cellmap_flow.cli.main
=====================

.. py:module:: cellmap_flow.cli.main

.. autoapi-nested-parse::

   ``cellmap_flow``: the one command, with a subcommand for each job.

   
     infer <type>   start a model's inference server and open the viewer on it
     yaml           the same for the models a YAML file lists
     add REF        the model entry for a path, URL, repo or model name
     view           open a dataset in the viewer; pick models in the dashboard
     dashboard      serve the dashboard alone, for a viewer already running
     serve          serve one model's predictions (the launchers run this)
     blockwise      run models over a whole volume, writing predictions to disk
     finetune       the finetune tools: train, export-merged, build-corrections
     models         list the model types and their arguments
     plugins        register, unregister and list plugins
     envs           the environments models run in: list, install, check
     doctor         check the environment

   Before 0.3.0 these were separate console scripts (``cellmap_flow_yaml`` and
   the rest). Those names still work for one release: ``cli/aliases.py`` says
   where each went and runs it. So do this command's own earlier subcommands,
   hidden from ``--help``: ``cellmap_flow <type>``, ``run`` (cli/infer.py),
   ``list-models``, ``register``, ``unregister`` and ``list-plugins``.



Classes
-------

.. autoapisummary::

   cellmap_flow.cli.main.CellMapFlowGroup


Functions
---------

.. autoapisummary::

   cellmap_flow.cli.main.cli
   cellmap_flow.cli.main.dashboard
   cellmap_flow.cli.main.models
   cellmap_flow.cli.main.plugins_group
   cellmap_flow.cli.main.register_cmd
   cellmap_flow.cli.main.unregister_cmd
   cellmap_flow.cli.main.list_plugins_cmd
   cellmap_flow.cli.main.finetune
   cellmap_flow.cli.main.main


Module Contents
---------------

.. py:class:: CellMapFlowGroup(name: str | None = None, commands: collections.abc.MutableMapping[str, Command] | collections.abc.Sequence[Command] | None = None, invoke_without_command: bool = False, no_args_is_help: bool | None = None, subcommand_metavar: str | None = None, chain: bool = False, result_callback: Callable[..., Any] | None = None, **kwargs: Any)



   The cellmap_flow group. ``cellmap_flow <type>``, its per-type commands
   before 0.3.0, are built on request as deprecated aliases of ``infer``.


   .. py:method:: get_command(ctx, name)

      Given a context and a command name, this returns a :class:`Command`
      object if it exists or returns ``None``.



.. py:function:: cli()

   CellMap Flow: real-time model inference on EM data, in Neuroglancer.

   Each job is a subcommand; `cellmap_flow <command> --help` shows its
   options.

   
     cellmap_flow view -d /path/to/data.zarr
     cellmap_flow yaml config.yaml
     cellmap_flow infer dacapo -r my_run -i 100 -d /path/to/data
     cellmap_flow blockwise config.yaml


.. py:function:: dashboard(neuroglancer_url)

   Serve the dashboard alone, for a viewer already running.

   `view`, `yaml` and `infer` start the dashboard with the viewer they
   open; this is the dashboard on its own, as `cellmap_flow_app` served it
   before 0.3.0. It prints its URL, and writes it to the file named by
   SERVICE_URL_PATH when that is set. Ctrl+C stops it and kills the models
   it launched.


.. py:function:: models()

   List the model types and the arguments each takes.


.. py:function:: plugins_group()

   Register, unregister and list plugins.

   A plugin is a .py file defining subclasses of InputNormalizer,
   PostProcessor or ModelConfig; registering copies it to
   ~/.cellmap_flow/plugins/.


.. py:function:: register_cmd(filepath, force)

   Register a custom plugin (normalizer, postprocessor, or model config).

   FILEPATH is the path to a .py file defining subclasses of
   InputNormalizer, PostProcessor, or ModelConfig.

   .. rubric:: Example

   cellmap_flow plugins register my_normalizer.py


.. py:function:: unregister_cmd(name)

   Unregister a previously registered plugin by name.

   NAME is the plugin filename (with or without .py extension).

   .. rubric:: Example

   cellmap_flow plugins unregister my_normalizer


.. py:function:: list_plugins_cmd()

   List all registered plugins.


.. py:function:: finetune()

   The finetune tools. The dashboard's finetune tab runs `train` for you.


.. py:function:: main(args=None)

   The ``cellmap_flow`` console script: load the plugins, then run the
   command ``args`` (by default, the process's arguments) names.