From f137de005216cfc5476184c9bfa6c033b5621447 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Cl=C3=A9ment=20Robert?= <cr52@protonmail.com>
Date: Fri, 28 Jul 2023 14:44:22 +0200
Subject: [PATCH] BLD: switch to Cython 3.0, forbid deprecated Numpy C API in
 generated code

---
 pyproject.toml                                |  4 +---
 setup.py                                      | 22 +++++++++++++++++--
 .../rockstar/rockstar_interface.pyx           |  4 ++--
 3 files changed, 23 insertions(+), 7 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 1f2f54e7..ab9e13a4 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,9 +1,7 @@
 [build-system]
 requires = [
   "setuptools>=61.2",
-  # see https://github.com/numpy/numpy/pull/18389
-  "wheel>=0.36.2",
-  "Cython>=0.29.21,<3.0",
+  "Cython>=3.0",
   "oldest-supported-numpy",
 ]
 
diff --git a/setup.py b/setup.py
index 838871dd..44616f03 100644
--- a/setup.py
+++ b/setup.py
@@ -41,11 +41,15 @@ def get_version(filename):
 else:
     std_libs = ["m"]
 
+
+define_macros = [("NPY_NO_DEPRECATED_API", "NPY_1_7_API_VERSION")]
+
 cython_extensions = [
     Extension(
         "yt_astro_analysis.ppv_cube.ppv_utils",
         ["yt_astro_analysis/ppv_cube/ppv_utils.pyx"],
         libraries=std_libs,
+        define_macros=define_macros,
     ),
 ]
 
@@ -57,10 +61,12 @@ def get_version(filename):
             "yt_astro_analysis/halo_analysis/halo_finding/fof/kd.c",
         ],
         libraries=std_libs,
+        define_macros=define_macros,
     ),
     Extension(
         "yt_astro_analysis.halo_analysis.halo_finding.hop.EnzoHop",
         glob.glob("yt_astro_analysis/halo_analysis/halo_finding/hop/*.c"),
+        define_macros=define_macros,
     ),
 ]
 
@@ -80,10 +86,12 @@ def get_version(filename):
         Extension(
             "yt_astro_analysis.halo_analysis.halo_finding.rockstar.rockstar_interface",
             sources=[os.path.join(rockstar_extdir, "rockstar_interface.pyx")],
+            define_macros=define_macros,
         ),
         Extension(
             "yt_astro_analysis.halo_analysis.halo_finding.rockstar.rockstar_groupies",
             sources=[os.path.join(rockstar_extdir, "rockstar_groupies.pyx")],
+            define_macros=define_macros,
         ),
     ]
     for ext in rockstar_extensions:
@@ -94,13 +102,20 @@ def get_version(filename):
     extensions += rockstar_extensions
 
 
+CYTHONIZE_KWARGS = {
+    "compiler_directives": {"language_level": 3},
+}
+
+
 class build_ext(_build_ext):
     # subclass setuptools extension builder to avoid importing cython and numpy
     # at top level in setup.py. See http://stackoverflow.com/a/21621689/1382869
     def finalize_options(self):
         from Cython.Build import cythonize
 
-        self.distribution.ext_modules[:] = cythonize(self.distribution.ext_modules)
+        self.distribution.ext_modules[:] = cythonize(
+            self.distribution.ext_modules, **CYTHONIZE_KWARGS
+        )
         _build_ext.finalize_options(self)
         # Prevent numpy from thinking it is still in its setup process
         # see http://stackoverflow.com/a/21621493/1382869
@@ -123,7 +138,10 @@ def run(self):
         # Make sure the compiled Cython files in the distribution are up-to-date
         from Cython.Build import cythonize
 
-        cythonize(cython_extensions)
+        cythonize(
+            cython_extensions,
+            **CYTHONIZE_KWARGS,
+        )
         _sdist.run(self)
 
 
diff --git a/yt_astro_analysis/halo_analysis/halo_finding/rockstar/rockstar_interface.pyx b/yt_astro_analysis/halo_analysis/halo_finding/rockstar/rockstar_interface.pyx
index 364144f1..a67a85d3 100644
--- a/yt_astro_analysis/halo_analysis/halo_finding/rockstar/rockstar_interface.pyx
+++ b/yt_astro_analysis/halo_analysis/halo_finding/rockstar/rockstar_interface.pyx
@@ -180,7 +180,7 @@ cdef import from "config_vars.h":
 # Forward declare
 cdef class RockstarInterface
 
-cdef void rh_analyze_halo(halo *h, particle *hp):
+cdef void rh_analyze_halo(halo *h, particle *hp) noexcept:
     # I don't know why, but sometimes we get halos with 0 particles.
     if h.num_p == 0: return
     cdef particleflat[:] pslice
@@ -190,7 +190,7 @@ cdef void rh_analyze_halo(halo *h, particle *hp):
         cb(rh.ds, parray)
     # This is where we call our functions
 
-cdef void rh_read_particles(char *filename, particle **p, np.int64_t *num_p):
+cdef void rh_read_particles(char *filename, particle **p, np.int64_t *num_p) noexcept:
     global SCALE_NOW
     cdef np.float64_t left_edge[6]
     cdef np.ndarray[np.int64_t, ndim=1] arri # index