Code

Cellfinder workflow tests#20

Code

Closed

sfmig wants to merge 53 commits intomainbrainglobe/brainglobe-workflows:mainfrom smg/cellfinder-workflow-testsbrainglobe/brainglobe-workflows:smg/cellfinder-workflow-testsCopy head branch name to clipboard

+476-5

Commits

Commits on Sep 18, 2023

• cellfinder workflow first draft

  sfmig

  committed
  8bfa73b

  Copy full SHA for 8bfa73b

• test data

  sfmig

  committed
  c317ec8

  Copy full SHA for c317ec8

• rename

  sfmig

  committed
  b64d518

  Copy full SHA for b64d518

• Merge branch 'main' into smg/cellfinder-workflow

  sfmig

  committed
  3925755

  Copy full SHA for 3925755

Commits on Sep 20, 2023

• delete test data from repo

  sfmig

  committed
  027d675

  Copy full SHA for 027d675

• rename init

  sfmig

  committed
  23f3a12

  Copy full SHA for 23f3a12

• rename and reduce workflow to main version

  sfmig

  committed
  10cac14

  Copy full SHA for 10cac14

• exclude notebooks from sdist

  sfmig

  committed
  0a34c72

  Copy full SHA for 0a34c72

• precommit fixes

  sfmig

  committed
  adfc179

  Copy full SHA for adfc179

Commits on Sep 21, 2023

• change brainglobe_scripts references in pyproject.toml

  sfmig

  committed
  cf1ed9d

  Copy full SHA for cf1ed9d

Commits on Oct 2, 2023

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

  sfmig

  committed
  113c668

  Copy full SHA for 113c668

• 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).

  sfmig

  committed
  fdedb44

  Copy full SHA for fdedb44

• add logging info

  sfmig

  committed
  c9bc5de

  Copy full SHA for c9bc5de

• add smoke tests for running the workflow with different options for the input config

  sfmig

  committed
  cab653b

  Copy full SHA for cab653b

• add smoketests for setup

  sfmig

  committed
  8b9c169

  Copy full SHA for 8b9c169

• add logging message for fetching from GIN

  sfmig

  committed
  9ab1e34

  Copy full SHA for 9ab1e34

• remove class for tests

  sfmig

  committed
  39754ea

  Copy full SHA for 39754ea

• refactor the input data retrieval

  sfmig

  committed
  4959cb6

  Copy full SHA for 4959cb6

• add pooch as dependency

  sfmig

  committed
  e4d7ced

  Copy full SHA for e4d7ced

• add cellfinder-core dependency

  sfmig

  committed
  07f6772

  Copy full SHA for 07f6772

• fix typo in Pathlike

  sfmig

  committed
  0e5054b

  Copy full SHA for 0e5054b

• replace caplog level setting with context manager option

  sfmig

  committed
  bece87e

  Copy full SHA for bece87e

• specify logger to try and fix pytest caplog error

  sfmig

  committed
  b3c5d5e

  Copy full SHA for b3c5d5e

• cellfinder workflow first draft

  sfmig

  committed
  08c0e1b

  Copy full SHA for 08c0e1b

• test data

  sfmig

  committed
  852ee04

  Copy full SHA for 852ee04

• rename

  sfmig

  committed
  25883ef

  Copy full SHA for 25883ef

• delete test data from repo

  sfmig

  committed
  7b97560

  Copy full SHA for 7b97560

• rename init

  sfmig

  committed
  c87f9f2

  Copy full SHA for c87f9f2

• rename and reduce workflow to main version

  sfmig

  committed
  61bbbeb

  Copy full SHA for 61bbbeb

• exclude notebooks from sdist

  sfmig

  committed
  aedb87d

  Copy full SHA for aedb87d

• precommit fixes

  sfmig

  committed
  7b6e882

  Copy full SHA for 7b6e882

• change brainglobe_scripts references in pyproject.toml

  sfmig

  committed
  f1836ff

  Copy full SHA for f1836ff

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

  sfmig

  committed
  16e6312

  Copy full SHA for 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).

  sfmig

  committed
  4de8497

  Copy full SHA for 4de8497

• add logging info

  sfmig

  committed
  5844ebf

  Copy full SHA for 5844ebf

• add logging message for fetching from GIN

  sfmig

  committed
  9192df3

  Copy full SHA for 9192df3

• refactor the input data retrieval

  sfmig

  committed
  59d9ca0

  Copy full SHA for 59d9ca0

• add pooch as dependency

  sfmig

  committed
  06ec524

  Copy full SHA for 06ec524

• add cellfinder-core dependency

  sfmig

  committed
  c85c2d5

  Copy full SHA for c85c2d5

• fix typo in Pathlike

  sfmig

  committed
  8e13570

  Copy full SHA for 8e13570

Commits on Oct 3, 2023

• teardown for env var fixture

  sfmig

  committed
  02b2a84

  Copy full SHA for 02b2a84

Commits on Oct 4, 2023

• add logger_str as fixture. changed prep_json to check if object is Path (to include WindowsPath)

  sfmig

  committed
  9d0c6c2

  Copy full SHA for 9d0c6c2

• remove logger.propagate setting to True (it's the default value)

  sfmig

  committed
  ff3532e

  Copy full SHA for ff3532e

• remove some comments and TODOs

  sfmig

  committed
  c8f22ff

  Copy full SHA for c8f22ff

• timestamp output directory

  sfmig

  committed
  446d959

  Copy full SHA for 446d959

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

  sfmig

  committed
  a4bcd51

  Copy full SHA for a4bcd51

• remove option to pass a config dict to setup_workflow

  sfmig

  committed
  ac14d84

  Copy full SHA for ac14d84

• add description of the script

  sfmig

  committed
  607dc0a

  Copy full SHA for 607dc0a

• remove some stray comments

  sfmig

  committed
  bb66598

  Copy full SHA for bb66598

• Merge branch 'smg/cellfinder-workflow-only' into smg/cellfinder-workflow-tests

  sfmig

  committed
  abd9e4c

  Copy full SHA for abd9e4c

• fix output_path with timestamp error. added function to generate configs on desired cache dirs.

  sfmig

  committed
  5555fba

  Copy full SHA for 5555fba

• add check for output directory to tests

  sfmig

  committed
  654ff31

  Copy full SHA for 654ff31

Commits on Oct 5, 2023

• rename json factory function

  sfmig

  committed
  3af3b8a

  Copy full SHA for 3af3b8a