update cli sections

news/cli_headers.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* <news item>
+
+**Changed:**
+
+* Changed CLI sections from "Network Planning", "Quickrun Exectutor" and "Miscellaneous" to "Planning & Setup", "Execution", "Results Gathering", and "Miscellaneous".
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

src/openfecli/cli.py

@@ -14,7 +14,7 @@
 
 class OpenFECLI(CLI):
     # COMMAND_SECTIONS = ["Setup", "Simulation", "Orchestration", "Analysis"]
-    COMMAND_SECTIONS = ["Network Planning", "Quickrun Executor", "Miscellaneous"]
+    COMMAND_SECTIONS = ["Planning & Setup", "Execution", "Results Gathering", "Miscellaneous"]
 
     def get_loaders(self):
         commands = str(pathlib.Path(__file__).parent.resolve() / "commands")

src/openfecli/commands/gather.py

@@ -803,11 +803,7 @@ def gather(
         rich_print_to_stdout(df)
 
 
-PLUGIN = OFECommandPlugin(
-    command=gather,
-    section="Quickrun Executor",
-    requires_ofe=(0, 6),
-)
+PLUGIN = OFECommandPlugin(command=gather, section="Results Gathering", requires_ofe=(0, 6))
 
 if __name__ == "__main__":
     gather()

src/openfecli/commands/gather_abfe.py

@@ -360,8 +360,4 @@ def gather_abfe(
         rich_print_to_stdout(df)
 
 
-PLUGIN = OFECommandPlugin(
-    command=gather_abfe,
-    section="Quickrun Executor",
-    requires_ofe=(0, 6),
-)
+PLUGIN = OFECommandPlugin(command=gather_abfe, section="Results Gathering", requires_ofe=(0, 6))

src/openfecli/commands/gather_septop.py

@@ -451,8 +451,4 @@ def gather_septop(
         rich_print_to_stdout(df)
 
 
-PLUGIN = OFECommandPlugin(
-    command=gather_septop,
-    section="Quickrun Executor",
-    requires_ofe=(0, 6),
-)
+PLUGIN = OFECommandPlugin(command=gather_septop, section="Results Gathering", requires_ofe=(0, 6))

src/openfecli/commands/generate_partial_charges.py

@@ -94,4 +94,4 @@ def charge_molecules(molecules, yaml_settings, output, n_cores, overwrite_charge
             output.write(mol.to_sdf())
 
 
-PLUGIN = OFECommandPlugin(command=charge_molecules, section="Miscellaneous", requires_ofe=(0, 3))
+PLUGIN = OFECommandPlugin(command=charge_molecules, section="Planning & Setup", requires_ofe=(1, 3))

src/openfecli/commands/plan_rbfe_network.py

@@ -263,5 +263,5 @@ def plan_rbfe_network(
 
 
 PLUGIN = OFECommandPlugin(
-    command=plan_rbfe_network, section="Network Planning", requires_ofe=(0, 3)
+    command=plan_rbfe_network, section="Planning & Setup", requires_ofe=(0, 3)
 )

src/openfecli/commands/plan_rhfe_network.py

@@ -216,5 +216,5 @@ def plan_rhfe_network(
 
 
 PLUGIN = OFECommandPlugin(
-    command=plan_rhfe_network, section="Network Planning", requires_ofe=(0, 3)
+    command=plan_rhfe_network, section="Planning & Setup", requires_ofe=(0, 3)
 )

src/openfecli/commands/quickrun.py

@@ -203,7 +203,7 @@ def quickrun(transformation, work_dir, output, resume):
         )
 
 
-PLUGIN = OFECommandPlugin(command=quickrun, section="Quickrun Executor", requires_ofe=(0, 3))
+PLUGIN = OFECommandPlugin(command=quickrun, section="Execution", requires_ofe=(0, 3))
 
 if __name__ == "__main__":
     quickrun()

src/openfecli/commands/status.py

@@ -73,4 +73,4 @@ def status(task_db_path: pathlib.Path):
     status_main(task_db_path=task_db_path)
 
 
-PLUGIN = OFECommandPlugin(command=status, section="Quickrun Executor", requires_ofe=(0, 3))
+PLUGIN = OFECommandPlugin(command=status, section="Execution", requires_ofe=(1, 13))

src/openfecli/commands/view_ligand_network.py

@@ -33,6 +33,6 @@ def view_ligand_network(ligand_network: os.PathLike):
 
 PLUGIN = OFECommandPlugin(
     command=view_ligand_network,
-    section="Network Planning",
+    section="Planning & Setup",
     requires_ofe=(0, 7, 0),
 )

src/openfecli/commands/worker.py

@@ -130,4 +130,4 @@ def worker(warehouse_path: pathlib.Path, scratch: pathlib.Path | None):
     worker_main(warehouse_path=warehouse_path, scratch=scratch)
 
 
-PLUGIN = OFECommandPlugin(command=worker, section="Quickrun Executor", requires_ofe=(0, 3))
+PLUGIN = OFECommandPlugin(command=worker, section="Execution", requires_ofe=(1, 13))

src/openfecli/tests/test_cli.py

@@ -50,7 +50,7 @@ def test_command_sections(self, cli):
         # This test does not ensure the order of the sections, and does not
         # prevent other sections from being added later. It only ensures
         # that the main 4 sections continue to exist.
-        included = ["Network Planning", "Quickrun Executor", "Miscellaneous"]
+        included = ["Planning & Setup", "Execution", "Results Gathering", "Miscellaneous"]
         for sec in included:
             assert sec in cli.COMMAND_SECTIONS