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Align CLI arguments with reader APIs for full parameter consistency #321

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Merged
LucaMarconato merged 11 commits into from
May 5, 2026
+476 −20
Merged

Align CLI arguments with reader APIs for full parameter consistency #321

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7e9196c
Initial plan
Copilot Sep 5, 2025
65e4f02
Fix CLI mismatches: add missing parameters for seqfish, visium, visiu…
Copilot Sep 5, 2025
232f0df
Add complete CLI/API alignment: JSON kwargs parameters for all readers
Copilot Sep 5, 2025
c48d483
Refactor CLI kwargs handling and fix macsima imread_kwargs gap
LucaMarconato May 4, 2026
18c60dc
add .gitignore
LucaMarconato May 5, 2026
9012952
Merge branch 'main' into copilot/fix-343cb2c5-5474-4b02-b011-67557f9c…
LucaMarconato May 5, 2026
e7e3632
Fix CLI/reader mismatches after main merge and add JSON kwargs tests
LucaMarconato May 5, 2026
7e5c71b
Add structural CLI/reader alignment test
LucaMarconato May 5, 2026
c109ed8
Replace unittest.mock with pytest-mock in CLI kwargs tests
LucaMarconato May 5, 2026
9f6e07a
Improve test_cli_alignment: symmetric check and limitation docs
LucaMarconato May 5, 2026
ce9e3b0
add pytest mock
LucaMarconato May 5, 2026
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3 changes: 0 additions & 3 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -45,10 +45,7 @@ uv.lock
profile.speedscope.json

# test datasets (e.g. Xenium ones)
# symlinks
data
# data folder
data/
tests/data
.venv
.uv.lock
3 changes: 2 additions & 1 deletion pyproject.toml
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Expand Up @@ -61,7 +61,8 @@ test = [
"pytest",
"pytest-cov",
# https://github.com/scverse/spatialdata-io/issues/334
"pyarrow!=22"
"pyarrow!=22",
"pytest-mock"
]
# this will be used by readthedocs and will make pip also look for pre-releases, generally installing the latest available version
# update: readthedocs doens't seem to try to install pre-releases even if when trying to install the pre optional-dependency. For
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