`config`¶

One home for constants that more than one notebook reads. collect writes the files named here, load reads them, and analysis notebooks import Cfg instead of restating a path. A knob that only one analysis uses stays in that analysis.

class Cfg:
    """Shared paths. Each line is a choice."""

    # Paths are anchored to the repo root,
    # so notebooks work from any working directory.
    ROOT = Path(__file__).resolve().parents[1]

    # Codex cell-type census, written by collect.download_codex.
    CENSUS = ROOT / "data" / "cell_types.csv.gz"
    # Other Codex tables, one <product>.csv.gz each,
    # written on demand by collect.download_codex.
    CODEX = ROOT / "data" / "codex"
    # Every pair of cells with at least one proofread end,
    # weighted by synapse count and sorted by presynaptic cell;
    # written by collect.collect_connections.
    # Read it lazily with load.scan_connections
    # and filter before collecting.
    CONNECTIONS = ROOT / "data" / "connections.parquet"
    # One file per batch of proofread cells while
    # collect.collect_connections runs;
    # a rerun skips the batches that are there,
    # and the merge deletes the folder.
    CONNECTIONS_PARTS = ROOT / "data" / "connections_parts"
    # One SWC file per root id, written by collect.collect_skeletons.
    SKELETONS = ROOT / "data" / "skeletons"
    # Codex side and column tables already under CODEX;
    # load reads them, and collect.download_codex writes them on demand.
    VISUAL_TYPES = CODEX / "visual_neuron_types.csv.gz"
    COLUMNS = CODEX / "column_assignment.csv.gz"
    # One row per proofread neuron,
    # the list that separates neurons from unproofread fragments.
    CLASSIFICATION = CODEX / "classification.csv.gz"
    FIGURES = ROOT / "figures"

pl.DataFrame(
    {
        "name": [_k for _k in vars(Cfg) if _k.isupper()],
        "value": [str(_v) for _k, _v in vars(Cfg).items() if _k.isupper()],
    }
)

shape: (10, 2)

name	value
str	str
"ROOT"	"/home/jaeho/projects/champalim…
"CENSUS"	"/home/jaeho/projects/champalim…
"CODEX"	"/home/jaeho/projects/champalim…
"CONNECTIONS"	"/home/jaeho/projects/champalim…
"CONNECTIONS_PARTS"	"/home/jaeho/projects/champalim…
"SKELETONS"	"/home/jaeho/projects/champalim…
"VISUAL_TYPES"	"/home/jaeho/projects/champalim…
"COLUMNS"	"/home/jaeho/projects/champalim…
"CLASSIFICATION"	"/home/jaeho/projects/champalim…
"FIGURES"	"/home/jaeho/projects/champalim…

config¶

`config`¶