diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml index 7ceefadb..ddb8df28 100644 --- 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 index 58d62ca8..b6f41c76 100644 --- 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 index d2cff320..59b6a7fd 100644 --- 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 git@github.com: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 index a28465c4..1e0945fb 100644 --- a/docs/source/installation.rst +++ b/docs/source/installation.rst @@ -2,6 +2,14 @@ Installation ============ +Install from anaconda +--------------------------------------- +flowerMD is available on `conda-forge `_ +:: + + $ 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 b/environment-dev.yml similarity index 75% rename from environment-gpu.yml rename to environment-dev.yml index 4fcf2d0c..9ca8771d 100644 --- a/environment-gpu.yml +++ b/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 b/environment.yml similarity index 77% rename from environment-cpu.yml rename to environment.yml index 942b2788..5f7a652b 100644 --- a/environment-cpu.yml +++ b/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