benchling-sdk 1.20__tar.gz → 1.21.0__tar.gz

{benchling_sdk-1.20 → benchling_sdk-1.21.0}/PKG-INFO

@@ -1,14 +1,13 @@
 Metadata-Version: 2.1
 Name: benchling-sdk
-Version: 1.20
+Version: 1.21.0
 Summary: SDK for interacting with the Benchling Platform.
 License: Apache-2.0
 Author: Benchling Support
 Author-email: support@benchling.com
-Requires-Python: >=3.8,<4.0
+Requires-Python: >=3.9,<4.0
 Classifier: License :: OSI Approved :: Apache Software License
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
@@ -17,7 +16,7 @@ Provides-Extra: python-jose
 Requires-Dist: PyYAML (>=6.0,<7.0)
 Requires-Dist: attrs (>=20.1.0)
 Requires-Dist: backoff (>=1.10.0,<3)
-Requires-Dist: benchling-api-client (==2.0.338)
+Requires-Dist: benchling-api-client (==2.0.342)
 Requires-Dist: certifi (>=2022.12.7)
 Requires-Dist: cryptography (>=42.0.0) ; extra == "cryptography"
 Requires-Dist: dataclasses-json (>=0.5.2,<0.6.0)

{benchling_sdk-1.20 → benchling_sdk-1.21.0}/benchling_sdk/apps/helpers/webhook_helpers.py

@@ -1,6 +1,6 @@
 import base64
 from datetime import datetime, timedelta, timezone
-from typing import cast, List, Protocol, Union
+from typing import Any, cast, List, Mapping, Optional, Protocol, Union
 
 from benchling_api_client.v2.benchling_client import BenchlingApiClient
 import httpx
@@ -93,7 +93,7 @@ def _production_webhook_jwks(app_definition_id: str) -> str:
 def _retrieve_jwks(
     app_installation_or_definition_id: str,
     jwk_url_provider: Union[JwkUrlProvider, LegacyJwkUrlProvider],
-    httpx_client: httpx.Client = None,
+    httpx_client: Optional[httpx.Client] = None,
 ):
     if httpx_client is None:
         httpx_client = _default_httpx_webhook_client()
@@ -106,8 +106,8 @@ def _retrieve_jwks(
 
 def jwks_by_app(
     app_id: str,
-    httpx_client: httpx.Client = None,
-    jwk_url_provider: LegacyJwkUrlProvider = None,
+    httpx_client: Optional[httpx.Client] = None,
+    jwk_url_provider: Optional[LegacyJwkUrlProvider] = None,
 ) -> jwk.JWKSet:
     """
     Get JWKs by App (Deprecated).
@@ -128,8 +128,8 @@ def jwks_by_app(
 
 def jwks_by_app_definition(
     app_definition_id: str,
-    httpx_client: httpx.Client = None,
-    jwk_url_provider: JwkUrlProvider = None,
+    httpx_client: Optional[httpx.Client] = None,
+    jwk_url_provider: Optional[JwkUrlProvider] = None,
 ) -> jwk.JWKSet:
     """
     Get JWKs for a Benchling App from its global app_definition_id.
@@ -146,7 +146,7 @@ def jwks_by_app_definition(
 
 
 def verify_app_installation(
-    app_id: str, data: str, headers: dict, jwk_function: LegacyGetJwksFunction = None
+    app_id: str, data: str, headers: Mapping[str, Any], jwk_function: Optional[LegacyGetJwksFunction] = None
 ) -> None:
     """
     Verify a webhook for an app installation (Deprecated).
@@ -162,7 +162,12 @@ def verify_app_installation(
     _verify(app_id, data, headers, jwk_function)
 
 
-def verify(app_definition_id: str, data: str, headers: dict, jwk_function: GetJwksFunction = None) -> None:
+def verify(
+    app_definition_id: str,
+    data: str,
+    headers: Mapping[str, Any],
+    jwk_function: Optional[GetJwksFunction] = None,
+) -> None:
     """
     Verify a webhook for a Benchling App from its global app_definition_id.
 
