synapseclient 4.5.0__tar.gz → 4.6.0__tar.gz

{synapseclient-4.5.0/synapseclient.egg-info → synapseclient-4.6.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: synapseclient
-Version: 4.5.0
+Version: 4.6.0
 Summary: A client for Synapse, a collaborative, open-source research platform that allows teams to share data, track analyses, and collaborate.
 Home-page: https://www.synapse.org
 Author: The Synapse Engineering Team
@@ -13,10 +13,10 @@ Project-URL: Changelog, https://python-docs.synapse.org/build/html/index.html#re
 Platform: any
 Classifier: Development Status :: 5 - Production/Stable
 Classifier: Programming Language :: Python
-Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
 Classifier: Operating System :: MacOS
 Classifier: Operating System :: Microsoft :: Windows
 Classifier: Operating System :: Unix
@@ -27,7 +27,7 @@ Classifier: License :: OSI Approved :: Apache Software License
 Classifier: Topic :: Software Development :: Libraries
 Classifier: Topic :: Scientific/Engineering
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
-Requires-Python: >=3.8
+Requires-Python: <3.13,>=3.9
 Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
 Requires-Dist: requests<3.0,>=2.22.0
 Requires-Dist: urllib3<2,>=1.26.18
@@ -35,6 +35,10 @@ Requires-Dist: deprecated<2.0,>=1.2.4
 Requires-Dist: opentelemetry-api>=1.21.0
 Requires-Dist: opentelemetry-sdk>=1.21.0
 Requires-Dist: opentelemetry-exporter-otlp-proto-http>=1.21.0
+Requires-Dist: opentelemetry-instrumentation-httpx>=0.48b0
+Requires-Dist: opentelemetry-instrumentation-requests>=0.48b0
+Requires-Dist: opentelemetry-instrumentation-threading>=0.48b0
+Requires-Dist: opentelemetry-instrumentation-urllib>=0.48b0
 Requires-Dist: nest-asyncio~=1.6.0
 Requires-Dist: asyncio-atexit~=1.0.1
 Requires-Dist: httpx~=0.27.0
@@ -67,7 +71,6 @@ Requires-Dist: pytest-cov~=4.1.0; extra == "tests"
 Requires-Dist: pandas<3.0,>=1.5; extra == "tests"
 Provides-Extra: pandas
 Requires-Dist: pandas<3.0,>=1.5; extra == "pandas"
-Requires-Dist: numpy<2.0.0; extra == "pandas"
 Provides-Extra: pysftp
 Requires-Dist: pysftp<0.3,>=0.2.8; extra == "pysftp"
 Provides-Extra: boto3
@@ -119,9 +122,9 @@ or by sending an email to [python-announce+subscribe@sagebase.org](mailto:python
 Installation
 ------------
 
-The Python Synapse client has been tested on 3.8, 3.9, 3.10 and 3.11 on Mac OS X, Ubuntu Linux and Windows.
+The Python Synapse client has been tested on versions 3.9, 3.10, 3.11 and 3.12 on Mac OS X, Ubuntu Linux and Windows.
 
-**Starting from Synapse Python client version 3.0, Synapse Python client requires Python >= 3.8**
+**Starting from Synapse Python client version 3.0, Synapse Python client requires Python >= 3.9**
 
 ### Install using pip
 
@@ -396,6 +399,7 @@ trace.set_tracer_provider(
 )
 trace.get_tracer_provider().add_span_processor(BatchSpanProcessor(OTLPSpanExporter()))
 tracer = trace.get_tracer("my_tracer")
+synapseclient.Synapse.enable_open_telemetry(True)
 
 @tracer.start_as_current_span("my_span_name")
 def main():

{synapseclient-4.5.0 → synapseclient-4.6.0}/README.md

@@ -36,9 +36,9 @@ or by sending an email to [python-announce+subscribe@sagebase.org](mailto:python
 Installation
 ------------
 
-The Python Synapse client has been tested on 3.8, 3.9, 3.10 and 3.11 on Mac OS X, Ubuntu Linux and Windows.
+The Python Synapse client has been tested on versions 3.9, 3.10, 3.11 and 3.12 on Mac OS X, Ubuntu Linux and Windows.
 
