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Use arrow-based schema for image work #5

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Merged
merged 5 commits into from
Oct 1, 2025
Merged

Use arrow-based schema for image work #5

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b446b04
add ome-arrow mvp
d33bs Oct 1, 2025
9526f5f
add lance work
d33bs Oct 1, 2025
b3e80f6
ome-arrow images in image table
d33bs Oct 1, 2025
29a16e4
with masks
d33bs Oct 1, 2025
3db35af
add crops and linting
d33bs Oct 1, 2025
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9 changes: 9 additions & 0 deletions CITATION.cff
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Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,15 @@ authors:
- given-names: Dave
family-names: Bunten
orcid: "https://orcid.org/0000-0001-6041-3665"
- given-names: Michael
family-names: Lippincott
orcid: 'https://orcid.org/0000-0002-8637-1448'
- given-names: Jenna
family-names: Tomkinson
orcid: 'https://orcid.org/0000-0003-2676-5813'
- given-names: Gregory
family-names: Way
orcid: 'https://orcid.org/0000-0002-0503-9348'
repository-code: "https://github.com/d33bs/serpula_rasa"
abstract: >-
Blank snake implementation prototype for image-based single-cell profiling
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10 changes: 10 additions & 0 deletions pyproject.toml
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Expand Up @@ -34,6 +34,14 @@ dependencies = [
"scikit-image>=0.24",
]

[dependency-groups]
dev = [
"pytest>=8.4.2",
]

[tool.setuptools.packages.find]
where = [ "src" ]

[tool.setuptools_scm]
root = "."
version_scheme = "no-guess-dev"
Expand Down Expand Up @@ -69,6 +77,8 @@ lint.select = [
]
lint.per-file-ignores."src/serpula_rasa/example.ipynb" = [ "PLR2004", "RUF059" ]
lint.per-file-ignores."src/serpula_rasa/example.py" = [ "PLR2004", "RUF059" ]
lint.per-file-ignores."src/serpula_rasa/image.py" = [ "PLR2004", "RUF059" ]
lint.per-file-ignores."tests/*" = [ "ANN001", "ANN201", "PLR2004" ]

[tool.pytest.ini_options]
pythonpath = [ "." ]
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659 changes: 425 additions & 234 deletions src/serpula_rasa/example.ipynb
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