Updated install instructions

Author: jparkpjw

README.md

@@ -26,9 +26,68 @@ M.D. Ward, M.I. Zimmerman, S. Swamidass, G.R. Bowman. [DiffNets: Self-supervised
 
 ## Recommended Installation
 
-Follow line-by-line instructions [here.](https://diffnets.readthedocs.io/en/latest/Installation.html)
+Clone both the DiffNets repo as well as the Enspara repo (which is a dependency of DiffNets) to your directory of choice:
+```bash
+cd /desired/path/for/packages
+git clone https://github.com/bowman-lab/enspara.git
+git clone https://github.com/bowman-lab/diffnets.git
+```
+
+Create a conda environment using the following command:
+
+```bash
+conda create -n diffnets python=3.11
+```
+
+Then activate the environment and install the following dependencies:
+
+```bash
+conda activate diffnets
+conda install -c conda-forge numpy=2.3 scipy=1.16 cython=3.2 pytest=9.0 matplotlib=3.10 pandas=2.3
+pip install mdtraj=1.11 mpi4py=4.1
+```
+
+Next install CUDA-enabled PyTorch:
+```bash
+pip install torch==2.2.2 torchvision==0.17.2 torchaudio==2.2.2 --index-url https://download.pytorch.org/whl/cu121
+```
+
+Alternatively you can use the provided `environment.yaml` file to create the conda environment in one go and activate it afterwards:
 
-While the above install should be simple to follow, a more concise install is in the works.
+```bash
+cd /path/to/diffnets
+conda env create -f environment.yaml
+conda activate diffnets
+```
+
+Note that other package versions might work but haven't been explicitly tested.
+
+Now install Enspara and check to make sure it was properly installed:
+
+```bash
+cd /path/to/enspara
+pip install -e .
+
+cd /any/directory
+python
+import enspara
+```
+
+If no messages pop up after this, then Enspara is properly installed! Now install DiffNets and test for proper installation:
+```bash
+cd /path/to/diffnets
+pip install -e .
+
+cd /any/directory
+python
+import diffnets
+```
+
+Again if no messages pop up, then DiffNets is properly installed!
+
+*The below install instructions are outdated. They have been left here for reference:
+Follow line-by-line instructions [here.](https://diffnets.readthedocs.io/en/latest/Installation.html)
+While the above install should be simple to follow, a more concise install is in the works.*
 
 ## Building the docs / Running the tests