-**Starting from Synapse Python client version 3.0, Synapse Python client requires Python >= 3.8**
+**Starting from Synapse Python client version 3.0, Synapse Python client requires Python >= 3.9**
 
 ### Install using pip
 
@@ -313,6 +313,7 @@ trace.set_tracer_provider(
 )
 trace.get_tracer_provider().add_span_processor(BatchSpanProcessor(OTLPSpanExporter()))
 tracer = trace.get_tracer("my_tracer")
+synapseclient.Synapse.enable_open_telemetry(True)
 
 @tracer.start_as_current_span("my_span_name")
 def main():

{synapseclient-4.5.0 → synapseclient-4.6.0}/setup.cfg

@@ -17,10 +17,10 @@ platforms = any
 classifiers = 
 	Development Status :: 5 - Production/Stable
 	Programming Language :: Python
-	Programming Language :: Python :: 3.8
 	Programming Language :: Python :: 3.9
 	Programming Language :: Python :: 3.10
 	Programming Language :: Python :: 3.11
+	Programming Language :: Python :: 3.12
 	Operating System :: MacOS
 	Operating System :: Microsoft :: Windows
 	Operating System :: Unix
@@ -36,7 +36,7 @@ classifiers =
 zip_safe = False
 include_package_data = True
 packages = find:
-python_requires = >=3.8
+python_requires = >=3.9, <3.13
 install_requires = 
 	requests>=2.22.0,<3.0
 	urllib3>=1.26.18,<2
@@ -44,6 +44,10 @@ install_requires =
 	opentelemetry-api>=1.21.0
 	opentelemetry-sdk>=1.21.0
 	opentelemetry-exporter-otlp-proto-http>=1.21.0
+	opentelemetry-instrumentation-httpx>=0.48b0
+	opentelemetry-instrumentation-requests>=0.48b0
+	opentelemetry-instrumentation-threading>=0.48b0
+	opentelemetry-instrumentation-urllib>=0.48b0
 	nest-asyncio~=1.6.0
 	asyncio-atexit~=1.0.1
 	httpx~=0.27.0
@@ -89,7 +93,6 @@ tests =
 	pandas>=1.5,<3.0
 pandas = 
 	pandas>=1.5,<3.0
-	numpy<2.0.0
 pysftp = 
 	pysftp>=0.2.8,<0.3
 boto3 = 

{synapseclient-4.5.0 → synapseclient-4.6.0}/synapseclient/__init__.py

@@ -31,12 +31,9 @@ from .table import (
 from .team import Team, TeamMember, UserGroupHeader, UserProfile
 from .wiki import Wiki
 
-# ref = importlib.resources.files(__name__).joinpath("synapsePythonClient")
-# with ref.open("r") as fp:
-#     __version__ = json.load(fp)["latestVersion"]
-# TODO: switch to the above after python 3.8 is deprecated
-with importlib.resources.path(__name__, "synapsePythonClient") as ref:
-    __version__ = json.load(open(ref))["latestVersion"]
+ref = importlib.resources.files(__name__).joinpath("synapsePythonClient")
+with ref.open("r") as fp:
+    __version__ = json.load(fp)["latestVersion"]
 
 __all__ = [
     # objects

{synapseclient-4.5.0 → synapseclient-4.6.0}/synapseclient/api/annotations.py

@@ -24,8 +24,9 @@ def set_annotations(
     Arguments:
         annotations: The annotations to set. This is expected to have the id, etag,
             and annotations filled in.
-        synapse_client: If not passed in or None this will use the last client from
-            the `.login()` method.
+        synapse_client: If not passed in and caching was not disabled by
+                `Synapse.allow_client_caching(False)` this will use the last created
+                instance from the Synapse class constructor.
 
     Returns: The annotations set in Synapse.
     """
@@ -58,8 +59,9 @@ async def set_annotations_async(
     Arguments:
         annotations: The annotations to set. This is expected to have the id, etag,
             and annotations filled in.
-        synapse_client: If not passed in or None this will use the last client from
-            the `.login()` method.
+        synapse_client: If not passed in and caching was not disabled by
+                `Synapse.allow_client_caching(False)` this will use the last created
+                instance from the Synapse class constructor.
 
     Returns: The annotations set in Synapse.
     """

{synapseclient-4.5.0 → synapseclient-4.6.0}/synapseclient/api/entity_bundle_services_v2.py

@@ -26,8 +26,9 @@ async def get_entity_id_bundle2(
             - includeAnnotations: True
             - includeFileHandles: True
             - includeRestrictionInformation: True
-        synapse_client: If not passed in or None this will use the last client from
-            the `.login()` method.
+        synapse_client: If not passed in and caching was not disabled by
+                `Synapse.allow_client_caching(False)` this will use the last created
+                instance from the Synapse class constructor.
 
