[fortran] Fix for function declarations in derived types (#834)

## Summary of Changes
There was a bug discovered in the CTSM source PhotosynthesisMod.F90
where a function is declared in a derived type but defined in the outer
module. This PR updates the variable context to support this case.

Additionally resolves a bug where function declarations and definitions
can have different case sensitivity.

### Related issues

Resolves ???

---------

Co-authored-by: titomeister <ferra@email.arizona.edu> 156e193

api/python/skema/img2mml/models/decoders/xfmer_decoder.html

@@ -365,7 +365,7 @@ <h3>Instance variables</h3>
 <h3>Methods</h3>
 <dl>
 <dt id="skema.img2mml.models.decoders.xfmer_decoder.Transformer_Decoder.create_pad_mask"><code class="name flex">
-<span>def <span class="ident">create_pad_mask</span></span>(<span>self, matrix: <built-in method tensor of type object at 0x7f93e855b500>, pad_token: int) ‑> <built-in method tensor of type object at 0x7f93e855b500></span>
+<span>def <span class="ident">create_pad_mask</span></span>(<span>self, matrix: <built-in method tensor of type object at 0x7f372515b500>, pad_token: int) ‑> <built-in method tensor of type object at 0x7f372515b500></span>
 </code></dt>
 <dd>
 <div class="desc"></div>

api/python/skema/img2mml/models/encoding/positional_encoding_for_xfmer.html

@@ -157,7 +157,7 @@ <h3>Class variables</h3>
 <h3>Methods</h3>
 <dl>
 <dt id="skema.img2mml.models.encoding.positional_encoding_for_xfmer.PositionalEncoding.forward"><code class="name flex">
-<span>def <span class="ident">forward</span></span>(<span>self, x: <built-in method tensor of type object at 0x7f93e855b500>) ‑> <built-in method tensor of type object at 0x7f93e855b500></span>
+<span>def <span class="ident">forward</span></span>(<span>self, x: <built-in method tensor of type object at 0x7f372515b500>) ‑> <built-in method tensor of type object at 0x7f372515b500></span>
 </code></dt>
 <dd>
 <div class="desc"><p>Defines the computation performed at every call.</p>

api/python/skema/program_analysis/CAST/fortran/ts2cast.html

@@ -134,13 +134,7 @@ <h1 class="title">Module <code>skema.program_analysis.CAST.fortran.ts2cast</code
         # TODO: Research the above
         outer_body_nodes = get_children_by_types(root, [&#34;function&#34;, &#34;subroutine&#34;])
         if len(outer_body_nodes) &gt; 0:
-            body = []
-            for body_node in outer_body_nodes:
-                child_cast = self.visit(body_node)
-                if isinstance(child_cast, List):
-                    body.extend(child_cast)
-                elif isinstance(child_cast, AstNode):
-                    body.append(child_cast)
+            body = self.generate_cast_body(outer_body_nodes)
             modules.append(
                 Module(
                     name=None,
@@ -208,14 +202,8 @@ <h1 class="title">Module <code>skema.program_analysis.CAST.fortran.ts2cast</code
         &#34;&#34;&#34;Visitor for program and module statement. Returns a Module object&#34;&#34;&#34;
         self.variable_context.push_context()
 
-        program_body = []
-        for child in node.children[1:-1]:  # Ignore the start and end program statement
-            child_cast = self.visit(child)
-            if isinstance(child_cast, List):
-                program_body.extend(child_cast)
-            elif isinstance(child_cast, AstNode):
-                program_body.append(child_cast)
-
+        program_body = self.generate_cast_body(node.children[1:-1])
+
         self.variable_context.pop_context()
 
         return Module(
@@ -260,7 +248,7 @@ <h1 class="title">Module <code>skema.program_analysis.CAST.fortran.ts2cast</code
         #     (function_result) - Optional
         #       (identifier)
         #  (body_node) ...
-
+     
         # Create a new variable context
         self.variable_context.push_context()
 
@@ -345,6 +333,19 @@ <h1 class="title">Module <code>skema.program_analysis.CAST.fortran.ts2cast</code
         # Pop variable context off of stack before leaving this scope
         self.variable_context.pop_context()
 
+
+        # If this is a class function, we need to associate the function def with the class
+        # We should also return None here so we don&#39;t duplicate the function def
+        if self.variable_context.is_class_function(name.name):
+            self.variable_context.copy_class_function(name.name,
+            FunctionDef(
+            name=name,
+            func_args=func_args,
+            body=body,
+            source_refs=[self.node_helper.get_source_ref(node)],
+        ))
+            return None
+
         return FunctionDef(
             name=name,
             func_args=func_args,
@@ -1049,20 +1050,17 @@ <h1 class="title">Module <code>skema.program_analysis.CAST.fortran.ts2cast</code
         # If we tell the variable context we are in a record definition, it will append the type name as a prefix to all defined variables.
         self.variable_context.enter_record_definition(record_name)
 
