Add CAREamics CI Script

scripts/check_compatibility_careamics.py

@@ -0,0 +1,127 @@
+import argparse
+from pathlib import Path
+
+import numpy as np
+import pydantic
+from careamics import __version__ as CAREAMICS_VERSION
+from careamics import CAREamist
+from careamics.model_io.bmz_io import load_from_bmz
+from bioimageio.spec import load_model_description
+from bioimageio.spec.generic.v0_2 import AttachmentsDescr
+
+from .script_utils import CompatibilityReportDict, check_tool_compatibility
+
+
+def check_compatibility_careamics_impl(
+    rdf_url: str,
+    sha256: str,
+) -> CompatibilityReportDict:
+    """Create a `CompatibilityReport` for a resource description.
+
+    Args:
+        rdf_url: URL to the rdf.yaml file
+        sha256: SHA-256 value of **rdf_url** content
+    """
+    model_desc = load_model_description(rdf_url)
+    if isinstance(model_desc.attachments, AttachmentsDescr):
+        attachment_file_names = [
+            Path(file.path).name
+            for file in model_desc.attachments.files
+            if file.path is not None
+        ]
+    elif isinstance(model_desc.attachments, list):
+        attachment_file_names = [
+            Path(attachment.source.path).name
+            for attachment in model_desc.attachments
+            if attachment.source.path is not None
+        ]
+    else:
+        # TODO: confirm all types of attachments (type checker still complaining)
+        report = CompatibilityReportDict(
+            status="failed",
+            error=None,
+            details="Could not process attachments.",
+        )
+        return report
+
+    # check type is tagged as CAREamics
+    if ("CAREamics" not in model_desc.tags) and ("careamics" not in model_desc.tags):
+        report = CompatibilityReportDict(
+            status="not-applicable",
+            error=None,
+            details="'Model' resource not tagged with 'CAREamics' or 'careamics'.",
+        )
+    # check config file is present in attachments
+    # TODO: update to careamics.yaml once files have been updated
+    elif not "config.yml" in attachment_file_names:
+        report = CompatibilityReportDict(
+            status="failed",
+            error=None,
+            details="CAREamics config file is not present in attachments.",
+        )
+    # download and test
+    else:
+        try:
+            model, config = load_from_bmz(rdf_url)
+        except (ValueError, pydantic.ValidationError) as e:
+            report = CompatibilityReportDict(
+                status="failed",
+                error="Error: {}".format(e),
+                details=("Could not load CAREamics configuration or model."),
+            )
+            return report
+
+        # no failure mode as config is already a Configuration object
+        careamist = CAREamist(config)
+        # TODO (CAREamics): make a model loading method, why doesn't this exist
+        careamist.model = model
+
+        # get input tensor
+        # TODO: type checker complaining because of difference between v0.4 and v0.5
+        #   test_tensor attribute does not exist for v0.4,
+        #   how can the tensor path be accessed?
+        input_path = model_desc.inputs[0].test_tensor.download().path
+        input_array = np.load(input_path)
+
+        try:
+            _ = careamist.predict(
+                source=input_array,
+                data_type="array",
+                axes="SCZYX" if "Z" in config.data_config.axes else "SCYX",
+            )
+        except Exception as e:
+            report = CompatibilityReportDict(
+                status="failed",
+                error="Error: {}".format(e),
+                details="Calling prediction failed.",
+            )
+            return report
+
+        report = CompatibilityReportDict(
+            status="passed",
+            error=None,
+            details="CAREamics compatibility checks completed successfully!",
+        )
+
+    return report
+
+
+def check_compatibility_careamics(all_version_path: Path, output_folder: Path) -> None:
+    """CAREamics compatibility check."""
+    check_tool_compatibility(
+        "CAREamics",
+        CAREAMICS_VERSION,
+        all_version_path=all_version_path,
+        output_folder=output_folder,
+        check_tool_compatibility_impl=check_compatibility_careamics_impl,
+        applicable_types={"model"},
+    )
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    _ = parser.add_argument("all_versions", type=Path)
+    _ = parser.add_argument("output_folder", type=Path)
+
+    args = parser.parse_args()
+    check_compatibility_careamics(args.all_versions, args.output_folder)