Edited README.md for the data directory; Modified setup.py to prevent…

… the data to be shipped with the package installation

ensemble_md/data/README.md

@@ -1,2 +1,39 @@
 # Example simulation inputs used in the REXEE paper
-This directory contains example simulation inputs used in the simulations reported in our paper, including those for the anthracene and CB7-10 systems. The data here will not be included when the package is installed.
+This directory contains example simulation inputs used in the simulations reported in our paper, including those for the anthracene and CB7-10 systems. The data here will not be included when the package is installed. Below is the structure of the `data` directory:
+
+```
+.
+├── CB7-10
+│   ├── complex
+│   │   ├── complex.gro
+│   │   ├── complex.top
+│   │   ├── fixed_weight.mdp
+│   │   ├── itp_files
+│   │   │   ├── 10_GMX.itp
+│   │   │   ├── 10atomtypes.itp
+│   │   │   └── cucurbit_7_uril_GMX.itp
+│   │   ├── params.yaml
+│   │   └── weight_updating.mdp
+│   └── solvent
+│       ├── fixed_weight.mdp
+│       ├── ligand.gro
+│       ├── ligand.top
+│       └── weight_updating.mdp
+├── README.md
+├── anthracene
+│   ├── anthracene.gro
+│   ├── anthracene.top
+│   ├── fixed_weight.mdp
+│   ├── HREX.mdp
+│   ├── params.yaml
+│   └── weight_updating.mdp
+└── instruction.md
+
+5 directories, 20 files
+```
+Here are some additional notes about the files: 
+- For each system, the provided GRO and TOP files were used for all simulations. 
+- The file `fixed_weight.mdp` was used for both fixed-weight EE and REXEE simulations for the anthracene system, and for the complex simulation of the CB7-10 system. Similarly, the file `weight_updating.mdp` was used for the weight-updating EE and REXEE simulations for the anthracene system, and for the complex simulation of the CB7-10 system. For the solvent leg of the CB7-10 system, only expanded ensemble simulations were performed. 
+- The file `params.yaml` contains REXEE parameters and can be used for both fixed-weight or weight-updating simulations. Relevant parameters were varied between tests for different REXEE simulations reported in the paper. 
+- For the CB7-10 system, the directory `itp_files` contains the ITP files referenced in `complex.top`, which is the topology file of the CB7-10 binding complex. 
+- The file `instruction.mdp` is just a file generated by the cookiecutter and is irrelevant to the project.

setup.py

@@ -64,8 +64,8 @@
 
     # Optional include package data to ship with your package
     # Customize MANIFEST.in if the general case does not suit your needs
-    # Comment out this line to prevent the files from being packaged with your software
-    include_package_data=True,
+    # Comment out this line or set include_package_data to False to prevent the files from being packaged with your software
+    include_package_data=False,
 
     # Allows `setup.py test` to work correctly with pytest
     setup_requires=[] + pytest_runner,