childmindresearch / bids2table

Efficiently index large-scale BIDS neuroimaging datasets and derivatives
https://childmindresearch.github.io/bids2table/
MIT License
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Add CLI prototype #1

Closed nx10 closed 1 year ago

nx10 commented 1 year ago

Adds a minimal CLI. Entrypoint gets registred when the package is pip installed.

$ b2t
usage: b2t [-h] -i INPUT -o OUTPUT [-u] [-c CORES] [-s]
b2t: error: the following arguments are required: -i/--input, -o/--output

$ b2t --help
usage: b2t [-h] -i INPUT -o OUTPUT [-u] [-c CORES] [-s]

options:
  -h, --help            show this help message and exit
  -i INPUT, --input INPUT
                        Path to BIDS dataset
  -o OUTPUT, --output OUTPUT
                        Path to output parquet dataset directory
  -u, --update          update dataset incrementally with only new or changed files.
  -c CORES, --cores CORES
                        number of parallel processes. If `None` or 1, run in the mainprocess. Setting to -1 runs in `os.cpu_count()` processes.
  -s, --suppress_warnings
                        suppress warnings

$ b2t -i my/bids/dir -o test_run -s
689it [00:02, 320.37it/s, tot=689, good=689, rec=333, err=0]
nx10 commented 1 year ago

updated according to review