rmcar17 / piqtree / 20168865821

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ENH: Add AliSim (#362)

* DEV: Expose `iq_simulate_alignment` into the `_piqtree`

* ENH: Add `IndelDistribution` classes

* MAINT: Fix `iqtree_str` for Lavalette Indel Distribution

* MAINT: Add `get_moltype` on models

* ENH: Add `simulate_alignment` (failures due to unrecognised models in IQ-TREE AliSim)

* MAINT: Allow for non-determinism when no random seed is specified

* TST: Skip certain substitution models

* MAINT: Fix deprecation warning, update cogent3

* MAINT: Further specify moltype return type

* MAINT: Gracefully handle unsupported models

* TST: Test indel size distribution and errors on unsupported models

* MAINT: Add `#pragma: no cover`s

* MAINT: Resolve typing error

* ENH: Add AliSim App
Fixes #381

* TST: Test root sequence

* DOC: Write docs pages for AliSim
Fixes #382

* DOC: Update docs to reflect that 0 now means a specific random seed

161 of 163 new or added lines in 9 files covered. (98.77%)

2141 of 2151 relevant lines covered (99.54%)

8.94 hits per line