🤖 Bump RDKit version to Release_2024_03_5 (#108)

* Set RDKit version to Release_2024_03_5

* Bump to 2024_03_4 (#105)

* Bump to 2024_03_4

* bump cmake to version 3.30.0

* set boost debug on

* cmake to 2.29

* Add fix for finding boost::numpy target

* Downgrade cmake to prevent issues with py3.8 and py3.9

* allow numpy 2.0 as install requirement

* Reenable arm64 macos runners on GH actions

* Bump github actions script

* Copy libs to /usr/lib path on MacOS

* Change permission of usr/lib dir

* Copy all libs to other directory for MacOS

* Fix stubs generation  on MacOS

* Fix freetype on macos

* Fix conan detection bug for cp38 arm64

* Fix 3D descriptor test

* Fix tests

---------

Co-authored-by: Create or Update Pull Request Action <create-or-update-pull-request@users.noreply.github.com>
Co-authored-by: Chris Kuenneth <44866753+kuelumbus@users.noreply.github.com>
Co-authored-by: Christopher Kuenneth <christopher.kuenneth@gmail.com>

Author: 3 people

setup.py

@@ -12,7 +12,7 @@
 from setuptools.command.build_ext import build_ext as build_ext_orig
 
 # RDKit version to build (tag from github repository)
-rdkit_tag = "Release_2024_03_4"
+rdkit_tag = "Release_2024_03_5"
 
 with open("README.md", "r", encoding="utf-8") as fh:
     long_description = fh.read()

tests/test_main.py

@@ -1,3 +1,5 @@
+import pytest
+
 def test_descriptor():
     from rdkit.Chem import Descriptors
     # Was 209 but changed to 211 in Release_2023_09_1
@@ -6,12 +8,17 @@ def test_descriptor():
 
 
 def test_3d_descriptors():
+    # from https://github.com/rdkit/rdkit/blob/master/rdkit/Chem/UnitTestDescriptors.py
     from rdkit import Chem
     from rdkit.Chem import AllChem, Descriptors3D
 
-    m2 = Chem.AddHs(Chem.MolFromSmiles("CC"))
-    AllChem.EmbedMolecule(m2, randomSeed=1)
-    assert round(Descriptors3D.NPR1(m2), 10) == 0.2553516286
+    mol = Chem.MolFromSmiles('CCCO')
+    
+    # test function returns expected outputs
+    AllChem.EmbedMolecule(mol, randomSeed=0xf00d)
+    descs = Descriptors3D.CalcMolDescriptors3D(mol)
+    assert 'InertialShapeFactor' in descs
+    assert 20.9582649071385 == pytest.approx(descs['PMI1'], 1e-4)
 
 
 def test_data_dir_and_chemical_features():