deriva-ml 1.14.26__py3-none-any.whl → 1.14.28__py3-none-any.whl

deriva_ml/dataset/dataset.py

@@ -211,6 +211,7 @@ class Dataset:
         dataset_path.update([{"RID": dataset, "Version": version["RID"]} for dataset, version in versions.items()])
 
     def _set_version_snapshot(self):
+        """Update the Snapshot column of the Dataset_Version table to the correct time."""
         dataset_version_path = self._model.catalog.getPathBuilder().schemas[self._ml_schema].tables["Dataset_Version"]
         versions = dataset_version_path.entities().fetch()
         dataset_version_path.update(
@@ -1023,7 +1024,7 @@ class Dataset:
                 self._logger.info(
                     "Downloading dataset %s for catalog: %s@%s"
                     % (
-                        'minid' if self._use_minid else 'bag',
+                        "minid" if self._use_minid else "bag",
                         dataset.rid,
                         str(dataset.version),
                     )

deriva_ml/execution/workflow.py

@@ -2,6 +2,7 @@ import inspect
 import logging
 import os
 import subprocess
+import sys
 from pathlib import Path
 from typing import Any
 
@@ -297,22 +298,46 @@ class Workflow(BaseModel):
                 pass
         return None, None
 
+    @staticmethod
+    def _in_repl():
+        # Standard Python interactive mode
+        if hasattr(sys, "ps1"):
+            return True
+
+        # Interactive mode forced by -i
+        if sys.flags.interactive:
+            return True
+
+        # IPython / Jupyter detection
+        try:
+            from IPython import get_ipython
+
+            if get_ipython() is not None:
+                return True
+        except ImportError:
+            pass
+
+        return False
+
     @staticmethod
     def _get_python_script() -> tuple[Path, bool]:
         """Return the path to the currently executing script"""
         is_notebook = True
         if not (filename := Workflow._get_notebook_path()):
             is_notebook = False
-            stack = inspect.stack()
+            stack = [
+                s.filename
+                for s in inspect.stack()
+                if ("pycharm" not in s.filename) and ("site-packages" not in s.filename)
+            ]
+            # 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():
+                # 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.
-            if len(stack) > 1:
-                filename = Path(stack[2].filename)
-                if not filename.exists():
-                    # Being called from the command line interpreter.
-                    filename = 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
@@ -352,19 +377,20 @@ class Workflow(BaseModel):
                 cwd=executable_path.parent,
                 capture_output=True,
                 text=True,
-                check=True,
+                check=False,
             )
             is_dirty = bool("M " in result.stdout.strip())  # Returns True if the output indicates a modified file
         except subprocess.CalledProcessError:
             is_dirty = False  # If the Git command fails, assume no changes
 
         """Get SHA-1 hash of latest commit of the file in the repository"""
+
         result = subprocess.run(
             ["git", "log", "-n", "1", "--pretty=format:%H--", executable_path],
-            cwd=executable_path.parent,
+            cwd=repo_root,
             capture_output=True,
             text=True,
-            check=True,
+            check=False,
         )
         sha = result.stdout.strip()
         url = f"{github_url}/blob/{sha}/{executable_path.relative_to(repo_root)}"

deriva_ml/model/database.py

@@ -126,8 +126,8 @@ class DatabaseModel(DerivaModel, metaclass=DatabaseModelMeta):
             dataset_versions = [
                 t for t in self.dbase.execute(f'SELECT "Dataset", "Version" FROM "{sql_dataset}"').fetchall()
             ]
-        dataset_versions = [(v[0], DatasetVersion.parse(v[1])) for v in dataset_versions]
 
+        dataset_versions = [(v[0], DatasetVersion.parse(v[1])) for v in dataset_versions]
         # Get most current version of each rid
         self.bag_rids = {}
         for rid, version in dataset_versions:

{deriva_ml-1.14.26.dist-info → deriva_ml-1.14.28.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: deriva-ml
-Version: 1.14.26
+Version: 1.14.28
 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-1.14.26.dist-info → deriva_ml-1.14.28.dist-info}/RECORD

