deriva-ml 1.9.0__py3-none-any.whl → 1.10.0__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/demo_catalog.py

@@ -295,7 +295,9 @@ def create_demo_catalog(
         dataset_table = deriva_ml.dataset_table
         dataset_table.annotations.update(
             Dataset(
-                deriva_ml.model, deriva_ml.cache_dir
+                deriva_ml.model,
+                cache_dir=deriva_ml.cache_dir,
+                working_dir=deriva_ml.working_dir,
             )._generate_dataset_annotations()
         )
         deriva_ml.model.apply()

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"]
@@ -1136,8 +1136,8 @@ class DerivaML(Dataset):
             return None
 
     def create_workflow(
-        self, name: str, workflow_type: str, description: str = "", create: bool = True
-    ) -> RID | None:
+        self, name: str, workflow_type: str, description: str = ""
+    ) -> Workflow:
         """Identify current executing program and return a workflow RID for it
 
         Determine the notebook or script that is currently being executed. Assume that  this is
@@ -1149,10 +1149,21 @@ class DerivaML(Dataset):
             name: The name of the workflow.
             workflow_type: The type of the workflow.
             description: The description of the workflow.
-            create: Whether to create a new workflow.
         """
         # Make sure type is correct.
         self.lookup_term(MLVocab.workflow_type, workflow_type)
+
+        try:
+            subprocess.run(
+                "git rev-parse --is-inside-work-tree",
+                capture_output=True,
+                text=True,
+                shell=True,
+                check=True,
+            )
+        except subprocess.CalledProcessError:
+            raise DerivaMLException("Not executing in a Git repository.")
+
         github_url, is_dirty = self._github_url()
 
         if is_dirty:
@@ -1174,14 +1185,13 @@ class DerivaML(Dataset):
             shell=True,
         ).stdout.strip()
 
-        workflow = Workflow(
+        return Workflow(
             name=name,
             url=github_url,
             checksum=checksum,
             description=description,
             workflow_type=workflow_type,
         )
-        return self.add_workflow(workflow) if create else None
 
     def _github_url(self) -> tuple[str, bool]:
         """Return a GitHUB URL for the latest commit of the script from which this routine is called.
@@ -1238,7 +1248,9 @@ class DerivaML(Dataset):
         return url, is_dirty
 
     # @validate_call
-    def create_execution(self, configuration: ExecutionConfiguration) -> "Execution":
+    def create_execution(
+        self, configuration: ExecutionConfiguration, dryrun: bool = False
+    ) -> "Execution":
         """Create an execution object
 
         Given an execution configuration, initialize the local compute environment to prepare for executing an
@@ -1249,6 +1261,7 @@ class DerivaML(Dataset):
 
         Args:
             configuration: ExecutionConfiguration:
+            dryrun: Do not create an execution record or upload results.
 
         Returns:
             An execution object.
@@ -1260,7 +1273,7 @@ class DerivaML(Dataset):
                 "Only one execution can be created for a Deriva ML instance."
             )
         else:
-            self._execution = Execution(configuration, self)
+            self._execution = Execution(configuration, self, dryrun=dryrun)
         return self._execution
 
     # @validate_call

deriva_ml/execution.py

@@ -30,7 +30,7 @@ from .deriva_definitions import (
 from .deriva_ml_base import DerivaML, FeatureRecord
 from .dataset_aux_classes import DatasetSpec, DatasetVersion, VersionPart
 from .dataset_bag import DatasetBag
-from .execution_configuration import ExecutionConfiguration
+from .execution_configuration import ExecutionConfiguration, Workflow
 from .execution_environment import get_execution_environment
 from .upload import (
     execution_metadata_dir,
@@ -96,6 +96,7 @@ class Execution:
         configuration: ExecutionConfiguration,
         ml_object: "DerivaML",
         reload: Optional[RID] = None,
+        dry_run: bool = False,
     ):
         """
 
@@ -107,6 +108,7 @@ class Execution:
         self.asset_paths: list[Path] = []
         self.configuration = configuration
         self._ml_object = ml_object
+        self._logger = ml_object._logger
         self.start_time = None
         self.stop_time = None
         self.status = Status.created
@@ -117,13 +119,23 @@ class Execution:
 
         self._working_dir = self._ml_object.working_dir
         self._cache_dir = self._ml_object.cache_dir
+        self._dry_run = dry_run
 
-        self.workflow_rid = self.configuration.workflow
-
-        if self._ml_object.resolve_rid(configuration.workflow).table.name != "Workflow":
-            raise DerivaMLException(
-                "Workflow specified in execution configuration is not a Workflow"
+        if isinstance(self.configuration.workflow, Workflow):
+            self.workflow_rid = (
+                self._ml_object.add_workflow(self.configuration.workflow)
+                if not self._dry_run
+                else "0000"
             )
+        else:
+            self.workflow_rid = self.configuration.workflow
+            if (
+                self._ml_object.resolve_rid(configuration.workflow).table.name
+                != "Workflow"
+            ):
+                raise DerivaMLException(
+                    "Workflow specified in execution configuration is not a Workflow"
+                )
 
