Fix CI and update dependencies

[Billyzhang1229]

.gitattributes

• Added *.ipynb linguist-vendored

.github/workflows/tests.yml

• Changed runs-on for the Lint job from ubuntu-18.04 to ubuntu-latest.
• Updated cancel-workflow-action from 0.6.0 to 0.12.1 in Lint job.
• Updated actions/checkout from v2 to v4.
• Updated pre-commit/action from v3.0.0 to v3.0.1 in Lint job.
• Updated Python versions in the test job to include 3.11 and remove 3.7.
• Updated cancel-workflow-action from 0.10.0 to 0.12.1 in test job.
• In deploy job, updated cancel-workflow-action from 0.10.0 to 0.12.1.
• Updated Python version from 3.9 to 3.10 in deploy job.

.pre-commit-config.yaml

• Upgraded pre-commit-hooks from v4.3.0 to v4.5.0.
• Upgraded reorder_python_imports from v3.1.0 to v3.12.0.
• Upgraded pyupgrade from v2.34.0 to v3.15.2, with arguments updated.
• Upgraded black from 22.6.0 to 24.3.0.
• Changed flake8 repository from GitLab to GitHub, upgrading from 3.9.2 to 6.1.0 with updated additional dependencies.
• Upgraded blacken-docs from v1.12.1 to 1.16.0, updating additional dependencies.

requirements/CI.txt

• numba upgraded from 0.55.2 to 0.59.1.
• tskit upgraded from 0.5.0 to 0.5.6.
• msprime upgraded from 1.2.0 to 1.3.1.
• sgkit upgraded from 0.5.0 to 0.7.0.

[coveralls]

Pull Request Test Coverage Report for Build 8414256226

Details

• 0 of 0 changed or added relevant lines in 0 files are covered.
• No unchanged relevant lines lost coverage.
• Overall coverage remained the same at 89.779%

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Totals
Change from base Build 3420596959:	0.0%
Covered Lines:	527
Relevant Lines:	587

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💛 - Coveralls