Update Instrument File Processing Functions

[Alrobbertz]

• Separates input, calibration, and output into three distinct functions
• Ensures calibration is done using the HermesData data container structure

[codecov]

Codecov Report

Attention: 12 lines in your changes are missing coverage. Please review.

Comparison is base (c6090d6) 91.07% compared to head (8c73799) 79.03%.

Files	Patch %	Lines
hermes_nemisis/calibration/calibration.py	56.25%	7 Missing ⚠️
hermes_nemisis/io/file_tools.py	85.29%	5 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##             main      #20       +/-   ##
===========================================
- Coverage   91.07%   79.03%   -12.04%     
===========================================
  Files           4        4               
  Lines          56       62        +6     
===========================================
- Hits           51       49        -2     
- Misses          5       13        +8     

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[dbarrous]

LGTM! Re: HERMES-SOC/hermes_eea#22

[ehsteve]

@Alrobbertz there is a conflict to resolve.