Update scipy patch

Remove Sulongisms

Author: msimacek

graalpython/lib-graalpython/patches/scipy/scipy-1.10.1.patch

@@ -1,139 +1,13 @@
-diff --git a/meson.build b/meson.build
-index ad18b245..24108760 100644
---- a/meson.build
-+++ b/meson.build
-@@ -11,7 +11,7 @@ project(
-     'buildtype=debugoptimized',
-     'c_std=c99',
-     'cpp_std=c++14',
--    'fortran_std=legacy',
-+    'fortran_std=none',
-     'blas=openblas',
-     'lapack=openblas'
-   ],
-@@ -66,6 +66,10 @@ if ff.has_argument('-Wno-conversion')
-   add_project_arguments('-Wno-conversion', language: 'fortran')
- endif
- 
-+if ff.has_argument('-fallow-argument-mismatch')
-+  add_project_arguments('-fallow-argument-mismatch', language: 'fortran')
-+endif
-+
- is_windows = host_machine.system() == 'windows'
- 
- # Intel compilers default to fast-math, so disable it if we detect Intel
-diff --git a/mesonpy_wrapper.py b/mesonpy_wrapper.py
-new file mode 100644
-index 00000000..afa33ecc
---- /dev/null
-+++ b/mesonpy_wrapper.py
-@@ -0,0 +1,86 @@
-+import mesonpy 
-+import os 
-+import sys
-+from contextlib import contextmanager
-+import subprocess
-+
-+
-+def get_flang_new_lib_dir():
-+    if sys.implementation.name == "graalpy" and __graalpython__.use_system_toolchain:
-+        return None, None
-+    try:
-+        output = subprocess.check_output(['flang-new', '--version'])
-+        flang_dir = output.splitlines()[-1].split()[-1].strip().decode("utf-8")
-+        return os.path.join(flang_dir, "flang-new"), os.path.normpath(os.path.join(flang_dir, '..', 'lib'))
-+    except Exception as e:
-+        print(f"INFO: flang-new not detected, could not find library path. Reason: {e}")
-+        return None, None
-+        
-+
-+def append_env_var(env, var, value):
-+    env[var] = '{} {}'.format(env.get(var, ''), value)
-+
-+
-+def get_build_env():
-+    env = {}
-+    flang_new, flang_lib_dir = get_flang_new_lib_dir()
-+    if flang_new:
-+        # until flang-new can compile propack we disable it (during runtime)
-+        env["USE_PROPACK"] = "0"
-+        env['CC'] = 'clang'
-+        env['CXX'] = 'clang++'
-+        # env['FC'] = flang_new
-+        env['FC'] = "flang-new"
-+        if sys.implementation.name == "graalpy":
-+            cflags = "-flto=full"
-+        else:
-+            ld = 'lld'
-+            cflags = "-flto=full -fuse-ld=lld -Wl,--mllvm=-lto-embed-bitcode=optimized,--lto-O0"
-+            env['CC_LD'] = ld
-+            env['CXX_LD'] = ld
-+            env['FC_LD'] = ld
-+        env['CFLAGS'] = cflags
-+        env['CXXFLAGS'] = cflags
-+        env['FFLAGS'] = cflags
-+        append_env_var(env, 'LDFLAGS', f'-L{flang_lib_dir}')
-+    return env
-+
-+
-+@contextmanager
-+def env_vars(env):
-+    # save and set 
-+    prev = {}
-+    for k, v in env.items():    
-+        prev[k] = os.environ.get(k, None)
-+        os.environ[k] = v
-+
-+    yield
-+
-+    # restore 
-+    for k, v in prev.items():
-+        if v is None:
-+            del os.environ[k]
-+        else:
-+            os.environ[k] = v
-+
-+
-+def get_config_settings(config_settings=None):
-+    if config_settings is None:
-+        config_settings = {}
-+    config_settings['compile-args'] = '-j4'
-+    config_settings['builddir'] = f'mesonbuild-{sys.implementation.name}'
-+    return config_settings
-+
-+
-+def build_wheel(wheel_directory, config_settings=None, metadata_directory=None):
-+    config_settings = get_config_settings(config_settings)
-+    scipy_build_env = get_build_env()
-+    with env_vars(scipy_build_env):
-+        return mesonpy.build_wheel(wheel_directory, config_settings=config_settings, metadata_directory=metadata_directory)
-+
-+
-+def build_sdist(sdist_directory, config_settings=None):
-+    config_settings = get_config_settings(config_settings)
-+    scipy_build_env = get_build_env()
-+    with env_vars(scipy_build_env):
-+        return mesonpy.build_sdist(sdist_directory, config_settings=config_settings)
 diff --git a/pyproject.toml b/pyproject.toml
-index 454a3c2e..94a754aa 100644
+index 454a3c2e..7c96eb11 100644
 --- a/pyproject.toml
 +++ b/pyproject.toml
-@@ -8,55 +8,21 @@
- #     "pybind11>=2.4.3,<2.5.0",
- 
- [build-system]
--build-backend = 'mesonpy'
-+# build-backend = 'mesonpy'
-+build-backend = 'mesonpy_wrapper'
-+backend-path = ["."]
- requires = [
-     "meson-python>=0.11.0,<0.13.0",
-     "Cython>=0.29.32,<3.0",
+@@ -15,48 +15,11 @@ requires = [
      # conservatively avoid issues from
      # https://github.com/pybind/pybind11/issues/4420
      "pybind11==2.10.1",
 -    "pythran>=0.12.0,<0.13.0",
-+    "pythran>=0.13.0",
++    "pythran==0.13.1",
      # `wheel` is needed for non-isolated builds, given that `meson-python`
      # doesn't list it as a runtime requirement (at least in 0.5.0)
      "wheel<0.39.0",
@@ -176,159 +50,6 @@ index 454a3c2e..94a754aa 100644
 -    "numpy; python_version>='3.12'",
 -    "numpy; python_version>='3.8' and platform_python_implementation=='PyPy'",
 +    "numpy==1.23.5",
-+    "ninja",
  ]
 
