Merge pull request #19 from Waltham-Data-Science/claude/apply-python-porting-guide-lVXML

Add pydantic validation decorators to epoch and ontology modules

Author: stevevanhooser

src/ndi/epoch/__init__.py

@@ -11,7 +11,7 @@
 """
 
 from .epoch import Epoch
-from .epochprobemap import EpochProbeMap
+from .epochprobemap import EpochProbeMap, build_devicestring, parse_devicestring
 from .epochprobemap_daqsystem import EpochProbeMapDAQSystem
 from .epochset import EpochSet
 from .functions import epochrange, findepochnode
@@ -21,6 +21,8 @@
     "EpochSet",
     "EpochProbeMap",
     "EpochProbeMapDAQSystem",
+    "build_devicestring",
     "epochrange",
     "findepochnode",
+    "parse_devicestring",
 ]

src/ndi/epoch/epoch.py

@@ -10,6 +10,9 @@
 from dataclasses import dataclass, field
 from typing import TYPE_CHECKING, Any
 
+import pydantic
+from pydantic import ConfigDict
+
 if TYPE_CHECKING:
     from ..time import ClockType
     from .epochprobemap import EpochProbeMap
@@ -210,6 +213,7 @@ def matches_probe(
         return False
 
 
+@pydantic.validate_call(config=ConfigDict(arbitrary_types_allowed=True))
 def is_epoch_or_empty(value: Any) -> bool:
     """
     Validate that a value is an Epoch or empty.

src/ndi/epoch/epochprobemap.py

@@ -11,6 +11,8 @@
 from dataclasses import dataclass
 from typing import Any
 
+import pydantic
+
 
 @dataclass
 class EpochProbeMap:
@@ -141,6 +143,7 @@ def __hash__(self) -> int:
         return hash((self.name, self.reference, self.type))
 
 
+@pydantic.validate_call
 def parse_devicestring(devicestring: str) -> dict[str, str]:
     """
     Parse a device string into components.
@@ -161,6 +164,7 @@ def parse_devicestring(devicestring: str) -> dict[str, str]:
     }
 
 
+@pydantic.validate_call
 def build_devicestring(
     name: str,
     deviceclass: str = "",

src/ndi/epoch/epochprobemap_daqsystem.py

@@ -13,6 +13,8 @@
 from pathlib import Path
 from typing import Any
 
+import pydantic
+
 from ..daq.daqsystemstring import DAQSystemString
 from .epochprobemap import EpochProbeMap
 
@@ -84,6 +86,7 @@ def serialize(self) -> str:
             ]
         )
 
+    @pydantic.validate_call
     def savetofile(self, filename: str) -> None:
         """
         Write this epoch probe map to a file.

src/ndi/epoch/epochset.py

@@ -9,12 +9,13 @@
 
 import hashlib
 from abc import ABC, abstractmethod
-from typing import TYPE_CHECKING, Any
+from typing import Annotated, Any
 
 import numpy as np
+import pydantic
+from pydantic import Field
 
-if TYPE_CHECKING:
-    from ..time import ClockType
+from ..time import ClockType
 
 
 class EpochSet(ABC):
@@ -149,7 +150,8 @@ def numepochs(self) -> int:
         et, _ = self.epochtable()
         return len(et)
 
-    def epochclock(self, epoch_number: int) -> list[ClockType]:
+    @pydantic.validate_call
+    def epochclock(self, epoch_number: Annotated[int, Field(ge=1)]) -> list[ClockType]:
         """
         Get clock types for an epoch.
 
@@ -163,13 +165,14 @@ def epochclock(self, epoch_number: int) -> list[ClockType]:
             IndexError: If epoch_number is out of range
         """
         et, _ = self.epochtable()
-        if epoch_number < 1 or epoch_number > len(et):
+        if epoch_number > len(et):
             raise IndexError(f"Epoch {epoch_number} out of range (1..{len(et)})")
 
         entry = et[epoch_number - 1]
         return entry.get("epoch_clock", [])
 
-    def t0_t1(self, epoch_number: int) -> list[tuple[float, float]]:
+    @pydantic.validate_call
+    def t0_t1(self, epoch_number: Annotated[int, Field(ge=1)]) -> list[tuple[float, float]]:
         """
         Get time range for an epoch.
 
@@ -183,13 +186,14 @@ def t0_t1(self, epoch_number: int) -> list[tuple[float, float]]:
             IndexError: If epoch_number is out of range
         """
         et, _ = self.epochtable()
-        if epoch_number < 1 or epoch_number > len(et):
+        if epoch_number > len(et):
             raise IndexError(f"Epoch {epoch_number} out of range (1..{len(et)})")
 
         entry = et[epoch_number - 1]
         return entry.get("t0_t1", [(np.nan, np.nan)])
 
-    def epochid(self, epoch_number: int) -> str:
+    @pydantic.validate_call
+    def epochid(self, epoch_number: Annotated[int, Field(ge=1)]) -> str:
         """
         Get epoch ID for an epoch number.
 
