From 7ee6aab18a748893a789a4b9ff964bbe6885f342 Mon Sep 17 00:00:00 2001
From: Adam Li <adam2392@gmail.com>
Date: Mon, 11 Mar 2024 17:44:10 -0400
Subject: [PATCH 1/6] Adding meson compiler directives

Signed-off-by: Adam Li <adam2392@gmail.com>
---
 meson.build              | 12 +++++++++--
 sktree/_lib/sklearn_fork |  2 +-
 sktree/meson.build       | 43 ++++++++++++++++++++++++++++++++++++++++
 3 files changed, 54 insertions(+), 3 deletions(-)

diff --git a/meson.build b/meson.build
index 420025437..26048bb3d 100644
--- a/meson.build
+++ b/meson.build
@@ -1,12 +1,12 @@
 project(
   'scikit-tree',
-  'c', 'cpp',
+  'c', 'cpp', 'cython',
   # Note that the git commit hash cannot be added dynamically here
   # That only happens when importing from a git repository.
   # See `sktree/__init__.py`
   version: '0.8.0dev0',
   license: 'BSD-3',
-  meson_version: '>= 0.64.0',
+  meson_version: '>= 1.1.0',
   default_options: [
     'buildtype=debugoptimized',
     'c_std=c99',
@@ -29,6 +29,14 @@ elif cc.get_id() == 'msvc'
   endif
 endif
 
+_global_c_args = cc.get_supported_arguments(
+  '-Wno-unused-but-set-variable',
+  '-Wno-unused-function',
+  '-Wno-conversion',
+  '-Wno-misleading-indentation',
+)
+add_project_arguments(_global_c_args, language : 'c')
+
 # We need -lm for all C code (assuming it uses math functions, which is safe to
 # assume for scikit-tree). For C++ it isn't needed, because libstdc++/libc++ is
 # guaranteed to depend on it. For Fortran code, Meson already adds `-lm`.
diff --git a/sktree/_lib/sklearn_fork b/sktree/_lib/sklearn_fork
index db5b137c1..b61ae3d54 160000
--- a/sktree/_lib/sklearn_fork
+++ b/sktree/_lib/sklearn_fork
@@ -1 +1 @@
-Subproject commit db5b137c1c1d2cb90aed2354dcb5b933e1df803b
+Subproject commit b61ae3d546ba4199dc3badf4bd89971d2d75e9df
diff --git a/sktree/meson.build b/sktree/meson.build
index aa46fe60f..1a0d5c4d4 100644
--- a/sktree/meson.build
+++ b/sktree/meson.build
@@ -29,6 +29,35 @@ if is_windows
   endif
 endif
 
+openmp_dep = dependency('OpenMP', language: 'c', required: false)
+
+if not openmp_dep.found()
+    warning(
+'''
+                ***********
+                * WARNING *
+                ***********
+
+It seems that scikit-tree cannot be built with OpenMP.
+
+- Make sure you have followed the installation instructions:
+
+    https://scikit-learn.org/dev/developers/advanced_installation.html
+
+- If your compiler supports OpenMP but you still see this
+  message, please submit a bug report at:
+
+    https://github.com/scikit-tree/scikit-tree/issues
+
+- The build will continue with OpenMP-based parallelism
+  disabled. Note however that some estimators will run in
+  sequential mode instead of leveraging thread-based
+  parallelism.
+
+                    ***
+''')
+endif
+
 # NumPy include directory - needed in all submodules
 incdir_numpy = run_command(py3,
   [
@@ -49,6 +78,20 @@ cc = meson.get_compiler('c')
 #   'source_fname',
 #   numpy_nodepr_api)
 numpy_nodepr_api = '-DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION'
+
+# XXX: ENABLE WHEN DEBUGGING
+boundscheck = 'False'
+
+scikit_learn_cython_args = [
+  '-X language_level=3', '-X boundscheck=' + boundscheck, '-X wraparound=False',
+  '-X initializedcheck=False', '-X nonecheck=False', '-X cdivision=True',
+  '-X profile=False',
+  # Needed for cython imports across subpackages, e.g. cluster pyx that
+  # cimports metrics pxd
+  '--include-dir', meson.global_build_root(),
+]
+cython_c_args += scikit_learn_cython_args
+
 cython_c_args += numpy_nodepr_api
 
 python_sources = [

From c8b139991510ee1fde818b71a1ab0d7a3b5e2135 Mon Sep 17 00:00:00 2001
From: Adam Li <adam2392@gmail.com>
Date: Mon, 11 Mar 2024 17:55:12 -0400
Subject: [PATCH 2/6] Fix compiling

Signed-off-by: Adam Li <adam2392@gmail.com>
---
 sktree/tree/_oblique_splitter.pxd             |  8 ++++--
 sktree/tree/_oblique_splitter.pyx             |  4 +--
 .../unsupervised/_unsup_oblique_splitter.pxd  | 28 +++++++++----------
 .../unsupervised/_unsup_oblique_splitter.pyx  |  1 -
 sktree/tree/unsupervised/_unsup_splitter.pxd  |  1 -
 sktree/tree/unsupervised/_unsup_splitter.pyx  |  7 +++--
 sktree/tree/unsupervised/_unsup_tree.pyx      | 14 +++++-----
 7 files changed, 32 insertions(+), 31 deletions(-)

