Cleanup/mypy cleanup

CLAUDE.md

@@ -0,0 +1,37 @@
+# Claude Instructions for circepy
+
+## Python Environment
+- Always use virtualenv for Python operations (don't rely on system Python or unauthenticated pip installs)
+- Activate the virtual environment before running Python commands or installing packages
+
+## Starting tasks - record testing state
+
+At the start of any task, record the state of tests as a baseline. It is not your job to fix pre-existing issues unless otherwise specified.
+
+Run tests with multiprocess for speed and store the state:
+```bash
+pytest -n auto --tb=short -v --json-report --json-report-file=.test_baseline.json
+```
+
+If the test state file is not created, check that pytest-xdist and pytest-json-report are installed in the virtualenv.
+
+## Pre-completion Checklist
+Before completing any task:
+
+1. Re-run pytest to verify no regressions:
+```bash
+pytest -n auto --tb=short -v --json-report --json-report-file=.test_final.json
+```
+
+Compare `.test_baseline.json` with `.test_final.json` — the final state should not show new failures.
+
+2. Run git pre-commit checks:
+```bash
+git pre-commit run --all-files
+```
+
+If pre-commit checks fail, fix the issues and re-run until they pass.
+
+## Git Workflow
+- Do not run `git commit` — the user will handle commits
+- Run pre-commit checks to validate code quality before marking tasks complete

circe/check/checkers/base_corelated_criteria_check.py

@@ -44,8 +44,8 @@ def _internal_check(self, expression: "CohortExpression", reporter: WarningRepor
                 if inclusion_rule.expression and inclusion_rule.expression.criteria_list:
                     for criteria in inclusion_rule.expression.criteria_list:
                         # Skip if criteria is still a dict (shouldn't happen after deserialization, but be defensive)
-                        if isinstance(criteria, dict):
-                            continue
+                        if isinstance(criteria, dict):  # type: ignore[unreachable]
+                            continue  # type: ignore[unreachable]
                         group_name = f"{self.INCLUSION_RULE}{inclusion_rule.name}"
                         self._check_criteria(criteria, group_name, reporter)
                         if hasattr(criteria, "criteria") and criteria.criteria:
@@ -60,16 +60,16 @@ def _check_criteria_group(self, criteria: "Criteria", group_name: str, reporter:
             reporter: The warning reporter to use
         """
         # Skip if criteria is still a dict (not yet deserialized)
-        if isinstance(criteria, dict):
-            return
+        if isinstance(criteria, dict):  # type: ignore[unreachable]
+            return  # type: ignore[unreachable]
 
         if hasattr(criteria, "correlated_criteria") and criteria.correlated_criteria:
             correlated = criteria.correlated_criteria
             if hasattr(correlated, "criteria_list") and correlated.criteria_list:
                 for corelated_criteria in correlated.criteria_list:
                     # Skip dicts
-                    if isinstance(corelated_criteria, dict):
-                        continue
+                    if isinstance(corelated_criteria, dict):  # type: ignore[unreachable]
+                        continue  # type: ignore[unreachable]
                     self._check_criteria(corelated_criteria, group_name, reporter)
                     if hasattr(corelated_criteria, "criteria") and corelated_criteria.criteria:
                         self._check_criteria_group(corelated_criteria.criteria, group_name, reporter)
@@ -78,8 +78,8 @@ def _check_criteria_group(self, criteria: "Criteria", group_name: str, reporter:
                     if hasattr(group, "criteria_list") and group.criteria_list:
                         for corelated_criteria in group.criteria_list:
                             # Skip dicts
-                            if isinstance(corelated_criteria, dict):
-                                continue
+                            if isinstance(corelated_criteria, dict):  # type: ignore[unreachable]
+                                continue  # type: ignore[unreachable]
                             self._check_criteria(corelated_criteria, group_name, reporter)
                             if hasattr(corelated_criteria, "criteria") and corelated_criteria.criteria:
                                 self._check_criteria_group(corelated_criteria.criteria, group_name, reporter)
@@ -99,7 +99,7 @@ def _check_criteria(
         """
         # Skip if criteria is still a dict (not yet deserialized)
         # This can happen when Pydantic doesn't fully deserialize polymorphic types
-        if isinstance(criteria, dict):
-            return
+        if isinstance(criteria, dict):  # type: ignore[unreachable]
+            return  # type: ignore[unreachable]
 
