Refactor parsing of results files

[wtbarnes]

Fixes #86

This pull requests does a few things though is mainly focused on refactoring the parsing of the results files to try and simplify things:

• Move all file parsing logic to standalone functions in pydrad/parse/util.py that return astropy.table.QTable objects rather than arrays
• Properties on Strand are only dynamically generated if there are many of them or if they are unknown ahead of time (e.g. for the .ine files). Otherwise they are explicitly listed on Profile.
• Quantities are now pulled out of the resulting tables by column name rather than relying on indexing an array. This should be more robust.
• All results files are now optional except for the .amr files. If the .phy files are not read (or not present), the thermodynamic quantities are computed from the conserved quantities in the .amr files. See Function for calculating thermodynamic variables from conserved variables #86.

TODOs:

• Docstrings for quantities on Profile
• Create issue to track case where .amr file has an additional column for the electron mass density

[codecov]

Codecov Report

Attention: Patch coverage is 75.00000% with 44 lines in your changes missing coverage. Please review.

Project coverage is 71.50%. Comparing base (557e41a) to head (16cbbdd).

Files with missing lines	Patch %	Lines
pydrad/parse/util.py	60.00%	18 Missing ⚠️
pydrad/parse/parse.py	87.71%	14 Missing ⚠️
pydrad/configure/configure.py	10.00%	9 Missing ⚠️
pydrad/visualize/animate.py	0.00%	3 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #176      +/-   ##
==========================================
+ Coverage   70.41%   71.50%   +1.08%     
==========================================
  Files          11       13       +2     
  Lines         730      800      +70     
==========================================
+ Hits          514      572      +58     
- Misses        216      228      +12     

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[jwreep]

A few minor suggestions that you can ignore if you want. This looks otherwise fine to me! Thanks for putting this together.

[jwreep]

There's definitely an uncertainty, but I don't know what it is!

The uncertainty from the abundance set (likely Feldman) + the uncertainty of the hydrogen and helium masses should propagate.

Perhaps we should make an issue to figure this out? I do like that this has the option of including it!

[wtbarnes]

Good point. I had this thought when I put in 0 for the uncertainty but didn't have any idea as to what this value may be. We can create another issue to track this.