From 5290acdff3f7a8855364c3a5c862fe5e5bb1908f Mon Sep 17 00:00:00 2001 From: Umesh Timalsina Date: Thu, 29 Oct 2020 15:39:59 -0500 Subject: [PATCH] Update README with conda install and status badges (#483) * Add conda install instructions * Add status badges * WIP- Add codecov badge * WIP- Add simple example * WIP- Fix foyer link * WIP- Fix minor typos and capitalization issues Co-authored-by: Co Quach <43968221+daico007@users.noreply.github.com> --- README.md | 41 +++++++++++++++++++++++++++++------------ docs/installation.rst | 9 +++++++++ 2 files changed, 38 insertions(+), 12 deletions(-) diff --git a/README.md b/README.md index cc51f3115..4e3bb0c45 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,27 @@ +![](https://anaconda.org/conda-forge/gmso/badges/license.svg) +[![](https://anaconda.org/conda-forge/gmso/badges/version.svg)](https://anaconda.org/conda-forge/gmso) +[![Build Status](https://dev.azure.com/mosdef/mosdef/_apis/build/status/mosdef-hub.gmso?branchName=master)](https://dev.azure.com/mosdef/mosdef/_build/latest?definitionId=9&branchName=master) +[![codecov](https://codecov.io/gh/mosdef-hub/gmso/branch/master/graph/badge.svg?token=rqPGwmXDzu)](undefined) + ## GMSO: General Molecular Simulation Object -Flexible storage of chemical topology for molecular simulation +Flexible storage of chemical topology for molecular simulation. +With few lines of `GMSO` code, together with [`mBuild`](https://mbuild.mosdef.org) and [`foyer`](https://foyer.mosdef.org), users can rapidly prototype arbitrary parameterized chemical systems and generate data files for a wide variety simulation engines. + +```python +import foyer +from mbuild.lib.molecules import Ethane +from gmso.external.convert_parmed import from_parmed +from gmso.formats.lammpsdata import write_lammpsdata +# Start with a mBuild compound +mb_ethane = Ethane() +oplsaa = foyer.Forcefield(name='oplsaa') +# atomtype the system with foyer, and convert the resulting structure to a topology +typed_ethane = from_parmed(oplsaa.apply(mb_ethane)) +typed_ethane.name = 'ethane' +# Write out lammps datafile +write_lammpsdata(typed_ethane, filename='ethane.lammps', atom_style='full') +``` Introduction @@ -69,17 +90,13 @@ Installation ------------ For full, detailed instructions, refer to the [documentation for installation](https://gmso.mosdef.org/en/latest/installation.html) -### `Conda` installation quickstart -_Note: `GMSO` is not on `conda` currently, but its dependencies are._ - +### `conda` installation quickstart +`GMSO` is available on `conda` and can be installed as: ```bash -git clone https://github.com/mosdef-hub/gmso.git -cd gmso -conda install -c omnia -c mosdef -c conda-forge --file requirements.txt -pip install -e . - ``` +conda install -c conda-forge gmso +``` -### `Pip` installation quickstart +### `pip` installation quickstart _Note: `GMSO` is not on `pypi` currently, but its dependencies are._ ```bash @@ -89,10 +106,10 @@ pip install -r requirements.txt pip install -e . ``` -These two quickstarts will install `GMSO` in [`editable` mode](https://pip.pypa.io/en/stable/reference/pip_install/#editable-installs), which means that as you edit the source code of `GMSO` those edits will be reflected in your installation. +`pip` quickstart will install `GMSO` in [`editable` mode](https://pip.pypa.io/en/stable/reference/pip_install/#editable-installs), which means that as you edit the source code of `GMSO` those edits will be reflected in your installation. Documentation ------------- -The full documentation can be found at [gmso.mosdef.org](https://gmso.mosdef.org) +The full documentation can be found at [gmso.mosdef.org](https://gmso.mosdef.org). diff --git a/docs/installation.rst b/docs/installation.rst index bcd28e208..506b0cdb8 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -2,6 +2,15 @@ Installation ============ +Installing with `conda `_ +-------------------------------------------------------- + +From ``GMSO`` version ``0.3.0``, you can use `conda `_ to install ``GMSO`` in your preferred environment. This will also install the dependencies of ``GMSO``. +:: + (your-env) $ conda install -c conda-forge gmso + + + Installing dependencies with `conda `_ ---------------------------------------------------------------------