cellmap_flow.cli.doctor
=======================

.. py:module:: cellmap_flow.cli.doctor

.. autoapi-nested-parse::

   Preflight check for the cellmap-flow environment.

   Run as ``cellmap_flow doctor`` (``--core-only`` skips the finetune checks),
   or ``python -m cellmap_flow.cli.doctor``. Reports what is installed, what is missing,
   and the exact command to fix each gap -- so a broken finetune environment
   surfaces up front rather than as a FileNotFoundError deep in an annotation
   route after you have already loaded a dataset and started painting.



Attributes
----------

.. autoapisummary::

   cellmap_flow.cli.doctor.OK
   cellmap_flow.cli.doctor.FAIL
   cellmap_flow.cli.doctor.WARN
   cellmap_flow.cli.doctor.NEUROGLANCER_FORK_MARKER
   cellmap_flow.cli.doctor.NEUROGLANCER_FORK_INSTALL
   cellmap_flow.cli.doctor.MINIO_INSTALL


Classes
-------

.. autoapisummary::

   cellmap_flow.cli.doctor.Result


Functions
---------

.. autoapisummary::

   cellmap_flow.cli.doctor.run_checks
   cellmap_flow.cli.doctor.main
   cellmap_flow.cli.doctor.report


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

.. py:data:: OK
   :value: '✓'


.. py:data:: FAIL
   :value: '✗'


.. py:data:: WARN
   :value: '!'


.. py:data:: NEUROGLANCER_FORK_MARKER
   :value: 'Paint Value'


.. py:data:: NEUROGLANCER_FORK_INSTALL
   :value: 'pip install git+https://github.com/briossant/neuroglancer@feature/voxel-annotation'


.. py:data:: MINIO_INSTALL
   :value: 'mamba install minio-server minio-client -c conda-forge'


.. py:class:: Result(name, status, detail='', fix='')

   .. py:attribute:: name


   .. py:attribute:: status


   .. py:attribute:: detail
      :value: ''



   .. py:attribute:: fix
      :value: ''



.. py:function:: run_checks(include_finetune=True)

.. py:function:: main(core_only)

   Check the environment: what is installed, what is missing, and how to fix it.


.. py:function:: report(results) -> int

   Print ``results`` and the fixes they call for; 1 if any is blocking, else 0.