.toml

@@ -6,25 +6,32 @@ build-backend = "setuptools.build_meta"
 name = "haddock3"
 version = "2024.10.0b6"
 description = "HADDOCK3"
-authors = [{name = "BonvinLab", email = "bonvinlab.support@uu.nl"}]
-license = {text = "Apache License 2.0"}
+readme = "README.md"
+authors = [{ name = "BonvinLab", email = "bonvinlab.support@uu.nl" }]
+license = { text = "Apache License 2.0" }
 classifiers = [
-    "Development Status :: 4 - Beta",
-    "License :: OSI Approved :: Apache Software License",
-    "Natural Language :: English",
-    "Operating System :: POSIX",
-    "Operating System :: POSIX :: Linux",
-    "Operating System :: MacOS",
-    "Intended Audience :: Science/Research",
-    "Topic :: Scientific/Engineering :: Bio-Informatics",
-    "Topic :: Scientific/Engineering :: Chemistry",
-    "Topic :: Scientific/Engineering :: Physics",
-    "Programming Language :: Python :: 3.9",
-    "Programming Language :: Python :: 3.10",
-    "Programming Language :: Python :: 3.11",
-    "Programming Language :: Python :: 3.12",
+  "Development Status :: 4 - Beta",
+  "License :: OSI Approved :: Apache Software License",
+  "Natural Language :: English",
+  "Operating System :: POSIX",
+  "Operating System :: POSIX :: Linux",
+  "Operating System :: MacOS",
+  "Intended Audience :: Science/Research",
+  "Topic :: Scientific/Engineering :: Bio-Informatics",
+  "Topic :: Scientific/Engineering :: Chemistry",
+  "Topic :: Scientific/Engineering :: Physics",
+  "Programming Language :: Python :: 3.9",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+]
+keywords = [
+  "Structural Biology",
+  "Biochemistry",
+  "Docking",
+  "Protein docking",
+  "Proteins",
 ]
-keywords = ["Structural Biology", "Biochemistry", "Docking", "Protein docking", "Proteins"]
 requires-python = ">=3.9, <3.13"
 dependencies = [
   'pdb-tools>=2.5.0',
@@ -37,7 +44,7 @@ dependencies = [
   'pandas==2.*',
   'plotly==5.24.1',
   'kaleido==0.2.1',
-  'freesasa>=2.2.1'
+  'freesasa>=2.2.1',
 ]
 
 [project.optional-dependencies]
@@ -49,15 +56,15 @@ dev = [
   "pytest-mock==3.14.0",
   "fastapi==0.115.0",
   "httpx==0.27.0",
-  "mpi4py==4.0.0"
+  "mpi4py==4.0.0",
 ]
 docs = [
   "sphinx>=2",
   "sphinx-argparse>=0.4.0",
   "sphinx_rtd_theme>=2.0.0",
   "CommonMark>=0.9.1",
   "mock>=5.0.2",
-  "myst-parser>=1.0.0"
+  "myst-parser>=1.0.0",
 ]
 
 [project.urls]
@@ -84,7 +91,7 @@ haddock3-restraints = "haddock.clis.cli_restraints:maincli"
 
 [tool.setuptools]
 packages = ["haddock"]
-package-dir = {"" = "src"}
+package-dir = { "" = "src" }
 include-package-data = true
 
 [tool.setuptools.package-data]