@@ -12,7 +12,7 @@ deriva_ml/core/exceptions.py,sha256=4MZNPOyN-UMaGeY9sqJDVwh_iOmz1ntp4usSyCNqVMg,
 deriva_ml/core/filespec.py,sha256=BQAAcRXfXq1lDcsKlokLOOXCBtEZpPgXxrFOIZYAgLg,4229
 deriva_ml/dataset/__init__.py,sha256=ukl2laJqa9J2AVqb4zlpIYc-3RaAlfRR33NMIQaoNrQ,104
 deriva_ml/dataset/aux_classes.py,sha256=9mZAln7_rrzaRbKhKA6dJOp3xeD6dHOC9NXOtJKROo4,6933
-deriva_ml/dataset/dataset.py,sha256=FnQG98eEr7mnUmo1ySgVRxRoyhbP5u_ZxuexdAcYxJY,64305
+deriva_ml/dataset/dataset.py,sha256=drL0YZovPpQC9G_eYe-fWuFQFysK2X-ad0vL4ZsYkf0,64396
 deriva_ml/dataset/dataset_bag.py,sha256=mPIZRX5aTbVRcJbCFtdkmlnexquF8NE-onbVK_8IxVk,14224
 deriva_ml/dataset/history.py,sha256=FK5AYYz11p4E4FWMVg4r7UPWOD4eobrq3b3xMjWF59g,3197
 deriva_ml/dataset/upload.py,sha256=Ad5JDfGvkIvefE-plP8SN9pNAxHzYrBoid5isz_bnNs,16411
@@ -20,10 +20,10 @@ 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=fd8dwCyDSpW_BOD_d0-zFs9yTNrbddwqD-xG3rKdvyU,13215
+deriva_ml/execution/workflow.py,sha256=E3npefABfJthlphH6QXHBjHGgDdRcoXzd7YowQOeUHg,13813
 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=cTe9rJHMCDo89_dmAT5aJGhzzLiK2DkXvCvZE6fczcM,14805
+deriva_ml/model/database.py,sha256=MlXQQFgFmGxZbRx-unRFoRttXwpJspV4v2AIgppttCU,14805
 deriva_ml/model/sql_mapper.py,sha256=_0QsJEVSgSPtxrWKSgjfPZCQ1aMVcjR_Tk2OxLhWEvY,1696
 deriva_ml/schema/__init__.py,sha256=yV-MfzCF3FA4OOz7mZwMM2q6-x1vgOJ057kUvikFF6E,130
 deriva_ml/schema/annotations.py,sha256=TuQ3vWFnK0160fRmtvsCkHx9qAcRa63MSyERB4x5a98,18197
@@ -32,9 +32,9 @@ 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-1.14.26.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-deriva_ml-1.14.26.dist-info/METADATA,sha256=nhgVSz2mmn24u8xsLlAQRu6wYa37-z4DJZNy3Fi8odM,1034
-deriva_ml-1.14.26.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-deriva_ml-1.14.26.dist-info/entry_points.txt,sha256=dkf_z7E4V6_3_5Xjsm0hcixNg6ASHDw6NfYQuBvF1Wc,363
-deriva_ml-1.14.26.dist-info/top_level.txt,sha256=I1Q1dkH96cRghdsFRVqwpa2M7IqJpR2QPUNNc5-Bnpw,10
-deriva_ml-1.14.26.dist-info/RECORD,,
+deriva_ml-1.14.28.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+deriva_ml-1.14.28.dist-info/METADATA,sha256=4OlbcNCpEy3cjuU_nekQ14A_feGdqhQinktMv3IwIMw,1034
+deriva_ml-1.14.28.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+deriva_ml-1.14.28.dist-info/entry_points.txt,sha256=dkf_z7E4V6_3_5Xjsm0hcixNg6ASHDw6NfYQuBvF1Wc,363
+deriva_ml-1.14.28.dist-info/top_level.txt,sha256=I1Q1dkH96cRghdsFRVqwpa2M7IqJpR2QPUNNc5-Bnpw,10
+deriva_ml-1.14.28.dist-info/RECORD,,