create spec file

[luiztauffer]

• [x] Separate the logic of creating spec file from run
• [x] add this as a cli functionality, this can be useful for developers and for automatic actions
• [x] remove the necessity of generate_spec.sh files in the apps directories

example usage, from the root dir of an apps repository:

protocaas make-app-spec-file --app-dir ./kilosort2_5/

the main.py file of the app:

import os
import protocaas.sdk as pr

try:
    import h5py
    import remfile
    import pynwb
    ...
except ImportError:
    # Do not raise import error if we are only generating the spec
    if os.environ.get('PROTOCAAS_GENERATE_SPEC', None) != '1':
        raise

app = pr.App(
    'kilosort2_5', 
    help="Kilosort 2.5 spike sorting",
    app_image="magland/pc-kilosort2_5",
    app_executable="/app/main"
)
...

[magland]

@luiztauffer I merged this and then I pushed a new commit that makes the naming consistent throughout: app_container and app_executable