diff --git a/sktree/tree/_oblique_splitter.pxd b/sktree/tree/_oblique_splitter.pxd
index 15feaea22..3f17b8c6b 100644
--- a/sktree/tree/_oblique_splitter.pxd
+++ b/sktree/tree/_oblique_splitter.pxd
@@ -30,6 +30,11 @@ cdef struct ObliqueSplitRecord:
     float64_t improvement          # Impurity improvement given parent node.
     float64_t impurity_left        # Impurity of the left split.
     float64_t impurity_right       # Impurity of the right split.
+    float64_t lower_bound       # Lower bound on value of both children for monotonicity
+    float64_t upper_bound       # Upper bound on value of both children for monotonicity
+    unsigned char missing_go_to_left  # Controls if missing values go to the left node.
+    intp_t n_missing            # Number of missing values for the feature being split on
+    intp_t n_constant_features  # Number of constant features in the split
 
     vector[float32_t]* proj_vec_weights  # weights of the vector (max_features,)
     vector[intp_t]* proj_vec_indices     # indices of the features (max_features,)
@@ -80,7 +85,6 @@ cdef class BaseObliqueSplitter(Splitter):
         self,
         float64_t impurity,   # Impurity of the node
         SplitRecord* split,
-        intp_t* n_constant_features,
         float64_t lower_bound,
         float64_t upper_bound,
     ) except -1 nogil
@@ -116,7 +120,6 @@ cdef class BestObliqueSplitter(ObliqueSplitter):
         self,
         float64_t impurity,   # Impurity of the node
         SplitRecord* split,
-        intp_t* n_constant_features,
         float64_t lower_bound,
         float64_t upper_bound,
     ) except -1 nogil
@@ -139,7 +142,6 @@ cdef class RandomObliqueSplitter(ObliqueSplitter):
         self,
         float64_t impurity,   # Impurity of the node
         SplitRecord* split,
-        intp_t* n_constant_features,
         float64_t lower_bound,
         float64_t upper_bound,
     ) except -1 nogil
diff --git a/sktree/tree/_oblique_splitter.pyx b/sktree/tree/_oblique_splitter.pyx
index aee43b1ce..23b6e722d 100644
--- a/sktree/tree/_oblique_splitter.pyx
+++ b/sktree/tree/_oblique_splitter.pyx
@@ -292,7 +292,6 @@ cdef class BestObliqueSplitter(ObliqueSplitter):
         self,
         float64_t impurity,
         SplitRecord* split,
-        intp_t* n_constant_features,
         float64_t lower_bound,
         float64_t upper_bound,
     ) except -1 nogil:
@@ -431,6 +430,7 @@ cdef class BestObliqueSplitter(ObliqueSplitter):
         deref(oblique_split).improvement = best_split.improvement
         deref(oblique_split).impurity_left = best_split.impurity_left
         deref(oblique_split).impurity_right = best_split.impurity_right
+        deref(oblique_split).n_constant_features = 0
         return 0
 
 cdef class RandomObliqueSplitter(ObliqueSplitter):
@@ -498,7 +498,6 @@ cdef class RandomObliqueSplitter(ObliqueSplitter):
         self,
         float64_t impurity,
         SplitRecord* split,
-        intp_t* n_constant_features,
         float64_t lower_bound,
         float64_t upper_bound,
     ) except -1 nogil:
@@ -656,6 +655,7 @@ cdef class RandomObliqueSplitter(ObliqueSplitter):
         deref(oblique_split).improvement = best_split.improvement
         deref(oblique_split).impurity_left = best_split.impurity_left
         deref(oblique_split).impurity_right = best_split.impurity_right
+        # deref(oblique_split).n_constant_features = 0
         return 0
 
 
diff --git a/sktree/tree/unsupervised/_unsup_oblique_splitter.pxd b/sktree/tree/unsupervised/_unsup_oblique_splitter.pxd
index 1e65a49b1..d2b47fde7 100644
--- a/sktree/tree/unsupervised/_unsup_oblique_splitter.pxd
+++ b/sktree/tree/unsupervised/_unsup_oblique_splitter.pxd
@@ -6,22 +6,23 @@ from libcpp.vector cimport vector
 from ..._lib.sklearn.tree._splitter cimport SplitRecord
 from ..._lib.sklearn.tree._utils cimport UINT32_t
 from ..._lib.sklearn.utils._typedefs cimport float32_t, float64_t, intp_t
+from .._oblique_splitter cimport ObliqueSplitRecord
 from ._unsup_splitter cimport UnsupervisedSplitter
 
+# cdef struct ObliqueSplitRecord:
+#     # Data to track sample split
+#     intp_t feature              # Which feature to split on.
+#     intp_t pos                  # Split samples array at the given position,
+#     #                           # i.e. count of samples below threshold for feature.
+#     #                           # pos is >= end if the node is a leaf.
+#     float64_t threshold            # Threshold to split at.
+#     float64_t improvement          # Impurity improvement given parent node.
+#     float64_t impurity_left        # Impurity of the left split.
+#     float64_t impurity_right       # Impurity of the right split.
+#     intp_t n_constant_features   # Number of constant features in the split.
 
-cdef struct ObliqueSplitRecord:
-    # Data to track sample split
-    intp_t feature              # Which feature to split on.
-    intp_t pos                  # Split samples array at the given position,
-    #                           # i.e. count of samples below threshold for feature.
-    #                           # pos is >= end if the node is a leaf.
-    float64_t threshold            # Threshold to split at.
-    float64_t improvement          # Impurity improvement given parent node.
-    float64_t impurity_left        # Impurity of the left split.
-    float64_t impurity_right       # Impurity of the right split.
-
-    vector[float32_t]* proj_vec_weights   # weights of the vector (max_features,)
-    vector[intp_t]* proj_vec_indices    # indices of the features (max_features,)
+#     vector[float32_t]* proj_vec_weights   # weights of the vector (max_features,)
+#     vector[intp_t]* proj_vec_indices    # indices of the features (max_features,)
 
