Adding py.typed file for mypy

[Jgmedina95]

• Adding py.typed file necessary for mypy
• Added mypy to the pre-commit file
• Fixed mypy typing issues raised (nothing major, mainly Optionals here and there)
• Added the path to the py.typed file in the setup.py file.

[Copilot]

Pull Request Overview

This PR adds a py.typed file for mypy and integrates mypy into the pre-commit checks, while also addressing minor typing issues across the codebase. Key changes include updating package_data in setup.py, modifying type annotations (e.g. to use Optional types), and updating the pre-commit configuration to include mypy.

Reviewed Changes

Copilot reviewed 7 out of 7 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
setup.py	Added "exmol/py.typed" to package_data and added a type: ignore comment on version.
paper1_CFs/RF.ipynb	Updated notebook kernelspec to a more standard Python 3 naming.
exmol/plot_utils.py	Added an explicit "return None" branch and updated type declaration for figure_kwargs.
exmol/exmol.py	Updated various type annotations, including a modified return type for name_morgan_bit and changes in get_functional_groups, plus improved inline type hints.
docs/source/conf.py	Added a type annotation for the exclude_patterns variable.
.pre-commit-config.yaml	Added configuration to run mypy as part of the pre-commit hooks.

[hgandhi2411]

Looks good. There are still optional args that are not py.typed.

[hgandhi2411]

May also be time to update description?

[Copilot]

Pull Request Overview

This PR adds support for mypy type checking by including a py.typed file, updates pre-commit hooks to run mypy, and makes several type annotation refinements and style updates.

• Added py.typed to package_data and updated setup.py accordingly
• Updated type annotations (e.g. Optional types and union return types) and adjusted API definitions in exmol/exmol.py
• Updated notebook metadata and fixed a call to a JAX utility in a notebook

Reviewed Changes

Copilot reviewed 8 out of 8 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
setup.py	Added comment ignore for version and included "exmol/py.typed" in package_data
paper3_Scents/GNNModelTrainingAndEvaluation.ipynb	Updated JAX utility call from jax.tree_leaves to jax.tree_util.tree_leaves
paper1_CFs/RF.ipynb	Updated notebook kernel metadata
exmol/plot_utils.py	Added an explicit return None for non-SVG branch and refined type annotation for kwargs
exmol/exmol.py	Updated several type annotations (e.g. Optional types, union annotations) and return types
docs/source/conf.py	Added type annotation for exclude_patterns
.pre-commit-config.yaml	Added mypy hook to pre-commit config

Comments suppressed due to low confidence (3)

exmol/exmol.py:496

• [nitpick] The use of the union type 'list | tuple' for selfies_mut suggests that the function may return either type. Ensure that downstream consumers can handle both cases.

selfies_mut: list | tuple = stoned.get_mutated_SELFIES(

exmol/exmol.py:500

• [nitpick] Similarly, using 'list | tuple' for smiles_back requires that any code using this variable correctly handles both possible types.

smiles_back: list | tuple = [sf.decoder(x) for x in selfies_mut]

.pre-commit-config.yaml:18

• [nitpick] Ensure that the specified mypy version (v1.15.0) in the pre-commit hook is fully compatible with your type annotations and configuration.

  - repo: https://github.com/pre-commit/mirrors-mypy