chemfp spherex command-line options

The following comes from chemfp spherex --help:

usage: chemfp spherex [-h] [-t FLOAT] [--num-picks N] [--dise]
                      [--dise-references FILENAME] [--dise-format FORMAT]
                      [--ranks FILENAME] [--ranks-default N]
                      [--ranks-format FORMAT] [--ranks-has-header]
                      [--in CANDIDATES_FORMAT] [--references FILENAME]
                      [--references-format FORMAT] [--pick-id PICK_ID]
                      [--pick-id-file FILENAME] [--randomize | --no-randomize]
                      [--seed N] [--mmap | --no-mmap] [--include-hits]
                      [--output FILENAME] [--out OUTPUT_FORMAT]
                      [--precision N] [--save-picks FILENAME]
                      [--save-picks-format FILENAME]
                      [--save-candidates FILENAME]
                      [--save-candidates-format FILENAME]
                      [--include-empty | --no-include-empty]
                      [--empty-score EMPTY_SCORE]
                      [--empty-hit-id EMPTY_HIT_ID]
                      [--pick-time | --no-pick-time] [--no-date] [--date STR]
                      [--times] [--progress | --no-progress]

Select diverse fingerprints using the sphere exclusion algorithm

positional arguments:
  candidates            fingerprint file containing candidates (fingerprints
                        to pick from)

  -h, --help            show this help message and exit
  -t FLOAT, --threshold FLOAT
                        Maximum similarity (default: 1.0)
  --num-picks N, -n N   Number of picks (default: 'all')
  --dise                Use directed sphere exclusion
  --dise-references FILENAME
                        DISE reference structures or fingerprints (default
                        uses the Gobbi & Lee structures)
  --dise-format FORMAT  format of the DISE reference file (default uses the
                        file extension, else 'fps')
  --ranks FILENAME      file containing fingerprint rank values
  --ranks-default N     default rank value if candidate id not found in the
                        ranks file (default: 2**32-1)
  --ranks-format FORMAT
                        format for the ranks file (only 'tsv' is supported)
  --ranks-has-header    skip the first line of the ranks file
                        Format of the candidates file (default uses filename
                        extension, or 'fps')
  --references FILENAME
                        Fingerprint file containing reference fingerprints to
                        avoid (the fingerprints you have)
  --references-format FORMAT
                        Format of the references file (default uses filename
                        extension, or 'fps')
  --pick-id PICK_ID     Initial candidate id (if no reference file). Can be
                        used more than once.
  --pick-id-file FILENAME
                        File containing initial candidate ids, one per line
  --randomize, --no-randomize
                        Use --randomize (default for undirected picking) to
                        randomly pick from the available candidates, or --no-
                        random (default for directed picking) to pick the
                        candidate with the smallest arena index.
  --seed N              Specify the random number generator seed between 0 and
                        2**64-1, inclusive, or use -1 to have one picked at
                        random (default: -1)
  --mmap, --no-mmap     Don't use mmap to read uncompressed FPB files. May
                        give better performance on networked file systems, at
                        the expense of higher memory use. (default: True)
  --include-hits        include ids and scores for fingerprints in each sphere
  --output FILENAME, -o FILENAME
                        Write output to the named file instead of stdout.
  --out OUTPUT_FORMAT   Output format. Must be one of 'chemfp' (the default),
                        'csv', 'tsv', or 'excel-tab', with optional
  --precision N         Number of digits in Tanimoto score (default: based on
                        the fingerprint size)
  --save-picks FILENAME
                        Write picked fingerprints to the named file.
  --save-picks-format FILENAME
                        Specify the format for the picked fingerprints.
  --save-candidates FILENAME
                        Write remaining candidate fingerprints to the named
  --save-candidates-format FILENAME
                        Specify the format for the remaining candidate
  --include-empty, --no-include-empty
                        In csv and tsv format with --include-hits, include
                        picks with no hits (the default) (default: True)
  --empty-score EMPTY_SCORE
                        The score if --include-empty outputs a pick with no
                        hits (default: 'NaN')
  --empty-hit-id EMPTY_HIT_ID
                        The hit id if --include-empty outputs a pick with no
                        hits (default: '*')
  --pick-time, --no-pick-time
                        include the elapsed time for each pick (default:
  --no-date             Do not include the 'date' metadata in the output
  --date STR            An ISO 8601 date (like '2022-02-07T11:10:15') to use
                        for the 'date' metadata in the output header
  --times               Write timing information to stderr
  --progress, --no-progress
                        Show a progress bar (default: show unless the output
                        is a terminal)