deriva-ml 1.14.36__tar.gz → 1.14.38__tar.gz

{deriva_ml-1.14.36 → deriva_ml-1.14.38}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: deriva-ml
-Version: 1.14.36
+Version: 1.14.38
 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-1.14.36 → deriva_ml-1.14.38}/src/deriva_ml/execution/execution.py

@@ -360,6 +360,14 @@ class Execution:
             with Path(cfile).open("w", encoding="utf-8") as config_file:
                 json.dump(self.configuration.model_dump(), config_file)
 
+            lock_file = Path(self.configuration.workflow.git_root) / "uv.lock"
+            if lock_file.exists():
+                _ = self.asset_file_path(
+                    MLAsset.execution_metadata,
+                    lock_file,
+                    ExecMetadataType.execution_config.value,
+                )
+
             for parameter_file in self.configuration.parameters:
                 self.asset_file_path(
                     MLAsset.execution_asset,
@@ -896,9 +904,7 @@ class Execution:
                     asset_path.write_bytes(file_name.read_bytes())
 
         # Persist the asset types into a file
-        with Path(
-            asset_type_path(self._working_dir, self.execution_rid, asset_table)
-        ).open("a") as asset_type_file:
+        with Path(asset_type_path(self._working_dir, self.execution_rid, asset_table)).open("a") as asset_type_file:
             asset_type_file.write(json.dumps({file_name.name: asset_types}) + "\n")
 
         return AssetFilePath(

{deriva_ml-1.14.36 → deriva_ml-1.14.38}/src/deriva_ml/execution/workflow.py

@@ -84,6 +84,7 @@ class Workflow(BaseModel):
     rid: RID | None = None
     checksum: str | None = None
     is_notebook: bool = False
+    git_root: Path | None = None
 
     _logger: logging.Logger = PrivateAttr(default=10)
 
@@ -125,6 +126,7 @@ class Workflow(BaseModel):
         if not self.url:
             path, self.is_notebook = Workflow._get_python_script()
             self.url, self.checksum = Workflow.get_url_and_checksum(path)
+            self.git_root = Workflow._get_git_root(path)
 
         self._logger = logging.getLogger("deriva_ml")
         return self
@@ -315,12 +317,9 @@ class Workflow(BaseModel):
             ]
             # Get the caller's filename, which is two up the stack from here.
             filename = Path(stack[-1])
-            if not filename.exists() or Workflow._in_repl():
+            if not (filename.exists() or Workflow._in_repl()):
                 # 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
         return filename, is_notebook
 
     @staticmethod

{deriva_ml-1.14.36 → deriva_ml-1.14.38}/src/deriva_ml/install_kernel.py

@@ -1,9 +1,13 @@
 # your_pkg/install_kernel.py
-import sys
 import re
+import sys
+from argparse import ArgumentParser
 from importlib import metadata
+from pathlib import Path
+
 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.
@@ -20,6 +24,7 @@ def _dist_name_for_this_package() -> str:
     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_].
@@ -28,19 +33,40 @@ def _normalize_kernel_name(name: str) -> str:
     name = re.sub(r"[^a-z0-9._-]+", "-", name)
     return name
 
+
+def _name_for_this_venv() -> str:
+    config_path = Path(sys.prefix) / "pyvenv.cfg"
+    with config_path.open() as f:
+        m = re.search("prompt *= *(?P<prompt>.*)", f.read())
+    return m["prompt"] if m else ""
+
+
 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"
+    parser = ArgumentParser()
+    parser.add_argument(
+        "--install-local",
+        action="store_true",
+        help="Create kernal in local venv directory instead of sys.prefix.",
+    )
+
+    dist_name = _name_for_this_venv()  # 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/..)
+    prefix_arg = {}
+    install_local = False
+    if install_local:
+        prefix_arg = {"prefix": sys.prefix}
+
     install_kernel(
-        user=False,                 # write under sys.prefix (the active env)
+        user=True,  # write under sys.prefix (the active env)
         kernel_name=kernel_name,
         display_name=display_name,
-        prefix=sys.prefix,
+        **prefix_arg,
     )
     print(f"Installed Jupyter kernel '{kernel_name}' with display name '{display_name}' under {sys.prefix!s}")
 
+
 if __name__ == "__main__":
-    main()
+    main()

{deriva_ml-1.14.36 → deriva_ml-1.14.38}/src/deriva_ml/schema/create_schema.py

@@ -298,7 +298,7 @@ def initialize_ml_schema(model: Model, schema_name: str = "deriva-ml"):
             },
             {
                 "Name": "Runtime_Env",
-                "Description": "Information about the execution environment",
+                "Description": "Information about the runtime environment",
             },
             {
                 "Name": "Execution_Metadata",

{deriva_ml-1.14.36 → deriva_ml-1.14.38}/src/deriva_ml.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: deriva-ml
-Version: 1.14.36
+Version: 1.14.38
 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-1.14.36 → deriva_ml-1.14.38}/tests/conftest.py

@@ -5,7 +5,6 @@ Pytest configuration and shared fixtures.
 import os
 
 import pytest
-from test_utils import MLCatalog, MLDatasetCatalog, create_jupyter_kernel, destroy_jupyter_kernel
 
 from deriva_ml import DerivaML
 from deriva_ml.demo_catalog import (
@@ -14,6 +13,8 @@ from deriva_ml.demo_catalog import (
     populate_demo_catalog,
 )
 
+from .test_utils import MLCatalog, MLDatasetCatalog, create_jupyter_kernel, destroy_jupyter_kernel
+
 
 @pytest.fixture(scope="session")
 def catalog_host():

{deriva_ml-1.14.36 → deriva_ml-1.14.38}/tests/execution/test_execution.py

@@ -134,7 +134,10 @@ class TestExecution:
             }
             for a in metadata_path.entities().fetch()
         ]
-        assert 2 == len(execution_metadata)
+        assert "uv.lock" in [d["Filename"] for d in execution_metadata]
+        assert "configuration.json" in [d["Filename"] for d in execution_metadata]
+
+        assert 3 == len(execution_metadata)
 
     def test_execution_upload(self, test_ml):
         ml_instance = test_ml

{deriva_ml-1.14.36 → deriva_ml-1.14.38}/tests/test_utils.py

@@ -3,7 +3,6 @@ import shutil
 from tempfile import TemporaryDirectory
 from urllib.parse import quote as urlquote
 
-from demo_catalog import create_demo_features
 from deriva.core.datapath import DataPathException
 from ipykernel.kernelspec import install
 from jupyter_client.kernelspec import KernelSpecManager
@@ -13,6 +12,7 @@ from deriva_ml.demo_catalog import (
     DatasetDescription,
     create_demo_catalog,
     create_demo_datasets,
+    create_demo_features,
     populate_demo_catalog,
 )