Refactor output

[keurfonluu]

• Changed: dedicated output classes (toughio.ElementOutput and toughio.ConnectionOutput) instead of mere namedtuple toughio.Output.
• Added: option time_steps to read a specific time step to avoid having to read the whole output file when working on a specific time step (so faster).
• Fixed: standard output reader for outputs generated by early versions of TOUGH2.

Reminders:

• Run invoke format to make sure the code follows the style guide,
• Add tests for new features or tests that would have caught the bug that you're fixing,
• Write detailed docstrings for all functions, classes and/or methods,
• If adding new functionality, unit test it and add it to the documentation.

[codecov]

Codecov Report

Attention: Patch coverage is 86.09272% with 42 lines in your changes are missing coverage. Please review.

Project coverage is 90.20%. Comparing base (4894d6d) to head (636014e).
Report is 16 commits behind head on master.

Files	Patch %	Lines
toughio/_io/output/_common.py	73.33%	24 Missing ⚠️
toughio/_io/output/tough/_tough.py	90.38%	5 Missing ⚠️
toughio/_io/output/_helpers.py	80.00%	4 Missing ⚠️
toughio/_io/output/petrasim/_petrasim.py	92.10%	3 Missing ⚠️
toughio/_cli/_export.py	60.00%	2 Missing ⚠️
toughio/_io/output/csv/_csv.py	95.34%	2 Missing ⚠️
toughio/_mesh/_mesh.py	71.42%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #170      +/-   ##
==========================================
- Coverage   90.21%   90.20%   -0.01%     
==========================================
  Files          97       97              
  Lines        6283     6433     +150     
==========================================
+ Hits         5668     5803     +135     
- Misses        615      630      +15     

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