YAML reader function

[connoramoreno]

Changes the location of the YAML reader function read_yaml_config. Previously, each ParaStell script had an identical read_yaml_config function to read YAML input. This PR moves this function to utils.py, and each script then imports it.

Closes #52
Closes #54

[connoramoreno]

It should be noted that this is a draft since the relative imports in each script seem to be causing issues when using YAML input from the command line. For example, assuming parastell.py and config.yaml are in the same directory, the command

python3 parastell.py config.yaml

results in the following error:

Traceback (most recent call last):
  File "/home/camoreno/parastell/parastell/parastell.py", line 6, in <module>
    from . import log
ImportError: attempted relative import with no known parent package

[gonuke]

I think we'll want to get to a point where we actually install this rather than just run from the source directory. Alternatively, we put the parastell directory in the python path?

[connoramoreno]

This is with parastell on PYTHONPATH, specifically the repository directory. This also uses the updated file structure.

[connoramoreno]

Executing from a different directory with config.yaml,

python3 ~/parastell/parastell/parastell.py config.yaml

results in the same error.

[connoramoreno]

I can change it so that we don't use relative imports; it's just strange that they seem to cause issues

[gonuke]

If that fixes it, I guess let's change it. Separately, I'd like to better understand these relative imports, because they should work.

[connoramoreno]

The relative imports work when ParaStell is imported as a module, but not when run from command line with a YAML input argument.

[connoramoreno]

It might be that relative imports are defined only for Python modules, but when these scripts are run from command line with a YAML argument, they might not be considered modules by Python anymore

[gonuke]

Yes... so I think the right way to do this is to generate a lightweight script that imports parastell and calls parastell.parastell()

if you make a file called stellarator with these contents and chmod u+x, it works.

#!/usr/bin/env python3

from parastell import parastell

parastell.parastell()

and make it executable.

I think there are simple ways to do this with setup tools as part of installation. But that may be for another time.

[connoramoreno]

I am planning to lump in the solution we discussed for #52 into this PR since it's so related, unless there are any objections.

[gonuke]

Just a minor comment on naming the executables.

[gonuke]

Also, if we figure out how to use pip install correctly, these can be automatically generated in the right place in the path.

[connoramoreno]

Would we rather make ParaStell pip-installable or condo-installable, given the dependency on conda packages? I'm not sure that some of our dependencies can be installed via pip.

[gonuke]

pip can also be used to install the software from the source code in a local place on the Python path. This is the mode I'm thinking of, not necessarily installing with pip from PyPi

[gonuke]

LGTM - thanks @connoramoreno