 
 cdef class UnsupervisedObliqueSplitter(UnsupervisedSplitter):
@@ -56,7 +57,6 @@ cdef class UnsupervisedObliqueSplitter(UnsupervisedSplitter):
         self,
         float64_t impurity,   # Impurity of the node
         SplitRecord* split,
-        intp_t* n_constant_features,
         float64_t lower_bound,
         float64_t upper_bound
     ) except -1 nogil
diff --git a/sktree/tree/unsupervised/_unsup_oblique_splitter.pyx b/sktree/tree/unsupervised/_unsup_oblique_splitter.pyx
index 53b2bbd43..3770b11c8 100644
--- a/sktree/tree/unsupervised/_unsup_oblique_splitter.pyx
+++ b/sktree/tree/unsupervised/_unsup_oblique_splitter.pyx
@@ -246,7 +246,6 @@ cdef class BestObliqueUnsupervisedSplitter(UnsupervisedObliqueSplitter):
         self,
         float64_t impurity,
         SplitRecord* split,
-        intp_t* n_constant_features,
         float64_t lower_bound,
         float64_t upper_bound,
     ) except -1 nogil:
diff --git a/sktree/tree/unsupervised/_unsup_splitter.pxd b/sktree/tree/unsupervised/_unsup_splitter.pxd
index 6a172dc4e..48bfe9a54 100644
--- a/sktree/tree/unsupervised/_unsup_splitter.pxd
+++ b/sktree/tree/unsupervised/_unsup_splitter.pxd
@@ -41,7 +41,6 @@ cdef class UnsupervisedSplitter(BaseSplitter):
         self,
         float64_t impurity,   # Impurity of the node
         SplitRecord* split,
-        intp_t* n_constant_features,
         float64_t lower_bound,
         float64_t upper_bound
     ) except -1 nogil
diff --git a/sktree/tree/unsupervised/_unsup_splitter.pyx b/sktree/tree/unsupervised/_unsup_splitter.pyx
index ca5fd0349..dafb950e1 100644
--- a/sktree/tree/unsupervised/_unsup_splitter.pyx
+++ b/sktree/tree/unsupervised/_unsup_splitter.pyx
@@ -178,7 +178,6 @@ cdef class BestUnsupervisedSplitter(UnsupervisedSplitter):
         self,
         float64_t impurity,
         SplitRecord* split,
-        intp_t* n_constant_features,
         float64_t lower_bound,
         float64_t upper_bound
     ) except -1 nogil:
@@ -225,7 +224,8 @@ cdef class BestUnsupervisedSplitter(UnsupervisedSplitter):
         cdef intp_t n_found_constants = 0
         # Number of features known to be constant and drawn without replacement
         cdef intp_t n_drawn_constants = 0
-        cdef intp_t n_known_constants = n_constant_features[0]
+        cdef intp_t n_known_constants = split.n_constant_features
+        # n_constant_features[0]
         # n_total_constants = n_known_constants + n_found_constants
         cdef intp_t n_total_constants = n_known_constants
         cdef intp_t partition_end
@@ -381,5 +381,6 @@ cdef class BestUnsupervisedSplitter(UnsupervisedSplitter):
 
         # Return values
         split[0] = best_split
-        n_constant_features[0] = n_total_constants
+        split.n_constant_features = n_total_constants
+        # n_constant_features[0] = n_total_constants
         return 0
diff --git a/sktree/tree/unsupervised/_unsup_tree.pyx b/sktree/tree/unsupervised/_unsup_tree.pyx
index 1236afcfc..46e9dc596 100644
--- a/sktree/tree/unsupervised/_unsup_tree.pyx
+++ b/sktree/tree/unsupervised/_unsup_tree.pyx
@@ -307,7 +307,8 @@ cdef class UnsupervisedBestFirstTreeBuilder(UnsupervisedTreeBuilder):
 
         cdef intp_t node_id
         cdef intp_t n_node_samples
-        cdef intp_t n_constant_features = 0
+        # cdef intp_t n_constant_features = 0
+        split_ptr.n_constant_features = 0
         cdef float64_t min_impurity_decrease = self.min_impurity_decrease
         cdef float64_t weighted_n_node_samples
         cdef bint is_leaf
@@ -326,7 +327,7 @@ cdef class UnsupervisedBestFirstTreeBuilder(UnsupervisedTreeBuilder):
                    )
 
         if not is_leaf:
-            splitter.node_split(impurity, split_ptr, &n_constant_features, 0., 0.)
+            splitter.node_split(impurity, split_ptr, 0., 0.)
 
             # assign local copy of SplitRecord to assign
             # pos, improvement, and impurity scores
@@ -443,7 +444,6 @@ cdef class UnsupervisedDepthFirstTreeBuilder(UnsupervisedTreeBuilder):
         cdef SplitRecord* split_ptr = <SplitRecord *>malloc(splitter.pointer_size())
 
         cdef float64_t impurity = INFINITY
-        cdef intp_t n_constant_features
         cdef bint is_leaf
         cdef bint first = 1
         cdef intp_t max_depth_seen = -1
@@ -473,7 +473,7 @@ cdef class UnsupervisedDepthFirstTreeBuilder(UnsupervisedTreeBuilder):
                 parent = stack_record.parent
                 is_left = stack_record.is_left
                 impurity = stack_record.impurity
-                n_constant_features = stack_record.n_constant_features
+                split_ptr.n_constant_features = stack_record.n_constant_features
 
                 n_node_samples = end - start
                 splitter.node_reset(start, end, &weighted_n_node_samples)
@@ -492,7 +492,7 @@ cdef class UnsupervisedDepthFirstTreeBuilder(UnsupervisedTreeBuilder):
                 is_leaf = is_leaf or impurity <= EPSILON
 
                 if not is_leaf:
-                    splitter.node_split(impurity, split_ptr, &n_constant_features, 0., 0.)
+                    splitter.node_split(impurity, split_ptr, 0., 0.)
 
