Update Cython patch to recythonize files after unpatched Cython

Author: msimacek

graalpython/lib-graalpython/patches/Cython/Cython-0.29.32.patch

@@ -1,8 +1,21 @@
 diff --git a/Cython/Build/Dependencies.py b/Cython/Build/Dependencies.py
-index 7eb55e2..76d4857 100644
+index 7eb55e2..1fbab30 100644
 --- a/Cython/Build/Dependencies.py
 +++ b/Cython/Build/Dependencies.py
-@@ -1094,6 +1094,8 @@ def cythonize(module_list, exclude=None, nthreads=0, aliases=None, quiet=False,
+@@ -1060,6 +1060,12 @@ def cythonize(module_list, exclude=None, nthreads=0, aliases=None, quiet=False,
+                 else:
+                     dep_timestamp, dep = deps.newest_dependency(source)
+                     priority = 2 - (dep in deps.immediate_dependencies(source))
++                # GraalPy change: force recythonize if not cythonized by our patched version
++                if os.path.exists(c_file):
++                    with open(c_file, 'rb') as f:
++                        # We modify the watermark to include graalpy
++                        if not b'graalpy' in f.read(100):
++                            c_timestamp = -1
+                 if force or c_timestamp < dep_timestamp:
+                     if not quiet and not force:
+                         if source == dep:
+@@ -1094,6 +1100,8 @@ def cythonize(module_list, exclude=None, nthreads=0, aliases=None, quiet=False,
          progress = progress_fmt.format(i+1, N)
          to_compile[i] = to_compile[i][1:] + (progress,)
 
@@ -101,6 +114,17 @@ index 7361a55..6c4d9d9 100644
          entry.in_cinclude = self.in_cinclude
          entry.create_wrapper = create_wrapper
          if name:
+diff --git a/Cython/Compiler/Version.py b/Cython/Compiler/Version.py
+index dcb561f..c2c06a0 100644
+--- a/Cython/Compiler/Version.py
++++ b/Cython/Compiler/Version.py
+@@ -6,4 +6,5 @@ from .. import __version__ as version
+ 
+ # For 'generated by' header line in C files.
+ 
+-watermark = str(version)
++# GraalPy change: watermark our patched version
++watermark = f'{version}-graalpy'
 diff --git a/Cython/Includes/cpython/datetime.pxd b/Cython/Includes/cpython/datetime.pxd
 index cd0f907..712cd92 100644
 --- a/Cython/Includes/cpython/datetime.pxd

graalpython/lib-graalpython/patches/Cython/Cython-0.29.37.patch

@@ -1,8 +1,21 @@
 diff --git a/Cython/Build/Dependencies.py b/Cython/Build/Dependencies.py
-index 92fa96a..2885a4f 100644
+index 92fa96a..8864b78 100644
 --- a/Cython/Build/Dependencies.py
 +++ b/Cython/Build/Dependencies.py
-@@ -1082,6 +1082,8 @@ def cythonize(module_list, exclude=None, nthreads=0, aliases=None, quiet=False,
+@@ -1048,6 +1048,12 @@ def cythonize(module_list, exclude=None, nthreads=0, aliases=None, quiet=False,
+                 else:
+                     dep_timestamp, dep = deps.newest_dependency(source)
+                     priority = 2 - (dep in deps.immediate_dependencies(source))
++                # GraalPy change: force recythonize if not cythonized by our patched version
++                if os.path.exists(c_file):
++                    with open(c_file, 'rb') as f:
++                        # We modify the watermark to include graalpy
++                        if not b'graalpy' in f.read(100):
++                            c_timestamp = -1
+                 if force or c_timestamp < dep_timestamp:
+                     if not quiet and not force:
+                         if source == dep:
+@@ -1082,6 +1088,8 @@ def cythonize(module_list, exclude=None, nthreads=0, aliases=None, quiet=False,
          progress = progress_fmt.format(i+1, N)
          to_compile[i] = to_compile[i][1:] + (progress,)
 
