deriva-ml 1.14.43__py3-none-any.whl → 1.14.44__py3-none-any.whl

deriva_ml/dataset/dataset.py

@@ -1289,8 +1289,8 @@ class Dataset:
                 {
                     "processor": "fetch",
                     "processor_params": {
-                        "query_path": f"/attribute/{spath}/!(URL::null::)/url:=URL,length:=Length,filename:=Filename,md5:=MD5",
-                        "output_path": f"asset/{table.name}",
+                        "query_path": f"/attribute/{spath}/!(URL::null::)/url:=URL,length:=Length,filename:=Filename,md5:=MD5,asset_rid:=RID",
+                        "output_path": "asset/{asset_rid}/" + table.name,
                     },
                 }
             )
@@ -1341,9 +1341,9 @@ class Dataset:
                     "source": {
                         "skip_root_path": False,
                         "api": "attribute",
-                        "path": f"{spath}/!(URL::null::)/url:=URL,length:=Length,filename:=Filename,md5:=MD5",
+                        "path": f"{spath}/!(URL::null::)/url:=URL,length:=Length,filename:=Filename,md5:=MD5, asset_rid:=RID",
                     },
-                    "destination": {"name": f"asset/{table.name}", "type": "fetch"},
+                    "destination": {"name": "asset/{asset_rid}/" + table.name, "type": "fetch"},
                 }
             )
         return exports

deriva_ml/dataset/upload.py

@@ -296,7 +296,6 @@ def upload_directory(model: DerivaModel, directory: Path | str) -> dict[Any, Fil
 
         with spec_file.open("w+") as cfile:
             json.dump(bulk_upload_configuration(model), cfile)
-        print("Creating GenericUploader...")
         uploader = GenericUploader(
             server={
                 "host": model.hostname,
@@ -318,7 +317,6 @@ def upload_directory(model: DerivaModel, directory: Path | str) -> dict[Any, Fil
             }
         finally:
             uploader.cleanup()
-            print(f"Cleanup called...{uploader}")
         return results
 
 

deriva_ml/run_notebook.py

@@ -10,7 +10,7 @@ import nbformat
 import papermill as pm
 import regex as re
 from deriva.core import BaseCLI
-from nbconvert import HTMLExporter
+from nbconvert import MarkdownExporter
 
 from deriva_ml import DerivaML, ExecAssetType, Execution, ExecutionConfiguration, MLAsset, Workflow
 
@@ -157,11 +157,16 @@ class DerivaMLRunNotebookCLI(BaseCLI):
             )
 
             # Generate an HTML version of the output notebook.
+            notebook_output_md = notebook_output.with_suffix(".md")
+            with notebook_output.open() as f:
+                nb = nbformat.read(f, as_version=4)
+            # Convert to Markdown
+            exporter = MarkdownExporter()
+            (body, resources) = exporter.from_notebook_node(nb)
+
+            with notebook_output_md.open("w") as f:
+                f.write(body)
             nb = nbformat.read(notebook_output, as_version=4)
-            html_exporter = HTMLExporter(template_name="classic")
-            body, resources = html_exporter.from_notebook_node(nb)
-            notebook_output_html = notebook_output.with_suffix(".html")
-            notebook_output_html.write_text(body, encoding="utf-8")
 
             execution.asset_file_path(
                 asset_name=MLAsset.execution_asset,
@@ -171,12 +176,12 @@ class DerivaMLRunNotebookCLI(BaseCLI):
 
             execution.asset_file_path(
                 asset_name=MLAsset.execution_asset,
-                file_name=notebook_output_html,
+                file_name=notebook_output_md,
                 asset_types=ExecAssetType.notebook_output,
             )
             execution.asset_file_path(
                 asset_name=MLAsset.execution_asset,
-                file_name=notebook_output_html,
+                file_name=notebook_output_md,
                 asset_types=ExecAssetType.notebook_output,
             )
             print("parameter....")