                     # assign local copy of SplitRecord to assign
                     # pos, improvement, and impurity scores
@@ -525,7 +525,7 @@ cdef class UnsupervisedDepthFirstTreeBuilder(UnsupervisedTreeBuilder):
                         "parent": node_id,
                         "is_left": 0,
                         "impurity": split.impurity_right,
-                        "n_constant_features": n_constant_features})
+                        "n_constant_features": split.n_constant_features})
 
                     # Push left child on stack
                     builder_stack.push({
@@ -535,7 +535,7 @@ cdef class UnsupervisedDepthFirstTreeBuilder(UnsupervisedTreeBuilder):
                         "parent": node_id,
                         "is_left": 1,
                         "impurity": split.impurity_left,
-                        "n_constant_features": n_constant_features})
+                        "n_constant_features": split.n_constant_features})
 
                 if depth > max_depth_seen:
                     max_depth_seen = depth

From 7c756776fbaaf7b97390d30004322edf53f3c29d Mon Sep 17 00:00:00 2001
From: Adam Li <adam2392@gmail.com>
Date: Wed, 13 Mar 2024 15:09:27 -0400
Subject: [PATCH 3/6] Try compiling here

Signed-off-by: Adam Li <adam2392@gmail.com>
---
 meson.build                                   | 30 ++++++----
 sktree/__init__.py                            |  1 +
 sktree/_build_utils/cythoner.py               | 40 -------------
 sktree/_lib/meson.build                       | 60 ++++++++++++-------
 sktree/datasets/meson.build                   |  2 +-
 sktree/datasets/tests/meson.build             |  2 +-
 sktree/ensemble/meson.build                   |  2 +-
 sktree/experimental/meson.build               |  2 +-
 sktree/experimental/tests/meson.build         |  2 +-
 sktree/meson.build                            | 54 ++++++++---------
 sktree/stats/meson.build                      |  2 +-
 sktree/stats/tests/meson.build                |  2 +-
 sktree/tests/meson.build                      |  2 +-
 sktree/tree/_oblique_tree.pxd                 |  2 +-
 sktree/tree/manifold/meson.build              | 25 ++++----
 sktree/tree/meson.build                       | 41 ++++++++-----
 sktree/tree/tests/meson.build                 |  2 +-
 .../tree/unsupervised/_unsup_oblique_tree.pxd |  2 +-
 sktree/tree/unsupervised/meson.build          | 41 ++++++++-----
 19 files changed, 162 insertions(+), 152 deletions(-)
 delete mode 100644 sktree/_build_utils/cythoner.py

diff --git a/meson.build b/meson.build
index 26048bb3d..58deed348 100644
--- a/meson.build
+++ b/meson.build
@@ -29,11 +29,17 @@ elif cc.get_id() == 'msvc'
   endif
 endif
 
+# Suppress warning for deprecated Numpy API.
+# (Suppress warning messages emitted by #warning directives).
+# Replace with numpy_nodepr_api after Cython 3.0 is out
+# '-Wno-maybe-uninitialized'
+# numpy_nodepr_api = '-DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION'
 _global_c_args = cc.get_supported_arguments(
   '-Wno-unused-but-set-variable',
   '-Wno-unused-function',
   '-Wno-conversion',
   '-Wno-misleading-indentation',
+  '-DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION',
 )
 add_project_arguments(_global_c_args, language : 'c')
 
@@ -58,22 +64,22 @@ r = run_command('mv', 'sktree/_lib/sklearn_fork/sklearn', 'sktree/_lib/sklearn',
 
 # Setup Python:
 # https://mesonbuild.com/Python-module.html
-py3_mod = import('python')
+py = import('python').find_installation(pure: false)
+# py3_mod = import('python')
 
-# NOTE: with Meson >=0.64.0 we can add `pure: false` here and remove that line
-# everywhere else, see https://github.com/mesonbuild/meson/pull/10783.
-py3 = py3_mod.find_installation(
-  'python3',
-  pure: false  # Will be installed next to binaries
-)
-# py3.install_env('venv')
+# # NOTE: with Meson >=0.64.0 we can add `pure: false` here and remove that line
+# # everywhere else, see https://github.com/mesonbuild/meson/pull/10783.
+# py3 = py3_mod.find_installation(
+#   'python3',
+#   pure: false  # Will be installed next to binaries
+# )
+# py.install_env('venv')
 
 # print some debugging output
-message(py3.full_path())
-message(py3.get_install_dir())
-if py3.language_version().version_compare('<3.9')
+message(py.full_path())
+message(py.get_install_dir())
+if py.language_version().version_compare('<3.9')
     error('At least Python 3.9 is required.')
 endif
-py3_dep = py3.dependency()
 
 subdir('sktree')
diff --git a/sktree/__init__.py b/sktree/__init__.py
index 9be0aff3b..793895f86 100644
--- a/sktree/__init__.py
+++ b/sktree/__init__.py
@@ -4,6 +4,7 @@
 import os
 import sys
 
