diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml new file mode 100644 index 000000000..ea6f54154 --- /dev/null +++ b/.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 diff --git a/README.md b/README.md index fa65b7319..d898166d7 100644 --- a/README.md +++ b/README.md @@ -1,10 +1,6 @@ # `haddock3` - +![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 ``` -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 diff --git a/pyproject.toml b/pyproject.toml index a0e39eac5..de2e654a3 100644 --- a/pyproject.toml +++ b/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] @@ -49,7 +56,7 @@ 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", @@ -57,7 +64,7 @@ docs = [ "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]