This PR properly compiles cython to remove pyximport

.gitignore

@@ -10,7 +10,8 @@ build/
 .DS_Store
 /site-packages/
 /tmp
-
+*.cpython*
+omas_cython.c
 omas/data-dictionary
 omas/Saxon*
 omas/imas_structures/*/*.xml

omas/omas_utils.py

@@ -868,21 +868,14 @@ def omas_global_quantities(imas_version=omas_rcparams['default_imas_version']):
     return _global_quantities[imas_version]
 
 
-# only attempt cython if effective user owns this copy of omas
-# disabled for Windows: need to add check for file ownership under Windows
-if os.name == 'nt' or os.geteuid() != os.stat(__file__).st_uid:
+# Import compiled Cython extension
+# Fall back to pure Python implementation if the compiled extension is not available
+try:
+    from .omas_cython import *
+except ImportError as _excp:
+    warnings.warn('Compiled Cython extension not available, falling back to pure Python: ' + str(_excp))
     with open(os.path.split(__file__)[0] + os.sep + 'omas_cython.pyx', 'r') as f:
         exec(f.read(), globals())
-else:
-    try:
-        import pyximport
-
-        pyximport.install(language_level=3)
-        from .omas_cython import *
-    except Exception as _excp:
-        warnings.warn('omas cython failed: ' + str(_excp))
-        with open(os.path.split(__file__)[0] + os.sep + 'omas_cython.pyx', 'r') as f:
-            exec(f.read(), globals())
 
 
 def l2ut(path):

omas/tests/test_omas_utils.py

@@ -117,6 +117,17 @@ def test_omas_info(self):
         ods_info_list = omas_info(get_list)
         assert all(item in ods_info_list for item in get_list)
 
+    def test_cython_extension_compiled(self):
+        """Test that the Cython extension was properly compiled and is being used"""
+        import omas.omas_cython as cython_module
+        # Check that we're using the compiled extension (.so file) not the .pyx source
+        assert hasattr(cython_module, '__file__'), "Cython module should have a __file__ attribute"
+        module_file = cython_module.__file__
+        # Compiled extension should end with .so (Linux/Mac) or .pyd (Windows)
+        assert module_file.endswith('.so') or module_file.endswith('.pyd'), \
+            f"Expected compiled extension (.so/.pyd), but got: {module_file}"
+        print(f"✓ Using compiled Cython extension: {module_file}")
+
     def test_p2l(self):
         assert p2l('0') == [0]
         assert p2l('equilibrium') == ['equilibrium']

pyproject.toml

@@ -0,0 +1,3 @@
+[build-system]
+requires = ["setuptools>=41.2", "Cython>=0.29", "numpy>=1.16.1"]
+build-backend = "setuptools.build_meta"

setup.py

@@ -1,6 +1,8 @@
 import os
 import glob
 import subprocess
+from setuptools import Extension
+from Cython.Build import cythonize
 
 install_requires = [
     'numpy>=1.16.1',
@@ -51,7 +53,7 @@
 
 packages = ['omas', 'omas.examples', 'omas.samples', 'omas.tests', 'omas.utilities']
 package_data = {
-    'omas': ['*.py', '*.pyx', 'version'],
+    'omas': ['*.py', 'version'],
     'omas.examples': ['*.py'],
     'omas.samples': ['*'],
     'omas.tests': ['*.py'],
@@ -109,6 +111,13 @@
 
 from setuptools import setup
 
+# Build Cython extension
+ext_modules = cythonize(
+    [Extension("omas.omas_cython", ["omas/omas_cython.pyx"])],
+    language_level=3,
+    compiler_directives={'embedsignature': True}
+)
+
 setup(
     name='omas',
     version=open(here + 'omas/version', 'r').read().strip(),
@@ -124,4 +133,6 @@
     package_data=package_data,
     install_requires=install_requires,
     extras_require=extras_require,
+    ext_modules=ext_modules,
+    setup_requires=['Cython>=0.29', 'numpy>=1.16.1'],
 )