feat: Add prototype code for validating fragement file

[Bento007]

Reason for Change

• prototype cellxgene schema CLI changes needed to validate fragments single-cell#721

Changes

• add cli command

$ cellxgene-schema validate-fragment -h                                                                                                    
Usage: cellxgene-schema validate-fragment [OPTIONS] H5AD_FILE FRAGMENT_FILE

  Check that an ATAC SEQ fragment follows the cellxgene data integration schema. If
  validation fails this command will return an exit status of 1 otherwise 0. When
  the '--generate-index' tag is present, the command will generate a tabix
  compatible version of the fragment and tabix index. The generated fragment will
  have the file suffix .bgz and the index will have the file suffix .bgz.tbi.

Options:
  -i, --generate-index  Generate index for fragment
  -h, --help            Show this message and exit.

• add requirements to run dask in local distributed mode
• add validation steps for ATAC-SEQ fragment file
• add tabix index generation steps.

Testing

• TESTS NEEDED

pip install git+https://github.com/chanzuckerberg/single-cell-curation/@tsmith/10x-ATAC#subdirectory=cellxgene_schema_cli

Remaining Work

chanzuckerberg/single-cell#724

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[codecov]

Codecov Report

Attention: Patch coverage is 84.02778% with 23 lines in your changes missing coverage. Please review.

Project coverage is 90.05%. Comparing base (f31d095) to head (e6be307).
Report is 43 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1095      +/-   ##
==========================================
- Coverage   90.52%   90.05%   -0.47%     
==========================================
  Files          18       19       +1     
  Lines        2068     2212     +144     
==========================================
+ Hits         1872     1992     +120     
- Misses        196      220      +24     

Components	Coverage Δ
cellxgene_schema_cli	91.06% <84.02%> (-0.79%)	⬇️
migration_assistant	91.26% <ø> (ø)
schema_bump_dry_run_genes	79.80% <ø> (ø)
schema_bump_dry_run_ontologies	99.53% <ø> (ø)

[github-actions]

This PR has not seen any activity in the past 2 weeks; if no one comments or reviews it in the next 3 days, this PR will be closed.

[github-actions]

This PR was closed because it has been inactive for 17 days, 3 days since being marked as stale. Please re-open if you still need this to be addressed.