updating input arguments in docs

Author: skfegan

docs/community_guide.rst

@@ -26,15 +26,15 @@ To run the full test suite, simply install ``pytest`` and run in root directory
 
     pytest
 
-To only run the unit tests in a particular part of program. For example only running test for solute part.
+To only run the unit tests in a particular part of program, for example only running tests for the levels functions:
 
 .. code-block:: bash
 
-    pytest CodeEntropy/tests/test_CodeEntropy.py
+    pytest CodeEntropy/tests/test_CodeEntropy/test_levels.py
 
 
-To only run the a specific test. e.g.
+To only run the a specific test, e.g.:
 
 .. code-block:: bash
 
-    pytest CodeEntropy/tests/test_CodeEntropy.py::test_CodeEntropy_parser_labForces
+    pytest CodeEntropy/tests/test_CodeEntropy/test_levels.py::test_select_levels

docs/config.yaml

@@ -2,13 +2,13 @@
 
 run1:
   top_traj_file: ["1AKI_prod.tpr", "1AKI_prod.trr"]
-  selection_string: 'not water'
+  selection_string: 'all'
   start: 0
   end: 500
   step: 1
   bin_width: 30
   temperature: 300
   verbose: True
-  thread: 
   force_partitioning: 0.5
   water_entropy: False
+  grouping: 'molecules'

docs/getting_started.rst

@@ -71,8 +71,8 @@ The top_traj_file argument is necessary to identify your simulation data, the ot
      - Default
      - Type
    * - ``--top_traj_file`` 
-     - Path to Structure/topology file(``AMBER PRMTOP``, ``GROMACS TPR`` or topology file with MDAnalysis readable dihedral information (not officially supported)) followed by Trajectory file(s) (``GROMAC TRR`` or ``AMBER NETCDF``) You will need to output the **coordinates** and **forces** to the **same file** . 
-     - Required
+     - Path to Structure/topology file followed by Trajectory file(s). Any MDAnalysis readable files should work  (for example ``GROMACS TPR and TRR`` or ``AMBER PRMTOP and NETCDF``). You will need to output the **coordinates** and **forces** to the **same file** . 
+     - Required, no default value
      - list of ``str`` 
    * - ``--selection_string``
      - Selection string for CodeEntropy such as protein or resid, refer to ``MDAnalysis.select_atoms`` for more information.
@@ -102,10 +102,6 @@ The top_traj_file argument is necessary to identify your simulation data, the ot
      - Enable verbose output
      - ``False``
      - ``bool``
-   * - ``--thread``
-     - How many multiprocess to use.
-     - ``1``: for single core execution
-     - ``int``
    * - ``--outfile``
      - Name of the file where the text format output will be written.
      - ``outfile.out``
@@ -118,6 +114,10 @@ The top_traj_file argument is necessary to identify your simulation data, the ot
      - Use Jas Kalayan's waterEntropy code to calculate the water conformational entropy
      - ``False``
      - ``bool``
+   * - ``--grouping``
+     - How to group molecules for averaging
+     - ``molecules``
+     - ``str``
 
 
 Example #1
@@ -147,3 +147,4 @@ To use the same settings as in Example #1, but override trajectory information,
 Or as an alternative, you could edit the config.yaml file and use the CodeEntropy command as in the first example.
 
 CodeEntropy creates job* directories for the output, where * is a job number choosen by the so that there are sequentially numbered directories when you rerun CodeEntropy in the same working directory.
+Each job* directory contains the output json file and a subdirectory with the log files.