diff --git a/docs/conf.py b/docs/conf.py index 1e6bd07df..f54790c22 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -193,7 +193,7 @@ else: repo = git.Repo.clone_from( "https://github.com/OpenFreeEnergy/ExampleNotebooks.git", - branch="2025.12.04", + branch="2026.01.26", to_path=example_notebooks_path, ) except Exception as e: diff --git a/docs/index.rst b/docs/index.rst index 600d84310..4a0cb6f69 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -25,12 +25,12 @@ Using this toolkit you can plan, execute, and analyze free energy calculations u Follow our installation guide to get **openfe** running on your machine! - .. grid-item-card:: :fas:`laptop-code` CLI + .. grid-item-card:: :fas:`laptop-code` CLI Quickstart :text-align: center - :link: reference/cli/index + :link: tutorials/rbfe_cli_tutorial :link-type: doc - Documentation for **openfe**\'s simple command line interface. + Get started with **openfe**\'s command line interface. .. grid-item-card:: :fas:`person-chalkboard` Tutorials :text-align: center @@ -53,12 +53,12 @@ Using this toolkit you can plan, execute, and analyze free energy calculations u How-to guides for common tasks. - .. grid-item-card:: :fas:`code` Python API + .. grid-item-card:: :fas:`code` API Reference :text-align: center - :link: reference/api/index + :link: reference/index :link-type: doc - Comprehensive details of the **openfe** Python API. + Comprehensive details of the **openfe** Python and CLI APIs. .. grid-item-card:: :fas:`gears` Protocols :text-align: center diff --git a/docs/reference/api/index.rst b/docs/reference/api/index.rst index 5b93b8739..d74b545dc 100644 --- a/docs/reference/api/index.rst +++ b/docs/reference/api/index.rst @@ -4,7 +4,7 @@ We have reproduced API documentation from the `gufe`_ package here for convenience. `gufe`_ serves as a foundation layer for openfe, providing abstract base classes and object models, and so might be more useful for developers. -OpenFE API Reference +Python API Reference ==================== .. toctree:: diff --git a/src/openfecli/parameters/plan_network_options.py b/src/openfecli/parameters/plan_network_options.py index 5798d69e4..b349d8972 100644 --- a/src/openfecli/parameters/plan_network_options.py +++ b/src/openfecli/parameters/plan_network_options.py @@ -205,7 +205,7 @@ def load_yaml_planner_options(path: Optional[str], context) -> PlanNetworkOption # TODO: do we want this in the docs anywhere? DEFAULT_YAML = """ - mapper: KartografAtomMapper + mapper: kartograf settings: atom_max_distance: 0.95 atom_map_hydrogens: true