{deriva_ml-1.14.43.dist-info → deriva_ml-1.14.44.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: deriva-ml
-Version: 1.14.43
+Version: 1.14.44
 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-1.14.43.dist-info → deriva_ml-1.14.44.dist-info}/RECORD

@@ -3,7 +3,7 @@ deriva_ml/bump_version.py,sha256=KpHmkpEztly2QHYL4dyaIGdEMyP4F0D89rawyh5EDTs,398
 deriva_ml/demo_catalog.py,sha256=JjPAIac_hKPh5krEhGJydjXquRnivi7kQoR8W4Khp-s,14928
 deriva_ml/feature.py,sha256=6-aphkxdKjWa9oPSGFWxHcwAc_8hmWj-7I4M178YG5Y,8470
 deriva_ml/install_kernel.py,sha256=b62XY0SLViYO_Zye5r1Pl9qhYZyu_fk4KAO8NS1pxgM,2165
-deriva_ml/run_notebook.py,sha256=2pGv6dNTH0TuCz7E6GBS4MMzF5IyH-Tbv1i46rsJLLQ,7923
+deriva_ml/run_notebook.py,sha256=U3Bz-PdYYMIo_KZwDwlyKJtnZEMKwJjLh5Jn-M8ChUI,8039
 deriva_ml/core/__init__.py,sha256=V_i90pc5PB1F4UdOO6DZWzpEFaZDTaPRU-EzKXQ19eI,787
 deriva_ml/core/base.py,sha256=5H0GEMlKXUVRXBYXJQ25kxdscB6uX1wIKSUAM_CBOhI,61228
 deriva_ml/core/constants.py,sha256=6wBJ8qMxe-dbCjRGrjUIX-RK0mTWrLDTeUpaVbLFoM8,888
@@ -14,10 +14,10 @@ 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=drL0YZovPpQC9G_eYe-fWuFQFysK2X-ad0vL4ZsYkf0,64396
+deriva_ml/dataset/dataset.py,sha256=AU27ZtzDSpCodtbq9T-8AtqiA-x8r78wQvFBOCgaqsQ,64451
 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=7C9v4CmH3OGjBKdPl-OPvygseuAEtDjy3atSwmhgGBs,16524
+deriva_ml/dataset/upload.py,sha256=i_7KLfRSd2-THqZ1aG2OFAFGoyb8dJBCZZ5t1ftrtMQ,16429
 deriva_ml/execution/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 deriva_ml/execution/environment.py,sha256=B7nywqxFTRUWgyu8n7rFoKcVC9on422kjeFG2FPQfvg,9302
 deriva_ml/execution/execution.py,sha256=JH2alK-7DoRzfGvjsrNhD_tZqoZkb736bxbbgXDP33o,44780
@@ -34,9 +34,9 @@ deriva_ml/schema/create_schema.py,sha256=9qK9_8SRQT-DwcEwTGSkhi3j2NaoH5EVgthvV2k
 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-1.14.43.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-deriva_ml-1.14.43.dist-info/METADATA,sha256=ktO6NAE5LHzYsCkS-CEK2OELB_Wqc97_3X7rhjLgrfY,1168
-deriva_ml-1.14.43.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-deriva_ml-1.14.43.dist-info/entry_points.txt,sha256=XsHSbfp7S1cKMjHoPUdFIaFcp9lHXHS6CV1zb_MEXkg,463
-deriva_ml-1.14.43.dist-info/top_level.txt,sha256=I1Q1dkH96cRghdsFRVqwpa2M7IqJpR2QPUNNc5-Bnpw,10
-deriva_ml-1.14.43.dist-info/RECORD,,
+deriva_ml-1.14.44.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+deriva_ml-1.14.44.dist-info/METADATA,sha256=Kq-OKAhKOm-JW2HbMoNsZIRWy8oT6v7-CYz4whIqCbo,1168
+deriva_ml-1.14.44.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+deriva_ml-1.14.44.dist-info/entry_points.txt,sha256=XsHSbfp7S1cKMjHoPUdFIaFcp9lHXHS6CV1zb_MEXkg,463
+deriva_ml-1.14.44.dist-info/top_level.txt,sha256=I1Q1dkH96cRghdsFRVqwpa2M7IqJpR2QPUNNc5-Bnpw,10
+deriva_ml-1.14.44.dist-info/RECORD,,