ENH add type annotations to frontend

[kroq-gar78]

This introduces type annotations to the user-facing API. Several functions, like cortex.quickshow and cortex.webshow, have numerous arguments with poorly defined inputs. This should now allow explicit type checking in user code.

This PR also provides a starting point for type annotations within the library, which should help maintenance.

I believe this also hard breaks support for Python 3.8, but since both 3.8 and 3.9 are EOL anyway, this PR drops support for both.

[mvdoc]

Awesome! We are testing on 3.8 and 3.9, but they both reached EOL. You can remove them from the matrix so we can run the tests on CI.

[kroq-gar78]

I'm actually really not sure what this line was supposed to be doing. Any ideas @mvdoc ?

[mvdoc]

It seems broken code to me. If it ever got to that except, then it would blow up because mask is undefined

[kroq-gar78]

Even in the original commit (f4f2fe9) I'm not sure what was supposed to happen... should we just delete the try/except?

[mvdoc]

Yeah I would just remove it

[Copilot]

Pull request overview

This PR introduces type annotations across pycortex’s user-facing APIs (notably WebGL viewing, dataset views, and export helpers) to enable better static type checking and provide a foundation for broader internal typing.

Changes:

• Add/expand type annotations across cortex.dataset, WebGL viewer entry points, and export utilities.
• Update packaging/config to support typing work (typing backports, mypy config) and adjust CI Python version matrices.
• Minor modernizations/cleanup (e.g., Python-2-era compatibility branches, NumPy API usage).

Reviewed changes

Copilot reviewed 22 out of 23 changed files in this pull request and generated 13 comments.

Show a summary per file

File	Description
setup.py	Changes how install_requires is read from requirements.txt.
requirements.txt	Adds typing_extensions conditional dependency.
pyproject.toml	Adds PEP 621 [project] metadata stub, mypy settings, and dev dependency group.
cortex/xfm.py	Replaces isstr(...) check with isinstance(..., str).
cortex/webgl/view.py	Adds typing to show(...) and some internal variables.
cortex/webgl/serve.py	Simplifies Queue import logic; adds type annotations to class attrs.
cortex/webgl/__init__.py	Updates DocLoader usage to support type checking via TYPE_CHECKING.
cortex/utils.py	Makes DocLoader generic (ParamSpec/TypeVar) and adds typed lazy loader for get_mapper.
cortex/quickflat/view.py	Adds typing to quickflat public helpers and internal utilities.
cortex/quickflat/composite.py	Replaces deprecated-ish np.in1d usage with np.isin.
cortex/options.py	Removes legacy Python 2 configparser fallback.
cortex/export/save_views.py	Adds typed dicts and function annotations for view export helper.
cortex/export/panels.py	Adds typed dicts and function annotations for panel plotting helper.
cortex/dataset/views.py	Adds overloads and more explicit typing for core view classes/utilities.
cortex/dataset/viewRGB.py	Adds typing and some additional runtime validation for RGB views.
cortex/dataset/view2D.py	Adds typing and extra runtime validation for 2D views.
cortex/dataset/dataset.py	Adds typing/overloads to dataset normalization and internals.
cortex/dataset/braindata.py	Adds typing (Self, NDArray types) and adjusts some return behavior.
cortex/dataset/__init__.py	Adds __future__.annotations and exports Dataview2D.
cortex/__init__.py	Updates Python-2 version check style.
.github/workflows/run_tests.yml	Updates tested Python versions and apt install flags.
.github/workflows/install_from_wheel.yml	Updates Python matrix for wheel build/install job.
.github/workflows/build_docs.yml	Updates docs build Python version and dependency install steps.

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[Copilot]

list_angles/list_surfaces are annotated as list[...], but list(zip(*angles_and_surfaces)) unpacks into tuples. Either convert to lists (e.g., list(...)) after unpacking or annotate them as tuples to keep the types consistent for static checking.

Suggested change

	list_angles, list_surfaces = list(zip(*angles_and_surfaces))
	list_angles, list_surfaces = map(list, zip(*angles_and_surfaces))

[Copilot]

viewer_params uses a mutable default (dict(...) containing mutable lists). Mutations will be shared across calls. Prefer defaulting to None and creating the dict inside the function.

Suggested change

	viewer_params: dict[str, Any]=dict(labels_visible=[], overlays_visible=["rois"]),
	viewer_params: dict[str, Any] | None = None,