Fg/ontology resource api#215
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sjfleming
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Apr 29, 2026
| { version = ">=2.2.0,<2.7.0", markers = "sys_platform == 'darwin'" }, | ||
| { version = ">=2.2.0,<2.7.0", markers = "sys_platform == 'linux'", source = "pytorch-cpu" } | ||
| { version = ">=2.2.0,<2.5.0", markers = "sys_platform == 'darwin'"}, | ||
| { version = ">=2.2.0,<2.5.0", markers = "sys_platform == 'linux'", source = "pytorch-cpu" } |
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I think this pytorch version limitation will be true until cellarium-ai/cellarium-ml#325
sjfleming
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Apr 29, 2026
| packaging = "24.2" | ||
| pydantic = "2.8.2" | ||
| pydantic-settings = "2.3.4" | ||
| numpy = "1.26.4" |
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did you remove a pinned numpy version? or is this somehow taken care of by poetry?
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Poetry does take care of it since it is a dependency of other dependencies (pytorch, anndata, etc). So there is pinned version of numpy in poetry.lock. It now decides which one to use, based on other dependencies.
sjfleming
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Apr 29, 2026
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Looks good, though admittedly I'm not sure I followed every detail :)
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Summary
This PR introduces a Cell Ontology Resource API (#214) and a new build-and-deploy workflow for CAS services.
New Features
create_cell_ontology_resource.pyscript — parses a CL OWL file and generates the precomputed JSON resourcebuild-and-deploy-workflow.yml— new reusable GitHub Actions workflow for building Docker images and deploying to GCP Artifact Registry / Cloud RunChanges
namefield toOntologicalColumnInfomodel (Alembic migration included)CASModelschema to exposeontological_columnsviaAliasPathCellOntologyResourceResponsePydantic schemacellarium_general_serviceandcellarium_generaldata manager with new ontology resource logicSecurity
build-and-deploy-workflow.ymlanddeploy-workflow.yml:inputs.image-tagis now assigned to anenv:variable instead of being interpolated directly intorun:blocksDependency Updates
torchandcellarium-mlfor compatibilitypoetry.lockandpyproject.tomlTests
test_create_cell_ontology_resource_script.py)test_cellarium_general_service.pyand related fixturesThis PR closes #214