From 45b51278fbe510a7c184ed0a214b7e9556acf215 Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Fri, 21 Aug 2026 12:54:33 -0700 Subject: [PATCH 1/4] update CLI header sections --- src/openfecli/cli.py | 2 +- src/openfecli/commands/gather.py | 6 +----- src/openfecli/commands/gather_abfe.py | 6 +----- src/openfecli/commands/gather_septop.py | 6 +----- src/openfecli/commands/generate_partial_charges.py | 2 +- src/openfecli/commands/plan_rbfe_network.py | 2 +- src/openfecli/commands/plan_rhfe_network.py | 2 +- src/openfecli/commands/quickrun.py | 2 +- src/openfecli/commands/status.py | 2 +- src/openfecli/commands/view_ligand_network.py | 2 +- src/openfecli/commands/worker.py | 2 +- 11 files changed, 11 insertions(+), 23 deletions(-) diff --git a/src/openfecli/cli.py b/src/openfecli/cli.py index d9bb11848..adc69ee63 100644 --- a/src/openfecli/cli.py +++ b/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") diff --git a/src/openfecli/commands/gather.py b/src/openfecli/commands/gather.py index 8112d7282..9f20997ef 100644 --- a/src/openfecli/commands/gather.py +++ b/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() diff --git a/src/openfecli/commands/gather_abfe.py b/src/openfecli/commands/gather_abfe.py index a08ac6018..a903f9ac9 100644 --- a/src/openfecli/commands/gather_abfe.py +++ b/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)) diff --git a/src/openfecli/commands/gather_septop.py b/src/openfecli/commands/gather_septop.py index 2b69e718f..97056b6ce 100644 --- a/src/openfecli/commands/gather_septop.py +++ b/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)) diff --git a/src/openfecli/commands/generate_partial_charges.py b/src/openfecli/commands/generate_partial_charges.py index d1a83580f..1f307e044 100644 --- a/src/openfecli/commands/generate_partial_charges.py +++ b/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)) diff --git a/src/openfecli/commands/plan_rbfe_network.py b/src/openfecli/commands/plan_rbfe_network.py index c13b93cb5..18fa554bd 100644 --- a/src/openfecli/commands/plan_rbfe_network.py +++ b/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) ) diff --git a/src/openfecli/commands/plan_rhfe_network.py b/src/openfecli/commands/plan_rhfe_network.py index 5b4ebf1ac..b1e0a99c7 100644 --- a/src/openfecli/commands/plan_rhfe_network.py +++ b/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) ) diff --git a/src/openfecli/commands/quickrun.py b/src/openfecli/commands/quickrun.py index 677552435..f8aa68277 100644 --- a/src/openfecli/commands/quickrun.py +++ b/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() diff --git a/src/openfecli/commands/status.py b/src/openfecli/commands/status.py index 31481f6ae..86335b555 100644 --- a/src/openfecli/commands/status.py +++ b/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, 12)) diff --git a/src/openfecli/commands/view_ligand_network.py b/src/openfecli/commands/view_ligand_network.py index 24125907a..0024cb8e1 100644 --- a/src/openfecli/commands/view_ligand_network.py +++ b/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), ) diff --git a/src/openfecli/commands/worker.py b/src/openfecli/commands/worker.py index c312e3ff0..4fc112454 100644 --- a/src/openfecli/commands/worker.py +++ b/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, 12)) From 1dec56ab3bbe418b385c94635b9f7e9b7c243029 Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Fri, 21 Aug 2026 12:59:46 -0700 Subject: [PATCH 2/4] add news item --- news/cli_headers.rst | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 news/cli_headers.rst diff --git a/news/cli_headers.rst b/news/cli_headers.rst new file mode 100644 index 000000000..661046bf8 --- /dev/null +++ b/news/cli_headers.rst @@ -0,0 +1,23 @@ +**Added:** + +* + +**Changed:** + +* Changed CLI sections from "Network Planning", "Quickrun Exectutor" and "Miscellaneous" to "Planning & Setup", "Execution", "Results Gathering", and "Miscellaneous". + +**Deprecated:** + +* + +**Removed:** + +* + +**Fixed:** + +* + +**Security:** + +* From f7ebf4a661dace3613a2fe08f6edd6f8bc8d2fbb Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Fri, 21 Aug 2026 13:07:36 -0700 Subject: [PATCH 3/4] bump recent additions to min openfe v1.13 --- src/openfecli/commands/status.py | 2 +- src/openfecli/commands/worker.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/openfecli/commands/status.py b/src/openfecli/commands/status.py index 86335b555..931cb74d2 100644 --- a/src/openfecli/commands/status.py +++ b/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="Execution", requires_ofe=(1, 12)) +PLUGIN = OFECommandPlugin(command=status, section="Execution", requires_ofe=(1, 13)) diff --git a/src/openfecli/commands/worker.py b/src/openfecli/commands/worker.py index 4fc112454..791b6d2c1 100644 --- a/src/openfecli/commands/worker.py +++ b/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="Execution", requires_ofe=(1, 12)) +PLUGIN = OFECommandPlugin(command=worker, section="Execution", requires_ofe=(1, 13)) From a91b8198dba42c2ad08975b5070108ebe21f3d5a Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Mon, 24 Aug 2026 07:52:25 -0700 Subject: [PATCH 4/4] update test --- src/openfecli/tests/test_cli.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/openfecli/tests/test_cli.py b/src/openfecli/tests/test_cli.py index 8c13ac8e7..421a2aed9 100644 --- a/src/openfecli/tests/test_cli.py +++ b/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