  [project]
-diff --git a/scipy/_lib/_ccallback_c.pyx b/scipy/_lib/_ccallback_c.pyx
-index 0704acc6..beb2bc72 100644
---- a/scipy/_lib/_ccallback_c.pyx
-+++ b/scipy/_lib/_ccallback_c.pyx
-@@ -210,15 +210,15 @@ cdef double sine(double x, void *user_data) nogil except *:
- import ctypes
- 
- plus1_t = ctypes.CFUNCTYPE(ctypes.c_double, ctypes.c_double, ctypes.POINTER(ctypes.c_int), ctypes.c_void_p)
--plus1_ctypes = ctypes.cast(<size_t>&plus1_cython, plus1_t)
-+# plus1_ctypes = ctypes.cast(<size_t>&plus1_cython, plus1_t)
- 
- plus1b_t = ctypes.CFUNCTYPE(ctypes.c_double, ctypes.c_double, ctypes.c_double,
-                             ctypes.POINTER(ctypes.c_int), ctypes.c_void_p)
--plus1b_ctypes = ctypes.cast(<size_t>&plus1b_cython, plus1b_t)
-+# plus1b_ctypes = ctypes.cast(<size_t>&plus1b_cython, plus1b_t)
- 
- plus1bc_t = ctypes.CFUNCTYPE(ctypes.c_double, ctypes.c_double, ctypes.c_double, ctypes.c_double,
-                             ctypes.POINTER(ctypes.c_int), ctypes.c_void_p)
--plus1bc_ctypes = ctypes.cast(<size_t>&plus1bc_cython, plus1bc_t)
-+# plus1bc_ctypes = ctypes.cast(<size_t>&plus1bc_cython, plus1bc_t)
- 
- sine_t = ctypes.CFUNCTYPE(ctypes.c_double, ctypes.c_double, ctypes.c_void_p)
--sine_ctypes = ctypes.cast(<size_t>&sine, sine_t)
-+# sine_ctypes = ctypes.cast(<size_t>&sine, sine_t)
-diff --git a/scipy/_lib/setup.py b/scipy/_lib/setup.py
-index 6fca8a66..95000399 100644
---- a/scipy/_lib/setup.py
-+++ b/scipy/_lib/setup.py
-@@ -55,8 +55,6 @@ def configuration(parent_package='',top_path=None):
-         # Generate a header file containing defines
-         config_cmd = config.get_config_cmd()
-         defines = []
--        if config_cmd.check_func('open_memstream', decl=True, call=True):
--            defines.append(('HAVE_OPEN_MEMSTREAM', '1'))
-         target = os.path.join(os.path.dirname(__file__), 'src',
-                               'messagestream_config.h')
-         with open(target, 'w') as f:
-diff --git a/scipy/_lib/src/messagestream_config.h.in b/scipy/_lib/src/messagestream_config.h.in
-index fe2a3876..1cdf6c79 100644
---- a/scipy/_lib/src/messagestream_config.h.in
-+++ b/scipy/_lib/src/messagestream_config.h.in
-@@ -1 +1 @@
--#define HAVE_OPEN_MEMSTREAM @has_openmemstream@
-+#define HAVE_OPEN_MEMSTREAM 0 // @has_openmemstream@
-\ No newline at end of file
-diff --git a/scipy/sparse/linalg/meson.build b/scipy/sparse/linalg/meson.build
-index 946cac0c..96852886 100644
---- a/scipy/sparse/linalg/meson.build
-+++ b/scipy/sparse/linalg/meson.build
-@@ -15,7 +15,7 @@ py3.install_sources([
-   subdir: 'scipy/sparse/linalg'
- )
- 
--subdir('_propack')
-+# subdir('_propack')
- subdir('_isolve')
- subdir('_dsolve')
- subdir('_eigen')
-diff --git a/scipy/special/meson.build b/scipy/special/meson.build
-index f92183f5..b1443aad 100644
---- a/scipy/special/meson.build
-+++ b/scipy/special/meson.build
-@@ -427,24 +427,24 @@ py3.extension_module('_test_internal',
