deriva-ml 1.9.0__py3-none-any.whl → 1.9.1__py3-none-any.whl

deriva_ml/database_model.py

@@ -84,7 +84,7 @@ class DatabaseModel(DerivaModel, metaclass=DatabaseModelMeta):
         except KeyError:
             raise DerivaMLException(f"Dataset {dataset_rid} not found")
 
-    def __init__(self, minid: DatasetMinid, bag_path: Path):
+    def __init__(self, minid: DatasetMinid, bag_path: Path, dbase_path: Path):
         """Create a new DatabaseModel.
 
         Args:
@@ -95,8 +95,7 @@ class DatabaseModel(DerivaModel, metaclass=DatabaseModelMeta):
         self.bag_path = bag_path
         self.minid = minid
         self.dataset_rid = minid.dataset_rid
-        dir_path = bag_path.parent
-        self.dbase_file = dir_path / f"{minid.version_rid}.db"
+        self.dbase_file = dbase_path / f"{minid.version_rid}.db"
         self.dbase = sqlite3.connect(self.dbase_file)
 
         super().__init__(

deriva_ml/dataset.py

@@ -67,11 +67,12 @@ class Dataset:
 
     _Logger = logging.getLogger("deriva_ml")
 
-    def __init__(self, model: DerivaModel, cache_dir: Path):
+    def __init__(self, model: DerivaModel, cache_dir: Path, working_dir: Path):
         self._model = model
         self._ml_schema = ML_SCHEMA
         self.dataset_table = self._model.schemas[self._ml_schema].tables["Dataset"]
         self._cache_dir = cache_dir
+        self._working_dir = working_dir
         self._logger = logging.getLogger("deriva_ml")
 
     def _is_dataset_rid(self, dataset_rid: RID, deleted: bool = False) -> bool:
@@ -783,7 +784,6 @@ class Dataset:
         snapshot: Optional[Dataset] = None,
         dataset_nesting_depth: Optional[int] = None,
     ) -> set[tuple[Table, ...]]:
-
         snapshot_catalog = snapshot if snapshot else self
 
         dataset_table = snapshot_catalog._model.schemas[self._ml_schema].tables[
@@ -831,9 +831,7 @@ class Dataset:
         nested_paths = set()
         if dataset_rid:
             for c in snapshot_catalog.list_dataset_children(dataset_rid=dataset_rid):
-                nested_paths |= self._collect_paths(
-                    c, snapshot=snapshot_catalog
-                )
+                nested_paths |= self._collect_paths(c, snapshot=snapshot_catalog)
         else:
             # Initialize nesting depth if not already provided.
             dataset_nesting_depth = (
@@ -979,7 +977,7 @@ class Dataset:
             if dataset.materialize
             else self._download_dataset_minid(minid)
         )
-        return DatabaseModel(minid, bag_path).get_dataset()
+        return DatabaseModel(minid, bag_path, self._working_dir).get_dataset()
 
     def _version_snapshot(self, dataset: DatasetSpec) -> str:
         """Return a catalog with snapshot for the specified dataset version"""

deriva_ml/deriva_ml_base.py

@@ -163,7 +163,7 @@ class DerivaML(Dataset):
         self.cache_dir.mkdir(parents=True, exist_ok=True)
 
         # Initialize dataset class.
-        super().__init__(self.model, self.cache_dir)
+        super().__init__(self.model, self.cache_dir, self.working_dir)
         self._logger = logging.getLogger("deriva_ml")
         self._logger.setLevel(logging_level)
 
@@ -257,7 +257,7 @@ class DerivaML(Dataset):
     def _get_notebook_path(self) -> Path | None:
         """Return the absolute path of the current notebook."""
 
-        server, session = self._get_notebook_session()
+        server, session = DerivaML._get_notebook_session()
         if server and session:
             self._check_nbstrip_status()
             relative_path = session["notebook"]["path"]

{deriva_ml-1.9.0.dist-info → deriva_ml-1.9.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: deriva-ml
-Version: 1.9.0
+Version: 1.9.1
 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
@@ -16,5 +16,14 @@ Requires-Dist: setuptools-scm<=6.0
 Requires-Dist: nbstripout
 Dynamic: license-file
 
-Deriva-ML is a python libary to simplify the process of creating and executing reproducible machine learning workflows
+# DerivaML
+Deriva-ML is a python library to simplify the process of creating and executing reproducible machine learning workflows
 using a deriva catalog.
+
+
+## Installing the GitHub CLI
+
+The script release.sh will create a new release tag in GitHub.  This script requires the 
+GitHUB CLI be installed. 
+
+See [https://cli.github.com](https://cli.github.com) for instructions on how to install and configure the CLI.

