deriva-ml 1.17.5__tar.gz → 1.17.7__tar.gz

{deriva_ml-1.17.5 → deriva_ml-1.17.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: deriva-ml
-Version: 1.17.5
+Version: 1.17.7
 Summary: Utilities to simplify use of Dervia and Pandas to create reproducable ML pipelines
 Author-email: ISRD <isrd-dev@isi.edu>
 Requires-Python: >=3.10

{deriva_ml-1.17.5 → deriva_ml-1.17.7}/src/deriva_ml/__init__.py

@@ -1,3 +1,5 @@
+# We will be loading get_version from setuptools_scm and it will emit a UserWarning about it being deprecated.
+
 from importlib.metadata import PackageNotFoundError, version
 from typing import TYPE_CHECKING
 

{deriva_ml-1.17.5 → deriva_ml-1.17.7}/src/deriva_ml/core/base.py

@@ -187,6 +187,7 @@ class DerivaML(Dataset):
         logger_config = DEFAULT_LOGGER_OVERRIDES
         # allow for reconfiguration of module-specific logging levels
         [logging.getLogger(name).setLevel(level) for name, level in logger_config.items()]
+        logging.getLogger("root").setLevel(deriva_logging_level)
         logging.getLogger("bagit").setLevel(deriva_logging_level)
         logging.getLogger("bdbag").setLevel(deriva_logging_level)
 
@@ -1439,7 +1440,9 @@ class DerivaML(Dataset):
         # Create and return a new workflow object
         return Workflow(name=name, workflow_type=workflow_type, description=description)
 
-    def create_execution(self, configuration: ExecutionConfiguration, dry_run: bool = False) -> "Execution":
+    def create_execution(
+        self, configuration: ExecutionConfiguration, workflow: Workflow | RID | None = None, dry_run: bool = False
+    ) -> "Execution":
         """Creates an execution environment.
 
         Given an execution configuration, initialize the local compute environment to prepare for executing an
@@ -1454,6 +1457,7 @@ class DerivaML(Dataset):
 
         Args:
             configuration: ExecutionConfiguration:
+            workflow: Workflow object representing the workflow to execute if not present in the ExecutionConfiguration.
             dry_run: Do not create an execution record or upload results.
 
         Returns:
@@ -1463,7 +1467,7 @@ class DerivaML(Dataset):
         from deriva_ml.execution.execution import Execution
 
         # Create and store an execution instance
-        self._execution = Execution(configuration, self, dry_run=dry_run)
+        self._execution = Execution(configuration, self, workflow=workflow, dry_run=dry_run)
         return self._execution
 
     def restore_execution(self, execution_rid: RID | None = None) -> Execution:

{deriva_ml-1.17.5 → deriva_ml-1.17.7}/src/deriva_ml/execution/__init__.py

@@ -1,7 +1,7 @@
 from typing import TYPE_CHECKING
 
 # Safe imports - no circular dependencies
-from deriva_ml.execution.execution_configuration import ExecutionConfiguration, AssetRIDConfig
+from deriva_ml.execution.execution_configuration import AssetRIDConfig, ExecutionConfiguration
 from deriva_ml.execution.workflow import Workflow
 
 if TYPE_CHECKING:
@@ -22,5 +22,5 @@ __all__ = [
     "Execution",  # Lazy-loaded
     "ExecutionConfiguration",
     "Workflow",
-    "AssetRIDConfig"
+    "AssetRIDConfig",
 ]

{deriva_ml-1.17.5 → deriva_ml-1.17.7}/src/deriva_ml/execution/execution.py

@@ -216,6 +216,7 @@ class Execution:
         self,
         configuration: ExecutionConfiguration,
         ml_object: DerivaML,
+        workflow: Workflow | RID | None = None,
         reload: RID | None = None,
         dry_run: bool = False,
     ):
@@ -227,6 +228,8 @@ class Execution:
         Args:
             configuration: Settings and parameters for the execution.
             ml_object: DerivaML instance managing the execution.
+            workflow: Optional workflow RID or Workflow object.  If not specified, the workflow RID is taken from
+              the ExecutionConfiguration object
             reload: Optional RID of existing execution to reload.
             dry_run: If True, don't create catalog records or upload results.
 
