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Add CLI support for running blockwise tasks#20

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JoeStrout wants to merge 2 commits intoe11bio:mainfrom
JoeStrout:cli_support
Open

Add CLI support for running blockwise tasks#20
JoeStrout wants to merge 2 commits intoe11bio:mainfrom
JoeStrout:cli_support

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Summary

  • Adds a run subcommand to volara-cli for running blockwise tasks directly from the command line, with
    support for YAML/JSON config files, dotted keys for nested fields, multi-value arguments, and shorthand
    expansion for nested Pydantic models.
  • Adds a CLI tutorial (with some small helper scripts for preparing & visualizing the data).
  • Fixes SQLite db code to read edge_attrs from stored metadata when not explicitly provided, avoiding assertion
    errors when reopening existing databases. (This lets us use the --db shorthand requested in issue Add CLI support #3.)

Details

  • Config files and CLI args can be mixed (CLI overrides config).
  • Shorthands: --db my.sqlite expands to {"db_type": "sqlite", "path": "my.sqlite"}
  • volara-cli run --help lists all available task types.
  • Added 32 new tests for config loading, arg parsing, shorthand resolution, and CLI integration.

Closes #3.

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Add CLI support

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