V4.13.0 rc dev

CLAUDE.md

@@ -102,6 +102,11 @@ synapseutils/          # Legacy bulk utilities (copy, sync, migrate, walk) — s
 
 Data flow: User → `operations/` factory → model async methods → `api/` service functions → `client.py` REST calls → Synapse API. Responses deserialized via `fill_from_dict()` on model instances.
 
+### Optional dependency imports
+pandas, boto3, pysftp, and other optional extras must never be imported at the top level of any module. Always import them lazily inside the functions/methods that need them. A top-level import of an optional dependency will crash the CLI and any code path that imports the module — even for unrelated operations like `synapse --version`.
+
+For type annotations referencing pandas types, use `DATA_FRAME_TYPE` and `SERIES_TYPE` from `core/typing_utils.py` rather than `pd.DataFrame` or `pd.Series`. These aliases resolve correctly at type-check time without requiring pandas at runtime.
+
 ## Constraints
 
 - Do not use Pydantic for models — the codebase uses stdlib dataclasses with custom serialization. Mixing would break the `@async_to_sync` decorator and `fill_from_dict()` pattern.

docs/guides/extensions/curator/metadata_contribution.md

@@ -126,7 +126,7 @@ import numpy as np
 df = pd.read_csv(csv_path)
 print(df)
 
-# Smoke-test stand-in: fills 4 rows with random integers regardless of column type.
+# Example only: fills 4 rows with random integers regardless of column type.
 # Replace this with real edits that match your task's schema before importing —
 # schema validation runs in Step 6 and will reject values that don't fit.
 df = pd.DataFrame(

docs/guides/extensions/curator/metadata_curation.md

@@ -115,7 +115,7 @@ entity_view_id, task_id = create_file_based_metadata_task(
     attach_wiki=False,                 # Creates a wiki in the folder with the entity view (Defaults to False)
     entity_view_name="Animal Study Files View",
     schema_uri=schema_uri,             # Schema found in Step 2
-    assignee_principal_id=123456     # Optional: Assign to a user or team
+    assignee_principal_id=123456,    # Optional: Assign to a user or team
     view_type_mask=ViewTypeMask.FILE   # Optional: include additional entity types in the view (ViewTypeMask.FILE | ViewTypeMask.DOCKER). (Defaults to ViewTypeMask.FILE)
 )
 
@@ -184,7 +184,7 @@ entity_view_id, task_id = create_file_based_metadata_task(
     attach_wiki=True,
     entity_view_name="Animal Study Files View",
     schema_uri=schema_uri,
-    assignee_principal_id=123456  # Optional: Assign to a user or team
+    assignee_principal_id=123456,  # Optional: Assign to a user or team
     view_type_mask=ViewTypeMask.FILE   # Optional: include additional entity types in the view (ViewTypeMask.FILE | ViewTypeMask.DOCKER). (Defaults to ViewTypeMask.FILE)
 )
 

docs/news.md

@@ -9,6 +9,67 @@ detailing some of the changes.
 the 4.x.x versions hidden behind optional feature flags or different import paths. Any
 breaking changes will not be included until v5.0.
 
