# Source code for brian2.codegen.runtime.cython_rt.cython_rt

    import platform

    import numpy

    from brian2.core.base import BrianObjectException
    from brian2.core.functions import Function
    from brian2.core.preferences import BrianPreference, prefs
    from brian2.core.variables import (
        ArrayVariable,
        AuxiliaryVariable,
        DynamicArrayVariable,
        Subexpression,
    )
    from brian2.utils.logger import get_logger
    from brian2.utils.stringtools import get_identifiers

    from ...codeobject import check_compiler_kwds, constant_or_scalar
    from ...cpp_prefs import get_compiler_and_args
    from ...generators.cython_generator import (
        CythonCodeGenerator,
        get_cpp_dtype,
        get_numpy_dtype,
    )
    from ...targets import codegen_targets
    from ...templates import Templater
    from ..numpy_rt import NumpyCodeObject
    from .extension_manager import cython_extension_manager

    __all__ = ["CythonCodeObject"]

    logger = get_logger(__name__)

    # Preferences
    prefs.register_preferences(
        "codegen.runtime.cython",
        "Cython runtime codegen preferences",
        multiprocess_safe=BrianPreference(
            default=True,
            docs="""
            Whether to use a lock file to prevent simultaneous write access
            to cython .pyx and .so files.
            """,
        ),
        cache_dir=BrianPreference(
            default=None,
            validator=lambda x: x is None or isinstance(x, str),
            docs="""
            Location of the cache directory for Cython files. By default,
            will be stored in a ``brian_extensions`` subdirectory
            where Cython inline stores its temporary files
            (the result of ``get_cython_cache_dir()``).
            """,
        ),
        delete_source_files=BrianPreference(
            default=True,
            docs="""
            Whether to delete source files after compiling. The Cython
            source files can take a significant amount of disk space, and
            are not used anymore when the compiled library file exists.
            They are therefore deleted by default, but keeping them around
            can be useful for debugging.
            """,
        ),
    )

    class CythonCodeObject(NumpyCodeObject):
        """
        Execute code using Cython.
        """

        templater = Templater(
            "brian2.codegen.runtime.cython_rt",
            ".pyx",
            env_globals={
                "cpp_dtype": get_cpp_dtype,
                "numpy_dtype": get_numpy_dtype,
                "dtype": numpy.dtype,
                "constant_or_scalar": constant_or_scalar,
            },
        )
        generator_class = CythonCodeGenerator
        class_name = "cython"

        def __init__(
            self,
            owner,
            code,
            variables,
            variable_indices,
            template_name,
            template_source,
            compiler_kwds,
            name="cython_code_object*",
        ):
            check_compiler_kwds(
                compiler_kwds,
                [
                    "libraries",
                    "include_dirs",
                    "library_dirs",
                    "runtime_library_dirs",
                    "sources",
                ],
                "Cython",
            )
            super().__init__(
                owner,
                code,
                variables,
                variable_indices,
                template_name,
                template_source,
                compiler_kwds={},  # do not pass the actual args
                name=name,
            )
            self.compiler, self.extra_compile_args = get_compiler_and_args()
            self.define_macros = list(prefs["codegen.cpp.define_macros"])
            self.extra_link_args = list(prefs["codegen.cpp.extra_link_args"])
            self.headers = []  # not actually used

            self.include_dirs = list(prefs["codegen.cpp.include_dirs"]) + compiler_kwds.get(
                "include_dirs", []
            )
            self.include_dirs = list(prefs["codegen.cpp.include_dirs"])

            self.library_dirs = list(prefs["codegen.cpp.library_dirs"]) + compiler_kwds.get(
                "library_dirs", []
            )

            self.runtime_library_dirs = list(
                prefs["codegen.cpp.runtime_library_dirs"]
            ) + compiler_kwds.get("runtime_library_dirs", [])

            self.libraries = list(prefs["codegen.cpp.libraries"]) + compiler_kwds.get(
                "libraries", []
            )
            self.sources = compiler_kwds.get("sources", [])

        @classmethod
        def is_available(cls):
            try:
                compiler, extra_compile_args = get_compiler_and_args()
                code = """
                #cython: language_level=3
                def main():
                    cdef int x
                    x = 0"""
                compiled = cython_extension_manager.create_extension(
                    code,
                    compiler=compiler,
                    extra_compile_args=extra_compile_args,
                    extra_link_args=prefs["codegen.cpp.extra_link_args"],
                    include_dirs=prefs["codegen.cpp.include_dirs"],
                    library_dirs=prefs["codegen.cpp.library_dirs"],
                    runtime_library_dirs=prefs["codegen.cpp.runtime_library_dirs"],
                )
                compiled.main()
                return True
            except Exception as ex:
                msg = (
                    f"Cannot use Cython, a test compilation failed: {str(ex)} "
                    f"({ex.__class__.__name__})"
                )
                if platform.system() != "Windows":
                    msg += (
                        "\nCertain compiler configurations (e.g. clang in a conda "
                        "environment on OS X) are known to be problematic. Note that "
                        "you can switch the compiler by setting the 'CC' and 'CXX' "
                        "environment variables. For example, you may want to try "
                        "'CC=gcc' and 'CXX=g++'."
                    )
                logger.warn(msg, "failed_compile_test")
                return False