         raise NotImplementedError("Subclasses must implement _check_criteria")

circe/check/checkers/comparisons.py

@@ -119,7 +119,7 @@ def compare_to(filter_val: "ObservationFilter", window: "Window") -> int:
             An integer representing the comparison result
         """
         if filter_val is None or window is None:
-            return 0
+            return 0  # type: ignore[unreachable]
 
         range1 = filter_val.post_days + filter_val.prior_days
         range2_start = 0
@@ -144,7 +144,7 @@ def is_before(window: "Window") -> bool:
             True if the window is before, False otherwise
         """
         if window is None:
-            return False
+            return False  # type: ignore[unreachable]
         return Comparisons.is_before_endpoint(window.start) and not Comparisons.is_after_endpoint(window.end)
 
     @staticmethod

circe/check/checkers/death_time_window_check.py

@@ -8,6 +8,8 @@
 Reference: JAVA_CLASS_MAPPINGS.md for Java equivalents.
 """
 
+from typing import Any
+
 from ..operations.operations import Operations
 from ..utils.criteria_name_helper import CriteriaNameHelper
 from ..warning_severity import WarningSeverity
@@ -122,7 +124,7 @@ def _check_criteria(
         """
         name = f"{group_name} {CriteriaNameHelper.get_criteria_name(criteria.criteria)}"
 
-        match_result = Operations.match(criteria.criteria)
+        match_result: Any = Operations.match(criteria.criteria)
         match_result.is_a(Death)
         match_result.then(
             lambda death: (

circe/check/checkers/drug_era_check.py

@@ -8,6 +8,8 @@
 Reference: JAVA_CLASS_MAPPINGS.md for Java equivalents.
 """
 
+from typing import Any
+
 from ..operations.operations import Operations
 from ..warning_severity import WarningSeverity
 from .base_corelated_criteria_check import BaseCorelatedCriteriaCheck
@@ -53,15 +55,15 @@ def _check_criteria(
             reporter: The warning reporter to use
         """
         # Handle case where criteria is still a dict (not yet deserialized)
-        if isinstance(criteria, dict):
+        if isinstance(criteria, dict):  # type: ignore[unreachable]
             # Skip validation for dict-based criteria - they need to be deserialized first
-            return
+            return  # type: ignore[unreachable]
 
         # Ensure criteria has a criteria attribute
         if not hasattr(criteria, "criteria") or not criteria.criteria:
             return
 
-        match_result = Operations.match(criteria.criteria)
+        match_result: Any = Operations.match(criteria.criteria)
         match_result.is_a(DrugEra)
         match_result.then(
             lambda c: (

circe/check/checkers/exit_criteria_check.py

@@ -8,6 +8,8 @@
 Reference: JAVA_CLASS_MAPPINGS.md for Java equivalents.
 """
 
+from typing import Any
+
 from ..operations.operations import Operations
 from .base_check import BaseCheck
 from .warning_reporter import WarningReporter
@@ -39,7 +41,7 @@ def _check(self, expression: "CohortExpression", reporter: WarningReporter) -> N
             expression: The cohort expression to check
             reporter: The warning reporter to use
         """
-        match_result = Operations.match(expression.end_strategy)
+        match_result: Any = Operations.match(expression.end_strategy)
         match_result.is_a(CustomEraStrategy)
         match_result.then(
             lambda s: (

circe/check/checkers/exit_criteria_days_offset_check.py

@@ -8,6 +8,8 @@
 Reference: JAVA_CLASS_MAPPINGS.md for Java equivalents.
 """
 
+from typing import Any
+
 from ..operations.operations import Operations
 from ..warning_severity import WarningSeverity
 from .base_check import BaseCheck
@@ -48,7 +50,7 @@ def _check(self, expression: "CohortExpression", reporter: WarningReporter) -> N
             expression: The cohort expression to check
             reporter: The warning reporter to use
         """
-        match_result = Operations.match(expression.end_strategy)
+        match_result: Any = Operations.match(expression.end_strategy)
         match_result.is_a(DateOffsetStrategy)
         match_result.then(
             lambda s: (

circe/check/checkers/initial_event_check.py

@@ -8,6 +8,8 @@
 Reference: JAVA_CLASS_MAPPINGS.md for Java equivalents.
 """
 
