overrides.shapely: Remove patch

Inheriting patches from nixpkgs is brittle and just a shortcut.
Instead patch the AST of the file that looks up the library paths
which should be much less brittle over time.

overrides/default.nix

@@ -1942,7 +1942,14 @@ lib.composeManyExtensions [
       shapely = super.shapely.overridePythonAttrs (
         old: {
           buildInputs = (old.buildInputs or [ ]) ++ [ pkgs.geos ];
-          inherit (pkgs.python3.pkgs.shapely) patches GEOS_LIBRARY_PATH;
+          inherit (pkgs.python3.pkgs.shapely) GEOS_LIBRARY_PATH;
+
+          GEOS_LIBC = lib.optionalString (!stdenv.isDarwin) "${stdenv.cc.libc}/lib/libc${stdenv.hostPlatform.extensions.sharedLibrary}.6";
+
+          # Fix library paths
+          postPatch = old.postPatch or "" + ''
+            ${self.python.pythonForBuild.interpreter} ${./shapely-rewrite.py} shapely/geos.py
+          '';
         }
       );
 

overrides/shapely-rewrite.py

@@ -0,0 +1,46 @@
+"""
+Rewrite libc/library path references to Nix store paths
+Nixpkgs uses a normal patch for this but we need to be less
+sensitive to changes between versions.
+"""
+from textwrap import dedent
+import sys
+import ast
+import os
+
+
+with open(sys.argv[1]) as f:
+    mod = ast.parse(f.read(), "geos.py")
+
+
+class LibTransformer(ast.NodeTransformer):
+    _lgeos_replaced = False
+
+    def visit_If(self, node):
+        if ast.unparse(node).startswith("if sys.platform.startswith('linux')"):
+            return ast.parse(
+                dedent(
+                    """
+            free = CDLL(%s).free
+            free.argtypes = [c_void_p]
+            free.restype = None
+            """
+                )
+                % (lambda x: "'" + x + "'" if x else None)(os.environ.get("GEOS_LIBC"))
+            )
+        return node
+
+    def visit_Assign(self, node):
+        _target = node.targets[0]
+        if (
+            not self._lgeos_replaced
+            and isinstance(_target, ast.Name)
+            and _target.id == "_lgeos"
+        ):
+            self._lgeos_replaced = True
+            return ast.parse("_lgeos = CDLL('%s')" % os.environ["GEOS_LIBRARY_PATH"])
+        return node
+
+
+with open(sys.argv[1], "w") as f:
+    f.write(ast.unparse(LibTransformer().visit(mod)))