+print("using current cython branch.")
 __version__ = "0.8.0dev0"
 logger = logging.getLogger(__name__)
 
diff --git a/sktree/_build_utils/cythoner.py b/sktree/_build_utils/cythoner.py
deleted file mode 100644
index ff3481064..000000000
--- a/sktree/_build_utils/cythoner.py
+++ /dev/null
@@ -1,40 +0,0 @@
-#!python
-""" Scipy variant of Cython command
-
-Cython, as applied to single pyx file.
-Expects two arguments, infile and outfile.
-Other options passed through to cython command line parser.
-"""
-
-import os
-import os.path as op
-import subprocess as sbp
-import sys
-
-
-def main():
-    in_fname, out_fname = (op.abspath(p) for p in sys.argv[1:3])
-
-    print("\n\ninside cythoner: ")
-    print("input file: ", in_fname)
-    print("output file: ", out_fname)
-    print(os.getcwd(), "\n\n")
-
-    sbp.run(
-        [
-            "cython",
-            "-3",
-            "--fast-fail",
-            "--output-file",
-            out_fname,
-            "--include-dir",
-            f"{os.getcwd()}",
-        ]
-        + sys.argv[3:]
-        + [in_fname],
-        check=True,
-    )
-
-
-if __name__ == "__main__":
-    main()
diff --git a/sktree/_lib/meson.build b/sktree/_lib/meson.build
index 10dade643..9e8c01786 100644
--- a/sktree/_lib/meson.build
+++ b/sktree/_lib/meson.build
@@ -4,20 +4,31 @@ if not fs.exists('sklearn')
 endif
 
 # install tree/ submodule
-extensions = [
-  '_tree',
-  '_utils',
-  '_criterion',
-  '_splitter',
-]
+tree_extension_metadata = {
+  '_tree':
+    {'sources': ['./sklearn/tree/' + '_tree.pyx'],
+     'override_options': ['cython_language=cpp', 'optimization=3']},
+  '_splitter':
+    {'sources': ['./sklearn/tree/' + '_splitter.pyx'],
+     'override_options': ['cython_language=cpp', 'optimization=3']},
+  '_criterion':
+    {'sources': ['./sklearn/tree/' + '_criterion.pyx'],
+     'override_options': ['cython_language=cpp', 'optimization=3']},
+  '_utils':
+    {'sources': ['./sklearn/tree/' + '_utils.pyx'],
+     'override_options': ['cython_language=cpp', 'optimization=3']},
+}
 
-foreach ext: extensions
-  py3.extension_module(ext,
-    cython_gen_cpp.process('./sklearn/tree/' + ext + '.pyx'),
-    c_args: cython_c_args,
-    include_directories: [incdir_numpy,],
-    install: true,
+
+foreach ext_name, ext_dict : tree_extension_metadata
+  py.extension_module(
+    ext_name,
+    ext_dict.get('sources'),
+    dependencies: [np_dep],
+    override_options : ext_dict.get('override_options', []),
+    cython_args: cython_c_args,
     subdir: 'sktree/_lib/sklearn/tree/',
+    install: true
   )
 endforeach
 
@@ -28,7 +39,7 @@ python_sources = [
   './sklearn/tree/_reingold_tilford.py',
 ]
 
-py3.install_sources(
+py.install_sources(
   python_sources,
   subdir: 'sktree/_lib/sklearn/tree'   # Folder relative to site-packages to install to
 )
@@ -38,7 +49,7 @@ python_sources = [
   '_forest.py',
 ]
 foreach py_source: python_sources
-  py3.install_sources(
+  py.install_sources(
     './sklearn/ensemble/' + py_source,
     subdir: 'sktree/_lib/sklearn/ensemble'
   )
@@ -51,10 +62,13 @@ extensions = [
 ]
 
 foreach ext: extensions
-  py3.extension_module(ext,
-    cython_gen_cpp.process('./sklearn/neighbors/' + ext + '.pyx'),
-    c_args: cython_c_args,
-    include_directories: [incdir_numpy,],
+  py.extension_module(
+    ext,
+    ['./sklearn/neighbors/' + ext + '.pyx'],
+    c_args: c_args,
+    dependencies: [np_dep],
+    cython_args: cython_c_args,
+    override_options : ['optimization=3', 'cython_language=cpp'],
     install: true,
     subdir: 'sktree/_lib/sklearn/neighbors/',
   )
@@ -67,10 +81,12 @@ extensions = [
 ]
 
 foreach ext: extensions
-  py3.extension_module(ext,
-    cython_gen_cpp.process('./sklearn/utils/' + ext + '.pyx'),
-    c_args: cython_c_args,
-    include_directories: [incdir_numpy,],
+  py.extension_module(ext,
+    ['./sklearn/utils/' + ext + '.pyx'],
+    c_args: c_args,
+    dependencies: [np_dep],
+    cython_args: cython_c_args,
+    override_options : ['optimization=3', 'cython_language=cpp'],
     install: true,
     subdir: 'sktree/_lib/sklearn/utils/',
   )
diff --git a/sktree/datasets/meson.build b/sktree/datasets/meson.build
index 8bd2882ff..4a5539827 100644
--- a/sktree/datasets/meson.build
+++ b/sktree/datasets/meson.build
@@ -4,7 +4,7 @@ python_sources = [
   'hyppo.py',
 ]
 
-py3.install_sources(
+py.install_sources(
   python_sources,
   pure: false,
   subdir: 'sktree/datasets'
diff --git a/sktree/datasets/tests/meson.build b/sktree/datasets/tests/meson.build
index 79b1833da..d450c3488 100644
--- a/sktree/datasets/tests/meson.build
+++ b/sktree/datasets/tests/meson.build
@@ -4,7 +4,7 @@ python_sources = [
   'test_multiview.py',
 ]
 
-py3.install_sources(
+py.install_sources(
   python_sources,
   pure: false,
   subdir: 'sktree/datasets/tests'
diff --git a/sktree/ensemble/meson.build b/sktree/ensemble/meson.build
index c5801c904..0e0cdf092 100644
--- a/sktree/ensemble/meson.build
+++ b/sktree/ensemble/meson.build
@@ -8,7 +8,7 @@ python_sources = [
   '_extensions.py',
 ]
 