@@ -196,7 +201,7 @@ def _has_valid_signature(to_verify: str, jwks: jwk.JWKSet, encoded_signatures: L
 def _verify(
     app_installation_or_definition_id: str,
     data: str,
-    headers: dict,
+    headers: Mapping[str, Any],
     jwk_function: Union[GetJwksFunction, LegacyGetJwksFunction],
 ) -> None:
     _verify_headers_present(headers)
@@ -226,7 +231,7 @@ def _der_signatures_from_versioned_signatures(versioned_signatures: str) -> List
     return der_signatures
 
 
-def _verify_headers_present(headers: dict) -> None:
+def _verify_headers_present(headers: Mapping[str, Any]) -> None:
     """
     Verify Headers Present.
 

{benchling_sdk-1.20 → benchling_sdk-1.21.0}/benchling_sdk/auth/client_credentials_oauth2.py

@@ -70,7 +70,7 @@ class ClientCredentialsOAuth2(AuthorizationMethod):
         self,
         client_id: str,
         client_secret: str,
-        token_url: str = None,
+        token_url: Optional[str] = None,
         httpx_client: Optional[httpx.Client] = None,
     ):
         """

{benchling_sdk-1.20 → benchling_sdk-1.21.0}/benchling_sdk/services/v2/stable/aa_sequence_service.py

@@ -111,7 +111,7 @@ class AaSequenceService(BaseService):
         creator_ids: Optional[Iterable[str]] = None,
         sort: Optional[ListAASequencesSort] = None,
         page_size: Optional[int] = None,
-        next_token: NextToken = None,
+        next_token: Optional[NextToken] = None,
         author_idsany_of: Optional[Iterable[str]] = None,
         returning: Optional[Iterable[str]] = None,
     ) -> Response[AaSequencesPaginatedList]:

{benchling_sdk-1.20 → benchling_sdk-1.21.0}/benchling_sdk/services/v2/stable/app_service.py

@@ -389,7 +389,7 @@ class AppService(BaseService):
         enabled: Optional[ListAppCanvasesEnabled] = None,
         archive_reason: Optional[str] = None,
         sort: Optional[Union[str, ListAppCanvasesSort]] = None,
-        next_token: NextToken = None,
+        next_token: Optional[NextToken] = None,
         page_size: Optional[int] = None,
     ) -> Response[AppCanvasesPaginatedList]:
         response = list_app_canvases.sync_detailed(
@@ -555,7 +555,7 @@ class AppService(BaseService):
         modified_at_gte: Optional[datetime] = None,
         sort: Optional[ListAppSessionsSort] = None,
         returning: Optional[Iterable[str]] = None,
-        next_token: NextToken = None,
+        next_token: Optional[NextToken] = None,
         page_size: Optional[int] = None,
     ) -> Response[AppSessionsPaginatedList]:
         response = list_app_sessions.sync_detailed(

{benchling_sdk-1.20 → benchling_sdk-1.21.0}/benchling_sdk/services/v2/stable/assay_result_service.py

@@ -71,7 +71,7 @@ class AssayResultService(BaseService):
         max_created_time: Optional[int] = None,
         entity_ids: Optional[Iterable[str]] = None,
         assay_run_ids: Optional[Iterable[str]] = None,
-        next_token: NextToken = None,
+        next_token: Optional[NextToken] = None,
         page_size: Optional[int] = None,
         ids: Optional[Iterable[str]] = None,
         storage_ids: Optional[Iterable[str]] = None,

{benchling_sdk-1.20 → benchling_sdk-1.21.0}/benchling_sdk/services/v2/stable/assay_run_service.py

