Updated installation instructions (#74)

* fixes #57
* Updated installation instructions using pip and mamba/conda (README and docs)

Author: amruthesht

README.md

@@ -27,64 +27,79 @@ IMDClient is bound by a [Code of Conduct](https://github.com/becksteinlab/imdrea
 
 ### Installation
 
-IMDClient is available via PyPi and can be installed with pip:
-```bash
+#### Install via mamba (recommended)
+To install the latest release of IMDClient from conda-forge:
+
+```
+mamba install -c conda-forge imdclient
+```
+
+#### Install via pip
+To install the latest release of IMDClient from PyPI:
+
+```
 pip install imdclient
 ```
 
-To build IMDClient from source,
-we highly recommend using virtual environments.
-If possible, we strongly recommend that you use
-[Anaconda](https://docs.conda.io/en/latest/) as your package manager.
-Below we provide instructions both for `conda` and
-for `pip`.
+---
+
+### Building from Source
+To build IMDClient from source, we highly recommend using virtual environments.
+If possible, we recommend that you use [mamba](https://mamba.readthedocs.io/en/latest/) as your package manager through [miniforge](https://github.com/conda-forge/miniforge). (You can substitute `conda` for `mamba` in the commands below if you prefer.)
 
-#### With conda
+Below we provide instructions both for `mamba` and for `pip`.
 
-Ensure that you have [conda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html) installed.
+#### Source build with mamba
+1. Ensure you have [mamba](https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html) installed.
 
-Create a virtual environment and activate it:
+2. Create and activate a new environment:
 
 ```
-conda create --name imdclient
-conda activate imdclient
+mamba create --name imdclient
+mamba activate imdclient
 ```
 
-<!-- Install the development and documentation dependencies:
+3. (Recommended) Install all dependencies using the provided environment YAML files for a clean and reproducible environment:
 
 ```
-conda env update --name imdreader --file devtools/conda-envs/test_env.yaml
-conda env update --name imdreader --file docs/requirements.yaml
-``` -->
+mamba env update --name imdclient --file devtools/conda-envs/test_env.yaml
+mamba env update --name imdclient --file docs/requirements.yaml
+```
 
-Build this package from source:
+4. Build and install IMDClient in editable mode:
 
 ```
 pip install -e .
 ```
 
-If you want to update your dependencies (which can be risky!), run:
+5. (Optional) Update dependencies:
 
 ```
-conda update --all
+mamba update --all
 ```
 
-And when you are finished, you can exit the virtual environment with:
+6. Deactivate the environment when finished:
 
 ```
-conda deactivate
+mamba deactivate
 ```
 
-#### With pip
+#### Source build with pip
+
+1. (Optional) Create and activate a virtual environment:
+
+```
+python -m venv venv
+source venv/bin/activate
+```
 
-To build the package from source, run:
+2. Install IMDClient from source:
 
 ```
 pip install .
 ```
 
-If you want to create a development environment, install
-the dependencies required for tests and docs with:
+3. (Optional) For development (tests and docs):
 
 ```
 pip install ".[test,doc]"
@@ -102,4 +117,5 @@ Copyright (c) 2024, Lawson
 
 Project based on the 
 [MDAnalysis Cookiecutter](https://github.com/MDAnalysis/cookiecutter-mda) version 0.1.
-<!-- Please cite [MDAnalysis](https://github.com/MDAnalysis/mdanalysis#citation) when using IMDReader in published work. --> 
+
+**If you use IMDClient in your research, please cite [IMDClient](https://github.com/Becksteinlab/imdclient) in your publications.**

docs/source/getting_started.rst

@@ -4,37 +4,68 @@ Getting Started
 Installation
 ############
 
-To build imdclient from source, we highly recommend using virtual environments.
-If possible, we strongly recommend that you use
-`Anaconda <https://docs.conda.io/en/latest/>`_ as your package manager.
-Below we provide instructions both for installing into a `conda` environment.
+Install via mamba (recommended)
+-------------------------------
 
-With conda
-----------
+To install the latest release of imdclient from conda-forge::
 
-Ensure that you have `conda <https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html>`_ installed.
+    mamba install -c conda-forge imdclient
 
-Create a virtual environment and activate it::
+Install via pip
+---------------
 
-    conda create --name imdclient
-    conda activate imdclient
+To install the latest release of imdclient from PyPI::
+
+    pip install imdclient
+
+Building from Source
+####################
+
+We highly recommend using virtual environments to source-build IMDClient. If possible, we recommend that you use `mamba <https://mamba.readthedocs.io/en/latest/>`_ as your package manager through `miniforge <https://github.com/conda-forge/miniforge>`_.
+
+Source build with mamba
+-----------------------
+
+Ensure that you have `mamba <https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html>`_ installed.
+
+Create and activate a new environment::
+
+    mamba create --name imdclient
+    mamba activate imdclient
+
+(Recommended) Install all dependencies using the provided environment YAML files for a clean and reproducible environment::
+
+    mamba env update --name imdclient --file devtools/conda-envs/test_env.yaml
+    mamba env update --name imdclient --file docs/requirements.yaml
 
 Build this package from source::
 
     pip install -e <path/to/repo>
 
+Source build with pip
+---------------------
+
+(Optional) Create and activate a virtual environment::
+
+    python -m venv venv
+    source venv/bin/activate
+
+Install imdclient from source::
+
+    pip install <path/to/repo>
+
 Development environment installation
 ------------------------------------
+For development or documentation builds, use the following commands after activating your environment:
 
-After creating and activating a conda environment as described, install 
-the package with documentation and testing dependencies::
+To install development and documentation dependencies::
 
-    pip install -e <path/to/repo>[doc, test]
+    pip install -e <path/to/repo>[doc,test]
 
-Then, to install the development dependencies::
+To update the development dependencies using mamba::
 
-    conda env update --name imdclient --file devtools/conda-envs/test_env.yaml
+    mamba env update --name imdclient --file devtools/conda-envs/test_env.yaml
 
-Or the documentation building dependencies::
+Or to update the documentation building dependencies::
 
-    conda env update --name imdclient --file docs/requirements.yaml
+    mamba env update --name imdclient --file docs/requirements.yaml