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chore: use keyword default arg in pydantic models #471

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jsstevenson merged 1 commit into from
May 18, 2026
Merged

chore: use keyword default arg in pydantic models #471

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44 changes: 28 additions & 16 deletions src/cool_seq_tool/mappers/exon_genomic_coords.py
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Original file line number Diff line number Diff line change
Expand Up @@ -63,7 +63,7 @@ class TxSegment(BaseModelForbidExtra):

exon_ord: StrictInt = Field(..., description="Exon number. 0-based.")
offset: StrictInt = Field(
0,
default=0,
description="The value added to or subtracted from the `genomic_location` to find the start or end of an exon.",
)
genomic_location: SequenceLocation = Field(
Expand Down Expand Up @@ -110,19 +110,23 @@ def check_seg_pos(cls, values: dict) -> dict: # noqa: N805
class GenomicTxSeg(BaseModelForbidExtra):
"""Model for representing a boundary for a transcript segment."""

seg: TxSegment | None = Field(None, description="Transcript segment.")
seg: TxSegment | None = Field(default=None, description="Transcript segment.")
gene: StrictStr | None = Field(
None, description="Valid, case-sensitive HGNC gene symbol."
default=None, description="Valid, case-sensitive HGNC gene symbol."
)
genomic_ac: StrictStr | None = Field(
default=None, description="RefSeq genomic accession."
)
tx_ac: StrictStr | None = Field(
default=None, description="RefSeq transcript accession."
)
genomic_ac: StrictStr | None = Field(None, description="RefSeq genomic accession.")
tx_ac: StrictStr | None = Field(None, description="RefSeq transcript accession.")
tx_status: TranscriptPriority | None = Field(
None, description="Transcript priority for RefSeq transcript accession"
default=None, description="Transcript priority for RefSeq transcript accession"
)
strand: Strand | None = Field(
None, description="The strand that the transcript accession exists on."
default=None, description="The strand that the transcript accession exists on."
)
errors: list[StrictStr] = Field([], description="Error messages.")
errors: list[StrictStr] = Field(default=[], description="Error messages.")

@model_validator(mode="before")
def check_errors(cls, values: dict) -> dict: # noqa: N805
Expand Down Expand Up @@ -175,19 +179,27 @@ class GenomicTxSegService(BaseModelForbidExtra):
"""Service model for genomic and transcript data."""

gene: StrictStr | None = Field(
None, description="Valid, case-sensitive HGNC gene symbol."
default=None, description="Valid, case-sensitive HGNC gene symbol."
)
genomic_ac: StrictStr | None = Field(
default=None, description="RefSeq genomic accession."
)
tx_ac: StrictStr | None = Field(
default=None, description="RefSeq transcript accession."
)
genomic_ac: StrictStr | None = Field(None, description="RefSeq genomic accession.")
tx_ac: StrictStr | None = Field(None, description="RefSeq transcript accession.")
tx_status: TranscriptPriority | None = Field(
None, description="Transcript priority for RefSeq transcript accession"
default=None, description="Transcript priority for RefSeq transcript accession"
)
strand: Strand | None = Field(
None, description="The strand that the transcript exists on."
default=None, description="The strand that the transcript exists on."
)
seg_start: TxSegment | None = Field(
default=None, description="Start transcript segment."
)
seg_end: TxSegment | None = Field(
default=None, description="End transcript segment."
)
seg_start: TxSegment | None = Field(None, description="Start transcript segment.")
seg_end: TxSegment | None = Field(None, description="End transcript segment.")
errors: list[StrictStr] = Field([], description="Error messages.")
errors: list[StrictStr] = Field(default=[], description="Error messages.")
service_meta: ServiceMeta = Field(..., description="Service metadata.")

@model_validator(mode="before")
Expand Down
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