Update dependencies (#2)

* Update dependencies and support Python 3.13 and

* Update linters and coder formatters

* Fix rare concurrency issue with tox writing coverage report

.github/workflows/run-checks.yml

@@ -17,6 +17,7 @@ jobs:
           - python-version: "3.10"
           - python-version: "3.11"
           - python-version: "3.12"
+          - python-version: "3.13"
     steps:
       - uses: actions/checkout@v4
 
@@ -60,7 +61,8 @@ jobs:
           source .venv/bin/activate
           coverage erase
           tox run-parallel -f py${{ matrix.python-version }} --parallel-no-spinner --parallel-live
-          coverage xml
+          coverage combine --data-file=.coverage
+          coverage xml --data-file=.coverage
 
       - name: Upload coverage reports to Codecov
         uses: codecov/codecov-action@v4