diff --git a/README.md b/README.md index 3818081a..32408a8f 100644 --- a/README.md +++ b/README.md @@ -5,6 +5,8 @@ [![GH Actions Status](https://github.com/volkamerlab/opencadd/workflows/CI/badge.svg)](https://github.com/volkamerlab/opencadd/actions?query=branch%3Amaster) [![codecov](https://codecov.io/gh/volkamerlab/opencadd/branch/master/graph/badge.svg)](https://codecov.io/gh/volkamerlab/opencadd/branch/master) [![Documentation Status](https://readthedocs.org/projects/opencadd/badge/?version=latest)](https://opencadd.readthedocs.io) +[![Conda Version](https://img.shields.io/conda/vn/conda-forge/opencadd.svg)](https://anaconda.org/conda-forge/opencadd) +[![License](https://img.shields.io/badge/License-MIT-blue.svg)](https://opensource.org/licenses/MIT) ![OpenCADD](/docs/_static/opencadd.png) diff --git a/docs/index.rst b/docs/index.rst index 3e920ee3..2dd89243 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -8,6 +8,28 @@ Welcome to OpenCADD's documentation! OpenCADD is a Python package for structural cheminformatics! +.. image:: + https://github.com/volkamerlab/opencadd/workflows/CI/badge.svg + :target: https://github.com/volkamerlab/opencadd/actions +.. image:: + https://codecov.io/gh/volkamerlab/opencadd/branch/master/graph/badge.svg + :target: https://codecov.io/gh/volkamerlab/opencadd/branch/master +.. image:: + https://readthedocs.org/projects/opencadd/badge/?version=latest + :target: https://opencadd.readthedocs.io/en/latest/ +.. image:: + https://img.shields.io/conda/vn/conda-forge/opencadd.svg + :target: https://anaconda.org/conda-forge/opencadd +.. image:: + https://img.shields.io/badge/License-MIT-blue.svg + :target: https://opensource.org/licenses/MIT + +.. raw:: html + +

+ Subpocket-based structural fingerprint for kinase pockets +

+ .. toctree:: :maxdepth: 1 :caption: User guide @@ -23,7 +45,7 @@ OpenCADD is a Python package for structural cheminformatics! .. toctree:: :maxdepth: 1 - :caption: Superposition + :caption: Structure: Superposition superposition tutorials/mda diff --git a/docs/installing.rst b/docs/installing.rst index 0693d543..ca8e4d26 100644 --- a/docs/installing.rst +++ b/docs/installing.rst @@ -1,29 +1,46 @@ Installing ========== -Eventually, we will have a ``conda`` package, but for now you need to create a new environment manually. +.. note:: -1. Install Miniconda for your OS if you don't have it already. -2. Download a `copy of this repository `_. -3. Create new conda environment:: + We are assuming you have a working ``mamba`` installation in your computer. + If this is not the case, please refer to their `official documentation `_. - conda env create -n opencadd -f devtools/conda-envs/test_env.yaml -4. Activate the new environment:: +Install from the conda package +------------------------------ + +1. Create a new conda environment called ``opencadd`` with the ``opencadd`` package and all its dependencies installed:: + + mamba create -n opencadd opencadd + +2. Activate the new conda environment:: + + conda activate opencadd + +.. 3. Test that your installation works:: + + superposer -h + + +Install from the latest development snapshot +-------------------------------------------- + +Install the latest development snapshot from the `GitHub repository's master branch `_. + + +1. Create a new conda environment called ``opencadd``:: + + mamba env create -f https://raw.githubusercontent.com/volkamerlab/opencadd/master/devtools/conda-envs/test_env.yaml -n opencadd + +2. Activate the new conda environment:: conda activate opencadd -5. Install the package with ``pip``:: +3. Install ``opencadd`` package via pip:: - python -m pip install https://github.com/volkamerlab/opencadd/archive/master.tar.gz + pip install https://github.com/volkamerlab/opencadd/archive/master.tar.gz -6. Run ``superposer -h`` to test it works. +.. 4. Test that your installation works:: -7. Workaround for MMLigner:: - conda config --add channels conda-forge - conda activate base - conda install conda-build - conda build devtools/conda-recipes/mmligner/ - (conda activate opencadd) - conda install -c local mmligner pip - python -m pip install -e . --no-deps \ No newline at end of file + superposer -h