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https://github.com/chanzuckerberg/cellxgene.git
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78176f9711
Add the `cellxgene schema apply` and `cellxgene schema validate` subcommands. The first takes an h5ad file and a yaml with config information and produces a new h5ad that follows the cellxgene data integration schema. The second takes an h5ad and checks if it follows the schema version written into its metadata. Both are currently marked as "experimental" as the primary intended users are still at CZI.
36 lines
973 B
Python
36 lines
973 B
Python
import click
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from .convert_to_cxg import convert_to_cxg
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from .launch import launch
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from .prepare import prepare
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from .upgrade import log_upgrade_check
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from .schema import schema_cli
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from .. import __version__
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@click.group(
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name="cellxgene",
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subcommand_metavar="COMMAND <args>",
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options_metavar="<options>",
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context_settings=dict(max_content_width=85, help_option_names=["-h", "--help"]),
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)
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@click.help_option("--help", "-h", help="Show this message and exit.")
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@click.version_option(
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version=__version__,
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prog_name="cellxgene",
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message="[%(prog)s] Version %(version)s",
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help="Show the software version and exit.",
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)
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@click.option(
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"--upgrade-check/--no-upgrade-check", default=True, show_default=True, help="Check for release upgrades on start.",
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)
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def cli(upgrade_check):
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if upgrade_check:
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log_upgrade_check()
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cli.add_command(launch)
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cli.add_command(prepare)
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cli.add_command(convert_to_cxg)
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cli.add_command(schema_cli)
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