@@ -67,7 +67,7 @@ class AssayRunService(BaseService):
         schema_id: str,
         min_created_time: Optional[int] = None,
         max_created_time: Optional[int] = None,
-        next_token: NextToken = None,
+        next_token: Optional[NextToken] = None,
         page_size: Optional[int] = None,
         ids: Optional[Iterable[str]] = None,
     ) -> Response[AssayRunsPaginatedList]:
@@ -152,7 +152,7 @@ class AssayRunService(BaseService):
         self,
         assay_run_id: str,
         modified_at: Optional[str] = None,
-        next_token: NextToken = None,
+        next_token: Optional[NextToken] = None,
     ) -> Response[AutomationFileInputsPaginatedList]:
         response = list_automation_input_generators.sync_detailed(
             client=self.client,
@@ -186,7 +186,7 @@ class AssayRunService(BaseService):
     def _automation_output_processors_page(
         self,
         assay_run_id: str,
-        next_token: NextToken = None,
+        next_token: Optional[NextToken] = None,
     ) -> Response[AutomationOutputProcessorsPaginatedList]:
         """Deprecated in favor of lab_automation.automation_output_processors."""
         log_deprecation(

{benchling_sdk-1.20 → benchling_sdk-1.21.0}/benchling_sdk/services/v2/stable/codon_usage_table_service.py

@@ -30,7 +30,7 @@ class CodonUsageTableService(BaseService):
         name_includes: Optional[str] = None,
         names_any_of: Optional[Iterable[str]] = [],
         page_size: Optional[int] = None,
-        next_token: NextToken = None,
+        next_token: Optional[NextToken] = None,
     ) -> Response[CodonUsageTablesPaginatedList]:
         response = list_codon_usage_tables.sync_detailed(
             client=self.client,

{benchling_sdk-1.20 → benchling_sdk-1.21.0}/benchling_sdk/services/v2/stable/custom_entity_service.py

@@ -93,7 +93,7 @@ class CustomEntityService(BaseService):
         creator_ids: Optional[Iterable[str]] = None,
         schema_fields: Optional[Dict[str, Any]] = None,
         page_size: Optional[int] = None,
-        next_token: NextToken = None,
+        next_token: Optional[NextToken] = None,
         author_idsany_of: Optional[Iterable[str]] = None,
         returning: Optional[Iterable[str]] = None,
     ) -> Response[CustomEntitiesPaginatedList]:

{benchling_sdk-1.20 → benchling_sdk-1.21.0}/benchling_sdk/services/v2/stable/dna_alignments_service.py

@@ -66,7 +66,7 @@ class DnaAlignmentsService(BaseService):
         sequence_ids: Optional[List[str]] = None,
         sort: Optional[ListDNAAlignmentsSort] = None,
         page_size: Optional[int] = None,
-        next_token: NextToken = None,
+        next_token: Optional[NextToken] = None,
     ) -> Response[DnaAlignmentsPaginatedList]:
         response = list_dna_alignments.sync_detailed(
             client=self.client,

{benchling_sdk-1.20 → benchling_sdk-1.21.0}/benchling_sdk/services/v2/stable/dna_oligo_service.py

@@ -89,7 +89,7 @@ class DnaOligoService(BaseService):
         schema_fields: Optional[Dict[str, Any]] = None,
         creator_ids: Optional[Iterable[str]] = None,
         page_size: Optional[int] = None,
-        next_token: NextToken = None,
+        next_token: Optional[NextToken] = None,
         author_idsany_of: Optional[Iterable[str]] = None,
         returning: Optional[Iterable[str]] = None,
         custom_notation_id: Optional[str] = None,

{benchling_sdk-1.20 → benchling_sdk-1.21.0}/benchling_sdk/services/v2/stable/dna_sequence_service.py

@@ -109,7 +109,7 @@ class DnaSequenceService(BaseService):
         creator_ids: Optional[Iterable[str]] = None,
         schema_fields: Optional[Dict[str, Any]] = None,
         page_size: Optional[int] = None,
-        next_token: NextToken = None,
+        next_token: Optional[NextToken] = None,
         author_idsany_of: Optional[Iterable[str]] = None,
         returning: Optional[Iterable[str]] = None,
     ) -> Response[DnaSequencesPaginatedList]:

{benchling_sdk-1.20 → benchling_sdk-1.21.0}/benchling_sdk/services/v2/stable/enzyme_service.py

@@ -29,7 +29,7 @@ class EnzymeService(BaseService):
         name_includes: Optional[str] = None,
         names_any_of: Optional[Iterable[str]] = [],
         page_size: Optional[int] = None,
-        next_token: NextToken = None,
+        next_token: Optional[NextToken] = None,
     ) -> Response[EnzymesPaginatedList]:
         response = list_enzymes.sync_detailed(
             client=self.client,