-py3.install_sources(
+py.install_sources(
   python_sources,
   pure: false,
   subdir: 'sktree/ensemble'
diff --git a/sktree/experimental/meson.build b/sktree/experimental/meson.build
index 2d1dde609..4dbbc4acc 100644
--- a/sktree/experimental/meson.build
+++ b/sktree/experimental/meson.build
@@ -6,7 +6,7 @@ python_sources = [
   'monte_carlo.py',
 ]
 
-py3.install_sources(
+py.install_sources(
   python_sources,
   pure: false,
   subdir: 'sktree/experimental'
diff --git a/sktree/experimental/tests/meson.build b/sktree/experimental/tests/meson.build
index c3fdd07c4..e3bbc474e 100644
--- a/sktree/experimental/tests/meson.build
+++ b/sktree/experimental/tests/meson.build
@@ -6,7 +6,7 @@ python_sources = [
   'test_monte_carlo.py',
 ]
 
-py3.install_sources(
+py.install_sources(
   python_sources,
   pure: false,
   subdir: 'sktree/experimental/tests'
diff --git a/sktree/meson.build b/sktree/meson.build
index 1a0d5c4d4..c719ffa36 100644
--- a/sktree/meson.build
+++ b/sktree/meson.build
@@ -2,6 +2,7 @@
 is_windows = host_machine.system() == 'windows'
 is_mingw = is_windows and cc.get_id() == 'gcc'
 
+c_args = []
 cython_c_args = []
 if is_windows
   # For mingw-w64, link statically against the UCRT.
@@ -59,14 +60,27 @@ It seems that scikit-tree cannot be built with OpenMP.
 endif
 
 # NumPy include directory - needed in all submodules
-incdir_numpy = run_command(py3,
-  [
-    '-c',
-    'import os; os.chdir(".."); import numpy; print(numpy.get_include())'
-  ],
-  check: true
-).stdout().strip()
-# inc_np = include_directories(incdir_numpy)
+incdir_numpy = meson.get_external_property('numpy-include-dir', 'not-given')
+if incdir_numpy == 'not-given'
+  incdir_numpy = run_command(py,
+    [
+      '-c',
+      '''
+import os
+import numpy as np
+try:
+  incdir = os.path.relpath(np.get_include())
+except Exception:
+  incdir = np.get_include()
+print(incdir)
+'''
+    ],
+    check: true
+  ).stdout().strip()
+endif
+
+inc_np = include_directories(incdir_numpy)
+np_dep = declare_dependency(include_directories: inc_np)
 
 cc = meson.get_compiler('c')
 
@@ -74,7 +88,7 @@ cc = meson.get_compiler('c')
 # NPY_API_VERSION in order not to break compilation for released versions
 # when NumPy introduces a new deprecation. Use in a meson.build file::
 #
-# py3.extension_module('_name',
+# py.extension_module('_name',
 #   'source_fname',
 #   numpy_nodepr_api)
 numpy_nodepr_api = '-DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION'
@@ -92,7 +106,7 @@ scikit_learn_cython_args = [
 ]
 cython_c_args += scikit_learn_cython_args
 
-cython_c_args += numpy_nodepr_api
+c_args += numpy_nodepr_api
 
 python_sources = [
   '__init__.py',
@@ -100,29 +114,11 @@ python_sources = [
   'conftest.py',
 ]
 
-py3.install_sources(
+py.install_sources(
   python_sources,
   subdir: 'sktree'
 )
 
-cython_cli = find_program('_build_utils/cythoner.py')
-
-cython_gen = generator(cython_cli,
-  arguments : ['@INPUT@', '@OUTPUT@'],
-  output : '@BASENAME@.c')
-
-cython_gen_cpp = generator(cython_cli,
-  arguments : ['@INPUT@', '@OUTPUT@', '--cplus'],
-  output : '@BASENAME@.cpp')
-
-c_undefined_ok = ['-Wno-maybe-uninitialized']
-
-# Suppress warning for deprecated Numpy API.
-# (Suppress warning messages emitted by #warning directives).
-# Replace with numpy_nodepr_api after Cython 3.0 is out
-cython_c_args += ['-Wno-cpp']
-cython_cpp_args = cython_c_args
-
 subdir('_lib')
 subdir('ensemble')
 subdir('experimental')
diff --git a/sktree/stats/meson.build b/sktree/stats/meson.build
index 5234538ec..b99353c80 100644
--- a/sktree/stats/meson.build
+++ b/sktree/stats/meson.build
@@ -7,7 +7,7 @@ python_sources = [
   'permuteforest.py',
 ]
 
-py3.install_sources(
+py.install_sources(
   python_sources,
   pure: false,
   subdir: 'sktree/stats'
diff --git a/sktree/stats/tests/meson.build b/sktree/stats/tests/meson.build
index 27a38d8b7..e4be1f212 100644
--- a/sktree/stats/tests/meson.build
+++ b/sktree/stats/tests/meson.build
@@ -6,7 +6,7 @@ python_sources = [
   'test_permuteforest.py',
 ]
 
-py3.install_sources(
+py.install_sources(
   python_sources,
   pure: false,
   subdir: 'sktree/stats/tests'
diff --git a/sktree/tests/meson.build b/sktree/tests/meson.build
index b3b8ce8eb..d9baa3418 100644
--- a/sktree/tests/meson.build
+++ b/sktree/tests/meson.build
@@ -9,7 +9,7 @@ python_sources = [
   'test_extensions.py',
 ]
 
