From fd7231d1fa112939396d0951900cace31adfb907 Mon Sep 17 00:00:00 2001 From: richard gowers Date: Mon, 8 May 2023 11:02:16 +0100 Subject: [PATCH] fixup execute_DAG docs to not raise warnings --- gufe/protocols/protocol.py | 2 +- gufe/protocols/protocoldag.py | 11 ++++------- 2 files changed, 5 insertions(+), 8 deletions(-) diff --git a/gufe/protocols/protocol.py b/gufe/protocols/protocol.py index d6e16deb..68bf15cc 100644 --- a/gufe/protocols/protocol.py +++ b/gufe/protocols/protocol.py @@ -75,7 +75,7 @@ class Protocol(GufeTokenizable): Takes a ``Settings`` object customised for this protocol on init. This configures the protocol for repeated execution on (pairs of) - ``ChemicalSystem`` objects. + :class:`ChemicalSystem` objects. This is an abstract base class; individual Protocol implementations should be subclasses of this class. The following methods should be diff --git a/gufe/protocols/protocoldag.py b/gufe/protocols/protocoldag.py index a878bf0f..ab930440 100644 --- a/gufe/protocols/protocoldag.py +++ b/gufe/protocols/protocoldag.py @@ -360,19 +360,16 @@ def execute_DAG(protocoldag: ProtocolDAG, *, keep_scratch: bool = False, raise_error: bool = True, ) -> ProtocolDAGResult: - """Execute the full DAG in-serial, in process. - - This is intended for debug use for Protocol developers. - Running locally is generally not useful for production purposes. + """Locally execute a full ProtocolDAG in-serial, in process. Parameters ---------- protocoldag : ProtocolDAG - The `ProtocolDAG` to execute. + The :class:``ProtocolDAG`` to execute. shared_basedir : Path Filesystem path to use for shared space that persists across whole DAG - execution. Used by `ProtocolUnit`s to pass file contents to dependent - `ProtocolUnit`s. + execution. Used by a `ProtocolUnit` to pass file contents to dependent + class:``ProtocolUnit`` instances. scratch_basedir : Path Filesystem path to use for `ProtocolUnit` `scratch` space. keep_shared : bool