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* Modify quickrun to allow resuming * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * store protocol dag using transformation key * use assert_click_success * Update the CLI quickrun help info * Add userguide documentation on how to use quickrun * this reference instead? * fix things a little bit * update the title * Update environment.yml * Update docs/guide/cli/quickrun.rst Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com> * update for new name for now * Update docs/guide/cli/quickrun.rst Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com> * update for new changes * Add to the execution guide instead * some fixes * Add `>` where it's a CLI command * formatting fixes --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Alyssa Travitz <alyssa.travitz@omsf.io> Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>
77 lines
3.1 KiB
ReStructuredText
77 lines
3.1 KiB
ReStructuredText
CLI basics
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==========
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The ``openfe`` command consists of several subcommands. This is similar to
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tools like ``gmx``, which has subcommands like ``gmx mdrun``, or ``conda``,
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which has subcommands like ``conda install``.
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To get a list of the subcommands and their descriptions, call ``openfe`` (or
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``openfe -h``):
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.. TODO autogenerate using sphinxcontrib-programoutput
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.. code:: none
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Usage: openfe [OPTIONS] COMMAND [ARGS]...
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This is the command line tool to provide easy access to functionality from
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the OpenFE Python library.
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Options:
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--version Show the version and exit.
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--log PATH logging configuration file
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-h, --help Show this message and exit.
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Network Planning Commands:
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plan-rhfe-network Plan a relative hydration free energy network, saved as
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JSON files for the quickrun command.
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plan-rbfe-network Plan a relative binding free energy network, saved as
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JSON files for the quickrun command.
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view-ligand-network Visualize a ligand network
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Quickrun Executor Commands:
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gather Gather result jsons for network of RFE results into a TSV file
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quickrun Run a given transformation, saved as a JSON file
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Miscellaneous Commands:
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fetch Fetch tutorial or other resource.
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charge-molecules Generate partial charges for a set of molecules.
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test Run the OpenFE test suite
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The ``--log`` option takes a logging configuration file and sets that
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logging behavior. If you use it, it must come before the subcommand name.
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You can find out more about each subcommand by putting ``--help`` *after*
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the subcommand name, e.g., ``openfe quickrun --help``, which returns
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.. code:: none
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Usage: openfe quickrun [OPTIONS] TRANSFORMATION
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Run the transformation (edge) in the given JSON file.
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Simulation JSON files can be created with the :ref:`cli_plan-rbfe-network`
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or from Python a :class:`.Transformation` can be saved using its to_json
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method::
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transformation.to_json("filename.json")
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That will save a JSON file suitable to be input for this command.
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Running this command will execute the simulation defined in the JSON file,
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creating a directory for each individual task (``Unit``) in the workflow.
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For example, when running the OpenMM HREX Protocol a directory will be
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created for each repeat of the sampling process (by default 3).
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Options:
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-d, --work-dir DIRECTORY Directory in which to store files in (defaults to
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current directory). If the directory does not
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exist, it will be created at runtime.
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-o PATH Filepath at which to create and write the JSON-
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formatted results.
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--resume Attempt to resume this transformation's execution
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using the cache.
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-h, --help Show this message and exit.
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For more details on various commands, see the :ref:`cli-reference`.
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