Merge pull request cmelab#98 from chrisjonesBSU/update-readme

Update `README` and documentation with new installation instructions.
chrisjonesBSU · Nov 16, 2023 · 531cd82 · 531cd82
2 parents a0db9e8 + f9b1ff4
commit 531cd82
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diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
@@ -6,13 +6,13 @@ on:
     branches: [ main ]
     paths:
       - flowermd/**
-      - environment-cpu.yml
+      - environment-dev.yml
       - .github/workflows/pytest.yml
   pull_request:
     branches: [ main ]
     paths:
       - flowermd/**
-      - environment-cpu.yml
+      - environment-dev.yml
       - .github/workflows/pytest.yml
   # Allows workflow to be manually triggered
   workflow_dispatch:
@@ -28,7 +28,7 @@ jobs:
     - name: Build environment
       uses: conda-incubator/setup-miniconda@v2
       with:
-        environment-file: environment-cpu.yml
+        environment-file: environment-dev.yml
         miniforge-variant: Mambaforge
         miniforge-version: 4.9.2-4
         use-mamba: true

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -25,7 +25,7 @@ We welcome all code contributions in the form of pull requests. If you are
 interested in contributing code, please follow the steps below:
 - Fork the repository (default branch is `main`)
 - Create a new branch for your feature/bug fix
-- Create the `flowermd` conda environment using the `environment-cpu.yml` or `environment-gpu.yml` file
+- Create the `flowermd` conda environment using the `environment-dev.yml` file
 - Make your changes
 - Install the latest version of pre-commit using `conda install -c conda-forge pre-commit` and run `pre-commit install` in the root directory of the repository
 - Commit your changes and make sure all the pre-commit hooks pass

diff --git a/README.md b/README.md
@@ -1,5 +1,7 @@
 [![pytest](https://github.com/cmelab/flowerMD/actions/workflows/pytest.yml/badge.svg)](https://github.com/cmelab/flowerMD/actions/workflows/pytest.yml)
 [![codecov](https://codecov.io/gh/cmelab/flowerMD/branch/main/graph/badge.svg?token=86LY9WHSH6)](https://codecov.io/gh/cmelab/flowerMD)
+[![Anaconda-Server Badge](https://anaconda.org/conda-forge/flowermd/badges/version.svg)](https://anaconda.org/conda-forge/flowermd)
+[![Anaconda-Server Badge](https://anaconda.org/conda-forge/flowermd/badges/latest_release_date.svg)](https://anaconda.org/conda-forge/flowermd)
 ## flowerMD: Flexible Library of Organic Workflows and Extensible Recipes for Molecular Dynamics
 flowerMD is a modular “wrapper” package for molecular dynamics (MD)
 simulation pipeline development, designed to enable fast, reproducible,
@@ -14,22 +16,43 @@ flowerMD agnostic to system identity, forcefield, and thermodynamic
 ensemble, and allowing for growth on an as-needed basis.
 
 
+Installing flowermd
+===================
 
-## Installation
+Installing `flowermd` from the `conda-forge` channel can be achieved by adding `conda-forge` to your channels with:
 
-### 1. Clone this repository: ###
+```
+conda config --add channels conda-forge
+conda config --set channel_priority strict
+```
+
+Once the `conda-forge` channel has been enabled, `flowermd` can be installed with `conda`:
+
+```
+conda install flowermd
+```
+
+or with `mamba`:
+
+```
+mamba install flowermd
+```
+
+**Installing from source for development:**
+
+Clone this repository:
 
 ```
 git clone [email protected]:cmelab/flowerMD.git
 cd flowerMD
 ```
 
-### 2. Set up and activate environment: ###
-#### a. Using HOOMD-blue from conda:
+Set up and activate environment:
+
 ```
-conda env create -f environment-cpu.yml
+conda env create -f environment-dev.yml
 conda activate flowermd
-python -m pip install .
+python -m pip install -e .
 ```
 
 ## Basic Usage

diff --git a/docs/source/installation.rst b/docs/source/installation.rst
@@ -2,6 +2,14 @@
 Installation
 ============
 
+Install from anaconda
+---------------------------------------
+flowerMD is available on `conda-forge <https://anaconda.org/conda-forge/flowermd>`_
+::
+
+    $ conda install -c conda-forge flowermd
+
+
 Install from source
 ---------------------------------------
 
@@ -14,6 +22,6 @@ Install from source
 2. Set up and activate environment:
 ::
 
-    $ conda env create -f environment-cpu.yml
+    $ conda env create -f environment.yml
     $ conda activate flowermd
     $ python -m pip install .
diff --git a/environment-gpu.yml → environment-dev.yml b/environment-gpu.yml → environment-dev.yml
@@ -1,17 +1,18 @@
-name: flowermd
+name: flowermd-dev
 channels:
   - conda-forge
 dependencies:
-  - foyer
+  - foyer >=0.12.0
   - fresnel
   - freud >=2.13.1
   - gmso >=0.11.2
   - gsd >=3.0
-  - hoomd=4.3=*gpu*
+  - hoomd=4.3
   - mbuild >=0.16.4
   - numpy
-  - openbabel
+  - openbabel >=3
   - pip
+  - pre-commit
   - py3Dmol
   - pytest
   - pytest-cov

diff --git a/environment-cpu.yml → environment.yml b/environment-cpu.yml → environment.yml
@@ -2,19 +2,17 @@ name: flowermd
 channels:
   - conda-forge
 dependencies:
-  - foyer
+  - foyer >=0.12.0
   - fresnel
   - freud >=2.13.1
   - gmso >=0.11.2
   - gsd >=3.0
-  - hoomd=4.3=*cpu*
+  - hoomd=4.3
   - mbuild >=0.16.4
   - numpy
-  - openbabel
+  - openbabel >=3
   - pip
   - py3Dmol
-  - pytest
-  - pytest-cov
   - python >=3.10
   - fresnel >=0.13.5
   - cmeutils >=1.0