chore: add unit tests for python pkg

[manzt]

• moves "core" logic into src/chromoscope/_viewer.py
• test: add unit tests
• add unit tests to ci

[manzt]

@sehilyi - on the python side, it might be worth looking at https://pydantic.dev/ to validate the config objects passed in

[sehilyi]

Thanks! I will merge this.

Would publishing this to PyPI requires adding API tokens to the GH repo?

[manzt]

Yup, maybe have a look at servir's release workflow. You'll need to publish manually once locally (hatch run build && hatch publish). But then on PyPI you can create an API token for this repo, and add a secret so that publish are made with tagged commits).

[manzt]

Oh, the other thing to mention about pydantic is that you can generate JSON schema from the models.

from typing import Literal, Union

from pydantic import BaseModel, Field, HttpUrl


class Config(BaseModel):
    id: str
    cancer: str
    assembly: Literal["hg38", "hg19"]
    sv: HttpUrl
    cnv: HttpUrl = Field(title="CNV", description="An URL of the CNV text file (.txt).")
    drivers: Union[HttpUrl, None] = Field(
        default=None,
        title="Drivers",
        description="An URL of a file that contains drivers (.txt).",
    )
    vcf: Union[HttpUrl, None] = Field(
        default=None,
        title="VCF",
        description="An URL of the point mutation file (.vcf).",
    )
    vcfIndex: Union[HttpUrl, None] = Field(
        default=None,
        title="VCF Index",
        description="An URL of the point mutation index file (.tbi).",
    )
    vcf2: Union[HttpUrl, None] = Field(
        default=None,
        title="VCF2",
        description="An URL of the the indel file (.vcf).",
    )
    vcf2Index: Union[HttpUrl, None] = Field(
        default=None,
        title="VCF2 Index",
        description="An URL of the indel index file (.tbi).",
    )
    bam: Union[HttpUrl, None] = Field(
        default=None,
        title="BAM",
        description="An URL of the BAM file (.bam)."
    )
    bamIndex: Union[HttpUrl, None] = Field(
        default=None,
        title="BAM Index",
        description="An URL of the BAM index file (.bai)."
    )
    note: Union[str, None] = Field(
        default=None,
        title="Note",
        description="A textual annotation.",
    )



if __name__ == "__main__":
    print(Config.schema_json(indent=2))

{
  "title": "Config",
  "type": "object",
  "properties": {
    "id": {
      "title": "Id",
      "type": "string"
    },
    "cancer": {
      "title": "Cancer",
      "type": "string"
    },
    "assembly": {
      "title": "Assembly",
      "enum": [
        "hg38",
        "hg19"
      ],
      "type": "string"
    },
    "sv": {
      "title": "Sv",
      "minLength": 1,
      "maxLength": 2083,
      "format": "uri",
      "type": "string"
    },
    "cnv": {
      "title": "CNV",
      "description": "An URL of the CNV text file (.txt).",
      "minLength": 1,
      "maxLength": 2083,
      "format": "uri",
      "type": "string"
    },
    "drivers": {
      "title": "Drivers",
      "description": "An URL of a file that contains drivers (.txt).",
      "minLength": 1,
      "maxLength": 2083,
      "format": "uri",
      "type": "string"
    },
    "vcf": {
      "title": "VCF",
      "description": "An URL of the point mutation file (.vcf).",
      "minLength": 1,
      "maxLength": 2083,
      "format": "uri",
      "type": "string"
    },
    "vcfIndex": {
      "title": "VCF Index",
      "description": "An URL of the point mutation index file (.tbi).",
      "minLength": 1,
      "maxLength": 2083,
      "format": "uri",
      "type": "string"
    },
    "vcf2": {
      "title": "VCF2",
      "description": "An URL of the the indel file (.vcf).",
      "minLength": 1,
      "maxLength": 2083,
      "format": "uri",
      "type": "string"
    },
    "vcf2Index": {
      "title": "VCF2 Index",
      "description": "An URL of the indel index file (.tbi).",
      "minLength": 1,
      "maxLength": 2083,
      "format": "uri",
      "type": "string"
    },
    "bam": {
      "title": "BAM",
      "description": "An URL of the BAM file (.bam).",
      "minLength": 1,
      "maxLength": 2083,
      "format": "uri",
      "type": "string"
    },
    "bamIndex": {
      "title": "BAM Index",
      "description": "An URL of the BAM index file (.bai).",
      "minLength": 1,
      "maxLength": 2083,
      "format": "uri",
      "type": "string"
    },
    "note": {
      "title": "Note",
      "description": "A textual annotation.",
      "type": "string"
    }
  },
  "required": [
    "id",
    "cancer",
    "assembly",
    "sv",
    "cnv"
  ]
}

This means you get auto-validation/parsing on the python side:

from chromosope import Config

unknown_config = [ ... ]

parsed = [Config(**item) for item in unknown_config]
parsed # now know the config is parsed correctly

and could equally generate validators for the JS side from the JSON schema.