Merge pull request #797 from OpenFreeEnergy/update-cli-docs

Update CLI help docs

docs/guide/cli/cli_basics.rst

@@ -12,26 +12,29 @@ subcommands and a brief description of them, use ``openfe (or
 .. code:: none
 
     Usage: openfe [OPTIONS] COMMAND [ARGS]...
-
+    
       This is the command line tool to provide easy access to functionality from
       the OpenFE Python library.
-
+    
     Options:
       --version   Show the version and exit.
       --log PATH  logging configuration file
       -h, --help  Show this message and exit.
-
-    Setup Commands:
-      plan-rhfe-network  Plan a relative hydration free energy network, saved in a
-                         dir with multiple JSON files
-      atommapping        Check the atom mapping of a given pair of ligands
-      plan-rbfe-network  Plan a relative binding free energy network, saved in a
-                         dir with multiple JSON files.
-
-    Simulation Commands:
-      gather    Gather DAG result jsons for network of RFE results into single TSV
-                file
+    
+    Network Planning Commands:
+      view-ligand-network  Visualize a ligand network
+      plan-rbfe-network    Plan a relative binding free energy network, saved as
+                           JSON files for the quickrun command.
+      plan-rhfe-network    Plan a relative hydration free energy network, saved as
+                           JSON files for the quickrun command.
+    
+    Quickrun Executor Commands:
+      gather    Gather result jsons for network of RFE results into a TSV file
       quickrun  Run a given transformation, saved as a JSON file
+    
+    Miscellaneous Commands:
+      fetch  Fetch tutorial or other resource.
+      test   Run the OpenFE test suite
 
 The ``--log`` option takes a logging configuration file and sets that
 logging behavior. If you use it, it must come before the subcommand name.
@@ -42,17 +45,26 @@ the subcommand name, e.g., ``openfe quickrun --help``, which returns
 .. code:: none
 
     Usage: openfe quickrun [OPTIONS] TRANSFORMATION
-
-      Run the transformation (edge) in the given JSON file in serial.
-
-      To save a transformation as JSON, create the transformation and then save it
-      with transformation.dump(filename).
-
+    
+      Run the transformation (edge) in the given JSON file.
+    
+      Simulation JSON files can be created with the :ref:`cli_plan-rbfe-network`
+      or from Python a :class:`.Transformation` can be saved using its dump
+      method::
+    
+          transformation.dump("filename.json")
+    
+      That will save a JSON file suitable to be input for this command.
+    
+      Running this command will execute the simulation defined in the JSON file,
+      creating a directory for each individual task (``Unit``) in the workflow.
+      For example, when running the OpenMM HREX Protocol a directory will be
+      created for each repeat of the sampling process (by default 3).
+    
     Options:
       -d, --work-dir DIRECTORY  directory to store files in (defaults to current
                                 directory)
       -o FILE                   output file (JSON format) for the final results
       -h, --help                Show this message and exit.
 
-
 For more details on various commands, see the :ref:`cli-reference`.