     Returns:
         The requested entity bundle matching
@@ -69,8 +70,9 @@ async def get_entity_id_version_bundle2(
             - includeAnnotations: True
             - includeFileHandles: True
             - includeRestrictionInformation: True
-        synapse_client: If not passed in or None this will use the last client from
-            the `.login()` method.
+        synapse_client: If not passed in and caching was not disabled by
+                `Synapse.allow_client_caching(False)` this will use the last created
+                instance from the Synapse class constructor.
 
     Returns:
         The requested entity bundle matching
@@ -103,8 +105,9 @@ async def post_entity_bundle2_create(
         request: The request for the bundle matching
             <https://rest-docs.synapse.org/rest/org/sagebionetworks/repo/model/entitybundle/v2/EntityBundleCreate.html>
         generated_by: The ID of the activity to associate with the entity.
-        synapse_client: If not passed in or None this will use the last client from
-            the `.login()` method.
+        synapse_client: If not passed in and caching was not disabled by
+                `Synapse.allow_client_caching(False)` this will use the last created
+                instance from the Synapse class constructor.
 
     Returns:
         The requested entity bundle matching
@@ -133,8 +136,9 @@ async def put_entity_id_bundle2(
         request: The request for the bundle matching
             <https://rest-docs.synapse.org/rest/org/sagebionetworks/repo/model/entitybundle/v2/EntityBundleCreate.html>
         generated_by: The ID of the activity to associate with the entity.
-        synapse_client: If not passed in or None this will use the last client from
-            the `.login()` method.
+        synapse_client: If not passed in and caching was not disabled by
+                `Synapse.allow_client_caching(False)` this will use the last created
+                instance from the Synapse class constructor.
 
     Returns:
         The requested entity bundle matching

{synapseclient-4.5.0 → synapseclient-4.6.0}/synapseclient/api/entity_factory.py

@@ -59,8 +59,9 @@ async def get_from_entity_factory(
             hop to the target of the link.
         entity_to_update: An existing entity class instance to update with data from
             Synapse.
-        synapse_client: If not passed in or None this will use the last client from
-            the `.login()` method.
+        synapse_client: If not passed in and caching was not disabled by
+                `Synapse.allow_client_caching(False)` this will use the last created
+                instance from the Synapse class constructor.
 
         Example: Using this function
             Download file into cache
@@ -127,7 +128,10 @@ async def get_from_entity_factory(
 
     # Check and warn for unmet access requirements
     _check_entity_restrictions(
-        bundle=bundle, synapse_id=bundle["entity"]["id"], download_file=download_file
+        bundle=bundle,
+        synapse_id=bundle["entity"]["id"],
+        download_file=download_file,
+        synapse_client=synapse_client,
     )
 
     return_data = await _cast_into_class_type(
@@ -166,8 +170,9 @@ async def _search_for_file_by_md5(
         md5: The MD5 of the file to retrieve. If not passed in, the MD5 will be
             calculated.
         limit_search: Limit the search to a specific project or folder.
-        synapse_client: If not passed in or None this will use the last client from
-            the `.login()` method.
+        synapse_client: If not passed in and caching was not disabled by
+                `Synapse.allow_client_caching(False)` this will use the last created
+                instance from the Synapse class constructor.
 
     Returns:
         A dictionary containing the entity bundle of the file found.
@@ -255,8 +260,9 @@ async def _cast_into_class_type(
             hop to the target of the link.
         entity_to_update: An existing entity class instance to update with data from
             Synapse.
-        synapse_client: If not passed in or None this will use the last client from
-            the `.login()` method.
+        synapse_client: If not passed in and caching was not disabled by
+                `Synapse.allow_client_caching(False)` this will use the last created
+                instance from the Synapse class constructor.
 
     Returns:
         A Synapse entity object.

{synapseclient-4.5.0 → synapseclient-4.6.0}/synapseclient/api/entity_services.py

@@ -22,8 +22,9 @@ async def post_entity(
         request: The request for the entity matching
             <https://rest-docs.synapse.org/rest/org/sagebionetworks/repo/model/Entity.html>
         generated_by: The ID of the activity to associate with the entity.
-        synapse_client: If not passed in or None this will use the last client from
-            the `.login()` method.
+        synapse_client: If not passed in and caching was not disabled by
+                `Synapse.allow_client_caching(False)` this will use the last created
+                instance from the Synapse class constructor.
 
