Update Ruff 11.13

[juanitorduz]

Fixes ixes #1095

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📚 Documentation preview 📚: https://pytensor--1462.org.readthedocs.build/en/1462/

[juanitorduz]

@ricardoV94

With some of the automated changes some tests break like

pytest -v tests/compile/test_profiling.py
================================================ test session starts ================================================
platform darwin -- Python 3.12.11, pytest-8.4.0, pluggy-1.6.0 -- /Users/juan.orduz/.local/share/mamba/envs/pytensor-env/bin/python3.12
cachedir: .pytest_cache
benchmark: 5.1.0 (defaults: timer=time.perf_counter disable_gc=False min_rounds=5 min_time=0.000005 max_time=1.0 calibration_precision=10 warmup=False warmup_iterations=100000)
rootdir: /Users/juan.orduz/Documents/pytensor
configfile: pyproject.toml
plugins: mock-3.14.1, benchmark-5.1.0, sphinx-0.6.3, cov-6.1.1
collected 2 items                                                                                                   

tests/compile/test_profiling.py::TestProfiling::test_profiling FAILED                                         [ 50%]
tests/compile/test_profiling.py::TestProfiling::test_ifelse PASSED                                            [100%]

===================================================== FAILURES ======================================================
___________________________________________ TestProfiling.test_profiling ____________________________________________

self = VMLinker(use_cloop=True, lazy=None, allow_partial_eval=None, allow_gc=True), profiler = None
input_storage = [[None], [None], [None]], output_storage = [[None], [None], [None], [None]]
storage_map = {val0: [None], val1: [None], val2: [None], Shape_i{0}.0: [None], ...}

    def make_all(
        self,
        profiler=None,
        input_storage=None,
        output_storage=None,
        storage_map=None,
    ):
        fgraph = self.fgraph
        order = self.schedule(fgraph)
    
        input_storage, output_storage, storage_map = map_storage(
            fgraph, order, input_storage, output_storage, storage_map
        )
        compute_map = {}
        for k in storage_map:
            compute_map[k] = [k.owner is None]
    
        thunks = []
    
        t0 = time.perf_counter()
        linker_make_thunk_time = {}
        impl = None
        if self.c_thunks is False:
            impl = "py"
        for node in order:
            try:
                thunk_start = time.perf_counter()
                # no-recycling is done at each VM.__call__ So there is
                # no need to cause duplicate c code by passing
                # no_recycling here.
                thunks.append(
>                   node.op.make_thunk(node, storage_map, compute_map, [], impl=impl)
                )

pytensor/link/vm.py:1230: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pytensor/link/c/op.py:125: in make_thunk
    return self.make_c_thunk(node, storage_map, compute_map, no_recycling)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
pytensor/link/c/op.py:84: in make_c_thunk
    outputs = cl.make_thunk(
pytensor/link/c/basic.py:1185: in make_thunk
    cthunk, module, in_storage, out_storage, error_storage = self.__compile__(
pytensor/link/c/basic.py:1102: in __compile__
    thunk, module = self.cthunk_factory(
pytensor/link/c/basic.py:1626: in cthunk_factory
    module = cache.module_from_key(key=key, lnk=self)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
pytensor/link/c/cmodule.py:1251: in module_from_key
    module = lnk.compile_cmodule(location)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
pytensor/link/c/basic.py:1527: in compile_cmodule
    module = c_compiler.compile_str(
...

[ricardoV94]

@juanitorduz can you show the full traceback, that doesn't give enough info

[ricardoV94]

Don't you still need different quotes inside?

Suggested change

	print(f'command "{" ".join(sys.argv)}" not recognized')
	print(f'command "{' '.join(sys.argv)}" not recognized')

[juanitorduz]

yeah, these are automatic changes, I need to investigate

[juanitorduz]

ok! This is a bit of a tricky PR as the automatic changes might be undesirable. I will take a closer look in another PR. Maybe increasing the ruff versions incrementally 🤔