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Cellfinder workflow CLI input argument with tests #23

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merged 74 commits into from
Oct 13, 2023
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8bfa73b
cellfinder workflow first draft
sfmig Sep 18, 2023
c317ec8
test data
sfmig Sep 18, 2023
b64d518
rename
sfmig Sep 18, 2023
3925755
Merge branch 'main' into smg/cellfinder-workflow
sfmig Sep 18, 2023
027d675
delete test data from repo
sfmig Sep 20, 2023
23f3a12
rename init
sfmig Sep 20, 2023
10cac14
rename and reduce workflow to main version
sfmig Sep 20, 2023
0a34c72
exclude notebooks from sdist
sfmig Sep 20, 2023
adfc179
precommit fixes
sfmig Sep 20, 2023
cf1ed9d
change brainglobe_scripts references in pyproject.toml
sfmig Sep 21, 2023
113c668
add config class and default config. Combine setup steps into one set…
sfmig Oct 2, 2023
fdedb44
set signal and parent dirs as strings (for read with dask). set list …
sfmig Oct 2, 2023
c9bc5de
add logging info
sfmig Oct 2, 2023
cab653b
add smoke tests for running the workflow with different options for t…
sfmig Oct 2, 2023
8b9c169
add smoketests for setup
sfmig Oct 2, 2023
9ab1e34
add logging message for fetching from GIN
sfmig Oct 2, 2023
39754ea
remove class for tests
sfmig Oct 2, 2023
4959cb6
refactor the input data retrieval
sfmig Oct 2, 2023
e4d7ced
add pooch as dependency
sfmig Oct 2, 2023
07f6772
add cellfinder-core dependency
sfmig Oct 2, 2023
0e5054b
fix typo in Pathlike
sfmig Oct 2, 2023
bece87e
replace caplog level setting with context manager option
sfmig Oct 2, 2023
b3c5d5e
specify logger to try and fix pytest caplog error
sfmig Oct 2, 2023
08c0e1b
cellfinder workflow first draft
sfmig Sep 18, 2023
852ee04
test data
sfmig Sep 18, 2023
25883ef
rename
sfmig Sep 18, 2023
7b97560
delete test data from repo
sfmig Sep 20, 2023
c87f9f2
rename init
sfmig Sep 20, 2023
61bbbeb
rename and reduce workflow to main version
sfmig Sep 20, 2023
aedb87d
exclude notebooks from sdist
sfmig Sep 20, 2023
7b6e882
precommit fixes
sfmig Sep 20, 2023
f1836ff
change brainglobe_scripts references in pyproject.toml
sfmig Sep 21, 2023
16e6312
add config class and default config. Combine setup steps into one set…
sfmig Oct 2, 2023
4de8497
set signal and parent dirs as strings (for read with dask). set list …
sfmig Oct 2, 2023
5844ebf
add logging info
sfmig Oct 2, 2023
9192df3
add logging message for fetching from GIN
sfmig Oct 2, 2023
59d9ca0
refactor the input data retrieval
sfmig Oct 2, 2023
06ec524
add pooch as dependency
sfmig Oct 2, 2023
c85c2d5
add cellfinder-core dependency
sfmig Oct 2, 2023
8e13570
fix typo in Pathlike
sfmig Oct 2, 2023
02b2a84
teardown for env var fixture
sfmig Oct 3, 2023
9d0c6c2
add logger_str as fixture. changed prep_json to check if object is Pa…
sfmig Oct 4, 2023
ff3532e
remove logger.propagate setting to True (it's the default value)
sfmig Oct 4, 2023
c8f22ff
remove some comments and TODOs
sfmig Oct 4, 2023
446d959
timestamp output directory
sfmig Oct 4, 2023
a4bcd51
make default config explicitly a module-level constant. separate defa…
sfmig Oct 4, 2023
ac14d84
remove option to pass a config dict to setup_workflow
sfmig Oct 4, 2023
607dc0a
add description of the script
sfmig Oct 4, 2023
bb66598
remove some stray comments
sfmig Oct 4, 2023
abd9e4c
Merge branch 'smg/cellfinder-workflow-only' into smg/cellfinder-workf…
sfmig Oct 4, 2023
5555fba
fix output_path with timestamp error. added function to generate conf…
sfmig Oct 4, 2023
654ff31
add check for output directory to tests
sfmig Oct 4, 2023
3af3b8a
rename json factory function
sfmig Oct 5, 2023
21ca8ed
change script to receive json as required CLI argument
sfmig Oct 5, 2023
8ded21a
add default json (WIP). refactor logger
sfmig Oct 6, 2023
b0336bd
add parent_dir optional argument to check outputs
sfmig Oct 6, 2023
f615da8
add default_config.json
sfmig Oct 6, 2023
432f1ee
refactor pytest fixtures to conftest.py. add adocstrings.
sfmig Oct 6, 2023
f7281bd
rename extract_dir
sfmig Oct 6, 2023
788ddd4
missed one name change
sfmig Oct 6, 2023
1e20b9b
add typing to fixtures and actually correct extract_dir_relative
sfmig Oct 6, 2023
094a912
add encoding for windows fix
sfmig Oct 6, 2023
5240d82
make fixture returning config for local data more explicit
sfmig Oct 6, 2023
2a05b61
remove some comments
sfmig Oct 6, 2023
3efef83
make data_url and data_hash into fixtures
sfmig Oct 6, 2023
07473bb
add type for outputs and docstrings
sfmig Oct 9, 2023
97f27fb
add default json config as fixture
sfmig Oct 9, 2023
c8d2468
add types to fixtures
sfmig Oct 9, 2023
069516a
make paths in config relative to install_path
sfmig Oct 9, 2023
43e6320
rename cfg to config for consistency
sfmig Oct 13, 2023
c23194f
clarify CLI is optional
sfmig Oct 13, 2023
481c1af
fix typo in list_background_files
sfmig Oct 13, 2023
ac932dc
remove notebooks from MANIFEST
sfmig Oct 13, 2023
f16c6b9
fix one cfg replacement for ok static typing
sfmig Oct 13, 2023
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1 change: 1 addition & 0 deletions MANIFEST.in
Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@ include README.md
exclude .pre-commit-config.yaml

recursive-include brainglobe_workflows *.py
include brainglobe_workflows/cellfinder/default_config.json

recursive-exclude * __pycache__
recursive-exclude * *.py[co]
Expand Down
2 changes: 1 addition & 1 deletion brainglobe_workflows/__init__.py
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
from importlib.metadata import PackageNotFoundError, version

try:
__version__ = version("brainglobe-scripts")
__version__ = version("brainglobe-workflows")
except PackageNotFoundError:

Check warning on line 5 in brainglobe_workflows/__init__.py

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brainglobe_workflows/__init__.py#L5

Added line #L5 was not covered by tests
# package is not installed
pass

Check warning on line 7 in brainglobe_workflows/__init__.py

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