Source code for spacr.main

"""Command-line entry point for ``python -m spacr``.

The module builds and dispatches spaCR's command-line subcommands. Every
window command opens the PySide6 application; with no subcommand it opens on
the Home tab.

Copyright © 2025 olafsson lab
"""

from __future__ import annotations

import argparse



[docs]
def build_parser() -> argparse.ArgumentParser:
    """Return the argparse parser exposing the ``spacr`` CLI subcommands.

    :returns: Parser accepting a single positional ``command`` argument.
    """
    parser = argparse.ArgumentParser(prog="spacr")
    parser.add_argument(
        "command",
        nargs="?",
        default="gui",
        choices=[
            "gui",
            "mask",
            "measure",
            "classify",
            "annotate",
            "sequencing",
            "umap",
            "make-masks",
            "version",
        ],
        help="Command to run.",
    )
    return parser



#: The subcommand a user types -> the Qt tab it should open on.
#:
#: `gui` names no tab: it opens on Home, which is what it always did.
_APP_KEYS = {
    "mask": "mask",
    "measure": "measure",
    "classify": "classify_merged",
    "annotate": "annotate",
    "sequencing": "map_barcodes",
    "umap": "umap",
    "make-masks": "make_masks",
}



[docs]
def main(argv: list[str] | None = None) -> int:
    """CLI entry point; dispatch to the requested spacr subcommand.

    :param argv: Argument list to parse. When None, ``sys.argv[1:]`` is used.
    :returns: ``0`` for the version command; window commands return the Qt
        launcher's integer exit status.
    :raises SystemExit: with code ``2`` when argparse rejects the arguments or
        a command accepted by the parser has no dispatcher. ``parser.error``
        never returns, so there is no exit code to hand back in either case.
    """
    parser = build_parser()
    args = parser.parse_args(argv)

    if args.command == "version":
        from .version import version_str
        print(version_str)
        return 0

    if args.command in ("gui", "mask", "measure", "classify", "annotate",
                        "sequencing", "umap", "make-masks"):
        from .qt import run

        key = _APP_KEYS.get(args.command)
        return int(run([key] if key else []) or 0)

    parser.error(f"Unknown command: {args.command}")



if __name__ == "__main__":
    raise SystemExit(main())
Source code for spacr.__main__

Source code for spacr.main
