Bump to python 3.12 (#1180)

* tests for python 3.12

* update numpy in in env

* python 3.12 requires protobuf 4

* add MacOS-13 along with macos-latest to test both arm and x86 mac

---------

Co-authored-by: root <root@DESKTOP-FO53E26>
Co-authored-by: Co Quach <43968221+daico007@users.noreply.github.com>
Co-authored-by: Co Quach <daico007@gmail.com>
Co-authored-by: chrisjonesBSU <chrisjones4@u.boisestate.edu>
Co-authored-by: Chris Jones <50423140+chrisjonesBSU@users.noreply.github.com>

.github/workflows/CI.yaml

@@ -18,11 +18,11 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [macOS-latest, ubuntu-latest]
-        python-version: ["3.9", "3.10", "3.11"]
+        os: [macOS-latest, macOS-13, ubuntu-latest]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
         include:
           - os: windows-latest
-            python-version: "3.11"
+            python-version: "3.12"
 
     defaults:
       run:

environment-dev-win.yml

@@ -14,13 +14,13 @@ dependencies:
   - mdtraj
   - networkx
   - nglview>=2.7
-  - numpy=1.24.2
+  - numpy=1.26.4
   - openbabel>=3.0.0
   - packmol=1!18.013
   - parmed>=3.4.3
   - pip
   - pre-commit
-  - protobuf<4
+  - protobuf
   - py3Dmol
   - pycifrw
   - pytest

environment-dev.yml

@@ -15,13 +15,13 @@ dependencies:
   - mdtraj
   - networkx
   - nglview>=3
-  - numpy=1.24.2
+  - numpy=1.26.4
   - openbabel>=3
   - packmol>=20
   - parmed>=3.4.3
   - pip
   - pre-commit
-  - protobuf<4
+  - protobuf
   - py3Dmol
   - pycifrw
   - pytest

environment.yml

@@ -3,7 +3,7 @@ channels:
   - conda-forge
 dependencies:
   - ele
-  - numpy=1.24.2
+  - numpy=1.26.4
   - packmol>=18
   - gmso>=0.9.0
   - parmed>=3.4.3

mbuild/tests/test_packing.py

@@ -397,7 +397,7 @@ def test_box_edge(self, h2o, methane):
         edge = 0.2
         bounds = [2, 2, 2, 1]
         sphere = mb.fill_sphere(
-            compound=h2o, n_compounds=100, sphere=bounds, edge=edge
+            compound=h2o, n_compounds=120, sphere=bounds, edge=edge
         )
         target_diameter = (bounds[3] - edge) * 2
         assert np.allclose(