Make some serializers optionals

[kripnerl]

Reasoning

OMAS should be (IMHO) a lightweight tool for; however, some of its dependencies make it bulky and have complicated dependencies.

Problem

I speak specifically about mojo-core. We have already encountered a second issue with that library. First was an obsolete dependency on urllib (which is fixed in the newer version) and second is now Windows poetry installations:

Installing botocore (1.31.33): Failed

  FileNotFoundError

  [Errno 2] No such file or directory: 'C:\\Users\\jh\\AppData\\Local\\Packages\\PythonSoftwareFoundation.Python.3.11_qbz5n2kfra8p0\\LocalCache\\Local\\pypoetry\\Cache\\virtualenvs\\cug-vessel-model-WXhTS8yu-py3.11\\Lib\\site-packages\\botocore\\data\\kinesis-video-archived-media\\2017-09-30\\endpoint-rule-set-1.json.gz'

  at C:\Program Files\WindowsApps\PythonSoftwareFoundation.Python.3.11_3.11.1776.0_x64__qbz5n2kfra8p0\Lib\pathlib.py:1044 in open
      1040│         the built-in open() function does.
      1041│         """
      1042│         if "b" not in mode:
      1043│             encoding = io.text_encoding(encoding)
    → 1044│         return io.open(self, mode, buffering, encoding, errors, newline)
      1045│
      1046│     def read_bytes(self):
      1047│         """
      1048│         Open the file in bytes mode, read it, and close the file.

Proposed solution

Add specialized backend as optional dependencies in setup.py:

...
install_requires = [
    'numpy>=1.16.1',
    'uncertainties',
    'pint',
    'netCDF4',
    'matplotlib',  # In principle, plotting could be also optional since some deployments do not require any plotting.
    'scipy',
    'h5py',
    'dnspython', # Not sure about this one - it is not used in the code, or I missed it. 
    'xarray',
    'setuptools>=41.2',  
    'Cython',
]

extras_require = {
    'machine': [
        'omfit_classes',
        'pexpect',
        'fortranformat',
        'pygacode',
    ],
    'hdc': ['pyhdc'],
    'imas': ['imas'],
    'uda': ['pyuda'],
    'mongo': ['pymongo'],
    'aws': ['boto3'],
    
    'build_structures': ['bs4', 'xmltodict', 'tqdm'], # xmltodict is used only in `omas_structures` and `tqdm` only when fetching data and the code more over is checking on the existence of the `tqdm`.  
    'build_documentation': ['Sphinx', 'sphinx-bootstrap-theme', 'sphinx-gallery', 'Pillow'],
}
...

[kripnerl]

If you agree, I will be very happy to open a pull request.

[orso82]

I am not sure how much the MongoDB interface is used. I suspect zero. If so, I'd be inclined to actually remove all that part of the source... others can comment

[kripnerl]

Hah. I was just recently thinking that it would be cool to test the MongoDB :-D. However, I assume this will remain only with dreams since the day is only 24 hours long ... So no. We are nor using nor (actively) planning using this.

[orso82]

Ok, well, perhaps we can start by making it an optional dependency as you suggested. Who knows that someday you'll find the time :P

Other comments for the PR:

• dnspython can probably go, I honestly forgot why it got there
• instead of aws can we use s3 ?

[github-actions]

Stale issue message

[kripnerl]

On hold, to be resolved soon.

[github-actions]

Stale issue message

[kripnerl]

Reopening with opened pull request: #330