deriva-ml 1.14.44__py3-none-any.whl → 1.14.46__py3-none-any.whl

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/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/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.dist-info → deriva_ml-1.14.46.dist-info}/METADATA

@@ -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.dist-info → deriva_ml-1.14.46.dist-info}/RECORD

@@ -3,9 +3,9 @@ deriva_ml/bump_version.py,sha256=KpHmkpEztly2QHYL4dyaIGdEMyP4F0D89rawyh5EDTs,398
 deriva_ml/demo_catalog.py,sha256=JjPAIac_hKPh5krEhGJydjXquRnivi7kQoR8W4Khp-s,14928
 deriva_ml/feature.py,sha256=6-aphkxdKjWa9oPSGFWxHcwAc_8hmWj-7I4M178YG5Y,8470
 deriva_ml/install_kernel.py,sha256=b62XY0SLViYO_Zye5r1Pl9qhYZyu_fk4KAO8NS1pxgM,2165
-deriva_ml/run_notebook.py,sha256=U3Bz-PdYYMIo_KZwDwlyKJtnZEMKwJjLh5Jn-M8ChUI,8039
+deriva_ml/run_notebook.py,sha256=QRO_CK9Q9qt_n-c0rxGdIRyTHjGOuZxt-wj0WQTnaAM,8171
 deriva_ml/core/__init__.py,sha256=V_i90pc5PB1F4UdOO6DZWzpEFaZDTaPRU-EzKXQ19eI,787
-deriva_ml/core/base.py,sha256=5H0GEMlKXUVRXBYXJQ25kxdscB6uX1wIKSUAM_CBOhI,61228
+deriva_ml/core/base.py,sha256=LI_ZLpVJwWx4DW2Wo7luALQauQ3xhBxFYHSKDAfNsag,61649
 deriva_ml/core/constants.py,sha256=6wBJ8qMxe-dbCjRGrjUIX-RK0mTWrLDTeUpaVbLFoM8,888
 deriva_ml/core/definitions.py,sha256=uq_8uYFBVBVHS691Ri2kdQsN37z0GNYTaZskJIb_ocM,1385
 deriva_ml/core/enums.py,sha256=sSN4B4OynbB-AXwxRszoFr-KWIWIAfhVa06EzAEHwVc,7194
@@ -20,7 +20,7 @@ deriva_ml/dataset/history.py,sha256=FK5AYYz11p4E4FWMVg4r7UPWOD4eobrq3b3xMjWF59g,
 deriva_ml/dataset/upload.py,sha256=i_7KLfRSd2-THqZ1aG2OFAFGoyb8dJBCZZ5t1ftrtMQ,16429
 deriva_ml/execution/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 deriva_ml/execution/environment.py,sha256=B7nywqxFTRUWgyu8n7rFoKcVC9on422kjeFG2FPQfvg,9302
-deriva_ml/execution/execution.py,sha256=JH2alK-7DoRzfGvjsrNhD_tZqoZkb736bxbbgXDP33o,44780
+deriva_ml/execution/execution.py,sha256=NJjjrxGsedv0zoe-T-LxfO_5UG83KOHaxU3SY5EJ0QQ,44928
 deriva_ml/execution/execution_configuration.py,sha256=Rw4VWkBCZN9yatvSKdTqEWTfu470lpcVKfHFR0uN0jI,6248
 deriva_ml/execution/workflow.py,sha256=7CwPrgs3FKQHiEVus0PpK9w5hVKLKZnCrlu_nT8GFe8,13604
 deriva_ml/model/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -34,9 +34,9 @@ deriva_ml/schema/create_schema.py,sha256=9qK9_8SRQT-DwcEwTGSkhi3j2NaoH5EVgthvV2k
 deriva_ml/schema/deriva-ml-reference.json,sha256=AEOMIgwKO3dNMMWHb0lxaXyamvfAEbUPh8qw0aAtsUQ,242460
 deriva_ml/schema/policy.json,sha256=5ykB8nnZFl-oCHzlAwppCFKJHWJFIkYognUMVEanfY8,1826
 deriva_ml/schema/table_comments_utils.py,sha256=4flCqnZAaqg_uSZ9I18pNUWAZoLfmMCXbmI5uERY5vM,2007
-deriva_ml-1.14.44.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-deriva_ml-1.14.44.dist-info/METADATA,sha256=Kq-OKAhKOm-JW2HbMoNsZIRWy8oT6v7-CYz4whIqCbo,1168
-deriva_ml-1.14.44.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-deriva_ml-1.14.44.dist-info/entry_points.txt,sha256=XsHSbfp7S1cKMjHoPUdFIaFcp9lHXHS6CV1zb_MEXkg,463
-deriva_ml-1.14.44.dist-info/top_level.txt,sha256=I1Q1dkH96cRghdsFRVqwpa2M7IqJpR2QPUNNc5-Bnpw,10
-deriva_ml-1.14.44.dist-info/RECORD,,
+deriva_ml-1.14.46.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+deriva_ml-1.14.46.dist-info/METADATA,sha256=jhm5D5-SqSJD-JVSMyqLcVPpjG3vY6MLJTIZacyt_Fc,1190
+deriva_ml-1.14.46.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+deriva_ml-1.14.46.dist-info/entry_points.txt,sha256=XsHSbfp7S1cKMjHoPUdFIaFcp9lHXHS6CV1zb_MEXkg,463
+deriva_ml-1.14.46.dist-info/top_level.txt,sha256=I1Q1dkH96cRghdsFRVqwpa2M7IqJpR2QPUNNc5-Bnpw,10
+deriva_ml-1.14.46.dist-info/RECORD,,