         for d in self.configuration.datasets:
             if self._ml_object.resolve_rid(d.rid).table.name != "Dataset":
@@ -142,6 +154,10 @@ class Execution:
         schema_path = self._ml_object.pathBuilder.schemas[self._ml_object.ml_schema]
         if reload:
             self.execution_rid = reload
+            if self.execution_rid == "0000":
+                self._dry_run = True
+        elif self._dry_run:
+            self.execution_rid = "0000"
         else:
             self.execution_rid = schema_path.Execution.insert(
                 [
@@ -189,7 +205,7 @@ class Execution:
             self.dataset_rids.append(dataset.rid)
         # Update execution info
         schema_path = self._ml_object.pathBuilder.schemas[self._ml_object.ml_schema]
-        if self.dataset_rids and not reload:
+        if self.dataset_rids and not (reload or self._dry_run):
             schema_path.Dataset_Execution.insert(
                 [
                     {"Dataset": d, "Execution": self.execution_rid}
@@ -203,7 +219,7 @@ class Execution:
             self._ml_object.download_asset(asset_rid=a, dest_dir=self._asset_dir())
             for a in self.configuration.assets
         ]
-        if self.asset_paths and not reload:
+        if self.asset_paths and not (reload or self._dry_run):
             self._update_execution_asset_table(self.configuration.assets)
 
         # Save configuration details for later upload
@@ -242,6 +258,11 @@ class Execution:
             msg: Additional information about the status
         """
         self.status = status
+        self._logger.info(msg)
+
+        if self._dry_run:
+            return
+
         self._ml_object.pathBuilder.schemas[self._ml_object.ml_schema].Execution.update(
             [
                 {
@@ -278,7 +299,7 @@ class Execution:
 
         self.start_time = datetime.now()
         self.uploaded_assets = None
-        self.update_status(Status.initializing, "Start ML algorithm ...")
+        self.update_status(Status.initializing, "Start execution  ...")
 
     def execution_stop(self) -> None:
         """Finish the execution and update the duration and status of execution."""
@@ -288,13 +309,11 @@ class Execution:
         minutes, seconds = divmod(remainder, 60)
         duration = f"{round(hours, 0)}H {round(minutes, 0)}min {round(seconds, 4)}sec"
 
-        if self._ml_object._is_notebook:
-            self._create_notebook_checkpoint()
-
         self.update_status(Status.completed, "Algorithm execution ended.")
-        self._ml_object.pathBuilder.schemas[self._ml_object.ml_schema].Execution.update(
-            [{"RID": self.execution_rid, "Duration": duration}]
-        )
+        if not self._dry_run:
+            self._ml_object.pathBuilder.schemas[
+                self._ml_object.ml_schema
+            ].Execution.update([{"RID": self.execution_rid, "Duration": duration}])
 
     def _upload_execution_dirs(self) -> dict[str, FileUploadState]:
         """Upload execution assets at _working_dir/Execution_asset.
@@ -402,6 +421,8 @@ class Execution:
             Uploaded assets with key as assets' suborder name, values as an
             ordered dictionary with RID and metadata in the Execution_Asset table.
         """
+        if self._dry_run:
+            return {}
         try:
             uploaded_assets = self._upload_execution_dirs()
             self.update_status(Status.completed, "Successfully end the execution.")

deriva_ml/execution_configuration.py

@@ -49,7 +49,7 @@ class ExecutionConfiguration(BaseModel):
 
     datasets: conlist(DatasetSpec) = []
     assets: list[RID | str] = []  # List of RIDs to model files.
-    workflow: RID
+    workflow: RID | Workflow
     description: str = ""
 
     model_config = ConfigDict(arbitrary_types_allowed=True)

{deriva_ml-1.9.0.dist-info → deriva_ml-1.10.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: deriva-ml
-Version: 1.9.0
+Version: 1.10.0
 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-1.10.0.dist-info}/RECORD

@@ -1,14 +1,14 @@
 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/demo_catalog.py,sha256=1442Lbxmlq45_fgFx0SZPag6dZLimXCk57-TRFee3VA,11064
 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=Yo52Sb_9rujH7ew9aJ_Ys84NZU-Tc3TGV_O--wnaUQA,47307
 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
+deriva_ml/execution.py,sha256=nPTQ__QHoBTz0gUu8k4CSEeCD4UvttZfy2oDJr9HxKY,30294
+deriva_ml/execution_configuration.py,sha256=yksebWFjAfrar2955L8_D6vUnQlfuvcyrqjOIrvWW90,3368
 deriva_ml/execution_environment.py,sha256=bCRKrCELDbGQDo7_FKfw7e8iMzVjSRZK3baKkqH5-_0,3264
 deriva_ml/feature.py,sha256=7e8WYPCfJSrGxJh9oUTduYSnB5ekybRhXa_0HIigS_w,5459
 deriva_ml/history.py,sha256=qTDLDs8Ow_6r7mDO0gZm0Fg81SWKOAgtCU5pzZoDRgM,2828
@@ -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-1.10.0.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+deriva_ml-1.10.0.dist-info/METADATA,sha256=EInfvOS4ru5OFfTQvNvFYVytQiuzHOXhiH3zISlNhmQ,942
+deriva_ml-1.10.0.dist-info/WHEEL,sha256=DK49LOLCYiurdXXOXwGJm6U4DkHkg4lcxjhqwRa0CP4,91
+deriva_ml-1.10.0.dist-info/entry_points.txt,sha256=ZiOvrYj022x544TQwi018ujeHRRDahNmwJnzn5ThacM,242
+deriva_ml-1.10.0.dist-info/top_level.txt,sha256=I1Q1dkH96cRghdsFRVqwpa2M7IqJpR2QPUNNc5-Bnpw,10
+deriva_ml-1.10.0.dist-info/RECORD,,

{deriva_ml-1.9.0.dist-info → deriva_ml-1.10.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (77.0.3)
+Generator: setuptools (78.0.2)
 Root-Is-Purelib: true
 Tag: py3-none-any