support python 3.13 bootstrapping from sources (#46983)

var/spack/repos/builtin/packages/clingo/PyEval_InitThreads.patch

@@ -1,12 +0,0 @@
-diff --git a/libpyclingo/pyclingo.cc b/libpyclingo/pyclingo.cc
-index ec4a33c6..ee903cd0 100644
---- a/libpyclingo/pyclingo.cc
-+++ b/libpyclingo/pyclingo.cc
-@@ -10463,7 +10463,6 @@ void addEmptyClass(Reference module, char const *name) {
- 
- PyObject *initclingo_() {
-     PY_TRY {
--        if (!PyEval_ThreadsInitialized()) { PyEval_InitThreads(); }
- #if PY_MAJOR_VERSION >= 3
-         Object m = PyModule_Create(&clingoModule);
- #else

var/spack/repos/builtin/packages/clingo/package.py

@@ -74,12 +74,20 @@ class Clingo(CMakePackage):
     patch("size-t.patch", when="%msvc")
     patch("vs2022.patch", when="%msvc@19.30:")
     patch("clingo_msc_1938_native_handle.patch", when="@:5.7.0 %msvc@19.38:")
-    patch("PyEval_InitThreads.patch", when="@spack,5.3:5.4 ^python@3.9:")
 
     def patch(self):
+        # In bootstrap/prototypes/*.json we don't want to have specs that work for any python
+        # version, so this conditional patch lives here instead of being its own directive.
+        if self.spec.satisfies("@spack,5.3:5.4 ^python@3.9:"):
+            filter_file(
+                "if (!PyEval_ThreadsInitialized()) { PyEval_InitThreads(); }",
+                "",
+                "libpyclingo/pyclingo.cc",
+                string=True,
+            )
         # Doxygen is optional but can't be disabled with a -D, so patch
         # it out if it's really supposed to be disabled
-        if "+docs" not in self.spec:
+        if self.spec.satisfies("~docs"):
             filter_file(
                 r"find_package\(Doxygen\)",
                 'message("Doxygen disabled for Spack build.")',