deriva-ml 1.14.44__tar.gz → 1.14.46__tar.gz

{deriva_ml-1.14.44 → deriva_ml-1.14.46}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: deriva-ml
-Version: 1.14.44
+Version: 1.14.46
 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
@@ -20,6 +20,7 @@ Requires-Dist: setuptools-scm>=8.0
 Requires-Dist: nbstripout
 Requires-Dist: papermill
 Requires-Dist: pandas-stubs==2.2.3.250527
+Requires-Dist: pyyaml
 Dynamic: license-file
 
 # DerivaML

{deriva_ml-1.14.44 → deriva_ml-1.14.46}/pyproject.toml

@@ -22,6 +22,7 @@ dependencies = [
     "nbstripout",
     "papermill",
     "pandas-stubs==2.2.3.250527",
+    "pyyaml"
 ]
 
 [project.scripts]

{deriva_ml-1.14.44 → deriva_ml-1.14.46}/src/deriva_ml/core/base.py

@@ -120,6 +120,7 @@ class DerivaML(Dataset):
         logging_level=logging.WARNING,
         credential=None,
         use_minid: bool = True,
+        check_auth: bool = True,
     ):
         """Initializes a DerivaML instance.
 
@@ -139,6 +140,7 @@ class DerivaML(Dataset):
             working_dir: Directory path for storing data used by or generated by any computations. If no value is
                 provided, will default to  ${HOME}/deriva_ml
             use_minid: Use the MINID service when downloading dataset bags.
+            check_auth: Check if the user has access to the catalog.
         """
         # Get or use provided credentials for server access
         self.credential = credential or get_credential(hostname)
@@ -150,6 +152,16 @@ class DerivaML(Dataset):
             credentials=self.credential,
             session_config=self._get_session_config(),
         )
+
+        try:
+            if check_auth and server.get_authn_session():
+                pass
+        except Exception:
+            raise DerivaMLException(
+                "You are not authorized to access this catalog. "
+                "Please check your credentials and make sure you have logged in."
+            )
+
         self.catalog = server.connect_ermrest(catalog_id)
         self.model = DerivaModel(self.catalog.getCatalogModel(), domain_schema=domain_schema)
 

{deriva_ml-1.14.44 → deriva_ml-1.14.46}/src/deriva_ml/execution/execution.py

@@ -385,6 +385,11 @@ class Execution:
         self.start_time = datetime.now()
         self.update_status(Status.pending, "Initialize status finished.")
 
+    @property
+    def working_dir(self) -> Path:
+        """Return the working directory for the execution."""
+        return self._execution_root
+
     @property
     def _execution_root(self) -> Path:
         """

{deriva_ml-1.14.44 → deriva_ml-1.14.46}/src/deriva_ml/run_notebook.py

@@ -9,6 +9,7 @@ from pathlib import Path
 import nbformat
 import papermill as pm
 import regex as re
+import yaml
 from deriva.core import BaseCLI
 from nbconvert import MarkdownExporter
 
@@ -28,7 +29,7 @@ class DerivaMLRunNotebookCLI(BaseCLI):
             "-f",
             type=Path,
             default=None,
-            help="JSON file with parameter values to inject into the notebook.",
+            help="JSON or YAML file with parameter values to inject into the notebook.",
         )
 
         self.parser.add_argument(
@@ -86,11 +87,14 @@ class DerivaMLRunNotebookCLI(BaseCLI):
         parameters = {key: self._coerce_number(val) for key, val in args.parameter}
 
         if parameter_file:
-            if not (parameter_file.is_file() and parameter_file.suffix == ".json"):
-                print("Parameter file must be an json file.")
-                exit(1)
-            with Path(parameter_file).open("r") as f:
-                parameters |= json.load(f)
+            with parameter_file.open("r") as f:
+                if parameter_file.suffix == ".json":
+                    parameters |= json.load(f)
+                elif parameter_file.suffix == ".yaml":
+                    parameters |= yaml.safe_load(f)
+                else:
+                    print("Parameter file must be an json or YAML file.")
+                    exit(1)
 
         if not (notebook_file.is_file() and notebook_file.suffix == ".ipynb"):
             print(f"Notebook file must be an ipynb file: {notebook_file.name}.")

{deriva_ml-1.14.44 → deriva_ml-1.14.46}/src/deriva_ml.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: deriva-ml
-Version: 1.14.44
+Version: 1.14.46
 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
@@ -20,6 +20,7 @@ Requires-Dist: setuptools-scm>=8.0
 Requires-Dist: nbstripout
 Requires-Dist: papermill
 Requires-Dist: pandas-stubs==2.2.3.250527
+Requires-Dist: pyyaml
 Dynamic: license-file
 
 # DerivaML

{deriva_ml-1.14.44 → deriva_ml-1.14.46}/src/deriva_ml.egg-info/requires.txt

@@ -12,3 +12,4 @@ setuptools-scm>=8.0
 nbstripout
 papermill
 pandas-stubs==2.2.3.250527
+pyyaml

{deriva_ml-1.14.44 → deriva_ml-1.14.46}/uv.lock

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