Design¶

The package is organized as:

• src/xnatcli/cli.py — argparse setup and subcommand dispatch.
• src/xnatcli/login.py — interactive credential capture, verification, and on-disk storage; also exposes load_credentials for the other subcommands.
• src/xnatcli/download.py — experiment download.
• src/xnatcli/query.py — CSV listing of (project, subject, experiment) triplets.
• src/xnatcli/mriconfig.py — runs dcm2bids_helper against a downloaded experiment directory.
• src/xnatcli/mriconvert.py — converts downloaded XNAT sessions to BIDS via dcm2bids.
• src/xnatcli/cubids.py — runs CuBIDS add-nifti-info and group on a BIDS dataset.
• src/xnatcli/bidsmap.py — generates/updates a participant/session mapping TSV for a mriconvert-produced BIDS dataset and, with -o, applies renames by copying the dataset to a new tree (uses pandas).
• src/xnatcli/physioconvert.py — converts physio recordings associated (via mriconvert's mriconvert_qc.tsv physio column) with a BIDS dataset, placing them directly alongside their paired scan (uses phys2bids).

Credentials live in ~/.xnatcli/credentials.cfg, a plain-text configparser file with a single [xnatcli] section storing server, username, and password. The file is created via os.open with mode 0o600 and re-chmod-ed to 0o600 after writing so only the owner can read or write it. (On Windows, os.chmod only toggles the read-only bit — the permissions model there is ACL-based; the 0o600 call still runs for portability.)