Update dependencies #minor (#112)

* use bluepysnap<3.0.0 * add python_requires='>=3.8' * Use pydantic >= 2.5 * update sonata-network with snapV2 * use bluepysnap>=2.0.0 due to breaking changes
BlueBrain · Nov 30, 2023 · 8bc636f · 8bc636f
1 parent 25187af
commit 8bc636f
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diff --git a/bluecellulab/circuit/circuit_access.py b/bluecellulab/circuit/circuit_access.py
@@ -36,7 +36,6 @@
 from bluepysnap.exceptions import BluepySnapError
 from bluepysnap import Circuit as SnapCircuit
 import pandas as pd
-from pydantic import Extra
 from pydantic.dataclasses import dataclass
 
 from bluecellulab import circuit, neuron
@@ -54,7 +53,7 @@
 logger = logging.getLogger(__name__)
 
 
-@dataclass(config=dict(extra=Extra.forbid))
+@dataclass(config=dict(extra="forbid"))
 class EmodelProperties:
     threshold_current: float
     holding_current: float

diff --git a/bluecellulab/circuit/config/sections.py b/bluecellulab/circuit/config/sections.py
@@ -14,10 +14,9 @@
 """Classes to represent config sections."""
 
 from __future__ import annotations
-from typing import Optional
+from typing import Literal, Optional
 
-from pydantic import Extra, Field, validator
-from pydantic.typing import Literal
+from pydantic import field_validator, Field
 from pydantic.dataclasses import dataclass
 
 from libsonata._libsonata import Conditions as LibSonataConditions
@@ -34,22 +33,22 @@ def string_to_bool(value: str) -> bool:
     raise ValueError(f"Invalid boolean value {value}")
 
 
-@dataclass(frozen=True, config=dict(extra=Extra.forbid))
+@dataclass(frozen=True, config=dict(extra="forbid"))
 class ConditionEntry:
     """For mechanism specific conditions."""
     minis_single_vesicle: Optional[int] = Field(None, ge=0, le=1)
     init_depleted: Optional[int] = Field(None, ge=0, le=1)
 
 
-@dataclass(frozen=True, config=dict(extra=Extra.forbid))
+@dataclass(frozen=True, config=dict(extra="forbid"))
 class MechanismConditions:
     """For mechanism specific conditions."""
     ampanmda: Optional[ConditionEntry] = None
     gabaab: Optional[ConditionEntry] = None
     glusynapse: Optional[ConditionEntry] = None
 
 
-@dataclass(frozen=True, config=dict(extra=Extra.forbid))
+@dataclass(frozen=True, config=dict(extra="forbid"))
 class Conditions:
     mech_conditions: Optional[MechanismConditions] = None
     celsius: Optional[float] = None
@@ -125,7 +124,7 @@ def init_empty(cls) -> Conditions:
         )
 
 
-@dataclass(frozen=True, config=dict(extra=Extra.forbid))
+@dataclass(frozen=True, config=dict(extra="forbid"))
 class ConnectionOverrides:
     source: str
     target: str
@@ -135,7 +134,8 @@ class ConnectionOverrides:
     synapse_configure: Optional[str] = None
     mod_override: Optional[Literal["GluSynapse"]] = None
 
-    @validator("mod_override")
+    @field_validator("mod_override")
+    @classmethod
     def validate_mod_override(cls, value):
         """Make sure the mod file to override is present."""
         if isinstance(value, str) and not hasattr(bluecellulab.neuron.h, value):

diff --git a/bluecellulab/stimuli.py b/bluecellulab/stimuli.py
@@ -19,7 +19,7 @@
 from typing import Optional
 import warnings
 
-from pydantic import Extra, NonNegativeFloat, PositiveFloat, validator
+from pydantic import field_validator, NonNegativeFloat, PositiveFloat
 from pydantic.dataclasses import dataclass
 
 
@@ -92,7 +92,7 @@ def from_sonata(cls, pattern: str) -> Pattern:
             raise ValueError(f"Unknown pattern {pattern}")
 
