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Merged
atravitz merged 10 commits into from
Jan 26, 2026
Merged

make CLI starting guide easier to find from the landing page #1787

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988189c
make CLI starting guide easier to find from the landing page
atravitz Jan 10, 2026
fd7d6c4
Merge branch 'main' into docs/make_quickstart_easier_to_find
atravitz Jan 10, 2026
1fd788f
Python API -> API Docs
atravitz Jan 13, 2026
4527606
bump ci
atravitz Jan 15, 2026
836fc54
Merge branch 'main' into docs/make_quickstart_easier_to_find
atravitz Jan 16, 2026
ed8dc24
Merge branch 'main' into docs/make_quickstart_easier_to_find
atravitz Jan 20, 2026
e057a49
Merge branch 'main' of github.com:OpenFreeEnergy/openfe into docs/mak…
atravitz Jan 26, 2026
c0c8ab9
bump example notebooks pin to 2026.01.26
atravitz Jan 26, 2026
a5e4ced
change a word
atravitz Jan 26, 2026
8821175
clarifying language
atravitz Jan 26, 2026
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2 changes: 1 addition & 1 deletion docs/conf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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:
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12 changes: 6 additions & 6 deletions docs/index.rst
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Expand Up @@ -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
Expand All @@ -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
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2 changes: 1 addition & 1 deletion docs/reference/api/index.rst
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Expand Up @@ -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::
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2 changes: 1 addition & 1 deletion src/openfecli/parameters/plan_network_options.py
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Expand Up @@ -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
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