pyproject: add and fix ruff RUF issues

pyproject.toml

pytools/__init__.py

pytools/batchjob.py

pytools/datatable.py

pytools/debug.py

pytools/graph.py

pytools/lex.py

pytools/spatial_btree.py

pytools/tag.py

pytools/test/test_graph_tools.py

pytools/test/test_persistent_dict.py