{benchling_sdk-1.20 → benchling_sdk-1.21.0}/benchling_sdk/services/v2/stable/event_service.py

@@ -29,7 +29,7 @@ class EventService(BaseService):
         event_types: Optional[str] = None,
         poll: Optional[bool] = None,
         page_size: Optional[int] = None,
-        next_token: NextToken = None,
+        next_token: Optional[NextToken] = None,
     ) -> Response[EventsPaginatedList]:
         response = list_events.sync_detailed(
             client=self.client,

{benchling_sdk-1.20 → benchling_sdk-1.21.0}/benchling_sdk/services/v2/stable/feature_library_service.py

@@ -73,7 +73,7 @@ class FeatureLibraryService(BaseService):
         sort: Optional[ListFeatureLibrariesSort] = None,
         page_size: Optional[int] = None,
         returning: Optional[Iterable[str]] = None,
-        next_token: NextToken = None,
+        next_token: Optional[NextToken] = None,
     ) -> Response[FeatureLibrariesPaginatedList]:
         response = list_feature_libraries.sync_detailed(
             client=self.client,
@@ -166,7 +166,7 @@ class FeatureLibraryService(BaseService):
     def _features_page(
         self,
         page_size: Optional[int] = None,
-        next_token: NextToken = None,
+        next_token: Optional[NextToken] = None,
         name: Optional[str] = None,
         ids: Optional[Iterable[str]] = None,
         namesany_ofcase_sensitive: Optional[Iterable[str]] = None,

{benchling_sdk-1.20 → benchling_sdk-1.21.0}/benchling_sdk/services/v2/stable/lab_automation_service.py

@@ -131,7 +131,7 @@ class LabAutomationService(BaseService):
         automation_file_config_name: Optional[str],
         archive_reason: Optional[str],
         modified_at: Optional[str],
-        next_token: NextToken = None,
+        next_token: Optional[NextToken] = None,
     ) -> Response[AutomationOutputProcessorsPaginatedList]:
         response = list_automation_output_processors.sync_detailed(
             client=self.client,
@@ -147,8 +147,8 @@ class LabAutomationService(BaseService):
     def automation_output_processors(
         self,
         assay_run_id: str,
-        automation_file_config_name: str = None,
-        archive_reason: str = None,
+        automation_file_config_name: Optional[str] = None,
+        archive_reason: Optional[str] = None,
         modified_at: Optional[str] = None,
     ) -> PageIterator[AutomationOutputProcessor]:
         """

{benchling_sdk-1.20 → benchling_sdk-1.21.0}/benchling_sdk/services/v2/stable/mixture_service.py

@@ -83,7 +83,7 @@ class MixtureService(BaseService):
         names_any_of_case_sensitive: Optional[Iterable[str]] = None,
         schema_fields: Optional[Dict[str, Any]] = None,
         page_size: Optional[int] = None,
-        next_token: NextToken = None,
+        next_token: Optional[NextToken] = None,
         author_idsany_of: Optional[Iterable[str]] = None,
     ) -> Response[MixturesPaginatedList]:
         response = list_mixtures.sync_detailed(

{benchling_sdk-1.20 → benchling_sdk-1.21.0}/benchling_sdk/services/v2/stable/molecule_service.py

@@ -84,7 +84,7 @@ class MoleculeService(BaseService):
         names_any_of: Optional[Iterable[str]] = None,
         schema_fields: Optional[Dict[str, Any]] = None,
         page_size: Optional[int] = None,
-        next_token: NextToken = None,
+        next_token: Optional[NextToken] = None,
         author_idsany_of: Optional[Iterable[str]] = None,
         chemical_substructuremol: Optional[str] = None,
         chemical_substructuresmiles: Optional[str] = None,

{benchling_sdk-1.20 → benchling_sdk-1.21.0}/benchling_sdk/services/v2/stable/monomer_service.py

