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klebgenomics / Kaptive

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use command -v instead of which in find_program #12

Closed EricDeveaud closed 7 months ago

EricDeveaud commented 4 years ago

Hello you may want to use command -v instead of which

while testing Kleborate in a minimal docker environement , Kaptive gave me the following error:

  File "/opt/gensoft/exe/Kleborate/2.0.0/venv/lib/python3.8/site-packages/kaptive/kaptive.py", line 173, in find_program
    process = subprocess.Popen(['which', name], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
  File "/opt/gensoft/adm/Python/3.8/lib/python3.8/subprocess.py", line 854, in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
  File "/opt/gensoft/adm/Python/3.8/lib/python3.8/subprocess.py", line 1702, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'which'

some more arguments: command is a shell buitin command is posix compliant which is an external binary that may or not available (I admit this may a rare case but it may exists, see above)

regards

Eric

tomdstanton commented 7 months ago

See #11