refactor!: clean up app (metaschema)

[korikuzma]

Close #162, #332, #429, #119, #428, #189, #309, #414, #475, #427

@jsstevenson sorry (again) 😅 . Need to pull in changes for metaschema branch that is needed for plenary work. I'm going to open now since it's large, but going to look through once more to make sure I didn't accidentally pull in things from prod that we didn't want and that we included everything.

Notes:

• Refactor app (refactor!: clean up app #474)
  • Mainly focused on cleanup related to to_vrs and normalize endpoints. Did not really look at gnomad_vcf_to_protein or copy_number_variation modules
  • Remove to canonical variation (no longer support)
  • Combined tests for tokenizers/classifiers/validators/translators into one module
  • Removed amino_acids.csv (accidentally left in)
  • Names changes
    • Coding DNA → cDNA
    • Polypeptide truncation → Protein Stop Gain
    • Silent Mutation → Reference Agree
    • Uncertain/Range → Ambiguous
    • HGVSDupDelModeEnum → HGVSDupDelModeOption
  • Validators no longer do any kind of translations to VRS representations. Translators will do this work
  • Classifier only returns exact matches and only returns a single classification rather than a list
  • Use regex patterns (in variation/regex.py) rather than multiple if/else conditions
  • Remove unused code
  • Create variation schemas for supported variation types. Uses consistent field naming
  • Cleaning up instance variables in classes
  • Only run fully justified allele normalization on VRS Alleles. Do not run on VRS Copy Number
  • Pulled tokenize, classify, validate, translate outside of subdirectories (variation/tokenizers, variation/classifiers, variation/validators, variation/translators) and moved to app root
  • baseline_copies is required in /hgvs_to_copy_number_count
  • cool-seq-tool update
    • Removes file path params from QueryHandler, can set these via environment variables
    • QueryHandler accepts only uta_db_url as param and removes uta_db_pwd
  • new dependencies for linting
  • ruff (replaced flake8)
  • black
• Add more support for gnomad vcf expressions in normalize ( feat: add more support for gnomad VCF expressions in normalize #479, refactor: gnomad vcf is classified as delins/sub/ref agree #489)
• Remove pyliftover from deps (covered by cool-seq-tool) (refactor: remove pyliftover from deps + remove unnecessary check #480)
• Fix default mode for hgvs dup del mode wrt rse (fix: default mode for hgvs dup del mode wrt rse #482)
• Fix default HGVS dup del mode - dels should be allele w lse (fix: hgvs dup del mode dels should be allele w lse #484)
• Use cool-seq-tool AnnotationLayer and rm CoordinateType (refactor: use cool-seq-tool AnnotationLayer and rm CoordinateType #485)
• Remove structural type from varaition descriptor (refactor!: remove structural type from variation descriptor #487)