@@ -101,6 +114,17 @@ index 7361a55..6c4d9d9 100644
          entry.in_cinclude = self.in_cinclude
          entry.create_wrapper = create_wrapper
          if name:
+diff --git a/Cython/Compiler/Version.py b/Cython/Compiler/Version.py
+index dcb561f..c2c06a0 100644
+--- a/Cython/Compiler/Version.py
++++ b/Cython/Compiler/Version.py
+@@ -6,4 +6,5 @@ from .. import __version__ as version
+ 
+ # For 'generated by' header line in C files.
+ 
+-watermark = str(version)
++# GraalPy change: watermark our patched version
++watermark = f'{version}-graalpy'
 diff --git a/Cython/Includes/cpython/datetime.pxd b/Cython/Includes/cpython/datetime.pxd
 index cd0f907..712cd92 100644
 --- a/Cython/Includes/cpython/datetime.pxd
@@ -154,7 +178,7 @@ index 099b3c4..0692df0 100644
          cval = ((PyComplexObject *)o)->cval;
      else
 diff --git a/Cython/Utility/Coroutine.c b/Cython/Utility/Coroutine.c
-index aaa8a8e..152e9dc 100644
+index aaa8a8e..e60a5e0 100644
 --- a/Cython/Utility/Coroutine.c
 +++ b/Cython/Utility/Coroutine.c
 @@ -531,8 +531,7 @@ static int __Pyx_PyGen__FetchStopIterationValue(CYTHON_UNUSED PyThreadState *$lo
@@ -221,7 +245,7 @@ index 93f577f..5dac1d7 100644
  #endif
      else if (PyMethod_Check(method)) {
 diff --git a/Cython/Utility/ModuleSetupCode.c b/Cython/Utility/ModuleSetupCode.c
-index cfff606..4a6a6ea 100644
+index cfff606..90876c6 100644
 --- a/Cython/Utility/ModuleSetupCode.c
 +++ b/Cython/Utility/ModuleSetupCode.c
 @@ -186,6 +186,48 @@

graalpython/lib-graalpython/patches/Cython/Cython-3.0.10.patch

@@ -1,8 +1,21 @@
 diff --git a/Cython/Build/Dependencies.py b/Cython/Build/Dependencies.py
-index 7de4065..e1589cd 100644
+index 7de4065..981011f 100644
 --- a/Cython/Build/Dependencies.py
 +++ b/Cython/Build/Dependencies.py
-@@ -1127,6 +1127,8 @@ def cythonize(module_list, exclude=None, nthreads=0, aliases=None, quiet=False,
+@@ -1090,6 +1090,12 @@ def cythonize(module_list, exclude=None, nthreads=0, aliases=None, quiet=False,
+                 else:
+                     dep_timestamp, dep = deps.newest_dependency(source)
+                     priority = 2 - (dep in deps.immediate_dependencies(source))
++                # GraalPy change: force recythonize if not cythonized by our patched version
++                if os.path.exists(c_file):
++                    with open(c_file, 'rb') as f:
++                        # We modify the watermark to include graalpy
++                        if not b'graalpy' in f.read(100):
++                            c_timestamp = -1
+                 if force or c_timestamp < dep_timestamp:
+                     if not quiet and not force:
+                         if source == dep:
+@@ -1127,6 +1133,8 @@ def cythonize(module_list, exclude=None, nthreads=0, aliases=None, quiet=False,
          progress = progress_fmt.format(i+1, N)
          to_compile[i] = to_compile[i][1:] + (progress,)
 
@@ -103,6 +116,17 @@ index 5f088dd..a258bdc 100644
          entry.in_cinclude = self.in_cinclude
          entry.create_wrapper = create_wrapper
          if name:
+diff --git a/Cython/Compiler/Version.py b/Cython/Compiler/Version.py
+index dcb561f..c2c06a0 100644
+--- a/Cython/Compiler/Version.py
++++ b/Cython/Compiler/Version.py
+@@ -6,4 +6,5 @@ from .. import __version__ as version
+ 
+ # For 'generated by' header line in C files.
+ 
+-watermark = str(version)
++# GraalPy change: watermark our patched version
++watermark = f'{version}-graalpy'
 diff --git a/Cython/Includes/cpython/datetime.pxd b/Cython/Includes/cpython/datetime.pxd
 index 3dce395..77f8356 100644
 --- a/Cython/Includes/cpython/datetime.pxd