Improve toughio.run

[keurfonluu]

• Added: option docker_args to pass additional arguments to docker run.
• Added: option petsc_args to pass to PETSc.
• Added: better error handling for executable and/or Docker.
• Fixed: capture and display standard output in IPython console.
• Added: option blocks to only read a selection blocks.
• Added: method __getitem__ for toughio.Mesh that returns a subset of a mesh given a slice.

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: 66 lines in your changes are missing coverage. Please review.

Files	Coverage Δ
toughio/_io/input/_helpers.py	82.85% <ø> (ø)
toughio/_io/input/tough/_read.py	96.34% <96.62%> (+0.06%)	⬆️
toughio/_run.py	56.12% <23.68%> (-20.35%)	⬇️
toughio/_mesh/_mesh.py	81.93% <2.85%> (-6.61%)	⬇️

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