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debug rtd build memory error (#1510)

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* try mambaforge build

* Revert "try mambaforge build"

This reverts commit 683e07f1ea.

* try explicit build

* try removing ambertools

* use the right env

* just add gufe pip install back

* add back openfe eco packages

* mock py3dmol

* add note for pip installs

* fix quote

* temporarily resort to SettingsBaseModel to get build

* specific imports

* dont use base settings placeholder
This commit is contained in:
Alyssa Travitz
2025-09-15 13:32:22 -07:00
committed by GitHub
parent 18314126a1
commit 1cb3ac79f1
4 changed files with 16 additions and 18 deletions
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12
docs/reference/api/openmm_rfe.rst
View File

@@ -9,7 +9,7 @@ implemented in OpenFE.
Protocol API specification
--------------------------
.. module:: openfe.protocols.openmm_rfe
.. module:: openfe.protocols.openmm_rfe.equil_rfe_methods
.. autosummary::
:nosignatures:
@@ -25,7 +25,7 @@ Protocol Settings
Below are the settings which can be tweaked in the protocol. The default settings (accessed using :meth:`RelativeHybridTopologyProtocol.default_settings`) will automatically populate a settings which we have found to be useful for running relative binding free energies using explicit solvent. There will however be some cases (such as when doing gas phase calculations) where you will need to tweak some of the following settings.
.. autopydantic_model:: RelativeHybridTopologyProtocolSettings
.. autopydantic_model:: openfe.protocols.openmm_rfe.equil_rfe_settings.RelativeHybridTopologyProtocolSettings
:model-show-json: False
:model-show-field-summary: False
:model-show-config-member: False
@@ -41,11 +41,9 @@ Below are the settings which can be tweaked in the protocol. The default setting
Protocol Specific Settings Classes
----------------------------------
Below are Settings classes which are unique to the `RelativeHybridTopologyProtocol`.
Below are Settings classes which are unique to the ``RelativeHybridTopologyProtocol``.
.. module:: openfe.protocols.openmm_rfe.equil_rfe_settings
.. autopydantic_model:: AlchemicalSettings
.. autopydantic_model:: openfe.protocols.openmm_rfe.equil_rfe_settings.AlchemicalSettings
:model-show-json: False
:model-show-field-summary: False
:model-show-config-member: False
@@ -56,7 +54,7 @@ Below are Settings classes which are unique to the `RelativeHybridTopologyProtoc
:inherited-members: SettingsBaseModel
:member-order: bysource
.. autopydantic_model:: LambdaSettings
.. autopydantic_model:: openfe.protocols.openmm_rfe.equil_rfe_settings.LambdaSettings
:model-show-json: False
:model-show-field-summary: False
:model-show-config-member: False

11
docs/reference/api/openmm_solvation_afe.rst
View File

@@ -27,9 +27,7 @@ Protocol Settings
Below are the settings which can be tweaked in the protocol. The default settings (accessed using :meth:`AbsoluteSolvationProtocol.default_settings`) will automatically populate settings which we have found to be useful for running solvation free energy calculations. There will however be some cases (such as when calculating difficult to converge systems) where you will need to tweak some of the following settings.
.. module:: openfe.protocols.openmm_afe.equil_afe_settings
.. autopydantic_model:: AbsoluteSolvationSettings
.. autopydantic_model:: openfe.protocols.openmm_afe.equil_afe_settings.AbsoluteSolvationSettings
:model-show-json: False
:model-show-field-summary: False
:model-show-config-member: False
@@ -45,10 +43,9 @@ Below are the settings which can be tweaked in the protocol. The default setting
Protocol Specific Settings Classes
----------------------------------
Below are Settings classes which are unique to the `AbsoluteSolvationProtocol`.
Below are Settings classes which are unique to the ``AbsoluteSolvationProtocol``.
.. autopydantic_model:: AlchemicalSettings
.. autopydantic_model:: openfe.protocols.openmm_afe.equil_afe_settings.AlchemicalSettings
:model-show-json: False
:model-show-field-summary: False
:model-show-config-member: False
@@ -59,7 +56,7 @@ Below are Settings classes which are unique to the `AbsoluteSolvationProtocol`.
:inherited-members: SettingsBaseModel
:member-order: bysource
.. autopydantic_model:: LambdaSettings
.. autopydantic_model:: openfe.protocols.openmm_afe.equil_afe_settings.LambdaSettings
:model-show-json: False
:model-show-field-summary: False
:model-show-config-member: False