@@ -41,7 +41,7 @@ class MonomerService(BaseService):
     def _list_page(
         self,
         page_size: Optional[int] = None,
-        next_token: NextToken = None,
+        next_token: Optional[NextToken] = None,
         returning: Optional[Iterable[str]] = None,
     ) -> Response[MonomersPaginatedList]:
         response = list_monomers.sync_detailed(

{benchling_sdk-1.20 → benchling_sdk-1.21.0}/benchling_sdk/services/v2/stable/nucleotide_alignments_service.py

@@ -58,7 +58,7 @@ class NucleotideAlignmentsService(BaseService):
         sequence_ids: Optional[List[str]] = None,
         sort: Optional[ListNucleotideAlignmentsSort] = None,
         page_size: Optional[int] = None,
-        next_token: NextToken = None,
+        next_token: Optional[NextToken] = None,
     ) -> Response[NucleotideAlignmentsPaginatedList]:
         response = list_nucleotide_alignments.sync_detailed(
             client=self.client,

{benchling_sdk-1.20 → benchling_sdk-1.21.0}/benchling_sdk/services/v2/stable/oligo_service.py

@@ -95,7 +95,7 @@ class OligoService(BaseService):
         schema_fields: Optional[Dict[str, Any]] = None,
         creator_ids: Optional[Iterable[str]] = None,
         page_size: Optional[int] = None,
-        next_token: NextToken = None,
+        next_token: Optional[NextToken] = None,
         returning: Optional[Iterable[str]] = None,
     ) -> Response[OligosPaginatedList]:
         """Deprecate in favor of dna_oligos._dna_oligos_page or rna_oligos._rna_oligos_page."""

{benchling_sdk-1.20 → benchling_sdk-1.21.0}/benchling_sdk/services/v2/stable/request_service.py

@@ -69,7 +69,7 @@ class RequestService(BaseService):
         request_status: Optional[RequestStatus] = None,
         min_created_time: Optional[int] = None,
         max_created_time: Optional[int] = None,
-        next_token: NextToken = None,
+        next_token: Optional[NextToken] = None,
         page_size: Optional[int] = None,
         returning: Optional[Iterable[str]] = None,
     ) -> Response[RequestsPaginatedList]:
@@ -201,7 +201,7 @@ class RequestService(BaseService):
         self,
         entry_id: str,
         modified_at: Optional[str] = None,
-        next_token: NextToken = None,
+        next_token: Optional[NextToken] = None,
         page_size: Optional[int] = None,
     ) -> Response[RequestFulfillmentsPaginatedList]:
         response = list_request_fulfillments.sync_detailed(

{benchling_sdk-1.20 → benchling_sdk-1.21.0}/benchling_sdk/services/v2/stable/rna_oligo_service.py

@@ -98,7 +98,7 @@ class RnaOligoService(BaseService):
         schema_fields: Optional[Dict[str, Any]] = None,
         creator_ids: Optional[Iterable[str]] = None,
         page_size: Optional[int] = None,
-        next_token: NextToken = None,
+        next_token: Optional[NextToken] = None,
         author_idsany_of: Optional[Iterable[str]] = None,
         returning: Optional[Iterable[str]] = None,
         custom_notation_id: Optional[str] = None,

{benchling_sdk-1.20 → benchling_sdk-1.21.0}/benchling_sdk/services/v2/stable/rna_sequence_service.py

@@ -104,7 +104,7 @@ class RnaSequenceService(BaseService):
         creator_ids: Optional[Iterable[str]] = None,
         schema_fields: Optional[Dict[str, Any]] = None,
         page_size: Optional[int] = None,
-        next_token: NextToken = None,
+        next_token: Optional[NextToken] = None,
         author_idsany_of: Optional[Iterable[str]] = None,
         returning: Optional[Iterable[str]] = None,
         custom_notation_id: Optional[str] = None,

{benchling_sdk-1.20 → benchling_sdk-1.21.0}/benchling_sdk/services/v2/stable/workflow_flowchart_service.py

@@ -44,7 +44,7 @@ class WorkflowFlowchartService(BaseService):
         ids: Optional[Iterable[str]] = None,
         created_at: Optional[datetime.date] = None,
         page_size: Optional[int] = None,
-        next_token: NextToken = None,
+        next_token: Optional[NextToken] = None,
     ) -> Response[WorkflowFlowchartPaginatedList]:
         response = list_workflow_flowcharts.sync_detailed(
             client=self.client,