-py3.install_sources(
+py.install_sources(
   python_sources,
   pure: false,
   subdir: 'sktree/tests'
diff --git a/sktree/tree/_oblique_tree.pxd b/sktree/tree/_oblique_tree.pxd
index 50c7949bf..b94531813 100644
--- a/sktree/tree/_oblique_tree.pxd
+++ b/sktree/tree/_oblique_tree.pxd
@@ -33,7 +33,7 @@ cdef class ObliqueTree(Tree):
         SplitRecord* split_node,
         Node *node,
         intp_t node_id
-    )  nogil except -1
+    )  except -1 nogil
     cdef float32_t _compute_feature(
         self,
         const float32_t[:, :] X_ndarray,
diff --git a/sktree/tree/manifold/meson.build b/sktree/tree/manifold/meson.build
index 4e1ae7b85..91ed92a3d 100644
--- a/sktree/tree/manifold/meson.build
+++ b/sktree/tree/manifold/meson.build
@@ -1,18 +1,23 @@
-extensions = [
-    '_morf_splitter',
-]
+tree_extension_metadata = {
+  '_morf_splitter':
+    {'sources': ['_morf_splitter.pyx'],
+     'override_options': ['cython_language=cpp', 'optimization=3']},
+}
 
-foreach ext: extensions
-  py3.extension_module(ext,
-    cython_gen_cpp.process(ext + '.pyx'),
-    c_args: cython_c_args,
-    include_directories: [incdir_numpy],
-    install: true,
+foreach ext_name, ext_dict : tree_extension_metadata
+  py.extension_module(
+    ext_name,
+    ext_dict.get('sources'),
+    dependencies: [np_dep],
+    override_options : ext_dict.get('override_options', []),
+    c_args: c_args,
+    cython_args: cython_c_args,
     subdir: 'sktree/tree/manifold',
+    install: true,
   )
 endforeach
 
 
-py3.install_sources(
+py.install_sources(
   subdir: 'sktree/tree/manifold'   # Folder relative to site-packages to install to
 )
diff --git a/sktree/tree/meson.build b/sktree/tree/meson.build
index cc13bc1b4..9737016af 100644
--- a/sktree/tree/meson.build
+++ b/sktree/tree/meson.build
@@ -1,18 +1,31 @@
-extensions = [
-  '_sklearn_splitter',
-  '_oblique_splitter',
-  '_oblique_tree',
-  '_utils',
-  '_marginal',
-]
+tree_extension_metadata = {
+  '_sklearn_splitter':
+    {'sources': ['_sklearn_splitter.pyx'],
+     'override_options': ['cython_language=cpp', 'optimization=3']},
+  '_oblique_splitter':
+    {'sources': ['_oblique_splitter.pyx'],
+     'override_options': ['cython_language=cpp', 'optimization=3']},
+  '_oblique_tree':
+    {'sources': ['_oblique_tree.pyx'],
+     'override_options': ['cython_language=cpp', 'optimization=3']},
+  '_utils':
+    {'sources': ['_utils.pyx'],
+     'override_options': ['cython_language=cpp', 'optimization=3']},
+  '_marginal':
+    {'sources': ['_marginal.pyx'],
+     'override_options': ['cython_language=cpp', 'optimization=3']},
+}
 
-foreach ext: extensions
-  py3.extension_module(ext,
-    cython_gen_cpp.process(ext + '.pyx'),
-    c_args: cython_c_args,
-    include_directories: [incdir_numpy],
-    install: true,
+foreach ext_name, ext_dict : tree_extension_metadata
+  py.extension_module(
+    ext_name,
+    ext_dict.get('sources'),
+    dependencies: [np_dep],
+    override_options : ext_dict.get('override_options', []),
+    c_args: c_args,
+    cython_args: cython_c_args,
     subdir: 'sktree/tree',
+    install: true,
   )
 endforeach
 
@@ -25,7 +38,7 @@ python_sources = [
   '_marginalize.py',
 ]
 
-py3.install_sources(
+py.install_sources(
   python_sources,
   subdir: 'sktree/tree'   # Folder relative to site-packages to install to
 )
diff --git a/sktree/tree/tests/meson.build b/sktree/tree/tests/meson.build
index c88eeda7c..44717eb2a 100644
--- a/sktree/tree/tests/meson.build
+++ b/sktree/tree/tests/meson.build
@@ -9,7 +9,7 @@ python_sources = [
   'test_multiview.py',
 ]
 
-py3.install_sources(
+py.install_sources(
   python_sources,
   pure: false,
   subdir: 'sktree/tree/tests'
diff --git a/sktree/tree/unsupervised/_unsup_oblique_tree.pxd b/sktree/tree/unsupervised/_unsup_oblique_tree.pxd
index 5292551b9..93b50600a 100644
--- a/sktree/tree/unsupervised/_unsup_oblique_tree.pxd
+++ b/sktree/tree/unsupervised/_unsup_oblique_tree.pxd
@@ -32,7 +32,7 @@ cdef class UnsupervisedObliqueTree(UnsupervisedTree):
         SplitRecord* split_node,
         Node *node,
         intp_t node_id,
-    )  nogil except -1
+    )  except -1 nogil
     cdef float32_t _compute_feature(
         self,
         const float32_t[:, :] X_ndarray,
diff --git a/sktree/tree/unsupervised/meson.build b/sktree/tree/unsupervised/meson.build
index bf87d72df..0d9534e9d 100644
--- a/sktree/tree/unsupervised/meson.build
+++ b/sktree/tree/unsupervised/meson.build
@@ -1,22 +1,35 @@
-extensions = [
-  '_unsup_criterion',
-  '_unsup_splitter',
-  '_unsup_tree',
-  '_unsup_oblique_splitter',
-  '_unsup_oblique_tree',
-]
+tree_extension_metadata = {
+  '_unsup_criterion':
+    {'sources': ['_unsup_criterion.pyx'],
+     'override_options': ['cython_language=cpp', 'optimization=3']},
+  '_unsup_splitter':
+    {'sources': ['_unsup_splitter.pyx'],
+     'override_options': ['cython_language=cpp', 'optimization=3']},
+  '_unsup_tree':
+    {'sources': ['_unsup_tree.pyx'],
+     'override_options': ['cython_language=cpp', 'optimization=3']},
+  '_unsup_oblique_splitter':
+    {'sources': ['_unsup_oblique_splitter.pyx'],
+     'override_options': ['cython_language=cpp', 'optimization=3']},
+  '_unsup_oblique_tree':
+    {'sources': ['_unsup_oblique_tree.pyx'],
+     'override_options': ['cython_language=cpp', 'optimization=3']},
+}
 