        def compile_block(self, block):
            code = getattr(self.code, block, "").strip()
            if not code or "EMPTY_CODE_BLOCK" in code:
                return None
            return cython_extension_manager.create_extension(
                code,
                define_macros=self.define_macros,
                libraries=self.libraries,
                extra_compile_args=self.extra_compile_args,
                extra_link_args=self.extra_link_args,
                include_dirs=self.include_dirs,
                library_dirs=self.library_dirs,
                runtime_library_dirs=self.runtime_library_dirs,
                compiler=self.compiler,
                owner_name=f"{self.owner.name}_{self.template_name}",
                sources=self.sources,
            )

        def run_block(self, block):
            compiled_code = self.compiled_code[block]
            if compiled_code:
                try:
                    return compiled_code.main(self.namespace)
                except Exception as exc:
                    message = (
                        "An exception occured during the execution of the "
                        f"'{block}' block of code object '{self.name}'.\n"
                    )
                    raise BrianObjectException(message, self.owner) from exc

        def _insert_func_namespace(self, func):
            impl = func.implementations[self]
            func_namespace = impl.get_namespace(self.owner)
            if func_namespace is not None:
                self.namespace.update(func_namespace)
            if impl.dependencies is not None:
                for dep in impl.dependencies.values():
                    self._insert_func_namespace(dep)

        def variables_to_namespace(self):
            # Variables can refer to values that are either constant (e.g. dt)
            # or change every timestep (e.g. t). We add the values of the
            # constant variables here and add the names of non-constant variables
            # to a list

            # A list containing tuples of name and a function giving the value
            self.nonconstant_values = []

            for name, var in self.variables.items():
                if isinstance(var, Function):
                    self._insert_func_namespace(var)
                if isinstance(var, (AuxiliaryVariable, Subexpression)):
                    continue
                try:
                    value = var.get_value()
                except (TypeError, AttributeError):
                    # A dummy Variable without value or a function
                    self.namespace[name] = var
                    continue

                if isinstance(var, ArrayVariable):
                    self.namespace[self.device.get_array_name(var, self.variables)] = value
                    self.namespace[f"_num{name}"] = var.get_len()
                    if var.scalar and var.constant:
                        self.namespace[name] = value.item()
                else:
                    self.namespace[name] = value

                if isinstance(var, DynamicArrayVariable):
                    dyn_array_name = self.generator_class.get_array_name(
                        var, access_data=False
                    )
                    # Adding logic to pass in the capsule object to namespace , we already have code set in generator to
                    # take the passed in object and work on it
                    capsule_name = f"{dyn_array_name}_capsule"
                    capsule = self.device.get_capsule(var)
                    self.namespace[capsule_name] = capsule
                    self.namespace[dyn_array_name] = self.device.get_value(
                        var, access_data=False
                    )

                # Also provide the Variable object itself in the namespace (can be
                # necessary for resize operations, for example)
                self.namespace[f"_var_{name}"] = var

            # Get all identifiers in the code -- note that this is not a smart
            # function, it will get identifiers from strings, comments, etc. This
            # is not a problem here, since we only use this list to filter out
            # things. If we include something incorrectly, this only means that we
            # will pass something into the namespace unnecessarily.
            all_identifiers = get_identifiers(self.code.run)
            # Filter out all unneeded objects
            self.namespace = {
                k: v for k, v in self.namespace.items() if k in all_identifiers
            }
            # There is one type of objects that we have to inject into the
            # namespace with their current value at each time step: dynamic
            # arrays that change in size during runs, where the size change is not
            # initiated by the template itself
            for name, var in self.variables.items():
                if isinstance(var, DynamicArrayVariable) and var.needs_reference_update:
                    array_name = self.device.get_array_name(var, self.variables)
                    if array_name in self.namespace:
                        self.nonconstant_values.append((array_name, var.get_value))
                    if f"_num{name}" in self.namespace:
                        self.nonconstant_values.append((f"_num{name}", var.get_len))

        def update_namespace(self):
            # update the values of the non-constant values in the namespace
            for name, func in self.nonconstant_values:
                self.namespace[name] = func()

    codegen_targets.add(CythonCodeObject)