Add Python 3.13 to CI, modernize type hints now that 3.10 is the minimum supported Python

[speediedan]

This branch adds/updates CI and project infra to support Python 3.13 and performs related cleanup.

Key changes

• Bump CI to run on Python 3.13 and adjust CI configuration accordingly.
• Bump Lightning dev SHA to pick up required upstream changes for CI compatibility.
• Modernize type hints in the codebase for newer Python versions.
• Automate cleaning of test warnings and add enhancements/options to CI helper scripts.
• Minor documentation cleanups related to the CI updates.

Commits in this branch (summary)

• 9975d10 — bump lightning dev sha, minor doc cleanup, set CI to use python 3.13
• ef57bac — automate test warnings cleanup process, enhance CI infra scripts with new options
• 7bc7007 — modernize type hints for python 3.10+

Why this change

Upgrading CI to include Python 3.13 ensures the project remains compatible with the latest Python release and catches regressions early. The Lightning dev SHA bump and type-hint modernization reduce friction during development and align the codebase with recent typing improvements.

Notes for reviewers / maintainers

• Check that the GitHub Actions workflows complete successfully on this branch.
• Verify no new type-related warnings are introduced under Python 3.13; the commits include type-hint modernizations but please review areas with complex typing.
• The commit that bumps the Lightning dev SHA may require downstream CI to use the same commit pin (this repo already supports commit pinning via CI overrides).

Files touched (high-level)

• GitHub Actions workflow files and/or CI helper scripts
• Small docs/README updates
• Type hint changes across source files

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📚 Documentation preview 📚: https://finetuning-scheduler--28.org.readthedocs.build/en/28/

[Copilot]

Pull request overview

This PR adds Python 3.13 support to the CI infrastructure and modernizes type hints throughout the codebase to use Python 3.10+ syntax. It also introduces automation for managing test warnings and enhances CI helper scripts.

Changes:

• Adds Python 3.13 to CI test matrix (replacing 3.12 as the maximum tested version)
• Modernizes type hints: Optional[X] → X | None, Union[X, Y] → X | Y, List[X] → list[X], Dict[K, V] → dict[K, V], Tuple[X, Y] → tuple[X, Y]
• Introduces automated warnings cleanup workflow with Python orchestrator and shell wrapper scripts
• Updates CI scripts with new options (--allow-failures, --run-all-and-examples, --log-dir)
• Bumps Lightning dev SHA for compatibility

Reviewed changes

Copilot reviewed 49 out of 49 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
.github/workflows/ci_test-full.yml	Updates CI matrix to test Python 3.10 and 3.13 (was 3.10 and 3.12)
scripts/build_fts_env.sh	Changes default Python from 3.12 to 3.13 for latest builds
src/finetuning_scheduler/*.py	Modernizes type hints across core modules
src/fts_examples/**/*.py	Modernizes type hints in example code
tests/helpers/expected_warns.py	Comments out obsolete warnings with TODO markers
tests/test_utils.sh	Adds allow_failures parameter for test execution control
tests/special_tests.sh	Adds --allow-failures and --log-dir options
scripts/automate_warnings_cleanup.py	New automation orchestrator for warnings management (1035 lines)
scripts/run_warnings_cleanup.sh	New wrapper script for warnings cleanup automation (191 lines)
scripts/gen_fts_coverage.sh	Adds --run-all-and-examples and --allow-failures options
requirements/ci/overrides.txt	Updates Lightning commit pin
pyproject.toml	Adds Python 3.13 classifier
Docker files and workflows	Updates Python version to 3.13 consistently
Documentation	Updates README, copilot instructions to reflect Python 3.13