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Cellfinder workflow#15

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sfmig wants to merge 20 commits intomainbrainglobe/brainglobe-workflows:mainfrom smg/cellfinder-workflowbrainglobe/brainglobe-workflows:smg/cellfinder-workflowCopy head branch name to clipboard

+312-5

Commits

Commits on Oct 2, 2023

• cellfinder workflow first draft

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  committed
  08c0e1b

• test data

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  852ee04

• rename

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  25883ef

• delete test data from repo

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  7b97560

• rename init

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  c87f9f2

• rename and reduce workflow to main version

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  61bbbeb

• exclude notebooks from sdist

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  aedb87d

• precommit fixes

  sfmig

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  7b6e882

• change brainglobe_scripts references in pyproject.toml

  sfmig

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  f1836ff

• add config class and default config. Combine setup steps into one setup workflow.

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  16e6312

• set signal and parent dirs as strings (for read with dask). set list signal and background files to None by default in dataclass (they need to be predefined).

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  4de8497

• add logging info

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  5844ebf

• add logging message for fetching from GIN

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  9192df3

• refactor the input data retrieval

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  59d9ca0

• add pooch as dependency

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  06ec524

• add cellfinder-core dependency

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  c85c2d5

• fix typo in Pathlike

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  8e13570

Commits on Oct 4, 2023

• timestamp output directory

  sfmig

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  446d959

• make default config explicitly a module-level constant. separate default config from input config in workflow setup.

  sfmig

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  a4bcd51

• remove option to pass a config dict to setup_workflow

  sfmig

  committed
  ac14d84