Merge branch 'wolberlab:main' into Code_class_restructure

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
+
+<!--
+The rules for this file:
+  * Authors are sorted chronologically, earliest to latest
+  * Please format it each entry as "Preferred name <GitHub username>"
+  * Your preferred name is whatever you wish to go by --
+    it does *not* have to be your legal name!
+  * Please start a new section for each new year
+  * Don't ever delete anything
+-->
+
+**2023**
+- Niklas Piet Doering <@NDoering99>
+- Leon Obendorf <@Habacef>
+- Marvin Taterra <@MarvinTaterra>
+
+**2022**
+- Valerij Talagayev <@talagayev>
+- Yu Chen <@xixichennn>
+- Gerhard Wolber <@gwolber>

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).
+
+<!--
+The rules for this file:
+  * entries are sorted newest-first.
+  * summarize sets of changes - don't reproduce every git log comment here.
+  * don't ever delete anything.
+  * keep the format consistent:
+    * do not use tabs but use spaces for formatting
+    * 79 char width
+    * YYYY-MM-DD date format (following ISO 8601)
+  * accompany each entry with github issue/PR number (Issue #xyz)
+-->
+
+## [Unreleased]
+
+### Authors
+<!-- GitHub usernames of contributors to this release -->
+
+### Added
+<!-- New added features -->
+
+### Fixed
+<!-- Bug fixes -->
+
+### Changed
+<!-- Changes in existing functionality -->
+
+### Deprecated
+<!-- Soon-to-be removed features -->
+
+### Removed
+<!-- Removed features -->

README.md

@@ -1,23 +1,31 @@
 OpenMMDL @ Molecular Design Lab
 ==============================
+
+<img src="https://github.com/wolberlab/OpenMMDL/blob/main/openmmdl/openmmdl_setup/static/OpenMMDL_logo_2.png" height="250">
+
 [//]: # (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]|
 
-<img src="https://github.com/wolberlab/OpenMMDL/blob/main/openmmdl/openmmdl_setup/static/OpenMMDL_logo_2.png" height="250">
 
 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

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

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 = [
 

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