deriva-ml 1.14.33__py3-none-any.whl → 1.14.35__py3-none-any.whl

deriva_ml/execution/workflow.py

@@ -100,9 +100,6 @@ class Workflow(BaseModel):
             - DERIVA_ML_WORKFLOW_CHECKSUM: Override the computed checksum
 
         Args:
-            name: Human-readable name for the workflow.
-            workflow_type: Type of workflow (must be a vocabulary term).
-            description: Optional description of workflow purpose.
 
         Returns:
             Workflow: New workflow instance with detected Git information.
@@ -240,6 +237,7 @@ class Workflow(BaseModel):
         """
 
         server, session = Workflow._get_notebook_session()
+
         if server and session:
             relative_path = session["notebook"]["path"]
             # Join the notebook directory with the relative path
@@ -321,8 +319,8 @@ class Workflow(BaseModel):
                 # Being called from the command line interpreter.
                 filename = Path.cwd() / Path("REPL")
             # Get the caller's filename, which is two up the stack from here.
-        else:
-            raise DerivaMLException("Looking for caller failed")  # Stack is too shallow
+            else:
+                raise DerivaMLException("Looking for caller failed")  # Stack is too shallow
         return filename, is_notebook
 
     @staticmethod

deriva_ml/feature.py

@@ -52,6 +52,7 @@ class FeatureRecord(BaseModel):
 
     class Config:
         arbitrary_types_allowed = True
+        extra = "forbid"
 
     @classmethod
     def feature_columns(cls) -> set[Column]:

deriva_ml/install_kernel.py

@@ -0,0 +1,46 @@
+# your_pkg/install_kernel.py
+import sys
+import re
+from importlib import metadata
+from ipykernel.kernelspec import install as install_kernel
+
+def _dist_name_for_this_package() -> str:
+    """
+    Try to resolve the distribution name that provides this package.
+    Works in editable installs and wheels.
+    """
+    # Top-level package name of this module (your_pkg)
+    top_pkg = __name__.split(".")[0]
+
+    # Map top-level packages -> distributions
+    pkg_to_dists = metadata.packages_distributions()
+    dists = pkg_to_dists.get(top_pkg) or []
+
+    # Fall back to project name in METADATA when mapping isn't available
+    dist_name = dists[0] if dists else metadata.metadata(top_pkg).get("Name", top_pkg)
+    return dist_name
+
+def _normalize_kernel_name(name: str) -> str:
+    """
+    Jupyter kernel directory names should be simple: lowercase, [-a-z0-9_].
+    """
+    name = name.strip().lower()
+    name = re.sub(r"[^a-z0-9._-]+", "-", name)
+    return name
+
+def main() -> None:
+    dist_name = _dist_name_for_this_package()               # e.g., "deriva-model-template"
+    kernel_name = _normalize_kernel_name(dist_name)         # e.g., "deriva-model-template"
+    display_name = f"Python ({dist_name})"
+
+    # Install into the current environment's prefix (e.g., .venv/share/jupyter/kernels/..)
+    install_kernel(
+        user=False,                 # write under sys.prefix (the active env)
+        kernel_name=kernel_name,
+        display_name=display_name,
+        prefix=sys.prefix,
+    )
+    print(f"Installed Jupyter kernel '{kernel_name}' with display name '{display_name}' under {sys.prefix!s}")
+
+if __name__ == "__main__":
+    main()

deriva_ml/run_notebook.py

@@ -95,7 +95,7 @@ class DerivaMLRunNotebookCLI(BaseCLI):
             exit(1)
 
         os.environ["DERIVA_HOST"] = args.host
-        os.environ["DERIVA_CATALOG_ID"] = args.catalog
+        os.environ["DERIVA_CATALOG"] = args.catalog
 
         # Create a workflow instance for this specific version of the script.
         # Return an existing workflow if one is found.
@@ -106,14 +106,14 @@ class DerivaMLRunNotebookCLI(BaseCLI):
             return
         else:
             notebook_parameters = (
-                {"host": args.host, "catalog_id": args.catalog, "catalog": args.catalog}
-                | {k: v["default"] for k, v in notebook_parameters.items()}
+                {k: v["default"] for k, v in notebook_parameters.items()}
+                | {"host": args.host, "hostname": args.host, "catalog_id": args.catalog, "catalog": args.catalog}
                 | parameters
             )
             print(f"Running notebook {notebook_file.name} with parameters:")
             for param, value in notebook_parameters.items():
                 print(f"  {param}:{value}")
-            self.run_notebook(notebook_file.resolve(), parameters, kernel=args.kernel, log=args.log_output)
+            self.run_notebook(notebook_file.resolve(), parameters, kernel=args.kernel[0], log=args.log_output)
 
     def run_notebook(self, notebook_file, parameters, kernel=None, log=False):
         url, checksum = Workflow.get_url_and_checksum(Path(notebook_file))

{deriva_ml-1.14.33.dist-info → deriva_ml-1.14.35.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: deriva-ml
-Version: 1.14.33
+Version: 1.14.35
 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
@@ -25,10 +25,9 @@ Deriva-ML is a python library to simplify the process of creating and executing
 using a deriva catalog.
 
 
-## Installing the GitHub CLI
+Complete on-line documentation for DerivaML can be found [here](https://informatics-isi-edu.github.io/deriva-ml/)
 
-The script release.sh will create a new release tag in GitHub.  This script requires the 
-GitHUB CLI be installed. 
+To get started using DerivaML, you can clone the [model template repository](https://github.com/informatics-isi-edu/deriva-ml-model-template), and modify it to suite your requirements.
 