-        # Note:
+        # Note: In derived type declarations, functions are only declared. The actual definition will be in the outer module.
         funcs = []
-        derived_type_procedures_node = get_first_child_by_type(
+        if derived_type_procedures_node := get_first_child_by_type(
             node, &#34;derived_type_procedures&#34;
-        )
-        if derived_type_procedures_node:
+        ):
             for procedure_node in get_children_by_types(
                 derived_type_procedures_node, [&#34;procedure_statement&#34;]
             ):
-                funcs.append(
-                    self.visit_name(
-                        get_first_child_by_type(procedure_node, &#34;method_name&#34;)
-                    )
-                )
+                function_name = self.node_helper.get_identifier(get_first_child_by_type(procedure_node, &#34;method_name&#34;, recurse=True))
+                funcs.append(self.variable_context.register_module_function(function_name))
+
 
         # A derived type can only have variable declarations in its body.
         fields = []
@@ -1290,12 +1288,14 @@ <h1 class="title">Module <code>skema.program_analysis.CAST.fortran.ts2cast</code
 
     def generate_cast_body(self, body_nodes: List):
         body = []
+
         for node in body_nodes:
             cast = self.visit(node)
+
             if isinstance(cast, AstNode):
                 body.append(cast)
             elif isinstance(cast, List):
-                body.extend(cast)
+                body.extend([element for element in cast if element is not None])
 
         # Gromet doesn&#39;t support empty bodies, so we should create a no_op instead
         if len(body) == 0:
@@ -1368,13 +1368,7 @@ <h2 class="section-title" id="header-classes">Classes</h2>
         # TODO: Research the above
         outer_body_nodes = get_children_by_types(root, [&#34;function&#34;, &#34;subroutine&#34;])
         if len(outer_body_nodes) &gt; 0:
-            body = []
-            for body_node in outer_body_nodes:
-                child_cast = self.visit(body_node)
-                if isinstance(child_cast, List):
-                    body.extend(child_cast)
-                elif isinstance(child_cast, AstNode):
-                    body.append(child_cast)
+            body = self.generate_cast_body(outer_body_nodes)
             modules.append(
                 Module(
                     name=None,
@@ -1442,14 +1436,8 @@ <h2 class="section-title" id="header-classes">Classes</h2>
         &#34;&#34;&#34;Visitor for program and module statement. Returns a Module object&#34;&#34;&#34;
         self.variable_context.push_context()
 
-        program_body = []
-        for child in node.children[1:-1]:  # Ignore the start and end program statement
-            child_cast = self.visit(child)
-            if isinstance(child_cast, List):
-                program_body.extend(child_cast)
-            elif isinstance(child_cast, AstNode):
-                program_body.append(child_cast)
-
+        program_body = self.generate_cast_body(node.children[1:-1])
+
         self.variable_context.pop_context()
 
         return Module(
@@ -1494,7 +1482,7 @@ <h2 class="section-title" id="header-classes">Classes</h2>
         #     (function_result) - Optional
         #       (identifier)
         #  (body_node) ...
-
+     
         # Create a new variable context
         self.variable_context.push_context()
 
@@ -1579,6 +1567,19 @@ <h2 class="section-title" id="header-classes">Classes</h2>
         # Pop variable context off of stack before leaving this scope
         self.variable_context.pop_context()
 
+
+        # If this is a class function, we need to associate the function def with the class
+        # We should also return None here so we don&#39;t duplicate the function def
+        if self.variable_context.is_class_function(name.name):
+            self.variable_context.copy_class_function(name.name,
+            FunctionDef(
+            name=name,
+            func_args=func_args,
+            body=body,
+            source_refs=[self.node_helper.get_source_ref(node)],
+        ))
+            return None
+
         return FunctionDef(
             name=name,
             func_args=func_args,
@@ -2283,20 +2284,17 @@ <h2 class="section-title" id="header-classes">Classes</h2>
         # If we tell the variable context we are in a record definition, it will append the type name as a prefix to all defined variables.
         self.variable_context.enter_record_definition(record_name)
 
-        # Note:
+        # Note: In derived type declarations, functions are only declared. The actual definition will be in the outer module.
         funcs = []
-        derived_type_procedures_node = get_first_child_by_type(
+        if derived_type_procedures_node := get_first_child_by_type(
             node, &#34;derived_type_procedures&#34;
-        )
-        if derived_type_procedures_node:
+        ):
             for procedure_node in get_children_by_types(
                 derived_type_procedures_node, [&#34;procedure_statement&#34;]
             ):
-                funcs.append(
-                    self.visit_name(
-                        get_first_child_by_type(procedure_node, &#34;method_name&#34;)
-                    )
-                )
+                function_name = self.node_helper.get_identifier(get_first_child_by_type(procedure_node, &#34;method_name&#34;, recurse=True))
+                funcs.append(self.variable_context.register_module_function(function_name))
+
 
