⬆️ Upgrade python version and dependencies

pwildenhain · web-flow · commit 1f91197e02b2 · 2025-02-07T13:13:15.000-05:00
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -20,7 +20,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ['3.8', '3.9', '3.10']
+        python-version: ['3.10', '3.11', '3.12']
 
     steps:
     - uses: actions/checkout@v2
diff --git a/.pylintrc b/.pylintrc
@@ -19,6 +19,7 @@ max-attributes=9
 
 # we're going to support as many arguments as the API calls have
 disable=too-many-arguments,
+        too-many-positional-arguments,
         # unfortunately this has to be disabled because of similar
         # import statements across different methods (which are
         # separated by different files by design)
diff --git a/poetry.lock b/poetry.lock
diff --git a/pyproject.toml b/pyproject.toml
@@ -27,20 +27,20 @@ packages = [
 ]
 
 [tool.poetry.dependencies]
-python = "^3.8"
+python = "^3.10"
 requests = "^2.20"
 semantic-version = "^2.8.5"
-pandas = {version = "^1.3.4", optional = true}
+pandas = {version = "^2.0.0", optional = true}
 
 [tool.poetry.extras]
 data_science = ["pandas"]
 
 [tool.poetry.group.dev.dependencies]
-pytest = "^6.2.5"
+pytest = "^7.0.0"
 pytest-cov = "^3.0.0"
 pytest-black = "^0.3.12"
 pytest-mypy = "^0.10.3"
-pytest-pylint = "^0.18.0"
+pytest-pylint = "^0.20.0"
 responses = "^0.14.0"
 pytest-mock = "^3.6.1"
 types-requests = "^2.26.1"
diff --git a/redcap/conftest.py b/redcap/conftest.py
@@ -3,6 +3,7 @@
 I don't think this is the ideal workflow, but it's the best I
 could come up with for having great, tested, examples
 """
+
 from pathlib import Path
 
 import pytest
diff --git a/redcap/methods/arms.py b/redcap/methods/arms.py
@@ -1,4 +1,5 @@
 """REDCap API methods for Project arms"""
+
 from typing import TYPE_CHECKING, Any, Dict, List, Literal, Optional, Union, cast
 
 from redcap.methods.base import Base, Json
@@ -15,7 +16,6 @@ def export_arms(
         format_type: Literal["json", "csv", "xml", "df"] = "json",
         arms: Optional[List[str]] = None,
     ):
-        # pylint: disable=line-too-long
         """
         Export the Arms of the Project
 
@@ -36,7 +36,6 @@ def export_arms(
             >>> proj.export_arms()
             [{'arm_num': 1, 'name': 'Arm 1'}]
         """
-        # pylint:enable=line-too-long
         payload = self._initialize_payload(content="arm", format_type=format_type)
         if arms:
             # Turn list of arms into dict, and append to payload
diff --git a/redcap/methods/base.py b/redcap/methods/base.py
@@ -1,4 +1,5 @@
 """The Base class for all REDCap methods"""
+
 from __future__ import annotations
 
 import json
@@ -227,12 +228,10 @@ def _filter_metadata(
         self,
         key: str,
         field_name: None = None,
-    ) -> list:
-        ...
+    ) -> list: ...
 
     @overload
-    def _filter_metadata(self, key: str, field_name: str) -> str:
-        ...
+    def _filter_metadata(self, key: str, field_name: str) -> str: ...
 
     def _filter_metadata(self, key: str, field_name: Optional[str] = None):
         """Safely filter project metadata based off requested column and field_name"""
diff --git a/redcap/methods/data_access_groups.py b/redcap/methods/data_access_groups.py
@@ -1,4 +1,5 @@
 """REDCap API methods for Project data access groups"""
+
 from typing import TYPE_CHECKING, Any, Dict, List, Literal, Optional, Union, cast
 
 from redcap.methods.base import Base, Json
diff --git a/redcap/methods/events.py b/redcap/methods/events.py
@@ -1,4 +1,5 @@
 """REDCap API methods for Project events"""
+
 from typing import TYPE_CHECKING, Any, Dict, List, Literal, Optional, Union, cast
 
 from redcap.methods.base import Base, Json
@@ -15,7 +16,6 @@ def export_events(
         format_type: Literal["json", "csv", "xml", "df"] = "json",
         arms: Optional[List[str]] = None,
     ):
-        # pylint: disable=line-too-long
         """
         Export the Events of the Project
 
