switch to ruff and fix issues

examples/airfoil3d.py

examples/box-in-box.py

examples/demo.py

examples/jw_meshtools.py

examples/mesh_ply.py

examples/nico_mesh.py

examples/test_ball.py

examples/test_cylinder.py

examples/test_gmsh_reader.py

examples/test_tet_torus.py

examples/test_tetgen_2.py

examples/test_tri_quadratic.py

examples/test_triangle.py

examples/test_triangle_refine.py

examples/test_triangle_with_specified_points.py

examples/tet-size-control.py

examples/tri-boundary-markers.py

examples/tri-refinement-spec.py

meshpy/common.py

meshpy/geometry.py