- # Must use `custom_target`, because `py3.install_sources` does not work with
- # generated sources - see https://github.com/mesonbuild/meson/issues/7372
- npz_files = [
--  [
--    '_data_boost',
--    'tests/data/boost/assoc_legendre_p_ipp/assoc_legendre_p.txt',
--    'boost',
--    'boost.npz'
--  ],
--  [
--    '_data_gsl',
--    'tests/data/gsl/mathieu_ab.txt',
--    'gsl',
--    'gsl.npz'
--  ],
--  [
--    '_data_local',
--    'tests/data/local/ellipkm1.txt',
--    'local',
--    'local.npz'
--  ],
-+  # [
-+  #   '_data_boost',
-+  #   'tests/data/boost/assoc_legendre_p_ipp/assoc_legendre_p.txt',
-+  #   'boost',
-+  #   'boost.npz'
-+  # ],
-+  # [
-+  #   '_data_gsl',
-+  #   'tests/data/gsl/mathieu_ab.txt',
-+  #   'gsl',
-+  #   'gsl.npz'
-+  # ],
-+  # [
-+  #   '_data_local',
-+  #   'tests/data/local/ellipkm1.txt',
-+  #   'local',
-+  #   'local.npz'
-+  # ],
- ]
- 
- foreach npz_file: npz_files
-diff --git a/tools/cythonize.py b/tools/cythonize.py
-index 402824cb..b6aba959 100755
---- a/tools/cythonize.py
-+++ b/tools/cythonize.py
-@@ -95,21 +95,19 @@ def process_pyx(fromfile, tofile, cwd):
-     if tofile.endswith('.cxx'):
-         flags += ['--cplus']
- 
--    try:
-+    try:    
-+        from Cython.Compiler.Main import setuptools_main
-+        prev_argv = sys.argv[1:]
-         try:
--            r = subprocess.call(['cython'] + flags + ["-o", tofile, fromfile], cwd=cwd)
--            if r != 0:
--                raise Exception('Cython failed')
--        except OSError as e:
--            # There are ways of installing Cython that don't result in a cython
--            # executable on the path, see gh-2397.
--            r = subprocess.call([sys.executable, '-c',
--                                 'import sys; from Cython.Compiler.Main import '
--                                 'setuptools_main as main; sys.exit(main())'] + flags +
--                                 ["-o", tofile, fromfile],
--                                cwd=cwd)
--            if r != 0:
--                raise Exception("Cython either isn't installed or it failed.") from e
-+            oldcwd = os.getcwd()
-+            os.chdir(cwd)
-+            sys.argv[1:] = flags + ["-o", tofile, fromfile]
-+            retcode = setuptools_main()
-+            if retcode:
-+                sys.exit(retcode)
-+        finally:
-+            sys.argv[1:] = prev_argv
-+            os.chdir(oldcwd)
-     except OSError as e:
-         raise OSError('Cython needs to be installed') from e
- 
-@@ -253,7 +251,7 @@ def find_process_files(root_dir):
-     lock = Lock()
- 
-     try:
--        num_proc = int(os.environ.get('SCIPY_NUM_CYTHONIZE_JOBS', cpu_count()))
-+        num_proc = int(os.environ.get('SCIPY_NUM_CYTHONIZE_JOBS', 1))
-         pool = Pool(processes=num_proc)
-     except ImportError as e:
-         # Allow building (single-threaded) on GNU/Hurd, which does not