 
-@dataclass(frozen=True, config=dict(extra=Extra.forbid))
+@dataclass(frozen=True, config=dict(extra="forbid"))
 class Stimulus:
     target: str
     delay: NonNegativeFloat
@@ -301,42 +301,43 @@ def from_sonata(cls, stimulus_entry: dict) -> Optional[Stimulus]:
             raise ValueError(f"Unknown pattern {pattern}")
 
 
-@dataclass(frozen=True, config=dict(extra=Extra.forbid))
+@dataclass(frozen=True, config=dict(extra="forbid"))
 class Noise(Stimulus):
     mean_percent: float
     variance: float
 
 
-@dataclass(frozen=True, config=dict(extra=Extra.forbid))
+@dataclass(frozen=True, config=dict(extra="forbid"))
 class Hyperpolarizing(Stimulus):
     ...
 
 
-@dataclass(frozen=True, config=dict(extra=Extra.forbid))
+@dataclass(frozen=True, config=dict(extra="forbid"))
 class Pulse(Stimulus):
     amp_start: float
     width: float
     frequency: float
 
 
-@dataclass(frozen=True, config=dict(extra=Extra.forbid))
+@dataclass(frozen=True, config=dict(extra="forbid"))
 class RelativeLinear(Stimulus):
     percent_start: float
 
 
-@dataclass(frozen=True, config=dict(extra=Extra.forbid))
+@dataclass(frozen=True, config=dict(extra="forbid"))
 class SynapseReplay(Stimulus):
     spike_file: str
     source: str
 
-    @validator("spike_file")
+    @field_validator("spike_file")
+    @classmethod
     def spike_file_exists(cls, v):
         if not Path(v).exists():
             raise ValueError(f"spike_file {v} does not exist")
         return v
 
 
-@dataclass(frozen=True, config=dict(extra=Extra.forbid))
+@dataclass(frozen=True, config=dict(extra="forbid"))
 class ShotNoise(Stimulus):
     rise_time: float
     decay_time: float
@@ -348,14 +349,15 @@ class ShotNoise(Stimulus):
     mode: ClampMode = ClampMode.CURRENT
     reversal: float = 0.0
 
-    @validator("decay_time")
+    @field_validator("decay_time")
+    @classmethod
     def decay_time_gt_rise_time(cls, v, values):
-        if v <= values["rise_time"]:
+        if v <= values.data["rise_time"]:
             raise ValueError("decay_time must be greater than rise_time")
         return v
 
 
-@dataclass(frozen=True, config=dict(extra=Extra.forbid))
+@dataclass(frozen=True, config=dict(extra="forbid"))
 class RelativeShotNoise(Stimulus):
     rise_time: float
     decay_time: float
@@ -367,14 +369,15 @@ class RelativeShotNoise(Stimulus):
     mode: ClampMode = ClampMode.CURRENT
     reversal: float = 0.0
 
-    @validator("decay_time")
+    @field_validator("decay_time")
+    @classmethod
     def decay_time_gt_rise_time(cls, v, values):
-        if v <= values["rise_time"]:
+        if v <= values.data["rise_time"]:
             raise ValueError("decay_time must be greater than rise_time")
         return v
 
 
-@dataclass(frozen=True, config=dict(extra=Extra.forbid))
+@dataclass(frozen=True, config=dict(extra="forbid"))
 class OrnsteinUhlenbeck(Stimulus):
     tau: float
     sigma: PositiveFloat
@@ -384,17 +387,18 @@ class OrnsteinUhlenbeck(Stimulus):
     mode: ClampMode = ClampMode.CURRENT
     reversal: float = 0.0
 
-    @validator("mean")
+    @field_validator("mean")
+    @classmethod
     def mean_in_range(cls, v, values):
-        if v < 0 and abs(v) > 2 * values["sigma"]:
+        if v < 0 and abs(v) > 2 * values.data["sigma"]:
             warnings.warn(
                 "mean is outside of range [0, 2*sigma],",
                 " ornstein uhlenbeck signal is mostly zero.",
             )
         return v
 
 
-@dataclass(frozen=True, config=dict(extra=Extra.forbid))
+@dataclass(frozen=True, config=dict(extra="forbid"))
 class RelativeOrnsteinUhlenbeck(Stimulus):
     tau: float
     mean_percent: float