Style errors with ruff v0.9.0

[seisman]

ruff v0.9.0 was released a few minutes ago. Refer to the blog post for details.

There are some new errors now:

ruff check pygmt doc/conf.py examples
pygmt/encodings.py:1:1: A005 Module `encodings` shadows a Python standard-library module
pygmt/helpers/tempfile.py:1:1: A005 Module `tempfile` shadows a Python standard-library module
pygmt/io.py:1:1: A005 Module `io` shadows a Python standard-library module
pygmt/src/select.py:1:1: A005 Module `select` shadows a Python standard-library module
Found 4 errors.
make: *** [Makefile:67: check] Error 1

We need to either fix them or ignore them