Update CI file and environments

.github/workflows/pytest.yml

@@ -29,8 +29,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [macos-latest, macOS-13, ubuntu-latest]
-        python-version: ['3.10', '3.11']
+        os: [macos-14, ubuntu-24.04]
+        python-version: ['3.10', '3.11', '3.12']
 
     runs-on: ${{ matrix.os }}
 
@@ -43,8 +43,8 @@ jobs:
       with:
         environment-file: environment-dev.yml
         python-version: ${{ matrix.python-version }}
-        miniforge-variant: Mambaforge
-        miniforge-version: 4.9.2-4
+        miniforge-variant: Miniforge3
+        miniforge-version: 24.11.0-0
         use-mamba: true
 
     - name: Install package
@@ -63,7 +63,7 @@ jobs:
 
   test-tutorials:
     if: ${{ github.event.issue.pull_request && github.event.comment.body== '/testtutorials'}}
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     steps:
     - name: Put a reaction to the comment
       run: gh api graphql --silent --raw-field query="mutation AddReaction {addReaction(input:{subjectId:\"$NODE_ID\",content:EYES}){reaction{content}subject{id}}}"
@@ -96,14 +96,14 @@ jobs:
         PR_NUMBER: ${{ github.event.issue.number }}
 
     - name: Check out repository
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
 
     - name: Build environment
-      uses: conda-incubator/setup-miniconda@v2
+      uses: conda-incubator/setup-miniconda@v3
       with:
         environment-file: environment-dev.yml
-        miniforge-variant: Mambaforge
-        miniforge-version: 4.9.2-4
+        miniforge-variant: Miniforge3
+        miniforge-version: 24.11.0-0
         use-mamba: true
 
     - name: Install package

environment-dev.yml

@@ -8,7 +8,7 @@ dependencies:
   - gmso >=0.12.0
   - gsd >=3.0
   - grits >=0.5.0
-  - hoomd >=4.5
+  - hoomd >=4.5, <5.0
   - mbuild >=0.17.0
   - numpy <2.0
   - openbabel >=3
@@ -18,6 +18,6 @@ dependencies:
   - pytest
   - pytest-cov
   - nbmake
-  - python >=3.10, <3.12
+  - python >=3.10, <3.13
   - fresnel >=0.13.5
   - cmeutils >=1.3

environment.yml

@@ -8,12 +8,12 @@ dependencies:
   - gmso >=0.12.0
   - gsd >=3.0
   - grits >=0.5.0
-  - hoomd >=4.5
+  - hoomd >=4.5, <5.0
   - mbuild >=0.17.0
   - numpy <2.0
   - openbabel >=3
   - pip
   - py3Dmol
-  - python >=3.10, <3.12
+  - python >=3.10, <3.13
   - fresnel >=0.13.5
   - cmeutils >=1.3

flowermd/tests/base/test_molecule.py

@@ -207,8 +207,8 @@ def test_polymer_different_chain_lengths(self, dimethylether_smiles):
             bond_orientation=[None, None],
         )
         assert polymer.n_particles == 53
-        assert len(polymer.molecules[0].labels["Compound"]) == 3
-        assert len(polymer.molecules[1].labels["Compound"]) == 4
+        assert len(polymer.molecules[0].children) == 3
+        assert len(polymer.molecules[1].children) == 4
 
     def test_polymer_different_num_mol(self, dimethylether_smiles):
         polymer = Polymer(
@@ -220,9 +220,9 @@ def test_polymer_different_num_mol(self, dimethylether_smiles):
             bond_orientation=[None, None],
         )
         assert polymer.n_particles == 55
-        assert len(polymer.molecules[0].labels["Compound"]) == 3
-        assert len(polymer.molecules[1].labels["Compound"]) == 2
-        assert len(polymer.molecules[2].labels["Compound"]) == 2
+        assert len(polymer.molecules[0].children) == 3
+        assert len(polymer.molecules[1].children) == 2
+        assert len(polymer.molecules[2].children) == 2
 
     def test_polymer_unequal_num_mol_length(self, dimethylether_smiles):
         with pytest.raises(ValueError):