-See [https://cli.github.com](https://cli.github.com) for instructions on how to install and configure the CLI.
 
+## References

{deriva_ml-1.14.33.dist-info → deriva_ml-1.14.35.dist-info}/RECORD

@@ -1,7 +1,8 @@
 deriva_ml/__init__.py,sha256=_aMdxGG4mRTcXodLZLNpXqH8v5uqMbqFUryE9KqNSB8,1158
 deriva_ml/demo_catalog.py,sha256=JjPAIac_hKPh5krEhGJydjXquRnivi7kQoR8W4Khp-s,14928
-deriva_ml/feature.py,sha256=L1XUXLWGnUGCjkxX5KsGu0I8SaUTJG7eDs__yUCWuCY,8445
-deriva_ml/run_notebook.py,sha256=BvLtkD_uizukqkAYoSUb1teIfuBWtKKcHSyJoAnAC4c,6496
+deriva_ml/feature.py,sha256=6-aphkxdKjWa9oPSGFWxHcwAc_8hmWj-7I4M178YG5Y,8470
+deriva_ml/install_kernel.py,sha256=LHAdy7s-m2jIvzptMpxLdHHkHc62Tn16e9MUWSGIznA,1651
+deriva_ml/run_notebook.py,sha256=XPZPtGDLv0Ej6dcqIwA1dx_ya1Z9kzsP7um473WtLpU,6519
 deriva_ml/core/__init__.py,sha256=V_i90pc5PB1F4UdOO6DZWzpEFaZDTaPRU-EzKXQ19eI,787
 deriva_ml/core/base.py,sha256=uG7xyVk12fXXWipusRmaBGplxbdlnN9sIOGAEHWD8i8,61090
 deriva_ml/core/constants.py,sha256=6wBJ8qMxe-dbCjRGrjUIX-RK0mTWrLDTeUpaVbLFoM8,888
@@ -20,7 +21,7 @@ deriva_ml/execution/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSu
 deriva_ml/execution/environment.py,sha256=B7nywqxFTRUWgyu8n7rFoKcVC9on422kjeFG2FPQfvg,9302
 deriva_ml/execution/execution.py,sha256=tXWkFLDoSre836x6MMkcmhtmr3zP5_VoSioQ72-XmvE,44298
 deriva_ml/execution/execution_configuration.py,sha256=Rw4VWkBCZN9yatvSKdTqEWTfu470lpcVKfHFR0uN0jI,6248
-deriva_ml/execution/workflow.py,sha256=Q5AvWOZLmveIobVKqTNo30HqpnLQ9Q9oy8klZBDKd3Q,13577
+deriva_ml/execution/workflow.py,sha256=AeCT4eYAnYvBIx-Ar-Cyg64YoPyIB8IJdg3lKkCiKCU,13390
 deriva_ml/model/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 deriva_ml/model/catalog.py,sha256=dzTBcRlqgEVkPY32AUax_iu75RgFiT4Pu5au7rmrv8k,14068
 deriva_ml/model/database.py,sha256=MlXQQFgFmGxZbRx-unRFoRttXwpJspV4v2AIgppttCU,14805
@@ -32,9 +33,9 @@ deriva_ml/schema/create_schema.py,sha256=0ydJSZEg3C3-m8hWPN6k2MoUvm-RWxAlKFzVChx
 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-1.14.33.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-deriva_ml-1.14.33.dist-info/METADATA,sha256=IbEngyEfOSCucoY9aRrvK4nuI9zNpTmg-Kh4XZ7fmW0,1065
-deriva_ml-1.14.33.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-deriva_ml-1.14.33.dist-info/entry_points.txt,sha256=dkf_z7E4V6_3_5Xjsm0hcixNg6ASHDw6NfYQuBvF1Wc,363
-deriva_ml-1.14.33.dist-info/top_level.txt,sha256=I1Q1dkH96cRghdsFRVqwpa2M7IqJpR2QPUNNc5-Bnpw,10
-deriva_ml-1.14.33.dist-info/RECORD,,
+deriva_ml-1.14.35.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+deriva_ml-1.14.35.dist-info/METADATA,sha256=ozEBGEehEvA6IHHD2u_vf8cupR-tJIvNdr9QDHjObV0,1122
+deriva_ml-1.14.35.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+deriva_ml-1.14.35.dist-info/entry_points.txt,sha256=Fg8f56jlXzbxzAqnIix7ntqZWmGdqmD11m1OOgiCXDM,420
+deriva_ml-1.14.35.dist-info/top_level.txt,sha256=I1Q1dkH96cRghdsFRVqwpa2M7IqJpR2QPUNNc5-Bnpw,10
+deriva_ml-1.14.35.dist-info/RECORD,,

{deriva_ml-1.14.33.dist-info → deriva_ml-1.14.35.dist-info}/entry_points.txt

@@ -2,5 +2,6 @@
 deriva-ml-alter-annotation = deriva_ml.schema_setup.alter_annotation:main
 deriva-ml-check-catalog-schema = deriva_ml.schema.check_schema:main
 deriva-ml-create-schema = deriva_ml.schema_setup.create_schema:main
+deriva-ml-install-kernel = deriva_ml.install_kernel:main
 deriva-ml-run-notebook = deriva_ml.run_notebook:main
 deriva-ml-table-comments-utils = deriva_ml.schema_setup.table_comments_utils:main