fix: avoid warnings about typing deprecations and escape sequences

[phaverty-ginkgo]

Description

Updates some typing inputs to beartype.typing as directed by warning messages.
Avoids a warning about an escape string by escaping as expected by docstring parser.

Motivation

Avoids these warnings:

<path>/python3.12/site-packages/jaxtyping/_decorator.py:71
  <path>/python3.12/site-packages/jaxtyping/_decorator.py:71: BeartypeDecorHintPep585DeprecationWarning: Function chai_lab.data.dataset.templates.align.align_2d() parameter "addtl_dims" PEP 484 type hint typing.Sequence[int] deprecated by PEP 585. This hint is scheduled for removal in the first Python version released after October 5th, 2025. To resolve this, import this hint from "beartype.typing" rather than "typing". For further commentary and alternatives, see also:
      https://beartype.readthedocs.io/en/latest/api_roar/#pep-585-deprecations
    return typechecker(fn)

.pixi/envs/dev/lib/python3.12/site-packages/jaxtyping/_decorator.py:71
.pixi/envs/dev/lib/python3.12/site-packages/jaxtyping/_decorator.py:71
  <path>/python3.12/site-packages/jaxtyping/_decorator.py:71: BeartypeDecorHintPep585DeprecationWarning: Function chai_lab.data.dataset.templates.load.get_template_data() parameter "template_hits" PEP 484 type hint typing.Iterator[chai_lab.data.parsing.templates.template_hit.TemplateHit] deprecated by PEP 585. This hint is scheduled for removal in the first Python version released after October 5th, 2025. To resolve this, import this hint from "beartype.typing" rather than "typing". For further commentary and alternatives, see also:
      https://beartype.readthedocs.io/en/latest/api_roar/#pep-585-deprecations
    return typechecker(fn)

.pixi/envs/dev/lib/python3.12/site-packages/jaxtyping/_decorator.py:71
.pixi/envs/dev/lib/python3.12/site-packages/jaxtyping/_decorator.py:71
  <path>/python3.12/site-packages/jaxtyping/_decorator.py:71: BeartypeDecorHintPep585DeprecationWarning: Function chai_lab.data.parsing.msas.aligned_pqt.merge_multi_a3m_to_aligned_dataframe() parameter "msa_a3m_files" PEP 484 type hint typing.Mapping[pathlib.Path, chai_lab.data.parsing.msas.data_source.MSADataSource] deprecated by PEP 585. This hint is scheduled for removal in the first Python version released after October 5th, 2025. To resolve this, import this hint from "beartype.typing" rather than "typing". For further commentary and alternatives, see also:
      https://beartype.readthedocs.io/en/latest/api_roar/#pep-585-deprecations
    return typechecker(fn)

.pixi/envs/dev/lib/python3.12/site-packages/chai_lab/ranking/ptm.py:100
  <path>/python3.12/site-packages/chai_lab/ranking/ptm.py:100: SyntaxWarning: invalid escape sequence '\i'
    ipTM is the max TM score over chains c \in C, restricting

Test plan

[arogozhnikov]

Hi, Peter, thanks for reporting.
Need to think about best way to ensure future compat with static type-checkers too - beartype.typing may/may not be the right path.