Command Provenance (uns_logger)

msmu functions decorated with uns_logger automatically append execution logs to mdata.uns["_cmd"].

At runtime, mdata.uns["_cmd"] is managed as dict[str, dict], where each entry contains:

• function: function name
• timestamp: execution timestamp
• msmu_version: installed msmu version
• python_version: runtime Python version
• payload: bound function arguments (including default values for omitted args)
• stdout: captured printed messages from the function (if any) (both print(...) and logging messages under the msmu logger)
• input_dimensions: input MuData dimensions (n_obs, n_vars, per-modality dimensions, layers)
• output_dimensions: output MuData dimensions (n_obs, n_vars, per-modality dimensions, layers)

Behavior

• print(...) output and logging output (from msmu loggers) are shown on screen and captured into _cmd (stdout).
• Reader functions (read_*, read_h5mu) also append _cmd entries.
• When reading .h5mu, _cmd is normalized back to runtime dict[str, dict] format.

Example

mdata = mm.pp.add_filter(
    mdata,
    modality="psm",
    on="var",
    column="q_value",
    keep="lt",
    value=0.01,
)

last = mdata.uns["_cmd"][max(mdata.uns["_cmd"], key=lambda k: int(k))]
print(last["function"])   # add_filter
print(last["payload"])    # arguments (including defaults)