     Returns:
         The requested entity matching
@@ -55,8 +56,9 @@ async def put_entity(
             <https://rest-docs.synapse.org/rest/org/sagebionetworks/repo/model/Entity.html>
         new_version: If true, a new version of the entity will be created.
         generated_by: The ID of the activity to associate with the entity.
-        synapse_client: If not passed in or None this will use the last client from
-            the `.login()` method.
+        synapse_client: If not passed in and caching was not disabled by
+                `Synapse.allow_client_caching(False)` this will use the last created
+                instance from the Synapse class constructor.
 
     Returns:
         The requested entity bundle matching
@@ -84,8 +86,9 @@ async def get_entity(
     """
     Arguments:
         entity_id: The ID of the entity.
-        synapse_client: If not passed in or None this will use the last client from
-            the `.login()` method.
+        synapse_client: If not passed in and caching was not disabled by
+                `Synapse.allow_client_caching(False)` this will use the last created
+                instance from the Synapse class constructor.
 
     Returns:
         The requested entity bundle matching
@@ -113,8 +116,9 @@ async def get_upload_destination(
 
     Arguments:
         entity_id: The ID of the entity.
-        synapse_client: If not passed in or None this will use the last client from
-            the `.login()` method.
+        synapse_client: If not passed in and caching was not disabled by
+                `Synapse.allow_client_caching(False)` this will use the last created
+                instance from the Synapse class constructor.
 
     Returns:
         The upload destination.
@@ -138,8 +142,9 @@ async def get_upload_destination_location(
     Arguments:
         entity_id: The ID of the entity.
         location: A storage location ID of the upload destination.
-        synapse_client: If not passed in or None this will use the last client from
-            the `.login()` method.
+        synapse_client: If not passed in and caching was not disabled by
+                `Synapse.allow_client_caching(False)` this will use the last created
+                instance from the Synapse class constructor.
 
     Returns:
         The upload destination.
@@ -162,8 +167,9 @@ async def create_access_requirements_if_none(
 
     Arguments:
         entity_id: The ID of the entity.
-        synapse_client: If not passed in or None this will use the last client from
-            the `.login()` method.
+        synapse_client: If not passed in and caching was not disabled by
+                `Synapse.allow_client_caching(False)` this will use the last created
+                instance from the Synapse class constructor.
     """
     from synapseclient import Synapse
 
@@ -195,8 +201,9 @@ async def delete_entity_generated_by(
     """
     Arguments:
         entity_id: The ID of the entity.
-        synapse_client: If not passed in or None this will use the last client from
-            the `.login()` method.
+        synapse_client: If not passed in and caching was not disabled by
+                `Synapse.allow_client_caching(False)` this will use the last created
+                instance from the Synapse class constructor.
 
     Returns: None
     """
@@ -219,8 +226,9 @@ async def get_entity_path(
 
     Arguments:
         entity_id: The ID of the entity.
-        synapse_client: If not passed in or None this will use the last client from
-            the `.login()` method.
+        synapse_client: If not passed in and caching was not disabled by
+                `Synapse.allow_client_caching(False)` this will use the last created
+                instance from the Synapse class constructor.
 
     Returns:
         Entity paths matching:
@@ -245,8 +253,9 @@ async def get_entities_by_md5(
 
     Arguments:
         md5: The MD5 of the entity.
-        synapse_client: If not passed in or None this will use the last client from
-            the `.login()` method.
+        synapse_client: If not passed in and caching was not disabled by
+                `Synapse.allow_client_caching(False)` this will use the last created
+                instance from the Synapse class constructor.
 
     Returns:
         Paginated results of:

{synapseclient-4.5.0 → synapseclient-4.6.0}/synapseclient/api/file_services.py

@@ -36,8 +36,9 @@ async def post_file_multipart(
         force_restart: Optional parameter. When True, any upload state for the given
             file will be cleared and a new upload will be started.
         endpoint: Server endpoint to call to.
-        synapse_client: If not passed in or None this will use the last client from
-            the `.login()` method.
+        synapse_client: If not passed in and caching was not disabled by
+                `Synapse.allow_client_caching(False)` this will use the last created
+                instance from the Synapse class constructor.
 
     Returns:
         The requested multipart upload status matching
@@ -87,8 +88,9 @@ async def put_file_multipart_add(
         md5_hex: The MD5 of the uploaded part represented as a hexadecimal string. If
             the provided MD5 does not match the MD5 of the uploaded part, the add
             will fail.
-        synapse_client: If not passed in or None this will use the last client from
-            the `.login()` method.
+        synapse_client: If not passed in and caching was not disabled by
+                `Synapse.allow_client_caching(False)` this will use the last created
+                instance from the Synapse class constructor.
 
