feat(starrynight): add mechanism for automatic update of bilayers schema

conductor/pyproject.toml

@@ -14,7 +14,7 @@ dependencies = [
   "pydantic~=2.8",
   "pydantic-settings~=2.4",
   "joblib~=1.3",
-  "cloudpahtlib[all]>0.18,<1.0",
+  "cloudpathlib[all]>=0.18,<1.0",
   "starrynight",
 ]
 

starrynight/pyproject.toml

@@ -14,14 +14,15 @@ dependencies = [
   "numpy<=1.26.4",
   "cloudpathlib[all]>=0.18,<1.0",
   "joblib<=1.4",
+  "linkml>=1.8"
 ]
 
 [project.optional-dependencies]
-cellprofiler = [
-  "cellprofiler-core",
-  "cellprofiler-library",
-  "Cellprofiler",
-]
+# cellprofiler = [
+#   "cellprofiler-core",
+#   "cellprofiler-library",
+#   "Cellprofiler",
+# ]
 dev = ["pytest", "ruff", "build", "twine"]
 
 [tools.uv.sources]

starrynight/src/starrynight/modules/registry.py

@@ -1,5 +1,9 @@
 """Modules registry."""
 
+from pathlib import Path
+
+import requests
+from linkml.generators import PydanticGenerator
 from pipecraft.node import UnitOfWork
 from pipecraft.pipeline import Pipeline
 from pydantic import BaseModel
@@ -29,3 +33,25 @@ class Config:
 
 
 MODULE_REGISTRY: dict[str, StarrynightModule] = {}
+
+VALIDATE_SCHEMA_URL = "https://raw.githubusercontent.com/bilayer-containers/bilayers/master/tests/test_config/validate_schema.yaml"
+
+
+def update_module_schema() -> None:
+    """Download and update the module schema from bilayers."""
+    schema_yaml = Path(__file__).parent.joinpath("validate_schema.yaml")
+    schema_path = Path(__file__).parent.joinpath("schema.py")
+    resp = requests.get(VALIDATE_SCHEMA_URL)
+    if resp.status_code == 200:
+        schema_yaml.open("wb").write(resp.content)
+    else:
+        raise Exception(
+            "Unable to Download and update the module schema from bilayers."
+        )
+
+    # Write generated pydantic schema
+    schema_path.open("w").write(PydanticGenerator(schema_yaml).serialize())
+
+
+if __name__ == "__main__":
+    update_module_schema()