diff --git a/AUTHORS.md b/AUTHORS.md new file mode 100644 index 00000000..a0bd5995 --- /dev/null +++ b/AUTHORS.md @@ -0,0 +1,30 @@ +# Authors + +OpenMMDL was created by Valerij Talagayev & Yu Chen in 2022. + + +All contributing authors are listed in this file below. +The repository history at https://github.com/wolberlab/OpenMMDL +and the CHANGELOG show individual code contributions. + +## Chronological list of authors + + + +**2023** +- Niklas Piet Doering <@NDoering99> +- Leon Obendorf <@Habacef> +- Marvin Taterra <@MarvinTaterra> + +**2022** +- Valerij Talagayev <@talagayev> +- Yu Chen <@xixichennn> +- Gerhard Wolber <@gwolber> diff --git a/CHANGELOG.md b/CHANGELOG.md new file mode 100644 index 00000000..5041f92b --- /dev/null +++ b/CHANGELOG.md @@ -0,0 +1,37 @@ +# Changelog +All notable changes to this project will be documented in this file. + +The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), +and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). + + + +## [Unreleased] + +### Authors + + +### Added + + +### Fixed + + +### Changed + + +### Deprecated + + +### Removed + diff --git a/README.md b/README.md index 41bb9264..967b9888 100644 --- a/README.md +++ b/README.md @@ -1,23 +1,31 @@ OpenMMDL @ Molecular Design Lab ============================== + + + [//]: # (Badges) -[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) -[![CI-CD](https://github.com/wolberlab/OpenMMDL/actions/workflows/CI-CD.yml/badge.svg)](https://github.com/wolberlab/OpenMMDL/actions/workflows/CI-CD.yml) -[![codecov](https://codecov.io/gh/talagayev/OpenMMDL/graph/badge.svg?token=950HZ93CKS)](https://codecov.io/gh/talagayev/OpenMMDL) -[![Documentation Status](https://readthedocs.org/projects/openmmdl/badge/?version=latest)](https://openmmdl.readthedocs.io) -[![License](https://img.shields.io/badge/License-MIT-blue.svg)](https://opensource.org/licenses/MIT) -[![CodeQL](https://github.com/wolberlab/OpenMMDL/actions/workflows/codeql.yml/badge.svg)](https://github.com/wolberlab/OpenMMDL/actions/workflows/codeql.yml) -[![Python 3.10](https://img.shields.io/badge/python-3.10-blue.svg)](https://www.python.org/downloads/release/python-3100/) +| **Release** | [![Last release tag][badge_release]][url_latest_release] ![GitHub commits since latest release (by date) for a branch][badge_commits_since]| +| :----------------- | :------- | +| **Availability** | [![Condaforge][badge_conda_forge]][url_conda_forge]| +| **Workflows** | ![CI_CD][badge_ci_cd] ![CodeQL][badge_codeql]| +| **Documentation** | [![docs][badge_docs]][url_docs] [![codecov][badge_codecov]][url_codecov]| +| **Dependencies** | [![rdkit][badge_rdkit]][url_rdkit] [![mdanalysis][badge_mda]][url_mda] [![Code style: black][badge_black]][url_black]| +| **License** | [![License: GPL v2][badge_license]][url_license]| - Interface to **OpenMM** for easy setup of molecular dynamic simulations of protein-ligand complexes http://openmmdl.readthedocs.io/ -## Install +## Installation via conda-forge + +**OpenMMDL** is implemented in conda-forge and can be installed for linux-based system with the following command line + + conda install -c conda-forge openmmdl + +## Installation via repository #### Clone this repository @@ -173,3 +181,27 @@ The Setup script is a modified version of [openmm-setup](https://github.com/open This Project is based on the [Computational Molecular Science Python Cookiecutter](https://github.com/molssi/cookiecutter-cms) version 1.1. + + +[badge_release]: https://img.shields.io/github/release-pre/wolberlab/openmmdl.svg +[badge_commits_since]: https://img.shields.io/github/commits-since/wolberlab/openmmdl/latest +[badge_ci_cd]: https://github.com/wolberlab/OpenMMDL/actions/workflows/CI-CD.yml/badge.svg +[badge_codeql]: https://github.com/wolberlab/OpenMMDL/actions/workflows/codeql.yml/badge.svg +[badge_docs]: https://readthedocs.org/projects/openmmdl/badge/?version=latest +[badge_codecov]: https://codecov.io/gh/talagayev/OpenMMDL/graph/badge.svg?token=950HZ93CKS +[badge_conda_forge]: https://img.shields.io/conda/vn/conda-forge/openmmdl.svg +[badge_rdkit]: https://img.shields.io/badge/Powered%20by-RDKit-3838ff.svg?