Merge pull request #100 from volkamerlab/update-readme-docs

Update README + docs incl. conda installation

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)
 

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
+
+   <p align="center">
+   <img src="_static/opencadd.png" alt="Subpocket-based structural fingerprint for kinase pockets" width="600"/>
+   </p>
+
 .. 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

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 <https://github.com/volkamerlab/opencadd/archive/master.zip>`_.
-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 <https://mamba.readthedocs.io/en/latest/installation.html#mamba>`_. 
 
-    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 <https://github.com/volkamerlab/opencadd>`_.
+
+
+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
+    superposer -h