1043 enforce default formatting (#1060)

* feat: adding flake8 extension that checks for default= and ...

Still needs work, this catches situations that it shouldn't catch

* chore: missing default=

* chore: realized there is a special linters section

Author: dbirman

.flake8

@@ -5,3 +5,7 @@ exclude =
     build
 max-complexity = 10
 max-line-length = 120
+
+[flake8:local-plugins]
+extension =
+    PF = aind_flake8_extensions.plugin:run_ast_checks

pyproject.toml

@@ -33,7 +33,8 @@ linters = [
     'coverage',
     'flake8',
     'interrogate',
-    'isort'
+    'isort',
+    'aind-flake8-extensions'
 ]
 
 docs = [

src/aind_data_schema/components/devices.py

@@ -528,7 +528,7 @@ class Laser(Device):
     power_unit: PowerUnit = Field(default=PowerUnit.MW, title="Power unit")
     coupling: Optional[Coupling] = Field(default=None, title="Coupling")
     coupling_efficiency: Optional[Decimal] = Field(
-        None,
+        default=None,
         title="Coupling efficiency (percent)",
         ge=0,
         le=100,

src/aind_data_schema/components/stimulus.py

@@ -40,7 +40,7 @@ class OptoStimulation(AindModel):
     pulse_train_duration_unit: TimeUnit = Field(default=TimeUnit.S, title="Pulse train duration unit")
     fixed_pulse_train_interval: bool = Field(..., title="Fixed pulse train interval")
     pulse_train_interval: Optional[Decimal] = Field(
-        None, title="Pulse train interval (s)", description="Time between pulse trains"
+        default=None, title="Pulse train interval (s)", description="Time between pulse trains"
     )
     pulse_train_interval_unit: TimeUnit = Field(default=TimeUnit.S, title="Pulse train interval unit")
     baseline_duration: Decimal = Field(

src/aind_data_schema/core/instrument.py

@@ -38,7 +38,7 @@ class Instrument(AindCoreModel):
     schema_version: Literal["1.0.0"] = Field("1.0.0")
 
     instrument_id: Optional[str] = Field(
-        None,
+        default=None,
         description="Unique instrument identifier, name convention: <room>-<apparatus name>-<date modified YYYYMMDD>",
         title="Instrument ID",
     )
@@ -58,12 +58,12 @@ class Instrument(AindCoreModel):
     scanning_stages: List[ScanningStage] = Field(default=[], title="Scanning motorized stages")
     additional_devices: List[AdditionalImagingDevice] = Field(default=[], title="Additional devices")
     calibration_date: Optional[date] = Field(
-        None,
+        default=None,
         description="Date of most recent calibration",
         title="Calibration date",
     )
     calibration_data: Optional[str] = Field(
-        None,
+        default=None,
         description="Path to calibration data from most recent calibration",
         title="Calibration data",
     )

src/aind_data_schema/core/procedures.py

@@ -241,7 +241,7 @@ class SpecimenProcedure(AindModel):
 
     procedure_type: SpecimenProcedureType = Field(..., title="Procedure type")
     procedure_name: Optional[str] = Field(
-        None, title="Procedure name", description="Name to clarify specific procedure used as needed"
+        default=None, title="Procedure name", description="Name to clarify specific procedure used as needed"
     )
     specimen_id: str = Field(..., title="Specimen ID")
     start_date: date = Field(..., title="Start date")

src/aind_data_schema/core/subject.py

@@ -98,7 +98,7 @@ class Subject(AindCoreModel):
     sex: Sex = Field(..., title="Sex")
     date_of_birth: date_type = Field(..., title="Date of birth")
     genotype: Optional[str] = Field(
-        None,
+        default=None,
         description="Genotype of the animal providing both alleles",
         title="Genotype",
     )
@@ -112,12 +112,12 @@ class Subject(AindCoreModel):
         title="Source",
     )
     rrid: Optional[PIDName] = Field(
-        None,
+        default=None,
         description="RRID of mouse if acquired from supplier",
         title="RRID",
     )
     restrictions: Optional[str] = Field(
-        None,
+        default=None,
         description="Any restrictions on use or publishing based on subject source",
         title="Restrictions",
     )