+from typing import Any
+
 from ..operations.operations import Operations
 from .base_check import BaseCheck
 from .warning_reporter import WarningReporter
@@ -37,7 +39,7 @@ def _check(self, expression: "CohortExpression", reporter: WarningReporter) -> N
             expression: The cohort expression to check
             reporter: The warning reporter to use
         """
-        match_result = Operations.match(expression)
+        match_result: Any = Operations.match(expression)
         match_result.when(
             lambda e: (
                 e.primary_criteria is None

circe/check/checkers/no_exit_criteria_check.py

@@ -8,6 +8,8 @@
 Reference: JAVA_CLASS_MAPPINGS.md for Java equivalents.
 """
 
+from typing import Any
+
 from ..operations.operations import Operations
 from ..warning_severity import WarningSeverity
 from .base_check import BaseCheck
@@ -46,7 +48,7 @@ def _check(self, expression: "CohortExpression", reporter: WarningReporter) -> N
             expression: The cohort expression to check
             reporter: The warning reporter to use
         """
-        match_result = Operations.match(expression)
+        match_result: Any = Operations.match(expression)
         match_result.when(
             lambda e: (
                 e.primary_criteria

circe/check/checkers/ocurrence_check.py

@@ -8,7 +8,7 @@
 Reference: JAVA_CLASS_MAPPINGS.md for Java equivalents.
 """
 
-from typing import TYPE_CHECKING
+from typing import TYPE_CHECKING, Any
 
 from ..operations.operations import Operations
 from ..warning_severity import WarningSeverity
@@ -52,6 +52,6 @@ def _check_criteria(
             reporter: The warning reporter to use
         """
         if criteria.occurrence:
-            match_result = Operations.match(criteria.occurrence)
+            match_result: Any = Operations.match(criteria.occurrence)
             match_result.when(lambda o: o.type == self.AT_LEAST and o.count == 0)
             match_result.then(lambda o: reporter(self.AT_LEAST_0_WARNING))

circe/check/checkers/range_check.py

@@ -69,8 +69,8 @@ def _check_inclusion_rules(self, expression: "CohortExpression", reporter: Warni
                 if rule.expression and rule.expression.criteria_list:
                     for criteria in rule.expression.criteria_list:
                         # Handle both dict and CorelatedCriteria objects
-                        if isinstance(criteria, dict):
-                            start_window = criteria.get("startWindow") or criteria.get("start_window")
+                        if isinstance(criteria, dict):  # type: ignore[unreachable]
+                            start_window = criteria.get("startWindow") or criteria.get("start_window")  # type: ignore[unreachable]
                             end_window = criteria.get("endWindow") or criteria.get("end_window")
                         else:
                             start_window = getattr(criteria, "start_window", None) or getattr(

circe/check/checkers/range_checker_factory.py

@@ -8,7 +8,7 @@
 Reference: JAVA_CLASS_MAPPINGS.md for Java equivalents.
 """
 
-from typing import Callable, Optional
+from typing import Any, Callable, Optional
 
 from ..constants import Constants
 from ..operations.operations import Operations
@@ -613,7 +613,7 @@ def warning(template: str) -> None:
 
         if isinstance(range_val, DateRange):
             # Date range checks
-            match_result = Operations.match(range_val)
+            match_result: Any = Operations.match(range_val)
             match_result.when(lambda r: r.value is not None and not Comparisons.is_date_valid(r.value)).then(
                 lambda x: warning(self.WARNING_DATE_IS_INVALID)
             )
@@ -639,7 +639,7 @@ def warning(template: str) -> None:
             )
         elif isinstance(range_val, NumericRange):
             # Numeric range checks
-            match_result = Operations.match(range_val)
+            match_result: Any = Operations.match(range_val)
             match_result.when(lambda r: r.op is not None and r.op.endswith("bt")).then(
                 lambda r: (
                     Operations.match(r)
@@ -673,7 +673,7 @@ def check_range(self, period: Optional["Period"], criteria_name: str, attribute:
         def warning(template: str) -> None:
             self._reporter(template, self._group_name, criteria_name, attribute)
 
-        match_result = Operations.match(period)
+        match_result: Any = Operations.match(period)
         match_result.when(
             lambda x: x.start_date is not None and not Comparisons.is_date_valid(x.start_date)
         ).then(lambda x: warning(self.WARNING_DATE_IS_INVALID))

circe/check/checkers/time_window_check.py

@@ -8,7 +8,7 @@
 Reference: JAVA_CLASS_MAPPINGS.md for Java equivalents.
 """
 