{deriva_ml-1.9.0.dist-info → deriva_ml-1.9.1.dist-info}/RECORD

@@ -1,11 +1,11 @@
 deriva_ml/__init__.py,sha256=r1Z9N5vtZkAET7emqhpAx2bf_xJUp5wHOc4_DIplsG8,1082
-deriva_ml/database_model.py,sha256=HaJoxKSogc-xLGaZfEviqRAWO9wUy52h7yK8by6FKxM,14838
-deriva_ml/dataset.py,sha256=XIXyTej55WduvEOGitG5SJIfPYrQu36cXjCoCNHNMwQ,60746
+deriva_ml/database_model.py,sha256=58iweWRteLeKKjjeNA9_e7TbUb4Av92lxH2zKvZzwA8,14823
+deriva_ml/dataset.py,sha256=h7Zkhnhy66GhPg6O1ud-YCx-jFKAabWF-nwuIDsR8SU,60785
 deriva_ml/dataset_aux_classes.py,sha256=YxjQnu2kS9kK_f8bGqhmgE6ty9GNeitCxfvReT9vaM0,6537
 deriva_ml/dataset_bag.py,sha256=aOJxFA9t5apjE5BNBrk8Pi9R1Cp8AWnnaL-10P8ELrQ,11515
 deriva_ml/demo_catalog.py,sha256=zQAHWSvrVPxMg-vyRUqoC0Jj5RhfGjkBwXW3mBksLhA,10986
 deriva_ml/deriva_definitions.py,sha256=jNiInYA2Cb1GE4OOT1CofxBygdLDSOmNsw5Wl6NbZQE,8943
-deriva_ml/deriva_ml_base.py,sha256=B0_0R0tgx4o30VM-QSSKIGy2BN5kOBcYKuYGvmPkwMg,46953
+deriva_ml/deriva_ml_base.py,sha256=nzPzn_iLQIUJDCxTdRgAVEWqS7LbRTZriofWYmdEYe8,46975
 deriva_ml/deriva_model.py,sha256=B4gwr3-92IQU-mEZlusgNEnRyulD96esWGS67q9MzHk,12024
 deriva_ml/execution.py,sha256=on8hAtuZr9qFiyxuk_vDCmnRJ9Cv4kFOgHK4HY4CmV8,29585
 deriva_ml/execution_configuration.py,sha256=vsdL31J09dz7CQDd2rYXIjyBPwNlgAWvrTqsXNWi82g,3357
@@ -19,9 +19,9 @@ deriva_ml/schema_setup/annotations.py,sha256=v0gTpmWYxRqsQ-bcnQzsr8WowGv2pi9pZUs
 deriva_ml/schema_setup/create_schema.py,sha256=BRdYeWW5I8HxuATkB1hkKuIw4n-JQu620xod7EQoVSE,10674
 deriva_ml/schema_setup/policy.json,sha256=77sf0Imy6CAQV0_VwwbA56_KROJ05WXsvT-Wjtkk538,1633
 deriva_ml/schema_setup/table_comments_utils.py,sha256=-2_ubEpoH7ViLVb-ZfW9wZbQ26DTKNgjkCABMzGu4i4,2140
-deriva_ml-1.9.0.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-deriva_ml-1.9.0.dist-info/METADATA,sha256=REDBcboXpGhYbG7bVaICPhZP81cDLoSiCdiY7PX8GrQ,669
-deriva_ml-1.9.0.dist-info/WHEEL,sha256=1tXe9gY0PYatrMPMDd6jXqjfpz_B-Wqm32CPfRC58XU,91
-deriva_ml-1.9.0.dist-info/entry_points.txt,sha256=ZiOvrYj022x544TQwi018ujeHRRDahNmwJnzn5ThacM,242
-deriva_ml-1.9.0.dist-info/top_level.txt,sha256=I1Q1dkH96cRghdsFRVqwpa2M7IqJpR2QPUNNc5-Bnpw,10
-deriva_ml-1.9.0.dist-info/RECORD,,
+deriva_ml-1.9.1.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+deriva_ml-1.9.1.dist-info/METADATA,sha256=zdDl9mmw2-DwvfYyWtq3vKnsB175gRFUsfHvRNLOGLg,941
+deriva_ml-1.9.1.dist-info/WHEEL,sha256=1tXe9gY0PYatrMPMDd6jXqjfpz_B-Wqm32CPfRC58XU,91
+deriva_ml-1.9.1.dist-info/entry_points.txt,sha256=ZiOvrYj022x544TQwi018ujeHRRDahNmwJnzn5ThacM,242
+deriva_ml-1.9.1.dist-info/top_level.txt,sha256=I1Q1dkH96cRghdsFRVqwpa2M7IqJpR2QPUNNc5-Bnpw,10
+deriva_ml-1.9.1.dist-info/RECORD,,