refactor commands/scripts to expose only one named mne

[agramfort]

as suggested by @yarikoptic

[yarikoptic]

this might lead to various unpleasant side effects happen there are spaces in the arguments etc. I guess it would be better to use subprocess.Popen or may be runpy would fit here?

[yarikoptic]

probably the easiest would be to use 'subprocess.call([cmdpath] + sys.argv[2:])', not sure if adding ', shell=True' is needed here

note: updated to add cmdpath

[larsoner]

We have a convenience wrapper for subprocess.popen in utils.py that could probably be used.

[agramfort]

ok now using Popen and hacking the usage message to recommand the "mne browse_raw" syntax.

[agramfort]

usage example

$mne browse_raw -h
Usage: mne browse_raw [options]

Options:
  -h, --help            show this help message and exit
  --raw=FILE            Input raw FIF file
  --proj=FILE           Projector file
  --eve=FILE            Events file
  -d DURATION, --duration=DURATION
                        Time window for plotting (sec)
  -t START, --start=START
                        Initial start time for plotting
  -n N_CHANNELS, --n_channels=N_CHANNELS
                        Number of channels to plot at a time
  -o ORDER, --order=ORDER
                        Order for plotting ('type' or 'original')
  -p PRELOAD, --preload=PRELOAD
                        Preload raw data (for faster navigaton)
  -s SHOW_OPTIONS, --show_options=SHOW_OPTIONS
                        Show projection options dialog
  --version             Return script version

[agramfort]

should be good to go ...

[dengemann]

Please wait and let me try tomorrow. I'll let you know how it goes.

[dengemann]

filtering is not needed here, os.listdir will be 50 % faster

[dengemann]

The following commands fail on my box (error prevents print help)

1. flash_bem_model

Traceback (most recent call last):
  File "/Users/dengemann/anaconda/python.app/Contents/lib/python2.7/site-packages/mne/commands/mne_flash_bem_model.py", line 136, in <module>
    flash05 = os.path.abspath(options.flash05)
  File "/Users/dengemann/anaconda/python.app/Contents/lib/python2.7/posixpath.py", line 352, in abspath
    if not isabs(path):
  File "/Users/dengemann/anaconda/python.app/Contents/lib/python2.7/posixpath.py", line 61, in isabs
    return s.startswith('/')
AttributeError: 'NoneType' object has no attribute 'startswith'


2. clean_eog_ecg

Traceback (most recent call last):
  File "/Users/dengemann/anaconda/python.app/Contents/lib/python2.7/site-packages/mne/commands/mne_clean_eog_ecg.py", line 147, in <module>
    clean_ecg_eog(raw_in, raw_out, eog=eog, ecg=ecg)
  File "/Users/dengemann/anaconda/python.app/Contents/lib/python2.7/site-packages/mne/commands/mne_clean_eog_ecg.py", line 39, in clean_ecg_eog
    raw_in = mne.fiff.Raw(in_fif_fname)
  File "/Users/dengemann/anaconda/python.app/Contents/lib/python2.7/site-packages/mne/utils.py", line 360, in dec
    return function(*args, **kwargs)
  File "/Users/dengemann/anaconda/python.app/Contents/lib/python2.7/site-packages/mne/fiff/raw.py", line 89, in __init__
    fnames = [op.abspath(fnames)] if not op.isabs(fnames) else [fnames]
  File "/Users/dengemann/anaconda/python.app/Contents/lib/python2.7/posixpath.py", line 61, in isabs
    return s.startswith('/')
AttributeError: 'NoneType' object has no attribute 'startswith'


3. surf2bem

/Users/dengemann/anaconda/python.app/Contents/lib/python2.7/site-packages/mne/datasets/utils.py:173: UserWarning: Sample dataset (version 0.6) is older than mne-python (version 0.7.git). If the examples fail, you may need to update the sample dataset by using force_update=True
  % (data_version, mne_version))
Traceback (most recent call last):
  File "/Users/dengemann/anaconda/python.app/Contents/lib/python2.7/site-packages/mne/commands/mne_surf2bem.py", line 39, in <module>
    points, tris = mne.read_surface(options.surf)
  File "/Users/dengemann/anaconda/python.app/Contents/lib/python2.7/site-packages/mne/utils.py", line 360, in dec
    return function(*args, **kwargs)
  File "/Users/dengemann/anaconda/python.app/Contents/lib/python2.7/site-packages/mne/surface.py", line 564, in read_surface
    with open(fname, "rb") as fobj:
TypeError: coercing to Unicode: need string or buffer, NoneType found
Converting None to BEM FIF file.

[dengemann]

However these particular scripts are broken themselves, it's not due to the new master command.

[dengemann]

Thanks @agramfort ! I'll open new issues for the points I mentioned.