@@ -37,7 +37,6 @@ def export_events(
             [{'event_name': 'Event 1', 'arm_num': 1, 'unique_event_name': 'event_1_arm_1',
             'custom_event_label': '', 'event_id': ...}, {'event_name': 'Event 2', ...}]
         """
-        # pylint:enable=line-too-long
         payload = self._initialize_payload(content="event", format_type=format_type)
         if arms:
             # Turn list of arms into dict, and append to payload
diff --git a/redcap/methods/field_names.py b/redcap/methods/field_names.py
@@ -1,4 +1,5 @@
 """REDCap API methods for Project field names"""
+
 from typing import TYPE_CHECKING, Any, Dict, Literal, Optional, Union, cast
 
 from redcap.methods.base import Base, Json
diff --git a/redcap/methods/files.py b/redcap/methods/files.py
@@ -14,11 +14,7 @@ class Files(Base):
 
     def _check_file_field(self, field: str) -> None:
         """Check that field exists and is a file field"""
-        # Since we initialize self.field_names as None, pylint worries that this will
-        # produce an error
-        # pylint: disable=unsupported-membership-test
         is_field = field in self.field_names
-        # pylint: enable=unsupported-membership-test
         is_file = self._filter_metadata(key="field_type", field_name=field) == "file"
         if not (is_field and is_file):
             msg = f"'{ field }' is not a field or not a 'file' field"
diff --git a/redcap/methods/instruments.py b/redcap/methods/instruments.py
@@ -1,4 +1,5 @@
 """REDCap API methods for Project instruments"""
+
 from typing import TYPE_CHECKING, Any, Dict, List, Literal, Optional, Union, cast
 
 from redcap.methods.base import Base, FileMap
diff --git a/redcap/methods/logging.py b/redcap/methods/logging.py
@@ -1,4 +1,5 @@
 """REDCap API methods for Project field names"""
+
 from datetime import datetime
 from typing import TYPE_CHECKING, Any, Dict, Literal, Optional, Union, cast
 
diff --git a/redcap/methods/metadata.py b/redcap/methods/metadata.py
@@ -1,4 +1,5 @@
 """REDCap API methods for Project metadata"""
+
 from typing import (
     TYPE_CHECKING,
     Any,
diff --git a/redcap/methods/project_info.py b/redcap/methods/project_info.py
@@ -1,4 +1,5 @@
 """REDCap API methods for Project info"""
+
 from typing import TYPE_CHECKING, Any, Dict, Literal, Optional, Union, cast
 
 from redcap.methods.base import Base, Json
diff --git a/redcap/methods/records.py b/redcap/methods/records.py
@@ -1,4 +1,5 @@
 """REDCap API methods for Project records"""
+
 from datetime import datetime
 
 from typing import (
diff --git a/redcap/methods/repeating.py b/redcap/methods/repeating.py
@@ -1,4 +1,5 @@
 """REDCap API methods for Project repeating instruments"""
+
 from typing import TYPE_CHECKING, Any, Dict, List, Optional, Union, Literal, cast
 
 from redcap.methods.base import Base
diff --git a/redcap/methods/reports.py b/redcap/methods/reports.py
@@ -1,4 +1,5 @@
 """REDCap API methods for Project reports"""
+
 from typing import TYPE_CHECKING, Any, Dict, Literal, Optional, Union, cast
 
 from redcap.methods.base import Base, Json
diff --git a/redcap/methods/surveys.py b/redcap/methods/surveys.py
@@ -1,4 +1,5 @@
 """REDCap API methods for Project surveys"""
+
 from typing import TYPE_CHECKING, Any, Dict, Literal, Optional, Union, cast
 
