Improved Source File and Code Structure Modelling

Closes #7 (closed) , #4 (closed)

This MR brings a significant refactoring and several extensions to the modelling of source file structure and contents in the SFG IR, as well as to the way these are constructed by the composer internally.

IR

Replace ir.source_components by ir.entities and ir.syntax

• ir.entities defines C++ code entities independently from their place in the output file syntax. It defines namespaces (including kernel namespaces and the global namespace), functions, kernels, classes and their members (methods, constructors). It also places these entities in parent-child-relationsships.
• ir.syntax defines the class SfgSourceFile to represent source files. It also contains the representation of the above entities as syntactic objects: namespace blocks (one namespace can have multiple blocks), entity declaration and definition nodes, class body and visibility block nodes.

Context and Composer

• The context now manages up to two source files (header and implementation)
• The composer navigates their syntax structure using a cursor
• sfg.namespace can now be called multiple times and be used as a context manager to enter and exit nested namespaces
• Remove sfg.define_once since it can no longer reliably check definitions for uniqueness
• The previously fixed structure "first kernel namespaces, then all the rest" of output files is broken up - syntax elements are now placed in the order they are created in

Generator and Emission

• Replace the old file printers and emitters with a minimal, entirely syntax-oriented printer
• Update SourceFileGenerator to prepare the file objects for the context and correctly invoke the printer

Configuration

• Users can now define a sort key for sorting #includes via the SfgConfig - if one is specified, clang-format header sorting will be automatically disabled

src/pystencilssfg/composer/basic_composer.py

 from __future__ import annotations
 from typing import Sequence, TypeAlias
 from abc import ABC, abstractmethod
-import numpy as np
 import sympy as sp
 from functools import reduce
 from warnings import warn
@@ -33,10 +32,6 @@ from ..ir.source_components import (
     SfgFunction,
     SfgKernelNamespace,
     SfgKernelHandle,
-    SfgClass,
-    SfgConstructor,
-    SfgMemberVariable,
-    SfgClassKeyword,
     SfgEntityDecl,
     SfgEntityDef,
     SfgNamespaceBlock,
@@ -86,7 +81,7 @@ SequencerArg: TypeAlias = tuple | ExprLike | SfgCallTreeNode | SfgNodeBuilder
 class KernelsAdder:
     def __init__(self, ctx: SfgContext, loc: SfgNamespaceBlock):
         self._ctx = ctx
-        self._loc = SfgNamespaceBlock
+        self._loc = loc
         assert isinstance(loc.namespace, SfgKernelNamespace)
         self._kernel_namespace = loc.namespace
 
@@ -110,6 +105,8 @@ class KernelsAdder:
         khandle = SfgKernelHandle(kernel_name, self._kernel_namespace, kernel)
         self._kernel_namespace.add_kernel(khandle)
 
+        self._loc.elements.append(SfgEntityDef(khandle))
+
         for header in kernel.required_headers:
             assert self._ctx.impl_file is not None
             self._ctx.impl_file.includes.append(HeaderFile.parse(header))
@@ -242,7 +239,7 @@ class SfgBasicComposer(SfgIComposer):
         self._cursor.write_impl(kns_block)
         return KernelsAdder(self._ctx, kns_block)
 
-    def include(self, header_file: str | HeaderFile, private: bool = False):
+    def include(self, header: str | HeaderFile, private: bool = False):
         """Include a header file.
 
         Args:
@@ -262,7 +259,7 @@ class SfgBasicComposer(SfgIComposer):
                 #include <vector>
                 #include "custom.h"
         """
-        header_file = HeaderFile.parse(header_file)
+        header_file = HeaderFile.parse(header)
 
         if private:
             if self._ctx.impl_file is None:
@@ -273,21 +270,6 @@ class SfgBasicComposer(SfgIComposer):
         else:
             self._ctx.header_file.includes.append(header_file)
 
-    def numpy_struct(
-        self, name: str, dtype: np.dtype, add_constructor: bool = True
-    ) -> SfgClass:
-        """Add a numpy structured data type as a C++ struct
-
-        Returns:
-            The created class object
-        """
-        cls = self._struct_from_numpy_dtype(
-            name, dtype, add_constructor=add_constructor
-        )
-        self._cursor.add_entity(cls)
-        self._cursor.write_header(SfgEntityDecl(cls))
-        return cls
-
     def kernel_function(self, name: str, kernel: Kernel | SfgKernelHandle):
         """Create a function comprising just a single kernel call.
 
@@ -295,9 +277,11 @@ class SfgBasicComposer(SfgIComposer):
             ast_or_kernel_handle: Either a pystencils AST, or a kernel handle for an already registered AST.
         """
         if isinstance(kernel, Kernel):
-            kernel = self.kernels.add(kernel, name)
+            khandle = self.kernels.add(kernel, name)
+        else:
+            khandle = kernel
 
-        self.function(name)(self.call(kernel))
+        self.function(name)(self.call(khandle))
 
     def function(
         self,
@@ -536,41 +520,6 @@ class SfgBasicComposer(SfgIComposer):
         ]
         return SfgDeferredVectorMapping(components, rhs)
 
-    def _struct_from_numpy_dtype(
-        self, struct_name: str, dtype: np.dtype, add_constructor: bool = True
-    ):
-        cls = SfgClass(
-            struct_name,
-            self._cursor.current_namespace,
-            class_keyword=SfgClassKeyword.STRUCT,
-        )
-
-        fields = dtype.fields
-        if fields is None:
-            raise SfgException(f"Numpy dtype {dtype} is not a structured type.")
-
-        constr_params = []
-        constr_inits = []
-
-        for member_name, type_info in fields.items():
-            member_type = create_type(type_info[0])
-
-            member = SfgMemberVariable(member_name, member_type)
-
-            arg = SfgVar(f"{member_name}_", member_type)
-
-            cls.default.append_member(member)
-
-            constr_params.append(arg)
-            constr_inits.append(f"{member}({arg})")
-
-        if add_constructor:
-            cls.default.append_member(
-                SfgEntityDef(SfgConstructor(constr_params, constr_inits))
-            )
-
-        return cls
-
 
 def make_statements(arg: ExprLike) -> SfgStatements:
     return SfgStatements(str(arg), (), depends(arg), includes(arg))