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kausmees / GenoCAE

Convolutional autoencoder for genotype data
BSD 3-Clause "New" or "Revised" License
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Suggest: give an error message when an invalid CLI argument is given #7

Closed richelbilderbeek closed 3 years ago

richelbilderbeek commented 3 years ago

When I run GCAE from the command line with a nonsense argument, e.g. nonsense:

python run_gcae.py nonsense

I get to see the help file:

2021-06-24 06:34:30.118604: W tensorflow/stream_executor/platform/default/dso_loader.cc:59] Could not load dynamic library 'libcudart.so.10.1'; dlerror: libcudart.so.10.1: cannot open shared object file: No such file or directory
2021-06-24 06:34:30.118629: I tensorflow/stream_executor/cuda/cudart_stub.cc:29] Ignore above cudart dlerror if you do not have a GPU set up on your machine.
tensorflow version 2.3.3
Usage:
  run_gcae.py train --datadir=<name> --data=<name> --model_id=<name> --train_opts_id=<name> --data_opts_id=<name> --save_interval=<num> --epochs=<num> [--resume_from=<num> --trainedmodeldir=<name> ]
  run_gcae.py project --datadir=<name>   [ --data=<name> --model_id=<name>  --train_opts_id=<name> --data_opts_id=<name> --superpops=<name> --epoch=<num> --trainedmodeldir=<name>   --pdata=<name> --trainedmodelname=<name>]
  run_gcae.py plot --datadir=<name> [  --data=<name>  --model_id=<name> --train_opts_id=<name> --data_opts_id=<name>  --superpops=<name> --epoch=<num> --trainedmodeldir=<name>  --pdata=<name> --trainedmodelname=<name>]
  run_gcae.py animate --datadir=<name>   [ --data=<name>   --model_id=<name> --train_opts_id=<name> --data_opts_id=<name>  --superpops=<name> --epoch=<num> --trainedmodeldir=<name> --pdata=<name> --trainedmodelname=<name>]
  run_gcae.py evaluate --datadir=<name> --metrics=<name>  [  --data=<name>  --model_id=<name> --train_opts_id=<name> --data_opts_id=<name>  --superpops=<name> --epoch=<num> --trainedmodeldir=<name>  --pdata=<name> --trainedmodelname=<name>]

I think it is already friendly to show the help, yet I would not expect the output to be exactly the same as when doing python run_gcae.py --help. I suggest to add an error message (and error code) if an invalid CLI argument is given.

richelbilderbeek commented 3 years ago

Indeed this has been fixed, thanks!

Note to self of a test that now passes:

remotes::install_github("richelbilderbeek/gcaer")
gcaer::install_gcae()
args <- c("--nonsense")
expect_error(run_gcae(args), "Invalid command")