     Returns:
         Object matching
@@ -126,8 +128,9 @@ async def put_file_multipart_complete(
     Arguments:
         upload_id: The unique identifier of the file upload.
         endpoint: Server endpoint to call to.
-        synapse_client: If not passed in or None this will use the last client from
-            the `.login()` method.
+        synapse_client: If not passed in and caching was not disabled by
+                `Synapse.allow_client_caching(False)` this will use the last created
+                instance from the Synapse class constructor.
 
     Returns:
         Object matching
@@ -154,8 +157,9 @@ async def post_file_multipart_presigned_urls(
     Arguments:
         upload_id: The unique identifier of the file upload.
         part_numbers: The part numbers to get pre-signed URLs for.
-        synapse_client: If not passed in or None this will use the last client from
-            the `.login()` method.
+        synapse_client: If not passed in and caching was not disabled by
+                `Synapse.allow_client_caching(False)` this will use the last created
+                instance from the Synapse class constructor.
 
     Returns:
         Object matching
@@ -199,8 +203,9 @@ async def post_external_object_store_filehandle(
         storage_location_id: The optional storage location descriptor
         mimetype:            The Mimetype of the file, if known.
         md5:                 The file's content MD5, if known.
-        synapse_client: If not passed in or None this will use the last client from
-            the `.login()` method.
+        synapse_client: If not passed in and caching was not disabled by
+                `Synapse.allow_client_caching(False)` this will use the last created
+                instance from the Synapse class constructor.
 
     Returns:
         A FileHandle for objects that are stored externally.
@@ -243,8 +248,9 @@ async def post_external_filehandle(
         mimetype:     The Mimetype of the file, if known.
         md5:          The file's content MD5.
         file_size:    The size of the file in bytes.
-        synapse_client: If not passed in or None this will use the last client from
-            the `.login()` method.
+        synapse_client: If not passed in and caching was not disabled by
+                `Synapse.allow_client_caching(False)` this will use the last created
+                instance from the Synapse class constructor.
 
     Returns:
         A FileHandle for objects that are stored externally.
@@ -299,8 +305,9 @@ async def post_external_s3_file_handle(
             mutually exclusive with parent
         mimetype: Mimetype of the file, if known
         md5: MD5 of the file, if known
-        synapse_client: If not passed in or None this will use the last client from
-            the `.login()` method.
+        synapse_client: If not passed in and caching was not disabled by
+                `Synapse.allow_client_caching(False)` this will use the last created
+                instance from the Synapse class constructor.
 
     Returns:
         The created file handle.
@@ -360,8 +367,9 @@ async def get_file_handle(
 
     Arguments:
         file_handle_id: The ID of the file handle to look up.
-        synapse_client: If not passed in or None this will use the last client from
-            the `.login()` method.
+        synapse_client: If not passed in and caching was not disabled by
+                `Synapse.allow_client_caching(False)` this will use the last created
+                instance from the Synapse class constructor.
 
     Returns:
         A file handle retrieved from the file handle service.
@@ -392,8 +400,9 @@ async def get_file_handle_for_download_async(
         entity_type:     Type of object associated with a file e.g. FileEntity,
             TableEntity
             <https://rest-docs.synapse.org/rest/org/sagebionetworks/repo/model/file/FileHandleAssociateType.html>
-        synapse_client: If not passed in or None this will use the last client from
-            the `.login()` method.
+        synapse_client: If not passed in and caching was not disabled by
+                `Synapse.allow_client_caching(False)` this will use the last created
+                instance from the Synapse class constructor.
 
     Raises:
         SynapseFileNotFoundError: If the fileHandleId is not found in Synapse.
@@ -452,8 +461,9 @@ def get_file_handle_for_download(
         entity_type:     Type of object associated with a file e.g. FileEntity,
             TableEntity
             <https://rest-docs.synapse.org/rest/org/sagebionetworks/repo/model/file/FileHandleAssociateType.html>
-        synapse_client: If not passed in or None this will use the last client from
-            the `.login()` method.
+        synapse_client: If not passed in and caching was not disabled by
+                `Synapse.allow_client_caching(False)` this will use the last created
+                instance from the Synapse class constructor.
 
     Raises:
         SynapseFileNotFoundError: If the fileHandleId is not found in Synapse.