Update documentation

[mattjones315]

Updated documentation:

• Updated docstring in ILPSolver to make it clear that Gurobi is being used (i.e., there is no backup solver)
• Update documentation site to include several new modules (e.g., ClonalSpatialDataSimualtor, cas.pl.Tree3D)

[codecov[bot]]

Codecov Report

Patch coverage: 100.00% and project coverage change: +0.30% :tada:

Comparison is base (172f57d) 79.12% compared to head (7b214ca) 79.43%. Report is 4 commits behind head on master.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## master #221 +/- ## ========================================== + Coverage 79.12% 79.43% +0.30% ========================================== Files 89 89 Lines 7893 7895 +2 ========================================== + Hits 6245 6271 +26 + Misses 1648 1624 -24 ``` | [Files Changed](https://app.codecov.io/gh/YosefLab/Cassiopeia/pull/221?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=YosefLab) | Coverage Δ | | |---|---|---| | [cassiopeia/simulator/SpatialDataSimulator.py](https://app.codecov.io/gh/YosefLab/Cassiopeia/pull/221?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=YosefLab#diff-Y2Fzc2lvcGVpYS9zaW11bGF0b3IvU3BhdGlhbERhdGFTaW11bGF0b3IucHk=) | `100.00% <ø> (ø)` | | | [cassiopeia/solver/ILPSolver.py](https://app.codecov.io/gh/YosefLab/Cassiopeia/pull/221?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=YosefLab#diff-Y2Fzc2lvcGVpYS9zb2x2ZXIvSUxQU29sdmVyLnB5) | `44.60% <ø> (ø)` | | | [cassiopeia/plotting/local.py](https://app.codecov.io/gh/YosefLab/Cassiopeia/pull/221?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=YosefLab#diff-Y2Fzc2lvcGVpYS9wbG90dGluZy9sb2NhbC5weQ==) | `89.96% <100.00%> (+9.34%)` | :arrow_up: | | [cassiopeia/plotting/local\_3d.py](https://app.codecov.io/gh/YosefLab/Cassiopeia/pull/221?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=YosefLab#diff-Y2Fzc2lvcGVpYS9wbG90dGluZy9sb2NhbF8zZC5weQ==) | `78.50% <100.00%> (+0.04%)` | :arrow_up: |

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