Revert "rename easy_r*fe to r*fe"

This reverts commit 921ea66.

Author: atravitz

cookbook/bespoke_parameters_showcase.ipynb

@@ -89,7 +89,7 @@
     "        sysA = openfe.ChemicalSystem(sysA_dict, name=f\"{mapping.componentA.name}_{leg}\")\n",
     "        sysB = openfe.ChemicalSystem(sysB_dict, name=f\"{mapping.componentB.name}_{leg}\")\n",
     "\n",
-    "        prefix = \"rbfe_\"  # prefix is only to exactly reproduce CLI\n",
+    "        prefix = \"easy_rbfe_\"  # prefix is only to exactly reproduce CLI\n",
     "\n",
     "        transformation = openfe.Transformation(\n",
     "            stateA=sysA,\n",

cookbook/create_alchemical_network.ipynb

@@ -226,7 +226,7 @@
     "            mapping=mapping,\n",
     "            protocol=protocol,\n",
     "            # Using the same name as to_rbfe_alchemical_network()\n",
-    "            name=f\"rbfe_{system_a.name}_{system_b.name}\"\n",
+    "            name=f\"easy_rbfe_{system_a.name}_{system_b.name}\"\n",
     "        )\n",
     "    \n",
     "        transformations.append(transformation)"

rbfe_tutorial/cli_tutorial.md

@@ -73,13 +73,13 @@ network_setup
 ├── ligand_network.graphml
 ├── network_setup.json
 └── transformations/
-    ├── rbfe_lig_ejm_31_complex_lig_ejm_42_complex.json
-    ├── rbfe_lig_ejm_31_complex_lig_ejm_46_complex.json
-    ├── rbfe_lig_ejm_31_complex_lig_ejm_47_complex.json
-    ├── rbfe_lig_ejm_31_complex_lig_ejm_48_complex.json
-    ├── rbfe_lig_ejm_31_complex_lig_ejm_50_complex.json
-    ├── rbfe_lig_ejm_31_solvent_lig_ejm_42_solvent.json
-    ├── rbfe_lig_ejm_31_solvent_lig_ejm_46_solvent.json
+    ├── easy_rbfe_lig_ejm_31_complex_lig_ejm_42_complex.json
+    ├── easy_rbfe_lig_ejm_31_complex_lig_ejm_46_complex.json
+    ├── easy_rbfe_lig_ejm_31_complex_lig_ejm_47_complex.json
+    ├── easy_rbfe_lig_ejm_31_complex_lig_ejm_48_complex.json
+    ├── easy_rbfe_lig_ejm_31_complex_lig_ejm_50_complex.json
+    ├── easy_rbfe_lig_ejm_31_solvent_lig_ejm_42_solvent.json
+    ├── easy_rbfe_lig_ejm_31_solvent_lig_ejm_46_solvent.json
 [continues]
 ```
 
@@ -98,7 +98,7 @@ The files that describe each individual simulation we will run are located withi
 `network_setup/transformations/`. Each JSON file represents a single alchemical
 leg to run and contains all the necessary information to run that leg.
 Filenames indicate ligand names as taken from the SDF; for example, the file
-`rbfe_lig_ejm_31_complex_lig_ejm_42_complex.json` is the leg
+`easy_rbfe_lig_ejm_31_complex_lig_ejm_42_complex.json` is the leg
 associated with the transformation of the ligand `lig_ejm_31` into `lig_ejm_42`
 while in complex with the protein.
 
@@ -273,7 +273,7 @@ openfe
 