@@ -203,11 +207,12 @@ def epochid(self, epoch_number: int) -> str:
             IndexError: If epoch_number is out of range
         """
         et, _ = self.epochtable()
-        if epoch_number < 1 or epoch_number > len(et):
+        if epoch_number > len(et):
             raise IndexError(f"Epoch {epoch_number} out of range (1..{len(et)})")
 
         return et[epoch_number - 1].get("epoch_id", "")
 
+    @pydantic.validate_call
     def epochnumber(self, epoch_id: str) -> int:
         """
         Get epoch number for an epoch ID.
@@ -255,7 +260,8 @@ def matchedepochtable(
 
         return matches
 
-    def epochtableentry(self, epoch_number: int) -> dict[str, Any]:
+    @pydantic.validate_call
+    def epochtableentry(self, epoch_number: Annotated[int, Field(ge=1)]) -> dict[str, Any]:
         """
         Get a single epoch table entry.
 
@@ -269,7 +275,7 @@ def epochtableentry(self, epoch_number: int) -> dict[str, Any]:
             IndexError: If epoch_number is out of range
         """
         et, _ = self.epochtable()
-        if epoch_number < 1 or epoch_number > len(et):
+        if epoch_number > len(et):
             raise IndexError(f"Epoch {epoch_number} out of range (1..{len(et)})")
 
         return et[epoch_number - 1]

src/ndi/epoch/functions.py

@@ -10,9 +10,13 @@
 
 from typing import Any
 
+import pydantic
+from pydantic import ConfigDict
+
 from ..time import ClockType
 
 
+@pydantic.validate_call(config=ConfigDict(arbitrary_types_allowed=True))
 def epochrange(
     epochset_obj: Any,
     clocktype: ClockType,
@@ -118,6 +122,7 @@ def _resolve_epoch_index(
     raise ValueError(f"Epoch ID '{epoch}' not found")
 
 
+@pydantic.validate_call(config=ConfigDict(arbitrary_types_allowed=True))
 def findepochnode(
     epoch_node: dict[str, Any],
     epoch_node_array: list[dict[str, Any]],

src/ndi/ontology/__init__.py

@@ -15,9 +15,9 @@
 from __future__ import annotations
 
 import json
-from functools import lru_cache
-from pathlib import Path
-from typing import Any, Dict, List, Optional, Tuple
+from typing import Any
+
+import pydantic
 
 from .providers import PROVIDER_REGISTRY
 
@@ -115,6 +115,7 @@ def _load_prefix_map() -> dict[str, str]:
 _CACHE_MAX = 100
 
 
+@pydantic.validate_call
 def lookup(lookup_string: str) -> OntologyResult:
     """Look up a term in the appropriate ontology.
 

src/ndi/ontology/providers.py

@@ -13,6 +13,8 @@
 from typing import Any
 from urllib.parse import quote
 
+import pydantic
+
 # Registry populated at module load
 PROVIDER_REGISTRY: dict[str, type[OntologyProvider]] = {}
 
@@ -22,6 +24,7 @@ class OntologyProvider:
 
     name: str = ""
 
+    @pydantic.validate_call
     def lookup_term(self, term: str, prefix: str = "") -> Any:
         """Look up a term by ID or name. Override in subclasses."""
         from . import OntologyResult
@@ -49,6 +52,7 @@ class OLSProvider(OntologyProvider):
     ols_ontology: str = ""
     ols_prefix: str = ""
 
+    @pydantic.validate_call
     def lookup_term(self, term: str, prefix: str = "") -> Any:
 
         prefix = prefix or self.ols_prefix
@@ -139,6 +143,7 @@ class OMProvider(OLSProvider):
     ols_ontology = "om"
     ols_prefix = "OM"
 
+    @pydantic.validate_call
     def lookup_term(self, term: str, prefix: str = "") -> Any:
 
         # OM doesn't support numeric ID lookups
@@ -208,6 +213,7 @@ def _load_data(self) -> list[dict[str, str]]:
             NDICProvider._data = []
             return []
 
+    @pydantic.validate_call
     def lookup_term(self, term: str, prefix: str = "") -> Any:
         from . import OntologyResult
 
@@ -230,6 +236,7 @@ class NCImProvider(OntologyProvider):
     name = "NCIm"
     _CUI_PATTERN = re.compile(r"^C\d{7}$")
 
+    @pydantic.validate_call
     def lookup_term(self, term: str, prefix: str = "") -> Any:
         from . import OntologyResult
 
@@ -277,6 +284,7 @@ class NCBITaxonProvider(OntologyProvider):
 
     name = "NCBITaxon"
 
+    @pydantic.validate_call
     def lookup_term(self, term: str, prefix: str = "") -> Any:
         from . import OntologyResult
 
@@ -344,6 +352,7 @@ class WBStrainProvider(OntologyProvider):
 
     name = "WBStrain"
 
+    @pydantic.validate_call
     def lookup_term(self, term: str, prefix: str = "") -> Any:
         from . import OntologyResult
 
@@ -392,6 +401,7 @@ class RRIDProvider(OntologyProvider):
 
     name = "RRID"
 
+    @pydantic.validate_call
     def lookup_term(self, term: str, prefix: str = "") -> Any:
         from . import OntologyResult
 
@@ -423,6 +433,7 @@ class PubChemProvider(OntologyProvider):
 
     name = "PubChem"
 
+    @pydantic.validate_call
     def lookup_term(self, term: str, prefix: str = "") -> Any:
         from . import OntologyResult
 
@@ -541,6 +552,7 @@ def _load_ontology(self) -> dict[str, Any]:
         }
         return EMPTYProvider._cache
 
+    @pydantic.validate_call
     def lookup_term(self, term: str, prefix: str = "") -> Any:
         from ndi.fun.name_utils import name_to_variable_name