Enable Ruff formatting

[VeckoTheGecko]

Enable Ruff formatting for all Python files in codebase. Line length 88 for docs/*, 120 for the rest.

This PR is intended to isolate these changes (since they're non-breaking, but create a large diff), as well as to act as a place to flag any changes that are unreadable and would benefit from refactoring before being merged.

If a file is particularly bad, we can add them to an exclude list.

To disable the formatter for certain parts of the code, you can add comments to suppress the formatter.

See related discussion in #1653. Contributes to #1620

[VeckoTheGecko]

Just using this PR draft to look through changes and note blocks where code formatting should be disabled (e.g., visualising 2D arrays, or long equations) or code should be refactored.

Will force push and rework the commits in this PR with the changes after I've some some refactoring in fieldset.py in another PR

[VeckoTheGecko]

@erikvansebille I was wanting to run some tests locally, but got an error about not finding the compiler. I exported CC to match clang --version but still get the error. Have you seen this before?

    def _create_compile_process_(self, cmd, src, log):
        with open(log, "w") as logfile:
            try:
                subprocess.check_call(cmd, stdout=logfile, stderr=logfile)
            except OSError:
>               raise RuntimeError(f"OSError during compilation. Please check if compiler exists: {self._cc}")
E               RuntimeError: OSError during compilation. Please check if compiler exists: arm64-apple-darwin23.6.0

parcels/compilation/codecompiler.py:240: RuntimeError

[erikvansebille]

@erikvansebille I was wanting to run some tests locally, but got an error about not finding the compiler. I exported CC to match clang --version but still get the error. Have you seen this before?

    def _create_compile_process_(self, cmd, src, log):
        with open(log, "w") as logfile:
            try:
                subprocess.check_call(cmd, stdout=logfile, stderr=logfile)
            except OSError:
>               raise RuntimeError(f"OSError during compilation. Please check if compiler exists: {self._cc}")
E               RuntimeError: OSError during compilation. Please check if compiler exists: arm64-apple-darwin23.6.0

parcels/compilation/codecompiler.py:240: RuntimeError

No, haven't seen his specific error before. But I normally do export CC=gcc when I encounter compiler problems on macOS; that often seems to do the trick