Encapsulate MC/DC models in explicit Simulation instances

[ilhamv]

Summary of changes

This PR redesigns model construction around explicit mcdc.Simulation instances, replacing the global simulation singleton and the global settings, visualization, and run interfaces.

Each simulation now owns and compiles its complete object graph before transport. The associated compiler, input and output workflows, regression problems, public API documentation, and unit tests have been updated for the encapsulated workflow.

Types of changes

• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that changes existing functionality)
• Organization and beautification (changes which improve readability and/or accessibility)

Breaking API change

The singleton-based workflow:

mcdc.simulation.set_root_universe(cells=[cell])
mcdc.Source(...)
mcdc.Tally(...)
mcdc.settings.N_particle = 1_000
mcdc.run()

is replaced by:

simulation = mcdc.Simulation()
simulation.set_model([cell])
simulation.set_sources([source])
simulation.set_tallies([tally])
simulation.settings.N_particle = 1_000
simulation.run()

Models can also be compiled or visualized directly through the simulation instance.

Additional updates

• Defer continuous-energy material and physics-data initialization until simulation compilation.
• Normalize and validate Python and NumPy inputs used by sources and distributions.
• Integrate census-based tally recombination into the simulation output workflow.
• Update regression problems to use the explicit simulation API.
• Expand public API docstrings with examples covering model construction, visualization, and execution.
• Update unit tests for the encapsulated object and transport workflow.

Developer Checklist

• I have read the [contributing guide](https://mcdc.readthedocs.io/en/latest/contribution/index.html).
• My code follows the [code style](https://mcdc.readthedocs.io/en/latest/contribution/index.html#code-styling) of this project.
• I have updated the documentation as needed.
• I have updated CHANGELOG.md as needed.
• I have added or updated tests to cover my changes.
• All new and existing tests pass

Associated Issues and PRs

• closes Encapsulate simulation object management and redesign the Python object model #478 Rework Documentation Around the Layered Documentation Philosophy #477 Update some distribution sampling unit tests #449

Associated Developers

[ilhamv]

Considerable customizations in the docs are introduced to get a nice documentation of the key nested objects (settings and techniques) in the Simulation class.

[nglaser3]

@ilhamv, thank you for working on the encapsulation! I am a big fan of the added "examples" to the user facing object docstrings! I have a few super minor comments, but otherwise this looks great!

[ilhamv]

Thanks for the review, @nglaser3!