 from redcap.methods.base import Base, Json
diff --git a/redcap/methods/user_roles.py b/redcap/methods/user_roles.py
@@ -1,4 +1,5 @@
 """REDCap API methods for Project user roles"""
+
 from typing import (
     TYPE_CHECKING,
     Any,
@@ -43,11 +44,11 @@ def export_user_roles(
             [{'unique_role_name': ..., 'role_label': 'Test role', 'design': '0', 'alerts': '0',
             'user_rights': '0', 'data_access_groups': '0', 'reports': '0', 'stats_and_charts': '0',
             'manage_survey_participants': '0', 'calendar': '0', 'data_import_tool': '0',
-            'data_comparison_tool': '0', 'logging': '0', 'file_repository': '0',
-            'data_quality_create': '0', 'data_quality_execute': '0', 'api_export': '0',
-            'api_import': '0', 'mobile_app': '0', 'mobile_app_download_data': '0',
-            'record_create': '0', 'record_rename': '0', 'record_delete': '0',
-            'lock_records_customization': '0', 'lock_records': '0', ...,
+            'data_comparison_tool': '0', 'logging': '0', 'email_logging': '0',
+            'file_repository': '0', 'data_quality_create': '0', 'data_quality_execute': '0',
+            'api_export': '0', 'api_import': '0', 'api_modules': '0', 'mobile_app': '0',
+            'mobile_app_download_data': '0', 'record_create': '0', 'record_rename': '0',
+            'record_delete': '0', 'lock_records_customization': '0', 'lock_records': '0', ...,
             'forms': {'form_1': 2}, 'forms_export': {'form_1': 0}}]
         """
         payload = self._initialize_payload(content="userRole", format_type=format_type)
diff --git a/redcap/methods/users.py b/redcap/methods/users.py
@@ -1,4 +1,5 @@
 """REDCap API methods for Project users"""
+
 from typing import TYPE_CHECKING, Any, Dict, List, Literal, Optional, Union, cast
 
 from redcap.methods.base import Base, Json
diff --git a/redcap/request.py b/redcap/request.py
@@ -70,7 +70,7 @@ def __init__(
 
     @staticmethod
     def _get_format_key(
-        payload: Dict[str, Any]
+        payload: Dict[str, Any],
     ) -> Optional[Literal["json", "csv", "xml"]]:
         """Determine format of the response
 
@@ -101,8 +101,7 @@ def get_content(
         format_type: None,
         return_empty_json: Literal[True],
         return_bytes: Literal[False],
-    ) -> EmptyJson:
-        ...
+    ) -> EmptyJson: ...
 
     @overload
     @staticmethod
@@ -111,8 +110,7 @@ def get_content(
         format_type: None,
         return_empty_json: Literal[False],
         return_bytes: Literal[True],
-    ) -> bytes:
-        ...
+    ) -> bytes: ...
 
     @overload
     @staticmethod
@@ -132,8 +130,7 @@ def get_content(
         format_type: Literal["csv", "xml"],
         return_empty_json: Literal[False],
         return_bytes: Literal[False],
-    ) -> str:
-        ...
+    ) -> str: ...
 
     @staticmethod
     def get_content(
@@ -204,6 +201,8 @@ def execute(
         # xml is the default returnFormat for error messages
         elif self.fmt == "xml" or self.fmt is None:
             bad_request = "<error>" in str(content).lower()
+        else:
+            raise ValueError(f"Unsupported format { self.fmt }")
 
         if bad_request:
             raise RedcapError(content)
diff --git a/tests/integration/conftest.py b/tests/integration/conftest.py
@@ -1,4 +1,5 @@
 """Test fixtures for integration tests only"""
+
 # pylint: disable=redefined-outer-name
 from datetime import datetime
 import os
diff --git a/tests/integration/test_long_project.py b/tests/integration/test_long_project.py
@@ -1,4 +1,5 @@
 """Test suite for longitudinal REDCap Project against real REDCap server"""
+
 # pylint: disable=missing-function-docstring
 import os
 
diff --git a/tests/integration/test_simple_project.py b/tests/integration/test_simple_project.py
@@ -1,4 +1,5 @@
 """Test suite for simple REDCap Project against real REDCap server"""
+
 # pylint: disable=missing-function-docstring
 import os
 from io import StringIO
diff --git a/tests/unit/conftest.py b/tests/unit/conftest.py
@@ -1,4 +1,5 @@
 """Test fixtures for unit tests only"""
+
 from typing import Dict, Generator
 
 import pytest

Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,5 @@`
`1`	`1`	`"""REDCap API methods for Project data access groups"""`
	`2`	`+`
`2`	`3`	`from typing import TYPE_CHECKING, Any, Dict, List, Literal, Optional, Union, cast`
`3`	`4`
`4`	`5`	`from redcap.methods.base import Base, Json`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,5 @@`
`1`	`1`	`"""REDCap API methods for Project field names"""`
	`2`	`+`
`2`	`3`	`from typing import TYPE_CHECKING, Any, Dict, Literal, Optional, Union, cast`
`3`	`4`
`4`	`5`	`from redcap.methods.base import Base, Json`