         # A derived type can only have variable declarations in its body.
         fields = []
@@ -2524,12 +2522,14 @@ <h2 class="section-title" id="header-classes">Classes</h2>
 
     def generate_cast_body(self, body_nodes: List):
         body = []
+
         for node in body_nodes:
             cast = self.visit(node)
+
             if isinstance(cast, AstNode):
                 body.append(cast)
             elif isinstance(cast, List):
-                body.extend(cast)
+                body.extend([element for element in cast if element is not None])
 
         # Gromet doesn&#39;t support empty bodies, so we should create a no_op instead
         if len(body) == 0:
@@ -2568,12 +2568,14 @@ <h3>Methods</h3>
 </summary>
 <pre><code class="python">def generate_cast_body(self, body_nodes: List):
     body = []
+
     for node in body_nodes:
         cast = self.visit(node)
+
         if isinstance(cast, AstNode):
             body.append(cast)
         elif isinstance(cast, List):
-            body.extend(cast)
+            body.extend([element for element in cast if element is not None])
 
     # Gromet doesn&#39;t support empty bodies, so we should create a no_op instead
     if len(body) == 0:
@@ -2626,13 +2628,7 @@ <h3>Methods</h3>
     # TODO: Research the above
     outer_body_nodes = get_children_by_types(root, [&#34;function&#34;, &#34;subroutine&#34;])
     if len(outer_body_nodes) &gt; 0:
-        body = []
-        for body_node in outer_body_nodes:
-            child_cast = self.visit(body_node)
-            if isinstance(child_cast, List):
-                body.extend(child_cast)
-            elif isinstance(child_cast, AstNode):
-                body.append(child_cast)
+        body = self.generate_cast_body(outer_body_nodes)
         modules.append(
             Module(
                 name=None,
@@ -2772,20 +2768,17 @@ <h3>Methods</h3>
     # If we tell the variable context we are in a record definition, it will append the type name as a prefix to all defined variables.
     self.variable_context.enter_record_definition(record_name)
 
-    # Note:
+    # Note: In derived type declarations, functions are only declared. The actual definition will be in the outer module.
     funcs = []
-    derived_type_procedures_node = get_first_child_by_type(
+    if derived_type_procedures_node := get_first_child_by_type(
         node, &#34;derived_type_procedures&#34;
-    )
-    if derived_type_procedures_node:
+    ):
         for procedure_node in get_children_by_types(
             derived_type_procedures_node, [&#34;procedure_statement&#34;]
         ):
-            funcs.append(
-                self.visit_name(
-                    get_first_child_by_type(procedure_node, &#34;method_name&#34;)
-                )
-            )
+            function_name = self.node_helper.get_identifier(get_first_child_by_type(procedure_node, &#34;method_name&#34;, recurse=True))
+            funcs.append(self.variable_context.register_module_function(function_name))
+
 
     # A derived type can only have variable declarations in its body.
     fields = []
@@ -3173,7 +3166,7 @@ <h3>Methods</h3>
     #     (function_result) - Optional
     #       (identifier)
     #  (body_node) ...
-
+ 
     # Create a new variable context
     self.variable_context.push_context()
 
@@ -3258,6 +3251,19 @@ <h3>Methods</h3>
     # Pop variable context off of stack before leaving this scope
     self.variable_context.pop_context()
 
+
+    # If this is a class function, we need to associate the function def with the class
+    # We should also return None here so we don&#39;t duplicate the function def
+    if self.variable_context.is_class_function(name.name):
+        self.variable_context.copy_class_function(name.name,
+        FunctionDef(
+        name=name,
+        func_args=func_args,
+        body=body,
+        source_refs=[self.node_helper.get_source_ref(node)],
+    ))
+        return None
+
     return FunctionDef(
         name=name,
         func_args=func_args,
@@ -3587,14 +3593,8 @@ <h3>Methods</h3>
     &#34;&#34;&#34;Visitor for program and module statement. Returns a Module object&#34;&#34;&#34;
     self.variable_context.push_context()
 
-    program_body = []
-    for child in node.children[1:-1]:  # Ignore the start and end program statement
-        child_cast = self.visit(child)
-        if isinstance(child_cast, List):
-            program_body.extend(child_cast)
-        elif isinstance(child_cast, AstNode):
-            program_body.append(child_cast)
-
+    program_body = self.generate_cast_body(node.children[1:-1])
+
     self.variable_context.pop_context()
 
     return Module(