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQBAMAAADt3eJSAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAAFVBMVEXc3NwUFP8UPP9kZP+MjP+0tP////9ZXZotAAAAAXRSTlMAQObYZgAAAAFiS0dEBmFmuH0AAAAHdElNRQfmAwsPGi+MyC9RAAAAQElEQVQI12NgQABGQUEBMENISUkRLKBsbGwEEhIyBgJFsICLC0iIUdnExcUZwnANQWfApKCK4doRBsKtQFgKAQC5Ww1JEHSEkAAAACV0RVh0ZGF0ZTpjcmVhdGUAMjAyMi0wMy0xMVQxNToyNjo0NyswMDowMDzr2J4AAAAldEVYdGRhdGU6bW9kaWZ5ADIwMjItMDMtMTFUMTU6MjY6NDcrMDA6MDBNtmAiAAAAAElFTkSuQmCC +[badge_mda]: https://img.shields.io/badge/powered%20by-MDAnalysis-orange.svg?logoWidth=16&logo=data:image/x-icon;base64,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 +[badge_black]: https://img.shields.io/badge/code%20style-black-000000.svg +[badge_license]: https://img.shields.io/badge/License-MIT-blue.svg + +[url_latest_release]: https://github.com/wolberlab/openmmdl/releases +[url_ci_cd]: https://github.com/wolberlab/OpenMMDL/actions/workflows/CI-CD.yml +[url_codeql]: https://github.com/wolberlab/OpenMMDL/actions/workflows/codeql.yml +[url_docs]: https://github.com/wolberlab/OpenMMDL/actions/workflows/codeql.yml +[url_codecov]: https://github.com/wolberlab/OpenMMDL/actions/workflows/codeql.yml +[url_conda_forge]: https://anaconda.org/conda-forge/openmmdl +[url_rdkit]: https://www.rdkit.org/ +[url_mda]: https://www.mdanalysis.org +[url_black]: https://github.com/psf/black +[url_license]: https://opensource.org/licenses/MIT diff --git a/environment.yml b/environment.yml index a4459b39..b4961124 100644 --- a/environment.yml +++ b/environment.yml @@ -4,27 +4,26 @@ channels: - conda-forge # Add the conda-forge channel here dependencies: - - python=3.10 - pip - setuptools>=61.0 - versioningit~=2.0 - pytest>=6.1.2 - pytest-runner - - numpy=1.23.4 - - plip=2.3.0 + - numpy + - plip - requests>=2.28.1 - rdkit>=2022.03.5 - - mdtraj=1.9.7 - - pdbfixer=1.8.1 - - openff-toolkit=0.11.1 - - openmmforcefields=0.11.2 + - mdtraj + - pdbfixer + - openff-toolkit + - openmmforcefields - cudatoolkit>=11.7.0 - cuda-python>=11.7.1 - - MDAnalysis>=2.3.0 + - mdanalysis>=2.3.0 - pytest-shutil>=1.7.0 - flask>=2.2.2 - - cairosvg=2.7.1 - - nglview=3.0.6 + - cairosvg + - nglview - numba>=0.59.1 - jupyter # Add any additional runtime dependencies from pyproject.toml here diff --git a/pyproject.toml b/pyproject.toml index 8b7fa958..a1d548af 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,5 +1,5 @@ [build-system] -requires = ["setuptools>=61.0", "versioningit~=2.0"] +requires = ["setuptools>=61.0", "versioningit"] build-backend = "setuptools.build_meta" # Self-descriptive entries which should always be present @@ -18,7 +18,7 @@ classifiers = [ "License :: OSI Approved :: MIT License", "Programming Language :: Python :: 3", ] -requires-python = ">=3.8" +requires-python = ">=3.10" # Declare any run-time dependencies that should be installed with the package. dependencies = [ diff --git a/requirements.txt b/requirements.txt index ccd68ef8..f1aa420e 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,10 +1,10 @@ -numpy=1.23.4 +numpy=1.26.4 plip=2.3.0 requests>=2.28.1 rdkit>=2022.03.5 mdtraj=1.9.7 pdbfixer=1.8.1 -openff-toolkit=0.11.1 +openff-toolkit=0.16.0 openmmforcefields=0.11.2 cudatoolkit>=11.7.0 cuda-python>=11.7.1