cellmap_flow.cli.doctor

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

`OK`
`FAIL`
`WARN`
`NEUROGLANCER_FORK_MARKER`
`NEUROGLANCER_FORK_COMMIT`
`NEUROGLANCER_FORK_INSTALL`
`MINIO_INSTALL`

Classes

Result

Functions

`painting_unavailable`()	One line for the dashboard's start when the installed neuroglancer
`run_checks`([include_finetune])
`main`(core_only)	Check the environment: what is installed, what is missing, and how to fix it.
`report`(results) → int	Print `results` and the fixes they call for; 1 if any is blocking, else 0.

Module Contents

cellmap_flow.cli.doctor.OK = '✓'

cellmap_flow.cli.doctor.FAIL = '✗'

cellmap_flow.cli.doctor.WARN = '!'

cellmap_flow.cli.doctor.NEUROGLANCER_FORK_MARKER = 'Paint Value'

cellmap_flow.cli.doctor.NEUROGLANCER_FORK_COMMIT = 'fae54db8c667176a602a34f0d9d1028956009836'

cellmap_flow.cli.doctor.NEUROGLANCER_FORK_INSTALL = 'pip install git+https://github.com/briossant/neuroglancer@fae54db8c667176a602a34f0d9d1028956009836'

cellmap_flow.cli.doctor.MINIO_INSTALL = 'mamba install minio-server minio-client -c conda-forge'

class cellmap_flow.cli.doctor.Result(name, status, detail='', fix='')

name

status

detail = ''

fix = ''

cellmap_flow.cli.doctor.painting_unavailable(): One line for the dashboard’s start when the installed neuroglancer cannot paint (_check_neuroglancer_fork), with the install line; None when it can. dashboard.app.create_and_run_app logs it, so a pip install, which has upstream neuroglancer, hears at start why the Draw tab has no brush.

cellmap_flow.cli.doctor.run_checks(include_finetune=True)

cellmap_flow.cli.doctor.main(core_only): Check the environment: what is installed, what is missing, and how to fix it.

cellmap_flow.cli.doctor.report(results) → int: Print results and the fixes they call for; 1 if any is blocking, else 0.