@@ -234,7 +237,7 @@ class Execution:
             DerivaMLException: If initialization fails or configuration is invalid.
         """
 
-        self.asset_paths: list[AssetFilePath] = []
+        self.asset_paths: dict[str, list[AssetFilePath]] = {}
         self.configuration = configuration
         self._ml_object = ml_object
         self._model = ml_object.model
@@ -253,6 +256,8 @@ class Execution:
         self._dry_run = dry_run
 
         # Make sure we have a good workflow.
+        if workflow:
+            self.configuration.workflow = workflow
         if isinstance(self.configuration.workflow, Workflow):
             self._ml_object.lookup_term(MLVocab.workflow_type, configuration.workflow.workflow_type)
             self.workflow_rid = (

{deriva_ml-1.17.5 → deriva_ml-1.17.7}/src/deriva_ml/execution/execution_configuration.py

@@ -26,9 +26,11 @@ import json
 import sys
 from dataclasses import dataclass
 from pathlib import Path
+from typing import Any
 
 from hydra_zen import builds
-from pydantic import BaseModel, ConfigDict, Field
+from omegaconf import DictConfig
+from pydantic import BaseModel, ConfigDict, Field, field_validator
 
 from deriva_ml.core.definitions import RID
 from deriva_ml.dataset.aux_classes import DatasetSpec
@@ -67,7 +69,7 @@ class ExecutionConfiguration(BaseModel):
 
     datasets: list[DatasetSpec] = []
     assets: list[RID] = []
-    workflow: RID | Workflow
+    workflow: RID | Workflow | None = None
     description: str = ""
     argv: list[str] = Field(default_factory=lambda: sys.argv)
 
@@ -80,6 +82,10 @@ class ExecutionConfiguration(BaseModel):
     #          config_list: DatasetList = value
     #          value = config_list.datasets
     #      return value
+    @field_validator("assets", mode="before")
+    @classmethod
+    def validate_assets(cls, value: Any) -> Any:
+        return [v.rid if isinstance(v, DictConfig) or isinstance(v, AssetRID) else v for v in value]
 
     @staticmethod
     def load_configuration(path: Path) -> ExecutionConfiguration:

{deriva_ml-1.17.5 → deriva_ml-1.17.7}/src/deriva_ml/execution/workflow.py

@@ -3,6 +3,7 @@ import logging
 import os
 import subprocess
 import sys
+import warnings
 from pathlib import Path
 from typing import Any
 
@@ -130,7 +131,6 @@ class Workflow(BaseModel):
             self.git_root = Workflow._get_git_root(path)
 
         self.version = Workflow.get_dynamic_version(root=str(self.git_root or Path.cwd()))
-
         self._logger = logging.getLogger("deriva_ml")
         return self
 
@@ -392,10 +392,19 @@ class Workflow(BaseModel):
 
         Works under uv / Python 3.10+ by forcing setuptools to use stdlib distutils.
         """
-        # Ensure setuptools doesn't try to override stdlib distutils
+        # 1) Tell setuptools to use stdlib distutils (or no override) to avoid
+        #    the '_distutils_hack' assertion you hit.
         os.environ.setdefault("SETUPTOOLS_USE_DISTUTILS", "stdlib")
 
-        from setuptools_scm import get_version  # imported *after* env var is set
+        warnings.filterwarnings(
+            "ignore",
+            category=UserWarning,
+            module="_distutils_hack",
+        )
+        try:
+            from setuptools_scm import get_version
+        except Exception as e:  # ImportError or anything environment-specific
+            raise RuntimeError(f"setuptools_scm is not available: {e}") from e
 
         if root is None:
             # Adjust this to point at your repo root if needed

{deriva_ml-1.17.5 → deriva_ml-1.17.7}/src/deriva_ml/schema/create_schema.py

@@ -310,6 +310,7 @@ def initialize_ml_schema(model: Model, schema_name: str = "deriva-ml"):
             },
             {"Name": "File", "Description": "A file that is not managed by Hatrac"},
             {"Name": "Input_File", "Description": "A file input to an execution."},
+            {"Name": "Output_File", "Description": "A file output from an execution."},
             {"Name": "Model_File", "Description": "The ML model."},
             {
                 "Name": "Notebook_Output",

{deriva_ml-1.17.5 → deriva_ml-1.17.7}/src/deriva_ml.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: deriva-ml
-Version: 1.17.5
+Version: 1.17.7
 Summary: Utilities to simplify use of Dervia and Pandas to create reproducable ML pipelines
 Author-email: ISRD <isrd-dev@isi.edu>
 Requires-Python: >=3.10

{deriva_ml-1.17.5 → deriva_ml-1.17.7}/uv.lock

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