Raise Python floor to 3.11, test through 3.14, drop dead testing extra (2.2.0)

[YalanBi]

Summary

• breaking: dropped support for Python 3.10; requires-python is now >=3.11. CI now tests 3.11-3.14 (added 3.13 and 3.14), and the lint job now runs on 3.14 instead of 3.12.
• Verified real wheel availability for Python 3.14 across the whole dependency stack (numba, llvmlite, pyhmmer, CPAT, intervaltree) via pip download, not guessed, before committing to this.
• Removed the unused pyproject.toml [project.optional-dependencies] testing extra -- nothing installed from it (tox.ini uses requirements_dev.txt directly), and it referenced mypy, which isn't run anywhere in CI. Left [tool.mypy] config alone (separate, bigger call).
• Regenerated the requirements.txt lock file under Python 3.14.
• Checked intervaltree's maintenance health while in the area (a load-bearing dependency): actively maintained, no risk found, no code change needed.

Bumps version to 2.2.0.

Test plan

• tox -e py314 (the real isolated env CI uses) passes all 29 tests
• tox -e flake8 (now running on 3.14) passes clean
• Verified pip install . succeeds cleanly under Python 3.14 in a fresh venv
• python -m build + twine check dist/* pass at 2.2.0

[github-actions]

Dependency Review

The following issues were found:

• ✅ 0 vulnerable package(s)
• ✅ 0 package(s) with incompatible licenses
• ✅ 0 package(s) with invalid SPDX license definitions
• ⚠️ 1 package(s) with unknown licenses.

See the Details below.

License Issues

.github/workflows/lint.yml

Package	Version	License	Issue Type
actions/setup-python	7.*.*	Null	Unknown License

OpenSSF Scorecard

Package	Version	Score	Details
actions/actions/setup-python	7.*.*	🟢 6.6	Details Check Score Reason Code-Review 🟢 10 all changesets reviewed Maintained 🟢 10 18 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 10 CII-Best-Practices ⚠️ 0 no effort to earn an OpenSSF best practices badge detected Binary-Artifacts 🟢 10 no binaries found in the repo Dangerous-Workflow 🟢 10 no dangerous workflow patterns detected Packaging ⚠️ -1 packaging workflow not detected Fuzzing ⚠️ 0 project is not fuzzed License 🟢 10 license file detected Token-Permissions ⚠️ 0 detected GitHub workflow tokens with excessive permissions Pinned-Dependencies 🟢 7 dependency not pinned by hash detected -- score normalized to 7 Signed-Releases ⚠️ -1 no releases found Security-Policy 🟢 9 security policy file detected SAST 🟢 9 SAST tool is not run on all commits -- score normalized to 9 Branch-Protection ⚠️ 0 branch protection not enabled on development/release branches
pip/charset-normalizer	3.5.1	Unknown	Unknown
pip/idna	3.19	Unknown	Unknown
pip/llvmlite	0.49.0	Unknown	Unknown
pip/numba	0.67.0	Unknown	Unknown
pip/numpy	2.5.2	Unknown	Unknown
pip/pyhmmer	0.12.3	Unknown	Unknown

Scanned Files

• .github/workflows/lint.yml
• requirements.txt