Resolve "add type hints to api.v1.resources.allele.AlleleListResource"

Description

Pydantic model namespace created at api.schemas.pydantic.v1

• General pydantic scaffolding: api.schemas.pydantic.v1.common
  • BaseModel for general use, ExtraOK for when additional parameters are added to the resulting object without validation
  • misc enums that are likely to be reused
• Initial pydantic models for:
  • allele_assessments
  • allele_reports
  • alleles
  • annotations
  • common
  • genotypes
  • references
  • resources
  • samples
  • users
  • Validates successfully against AlleleDataLoader output
• Resource response validation
  • Resource response models in api.schemas.pydantic.v1.resources
  • Resource objects only need a decorator with the new model: @validate_output(PydanticResourceModel)
• Schema generation
  • pydantic2json.py - generates JSON Schema files from pydantic models
  • pydantic2ts.sh - generates TypeScript interfaces/types from pydantic models (via JSON Schemas)
• Pipfile
  • Updated:
    • mypy
    • typing-extensions
    • coverage
  • Added:
    • types-pytz
    • types-pyyaml
• Misc
  • Bugfix for #2102 (closed), found while creating initial models
  • Assorted formatting/clean up of shell scripts
  • Testing profile for devcontainer with deadline disabled

Related issues

Notes to review (code/docs/QA)

Tests

General

• Tests have been added that prove my fix is effective or that my feature works
• Related tests have been modified/removed

Hypothesis testing:

• Soak testing has been done
• Distribution between positive / negative cases has been checked

Database

• Includes changes to database schema
• Includes necessary database migrations

Configuration

• Includes changes to configuration
• Includes configuration migration instructions in documentation

Closes #2005 (closed), #2102 (closed)