+## 4.13.0
+
+## Highlights
+
+- `sync_to_synapse` / `sync_from_synapse` to enable bulk upload/download operations on OOP `Project` and `Folder` models.
+- Enabling programmatic Grid collaboration through CSV import/export to Grid sessions, and Grid session to CurationTask linking for Curator.
+- Object-oriented `DownloadList`, storage locations and migration are now supported.
+- Bug fixes for table queries, Recordset versioning, async messaging, and special-character handling in row stores.
+
+## Features
+
+- [SYNPY-1802] Add DownloadList OOP model and deprecate legacy methods by @andrewelamb in #1347
+- [SYNPY-1800] Add new sync_to_synapse method on StorableContainer by @andrewelamb in #1353
+- [SYNPY-1799, SYNPY-1804] Add manifest generation to sync_from_synapse by @danlu1 in #1354
+- [SYNPY-1809] Add generate_sync_manifest method by @andrewelamb in #1373
+- [DPE-1577] Support storage locations and migration in OOP models by @BryanFauble in #1315
+- [SYNPY-1781] Implement CSV import to Grid session by @linglp in #1360
+- [SYNPY-1782] Implement CSV download from Grid session by @linglp in #1366
+- [SYNPY-1783] Implement Grid synchronization by @linglp in #1368
+- [SYNPY-1760] Add ability to link Grid to CurationTask by @andrewelamb in #1383
+- [SYNPY-1841] Add fields for CurationTask search/filtering by @andrewelamb in #1384
+- [SYNPY-1836] Support configurable view_type_mask in file-based metadata task by @BryanFauble in #1374
+
+## Bug Fixes
+
+- [SYNPY-1835] Fix query() failure when a list column is all-NA by @BryanFauble in #1390
+- [SYNPY-1832] Fix bug causing RecordSet to be updated to v2 by @andrewelamb in #1378
+- [SYNPY-1838] Prevent create_record_based_metadata_task from creating a Grid entity by @andrewelamb in #1380
+- [SYNPY-1824] Fix syn.sendMessage in async context by @linglp in #1370
+- [SYNPY-1749] Allow quote, apostrophe and ellipsis in store_row_async by @danlu1 in #1316
+
+## Tech Debt
+
+- [SYNPY-1764] Add Trivy container vulnerability scanning by @BryanFauble in #1346, #1355, #1357
+- [SYNPY-1798] Update black to 26.3.1 and rerun pre-commit by @linglp in #1341
+- Add validate-release workflow by @xschildw in #1361
+- Fix circular dependencies by @andrewelamb in #1365
+- Fix flaky integration test test_wikiAttachment by @linglp in #1363
+- Fix flaky test test_get_docker_repo_by_id by @linglp in #1381
+- Remove explicit default columns when creating EntityView in curation tests by @linglp in #1377
+- Set higher requests version minimum by @andrewelamb in #1385
+
+## Documentation
+
+- [SYNPY-1810] Migrate all docs to new reference style by @thomasyu888 in #1386
+- [SYNPY-1508] Add tutorial for downloading files by Synapse ID concurrently by @thomasyu888 in #1337
+- [SYNPY-1375] Add Activity/Provenance tutorial by @thomasyu888 in #1351
+- [SYNPY-1402] Update reticulate tutorial for new OOP models/operations API by @thomasyu888 in #1352
+- [SYNPY-1480] Improve documentation around configuration file by @thomasyu888 in #1350
+- [SYNPY-1638] Clarify that the config file is not generated upon installation by @thomasyu888 in #1387
+- Promote the usage of MCP by @thomasyu888 in #1349
+- Curator documentation: add viewtype mask by @thomasyu888 in #1382
+- Add missing MY_PROXY_SECRET_KEY variable in tutorials by @rxu17 in #1375
+- Update project name in activity.py by @thomasyu888 in #1367
+
+## Other
+
+- Add initial CLAUDE.md for AI-assisted development by @BryanFauble in #1342
+
+Full Changelog: https://github.com/Sage-Bionetworks/synapsePythonClient/compare/v4.12.0...v4.13.0
+
 ## 4.12.0
 
 ## Highlights

synapseclient/models/mixins/table_components.py

@@ -13,7 +13,6 @@
 from io import BytesIO
 from typing import Any, Dict, List, Optional, Protocol, Tuple, Union
 
-import pandas as pd
 from tqdm import tqdm
 from tqdm.contrib.logging import logging_redirect_tqdm
 from typing_extensions import Self
@@ -139,7 +138,7 @@ def row_labels_from_rows(rows: List[Row]) -> List[Row]:
     )
 
 
-def convert_dtypes_to_json_serializable(df) -> pd.DataFrame:
+def convert_dtypes_to_json_serializable(df) -> "DATA_FRAME_TYPE":
     """
     Prepare a DataFrame for JSON/CSV serialization by cleaning special values
     and normalizing dtypes. Mutates the passed-in DataFrame in place (and also
@@ -201,6 +200,8 @@ def convert_dtypes_to_json_serializable(df) -> pd.DataFrame:
         df = convert_dtypes_to_json_serializable(df)
         print(df)
     """
+    test_import_pandas()
+    import pandas as pd
 
     def _serialize_json_value(x):
         if isinstance(x, (list, dict)):

synapseclient/synapsePythonClient

@@ -1,6 +1,6 @@
 {
   "client": "synapsePythonClient",
-  "latestVersion": "4.12.0",
+  "latestVersion": "4.13.0",
   "blacklist": [
     "0.0.0",
     "0.4.1",