 ```text
 results
-├── rbfe_lig_ejm_31_complex_lig_ejm_42_complex
+├── easy_rbfe_lig_ejm_31_complex_lig_ejm_42_complex
 │   ├── shared_RelativeHybridTopologyProtocolUnit-3ea82011-75f0-4bb6-b415-e7d05bd012f6
 │   │   ├── checkpoint.nc
 │   │   └── simulation.nc
@@ -283,8 +283,8 @@ results
 │   └── shared_RelativeHybridTopologyProtocolUnit-7a6def34-2967-4452-8d47-483bc7219c06
 │       ├── checkpoint.nc
 │       └── simulation.nc
-├── rbfe_lig_ejm_31_complex_lig_ejm_42_complex.json
-├── rbfe_lig_ejm_31_complex_lig_ejm_46_complex
+├── easy_rbfe_lig_ejm_31_complex_lig_ejm_42_complex.json
+├── easy_rbfe_lig_ejm_31_complex_lig_ejm_46_complex
 │   ├── shared_RelativeHybridTopologyProtocolUnit-ad113e55-5636-474e-9be3-ee77fe887e77
 │   │   ├── checkpoint.nc
 │   │   └── simulation.nc
@@ -294,7 +294,7 @@ results
 │   └── shared_RelativeHybridTopologyProtocolUnit-f848e671-fdd3-4b8d-8bd2-6eb5140e3ed3
 │       ├── checkpoint.nc
 │       └── simulation.nc
-├── rbfe_lig_ejm_31_complex_lig_ejm_46_complex.json
+├── easy_rbfe_lig_ejm_31_complex_lig_ejm_46_complex.json
 [continues]
 ```
 

rbfe_tutorial/python_tutorial.ipynb

@@ -472,7 +472,7 @@
     "        sysA = openfe.ChemicalSystem(sysA_dict, name=f\"{mapping.componentA.name}_{leg}\")\n",
     "        sysB = openfe.ChemicalSystem(sysB_dict, name=f\"{mapping.componentB.name}_{leg}\")\n",
     "        \n",
-    "        prefix = \"rbfe_\"  # prefix is only to exactly reproduce CLI\n",
+    "        prefix = \"easy_rbfe_\"  # prefix is only to exactly reproduce CLI\n",
     "        \n",
     "        transformation = openfe.Transformation(\n",
     "            stateA=sysA,\n",
@@ -523,24 +523,24 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "rbfe_lig_ejm_31_complex_lig_ejm_42_complex.json\n",
-      "rbfe_lig_ejm_31_complex_lig_ejm_46_complex.json\n",
-      "rbfe_lig_ejm_31_complex_lig_ejm_47_complex.json\n",
-      "rbfe_lig_ejm_31_complex_lig_ejm_48_complex.json\n",
-      "rbfe_lig_ejm_31_complex_lig_ejm_50_complex.json\n",
-      "rbfe_lig_ejm_31_solvent_lig_ejm_42_solvent.json\n",
-      "rbfe_lig_ejm_31_solvent_lig_ejm_46_solvent.json\n",
-      "rbfe_lig_ejm_31_solvent_lig_ejm_47_solvent.json\n",
-      "rbfe_lig_ejm_31_solvent_lig_ejm_48_solvent.json\n",
-      "rbfe_lig_ejm_31_solvent_lig_ejm_50_solvent.json\n",
-      "rbfe_lig_ejm_42_complex_lig_ejm_43_complex.json\n",
-      "rbfe_lig_ejm_42_solvent_lig_ejm_43_solvent.json\n",
-      "rbfe_lig_ejm_46_complex_lig_jmc_23_complex.json\n",
-      "rbfe_lig_ejm_46_complex_lig_jmc_27_complex.json\n",
-      "rbfe_lig_ejm_46_complex_lig_jmc_28_complex.json\n",
-      "rbfe_lig_ejm_46_solvent_lig_jmc_23_solvent.json\n",
-      "rbfe_lig_ejm_46_solvent_lig_jmc_27_solvent.json\n",
-      "rbfe_lig_ejm_46_solvent_lig_jmc_28_solvent.json\n"
+      "easy_rbfe_lig_ejm_31_complex_lig_ejm_42_complex.json\n",
+      "easy_rbfe_lig_ejm_31_complex_lig_ejm_46_complex.json\n",
+      "easy_rbfe_lig_ejm_31_complex_lig_ejm_47_complex.json\n",
+      "easy_rbfe_lig_ejm_31_complex_lig_ejm_48_complex.json\n",
+      "easy_rbfe_lig_ejm_31_complex_lig_ejm_50_complex.json\n",
+      "easy_rbfe_lig_ejm_31_solvent_lig_ejm_42_solvent.json\n",
+      "easy_rbfe_lig_ejm_31_solvent_lig_ejm_46_solvent.json\n",
+      "easy_rbfe_lig_ejm_31_solvent_lig_ejm_47_solvent.json\n",
+      "easy_rbfe_lig_ejm_31_solvent_lig_ejm_48_solvent.json\n",
+      "easy_rbfe_lig_ejm_31_solvent_lig_ejm_50_solvent.json\n",
+      "easy_rbfe_lig_ejm_42_complex_lig_ejm_43_complex.json\n",
+      "easy_rbfe_lig_ejm_42_solvent_lig_ejm_43_solvent.json\n",
+      "easy_rbfe_lig_ejm_46_complex_lig_jmc_23_complex.json\n",
+      "easy_rbfe_lig_ejm_46_complex_lig_jmc_27_complex.json\n",
+      "easy_rbfe_lig_ejm_46_complex_lig_jmc_28_complex.json\n",
+      "easy_rbfe_lig_ejm_46_solvent_lig_jmc_23_solvent.json\n",
+      "easy_rbfe_lig_ejm_46_solvent_lig_jmc_27_solvent.json\n",
+      "easy_rbfe_lig_ejm_46_solvent_lig_jmc_28_solvent.json\n"
      ]
     }
    ],