[GR-60283] Update more patches

PullRequest: graalpython/3643

Author: msimacek

graalpython/lib-graalpython/patches/catboost-1.2.3.patch

@@ -0,0 +1,33 @@
+diff --git a/setup.py b/setup.py
+index b936372..158056a 100644
+--- a/setup.py
++++ b/setup.py
+@@ -133,7 +133,7 @@ BUILD_OVERRIDE_BORING_SSL_ASM_PLATFORM = os.environ.get(
+ # to have been generated by building first *with* Cython support. Even if this
+ # is set to false, if the script detects that the generated `.c` file isn't
+ # present, then it will still attempt to use Cython.
+-BUILD_WITH_CYTHON = _env_bool_value("GRPC_PYTHON_BUILD_WITH_CYTHON", "False")
++BUILD_WITH_CYTHON = _env_bool_value("GRPC_PYTHON_BUILD_WITH_CYTHON", "True")
+ 
+ # Export this variable to use the system installation of openssl. You need to
+ # have the header files installed (in /usr/include/openssl) and during
+diff --git a/src/python/grpcio/grpc/_server.py b/src/python/grpcio/grpc/_server.py
+index c8af57c..ef862a2 100644
+--- a/src/python/grpcio/grpc/_server.py
++++ b/src/python/grpcio/grpc/_server.py
+@@ -1257,13 +1257,13 @@ def _process_event_and_continue(
+     state: _ServerState, event: cygrpc.BaseEvent
+ ) -> bool:
+     should_continue = True
+-    if event.tag is _SHUTDOWN_TAG:
++    if event.tag == _SHUTDOWN_TAG:
+         with state.lock:
+             state.due.remove(_SHUTDOWN_TAG)
+             if _stop_serving(state):
+                 should_continue = False
+     elif (
+-        event.tag is _REQUEST_CALL_TAG
++        event.tag == _REQUEST_CALL_TAG
+         or event.tag in state.registered_method_handlers.keys()
+     ):
+         registered_method_name = None

graalpython/lib-graalpython/patches/grpcio-1.66.1.patch

@@ -19,6 +19,11 @@ license = 'Apache-2.0'
 patch = 'blosc2.patch'
 license = 'Apache-2.0'
 
+[[catboost.rules]]
+version = '== 1.2.3'
+patch = 'catboost-1.2.3.patch'
+license = 'Apache-2.0'
+
 [[catboost.rules]]
 version = '== 1.2.2'
 patch = 'catboost-1.2.2.patch'
@@ -34,7 +39,7 @@ patch = 'cffi-1.15.1.patch'
 license = 'MIT'
 
 [[cffi.rules]]
-version = '== 1.16.0'
+version = '>= 1.16.0'
 patch = 'cffi-1.16.0.patch'
 license = 'MIT'
 
@@ -144,20 +149,16 @@ version = '== 1.60.0'
 patch = 'grpcio-1.60.0.patch'
 license = 'Apache-2.0'
 
+[[grpcio.rules]]
+# Force re-cythonize + other fixes
+version = '== 1.66.1'
+patch = 'grpcio-1.66.1.patch'
+license = 'Apache-2.0'
+
 [[h2o.rules]]
 patch = 'h2o.patch'
 license = 'Apache-2.0'
 
-[[h5py.rules]]
-version = '== 2.10.0'
-patch = 'h5py-2.10.0.patch'
-license = 'BSD-3-Clause'
-
-[[h5py.rules]]
-version = '== 3.10.0'
-patch = 'h5py-3.10.0.patch'
-license = 'BSD-3-Clause'
-
 [[hmmlearn.rules]]
 # Need to specify pybind11 build dependency, otherwise setuptools will install it unpatched
 patch = 'hmmlearn.patch'
@@ -190,7 +191,7 @@ patch = 'jiter.patch'
 license = 'MIT'
 
 [[joblib.rules]]
-version = '==1.4.0'
+version = '==1.4.*'
 patch = 'joblib-1.4.0.patch'
 license = 'BSD-3-Clause'
 
@@ -243,23 +244,6 @@ license = "BSD-3-Clause"
 install-priority = 0  # Don't make pip install prefer this version
 dist-type = "sdist"
 
-[[matplotlib.rules]]
-version = '== 3.5.3'
-patch = 'matplotlib-3.5.3.patch'
-license = 'PSF-2.0'
-
-[[matplotlib.rules]]
-version = '== 3.6.3'
-patch = 'matplotlib-3.6.3.patch'
-license = 'PSF-2.0'
-
-[[matplotlib.rules]]
-# pin 3.7.0
-install-priority = 10
-version = '== 3.7.0'
-patch = 'matplotlib-3.7.0.patch'
-license = 'PSF-2.0'
-
 [[meson-python.rules]]
 # Upstreamed
 version = '<= 0.16.0'
@@ -581,6 +565,12 @@ version = '== 0.3.3'
 patch = 'safetensors-0.3.3.patch'
 license = 'Apache-2.0'
 
+[[scikit-learn.rules]]
+version = '== 1.5.2'
+patch = 'scikit-learn-1.5.2.patch'
+license = 'BSD-3-Clause'
+dist-type = 'sdist'
+
 [[scikit-learn.rules]]
 version = '== 1.2.2'
 patch = 'scikit-learn-1.2.2.patch'

graalpython/lib-graalpython/patches/h5py-2.10.0.patch

@@ -0,0 +1,31 @@
+diff --git a/sklearn/_build_utils/__init__.py b/sklearn/_build_utils/__init__.py
+index ceb7244..0a0acc2 100644
+--- a/sklearn/_build_utils/__init__.py
++++ b/sklearn/_build_utils/__init__.py
+@@ -59,10 +59,10 @@ def cythonize_extensions(extension):
+     sklearn._OPENMP_SUPPORTED = check_openmp_support()
+ 
+     n_jobs = 1
+-    with contextlib.suppress(ImportError):
+-        import joblib
++    # with contextlib.suppress(ImportError):
++    #     import joblib
+ 
+-        n_jobs = joblib.cpu_count()
++    #     n_jobs = joblib.cpu_count()
+ 
+     # Additional checks for Cython
+     cython_enable_debug_directives = (
+diff --git a/sklearn/datasets/_svmlight_format_fast.pyx b/sklearn/datasets/_svmlight_format_fast.pyx
+index 103d43b..e2cc6da 100644
+--- a/sklearn/datasets/_svmlight_format_fast.pyx
++++ b/sklearn/datasets/_svmlight_format_fast.pyx
+@@ -80,7 +80,7 @@ def _load_svmlight_file(f, dtype, bint multilabel, bint zero_based,
+         if n_features and features[0].startswith(qid_prefix):
+             _, value = features[0].split(COLON, 1)
+             if query_id:
+-                query.resize(len(query) + 1)
++                query.resize(len(query) + 1, refcheck=False)
+                 query[len(query) - 1] = np.int64(value)
+             features.pop(0)
+             n_features -= 1