-foreach ext: extensions
-  py3.extension_module(ext,
-    cython_gen_cpp.process(ext + '.pyx'),
-    c_args: cython_c_args,
-    include_directories: [incdir_numpy],
-    install: true,
+foreach ext_name, ext_dict : tree_extension_metadata
+  py.extension_module(
+    ext_name,
+    ext_dict.get('sources'),
+    dependencies: [np_dep],
+    override_options : ext_dict.get('override_options', []),
+    c_args: c_args,
+    cython_args: cython_c_args,
     subdir: 'sktree/tree/unsupervised',
+    install: true,
   )
 endforeach
 
 
-py3.install_sources(
+py.install_sources(
   subdir: 'sktree/tree/unsupervised'   # Folder relative to site-packages to install to
 )

From f8c31049b277d5e0e05b3a43a680d4455572bf5b Mon Sep 17 00:00:00 2001
From: Adam Li <adam2392@gmail.com>
Date: Wed, 13 Mar 2024 15:49:06 -0400
Subject: [PATCH 4/6] Adding changelog

Signed-off-by: Adam Li <adam2392@gmail.com>
---
 doc/whats_new/v0.8.rst | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/doc/whats_new/v0.8.rst b/doc/whats_new/v0.8.rst
index 2637a0cf8..0da140f70 100644
--- a/doc/whats_new/v0.8.rst
+++ b/doc/whats_new/v0.8.rst
@@ -14,6 +14,11 @@ Changelog
 ---------
 - |Fix| Trunk simulators now correctly generate random values with a fixed seed,
     by `Sambit Panda`_ (:pr:`#236`)
+- |Efficiency| All scikit-tree estimators are now at least 2X faster than they were
+    in previous versions. This was due to adding in compiler-directives to turn on 
+    optimizations '-03' when compiling the C++ generated code from Cython. In addition,
+    we explicitly turned off bounds-checking and related runtime checks in the Cython code,
+    which would lead to performance degradation during runtime. by `Adam Li`_ (:pr:`#242`)
 
 Code and Documentation Contributors
 -----------------------------------

From 1fb9dc740280a9df944724edbc7dc737e5ddd576 Mon Sep 17 00:00:00 2001
From: Adam Li <adam2392@gmail.com>
Date: Wed, 13 Mar 2024 15:55:42 -0400
Subject: [PATCH 5/6] Clean up meson build

Signed-off-by: Adam Li <adam2392@gmail.com>
---
 meson.build | 12 ++----------
 1 file changed, 2 insertions(+), 10 deletions(-)

diff --git a/meson.build b/meson.build
index 58deed348..822d2413d 100644
--- a/meson.build
+++ b/meson.build
@@ -30,10 +30,11 @@ elif cc.get_id() == 'msvc'
 endif
 
 # Suppress warning for deprecated Numpy API.
-# (Suppress warning messages emitted by #warning directives).
 # Replace with numpy_nodepr_api after Cython 3.0 is out
 # '-Wno-maybe-uninitialized'
 # numpy_nodepr_api = '-DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION'
+
+# (Suppress warning messages emitted by #warning directives).
 _global_c_args = cc.get_supported_arguments(
   '-Wno-unused-but-set-variable',
   '-Wno-unused-function',
@@ -65,15 +66,6 @@ r = run_command('mv', 'sktree/_lib/sklearn_fork/sklearn', 'sktree/_lib/sklearn',
 # Setup Python:
 # https://mesonbuild.com/Python-module.html
 py = import('python').find_installation(pure: false)
-# py3_mod = import('python')
-
-# # NOTE: with Meson >=0.64.0 we can add `pure: false` here and remove that line
-# # everywhere else, see https://github.com/mesonbuild/meson/pull/10783.
-# py3 = py3_mod.find_installation(
-#   'python3',
-#   pure: false  # Will be installed next to binaries
-# )
-# py.install_env('venv')
 
 # print some debugging output
 message(py.full_path())

From d3f36ebef5f6780afac062a65ec9bbc0319e8119 Mon Sep 17 00:00:00 2001
From: Adam Li <adam2392@gmail.com>
Date: Wed, 13 Mar 2024 16:06:04 -0400
Subject: [PATCH 6/6] Fix windows wheels

Signed-off-by: Adam Li <adam2392@gmail.com>
---
 sktree/meson.build | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sktree/meson.build b/sktree/meson.build
index c719ffa36..7da2e8a17 100644
--- a/sktree/meson.build
+++ b/sktree/meson.build
@@ -26,7 +26,7 @@ if is_windows
     # Silence warnings emitted by PyOS_snprintf for (%zd), see
     # https://github.com/rgommers/scipy/issues/118.
     # Use as c_args for extensions containing Cython code
-    cython_c_args += ['-Wno-format-extra-args', '-Wno-format']
+    c_args += ['-Wno-format-extra-args', '-Wno-format']
   endif
 endif