diff --git a/README.md b/README.md index 13b1e3d..d665f17 100644 --- a/README.md +++ b/README.md @@ -14,11 +14,11 @@ Source code for [Davel, Connor M., Bernat, Timotej, Wagner, Jeffrey R., and Shir ## Installation Currently, this package only supports a "dirty" developer install using conda/mamba and `pip`. -First, install the `conda` environment manager (either the lightweight [Miniconda Distribution](https://docs.anaconda.com/free/miniconda/miniconda-install/) (recommended) or the bulkier [Anaconda Distribution](https://www.anaconda.com/download)). -Further, it is highly recommended (but optional) that you install the mamba package manager (either through [Miniforge or Conda](https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html)); this will greatly accelerate download times. +First, you will need to install the `conda` environment manager (either the lightweight [Miniconda Distribution](https://docs.anaconda.com/free/miniconda/miniconda-install/) (recommended) or the bulkier [Anaconda Distribution](https://www.anaconda.com/download)) if you don't already have it. +Further, it is highly recommended (but optional) that you also have the `mamba` package manager installed (either through [Miniforge or Conda](https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html)); this will greatly accelerate download times. -Once mamba is installed, you can proceed with the dirty `polymerist` install into a safe virtual environment (named "polymerist-env" here). -To install, execute the following set of commands in the CLI in whichever directory you'd like the dev installation to live: +Once `mamba` is installed, you can proceed with the dirty `polymerist` install into a safe virtual environment (named "polymerist-env" here). +To install, execute the following set of commands in a command line interface (CLI) in whichever directory you'd like the dev installation to live: ```sh git clone https://github.com/timbernat/polymerist cd polymerist @@ -26,9 +26,9 @@ mamba env create -n polymerist-env -f devtools/conda-envs/polymerist-env.yml mamba activate polymerist-env pip install -e . ``` -The third command will take **_at least_** a few minutes, and will make the terminal quite bust; remain calm, that's normal! +The third command will take **_at least_** a few minutes, and will make the CLI terminal quite busy; remain calm, that's normal! -Equivalent commands using just conda (in case mamba installation fails) are below. These will perform the same install, just much more slowly: +Equivalent commands using just `conda` (in case `mamba` has ot been installed) are below. These will perform the same installation, just much more slowly: ```sh git clone https://github.com/timbernat/polymerist cd polymerist @@ -37,9 +37,9 @@ conda activate polymerist-env pip install -e . ``` As an optional last step, it is recommended that you correctly set up paths to your [OpenEye License](https://docs.eyesopen.com/toolkits/python/quickstart-python/license.html), if you have access to one. -Portions of conformer-generation and partial-charge assignment in `polymerist` will work more effectively with the OpenEye toolkit installed and licensed, but the package is set up to not require these closed-source dependencies. +Portions of conformer-generation and partial-charge assignment in `polymerist` will work more effectively with the OpenEye toolkit installed and licensed, but 'polymerist' is set up to not require these closed-source dependencies. -From here, you should be able to run `polymerist`-dependent scripts in the polymerist-env environment active, either from the command line or from a [Jupyter Notebook](https://jupyter.org/)! +From here, you should be able to run `polymerist`-dependent scripts in the polymerist-env virtual environment active, either from the command line or from a [Jupyter Notebook](https://jupyter.org/)! ### Copyright