[WIP] Fixes for feedback (#62)

* correct cli tutorial name of directory

* ligand-network-viewer => view-ligand-network

rbfe_tutorial/cli_tutorial.md

@@ -68,7 +68,7 @@ network_setup
 ```
 
 The `ligand_network.graphml` file describes the atom mappings between the
-ligands. We can visualize it with the `openfe ligand-network-viewer` command:
+ligands. We can visualize it with the `openfe view-ligand-network` command:
 
 ```bash
 openfe ligand-network-viewer network_setup/ligand_network.graphml
@@ -104,8 +104,8 @@ run each simulation on your local machine with something like:
 
 ```bash
 # this will take a very long time! don't actually do it!
-for file in setup/transformations/*.json; do
-  relpath=${file:22}  # strip off "setup/transformations/"
+for file in network_setup/transformations/*.json; do
+  relpath=${file:30}  # strip off "network_setup/transformations/"
   dirpath=${relpath%.*}  # strip off final ".json"
   openfe quickrun $file -o results/$relpath -d results/$dirpath
 done
@@ -121,9 +121,9 @@ and submit a job script for the simplest SLURM use case:
 
 ```bash
 for file in setup/transformations/*.json; do
-  relpath=${file:22}  # strip off "setup/transformations/"
+  relpath=${file:30}  # strip off "network_setup/transformations/"
   dirpath=${relpath%.*}  # strip off final ".json"
-  jobpath="setup/transformations/${dirpath}.job"
+  jobpath="network_setup/transformations/${dirpath}.job"
   cmd="openfe quickrun $file -o results/$relpath -d results/$dirpath"
   echo -e "#!/usr/bin/env bash\n${cmd}" > $jobpath
   sbatch $jobpath

rbfe_tutorial/python_tutorial.ipynb

@@ -191,9 +191,7 @@
     "\n",
     "That information in included in a `Transformation`. Each of these transformations corresponds to a single leg of the simulation campaign, so for each edge in the `LigandNetwork`, we will create two `Transformation`s: one for vacuum and one for solvent.\n",
     "\n",
-    "In practice, this will be done for each edge of the `LigandNetwork` in a loop, but for illustrative purposes we'll dive into the details of creating a single transformation. In particular, we'll create the solvent leg for the pair of molecules we selecting for the mapping above.\n",
-    "\n",
-    "TODO: SWITCH TO PROTEIN COMPLEX LEG"
+    "In practice, this will be done for each edge of the `LigandNetwork` in a loop, but for illustrative purposes we'll dive into the details of creating a single transformation. In particular, we'll create the solvent leg for the pair of molecules we selecting for the mapping above."
    ]
   },
   {