{benchling_sdk-1.20 → benchling_sdk-1.21.0}/benchling_sdk/services/v2/stable/workflow_output_service.py

@@ -81,7 +81,7 @@ class WorkflowOutputService(BaseService):
         linked_item_ids_none_of: Optional[Iterable[str]] = None,
         archive_reason: Optional[str] = None,
         page_size: Optional[int] = None,
-        next_token: NextToken = None,
+        next_token: Optional[NextToken] = None,
     ) -> Response[WorkflowOutputsPaginatedList]:
         response = list_workflow_outputs.sync_detailed(
             client=self.client,

{benchling_sdk-1.20 → benchling_sdk-1.21.0}/benchling_sdk/services/v2/stable/workflow_task_group_service.py

@@ -70,7 +70,7 @@ class WorkflowTaskGroupService(BaseService):
         display_ids: Optional[Iterable[str]] = None,
         archive_reason: Optional[str] = None,
         page_size: Optional[int] = None,
-        next_token: NextToken = None,
+        next_token: Optional[NextToken] = None,
     ) -> Response[WorkflowTaskGroupsPaginatedList]:
         response = list_workflow_task_groups.sync_detailed(
             client=self.client,

{benchling_sdk-1.20 → benchling_sdk-1.21.0}/benchling_sdk/services/v2/stable/workflow_task_service.py

@@ -92,7 +92,7 @@ class WorkflowTaskService(BaseService):
         linked_item_ids_none_of: Optional[Iterable[str]] = None,
         archive_reason: Optional[str] = None,
         page_size: Optional[int] = None,
-        next_token: NextToken = None,
+        next_token: Optional[NextToken] = None,
     ) -> Response[WorkflowTasksPaginatedList]:
         response = list_workflow_tasks.sync_detailed(
             client=self.client,

{benchling_sdk-1.20 → benchling_sdk-1.21.0}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "benchling-sdk"
-version = "1.20"   # NOTE: This version number is ignored and does not correspond to releases (see README)
+version = "1.21.0"   # NOTE: This version number is ignored and does not correspond to releases (see README)
 description = "SDK for interacting with the Benchling Platform."
 authors = ["Benchling Support <support@benchling.com>"]
 packages = [{include = "benchling_sdk"}]
@@ -18,7 +18,7 @@ testpaths = [
 ]
 
 [tool.poetry.dependencies]
-python = "^3.8"
+python = "^3.9"
 backoff = ">=1.10.0, <3"
 dataclasses-json = "^0.5.2"
 httpx = ">=0.23.0"
@@ -28,7 +28,7 @@ PyYAML = "^6.0"
 # See issue: https://github.com/giampaolo/psutil/issues/2165
 psutil = {version = "^5.9.4", python = "^3.11" }
 jwcrypto = "^1.5.1"
-benchling-api-client = "2.0.338"
+benchling-api-client = "2.0.342"
 # Minimum version due to vulnerability in 2022.9.24
 certifi = ">=2022.12.7"
 # Cryptography extras - see ExtrasPackage.CRYPTOGRAPHY
@@ -48,7 +48,7 @@ black = "^22.3.0"
 isort = "^5.10.1"
 pre-commit = "^2.6.0"
 ipython = "^7.16.1"
-mypy = "^0.960"
+mypy = "^1.13"
 flake8 = "^3.8.3"
 taskipy = "^1.6.0"
 Jinja2 = "^3.1.2"
@@ -70,7 +70,7 @@ botocore-stubs = "1.28.4"
 # Used by flake8, version pinning is because v5 removes a deprecated call flake is currently using.
 importlib-metadata = "^4.13.0"
 sphinx-multiversion-pre-post-build = "^0.2.4"
-time-machine = "^2.8.2"
+time-machine = "^2.15.0"  # change to >=2.15.0 once we drop Python 3.8 support
 python-jose = "^3.3.0"
 gitpython = "^3.1.31"
 pytest-rerunfailures = "^12.0"