-from typing import Optional
+from typing import Any, Optional
 
 from ..operations.operations import Operations
 from ..utils.criteria_name_helper import CriteriaNameHelper
@@ -77,7 +77,7 @@ def _check_criteria(
         """
         name = f"{group_name} {CriteriaNameHelper.get_criteria_name(criteria.criteria)}"
 
-        match_result = Operations.match(criteria)
+        match_result: Any = Operations.match(criteria)
         match_result.when(
             lambda c: (
                 c.start_window is not None

circe/check/utils/criteria_name_helper.py

@@ -90,5 +90,5 @@ def get_criteria_name(criteria) -> str:
             .is_a(PayerPlanPeriod)
             .then_return(lambda c: Constants.Criteria.PAYER_PLAN_PERIOD)
             .value()
-            or "unknown criteria"
+            or "unknown criteria"  # type: ignore[unreachable]
         )

circe/cohortdefinition/builders/base.py

@@ -64,8 +64,6 @@ def get_criteria_sql_with_options(self, criteria: T, options: Optional[BuilderOp
                 )
             else:
                 query = query.replace("@additionalColumns", "")
-        else:
-            query = query.replace("@additionalColumns", "")
 
         return query
 

circe/cohortdefinition/builders/visit_occurrence.py

@@ -256,8 +256,6 @@ def resolve_where_clauses(
 
         return where_clauses
 
-        return where_clauses
-
     def embed_ordinal_expression(
         self,
         query: str,

circe/cohortdefinition/code_generator.py

@@ -106,7 +106,7 @@ def instance_is_pydantic(o):
     # Generate Imports
     import_lines = []
     # Group by module
-    module_map = {}
+    module_map: dict[str, list[str]] = {}
     for cls in required_classes:
         mod = cls.__module__
         if mod not in module_map:

circe/cohortdefinition/cohort_expression_query_builder.py

@@ -1471,9 +1471,9 @@ def get_criteria_sql(self, criteria: Criteria, options: Optional[BuilderOptions]
         Java equivalent: Various getCriteriaSql methods
         """
         # Handle case where criteria is still a dict (shouldn't happen, but be defensive)
-        if isinstance(criteria, dict):
+        if isinstance(criteria, dict):  # type: ignore[unreachable]
             # Try to deserialize it - import here to avoid circular dependency issues
-            from .criteria import ConditionEra as CE
+            from .criteria import ConditionEra as CE  # type: ignore[unreachable]
             from .criteria import ConditionOccurrence as CO
             from .criteria import Death as D
             from .criteria import DeviceExposure as DevE

circe/cohortdefinition/criteria.py

@@ -271,14 +271,6 @@ def _serialize_polymorphic(self, serializer, info):
 
         return {self.__class__.__name__: data}
 
-        # Get the serialized data using default serialization
-        data = serializer(self)
-        # Wrap in class name for polymorphic deserialization in Java
-        # Only wrap if this is a subclass (not the base Criteria class)
-        if self.__class__.__name__ != "Criteria":
-            return {self.__class__.__name__: data}
-        return data
-
     def accept(self, dispatcher: Any, options: Optional[Any] = None) -> str:
         """Accept method for visitor pattern."""
         return dispatcher.get_criteria_sql(self, options)
@@ -1146,7 +1138,7 @@ def deserialize_criteria_list(cls, v: Any) -> Any:
         # Helper window normalizer (same as before)
         def normalize_window(window_dict: dict) -> dict:
             if not isinstance(window_dict, dict):
-                return window_dict
+                return window_dict  # type: ignore[unreachable]
             normalized = {}
             if "UseEventEnd" in window_dict:
                 normalized["useEventEnd"] = window_dict["UseEventEnd"]

circe/cohortdefinition/printfriendly/markdown_render.py

@@ -238,7 +238,7 @@ def _format_number(self, value: Union[int, float]) -> str:
             Formatted string (e.g. "1,500" or "1.5")
         """
         if value is None:
-            return ""
+            return ""  # type: ignore[unreachable]
 
         # If matches integer, convert to int for clean formatting
         if isinstance(value, float) and value.is_integer():