Old / unwanted commands?

[michaelbornholdt]

Running python3 deepprofiler yields

Options:
  --root PATH          Root directory for DeepProfiler experiment
  --config TEXT        Path to existing config file
  --cores INTEGER      Number of CPU cores for parallel processing (all=0)
  --gpu TEXT           GPU device id
  --exp TEXT           Name of experiment
  --single-cells TEXT  Name of single cell export folder
  --metadata TEXT      Name of metadata file, default index.csv
  --logging TEXT       Path to file with comet.ml API key
  --help               Show this message and exit.

Commands:
  download-bbbc021
  export-sc
  prepare
  profile
  setup
  split
  train
  traintf2

Its not a big problem, but the first and last commands are outdated or maybe they do have a reason to be there, that I dont know of

[jccaicedo]

That's a good point!
The first command was to help people get started with bbbc021 as a reference dataset for experiments, but we probably don't need it anymore. The second command is still useful, but we could remove it from the main branch and keep it only in the tf2 branch while we decide how to transition more code to TFv2.

@Arkkienkeli does this make sense to you?

[michaelbornholdt]

I think since we want to make the example data a more core part of the first user experimence, it should be downloaded automatically when calling setup and then people can try out all the functions