Add pymatgen.io.openff module

.github/workflows/test.yml

@@ -48,69 +48,45 @@ jobs:
       - name: Check out repo
         uses: actions/checkout@v4
 
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
-        with:
-          python-version: ${{ matrix.python-version }}
-          cache: pip
-          cache-dependency-path: setup.py
+      - name: Set up micromamba
+        uses: mamba-org/setup-micromamba@main
+
+      - name: Create mamba environment
+        run: |
+          micromamba create -n pymatgen python=${{ matrix.python-version }} --yes
 
       - name: Install uv
-        run: pip install uv
+        run: micromamba run -n pymatgen pip install uv
 
       - name: Copy GULP to bin
         if: matrix.os == 'ubuntu-latest'
         run: |
           sudo cp cmd_line/gulp/Linux_64bit/* /usr/local/bin/
 
-      - name: Install Bader
+      - name: Install ubuntu-only conda dependencies
         if: matrix.os == 'ubuntu-latest'
         run: |
-          wget https://theory.cm.utexas.edu/henkelman/code/bader/download/bader_lnx_64.tar.gz
-          tar xvzf bader_lnx_64.tar.gz
-          sudo mv bader /usr/local/bin/
-        continue-on-error: true # This is not critical to succeed.
+          micromamba install -n pymatgen -c conda-forge enumlib packmol bader openbabel openff-toolkit --yes
 
-      - name: Install Enumlib
-        if: matrix.os == 'ubuntu-latest'
-        run: |
-          git clone --recursive https://github.com/msg-byu/enumlib
-          cd enumlib/symlib/src
-          export F90=gfortran
-          make
-          cd ../../src
-          make enum.x
-          sudo mv enum.x /usr/local/bin/
-          cd ..
-          sudo cp aux_src/makeStr.py /usr/local/bin/
-        continue-on-error: true # This is not critical to succeed.
-
-      - name: Install Packmol
-        if: matrix.os == 'ubuntu-latest'
-        run: |
-          wget -O packmol.tar.gz https://github.com/m3g/packmol/archive/refs/tags/v20.14.2.tar.gz
-          tar xvzf packmol.tar.gz
-          export F90=gfortran
-          cd packmol-20.14.2
-          ./configure
-          make
-          sudo mv packmol /usr/local/bin/
-          cd ..
-        continue-on-error: true # This is not critical to succeed.
-
-      - name: Install dependencies
+      - name: Install pymatgen and dependencies
         run: |
           # TODO remove temporary fix. added since uv install torch is flaky.
           # track https://github.com/astral-sh/uv/issues/1921 for resolution
-          pip install torch
+          micromamba run -n pymatgen uv pip install torch
 
-          uv pip install numpy cython --system
+          micromamba run -n pymatgen uv pip install numpy cython
 
-          uv pip install -e '.[dev,optional]' --system
+          micromamba run -n pymatgen uv pip install -e .[dev,optional]
 
           # TODO remove next line installing ase from main branch when FrechetCellFilter is released
-          uv pip install --upgrade 'git+https://gitlab.com/ase/ase' --system
+          micromamba run -n pymatgen uv pip install --upgrade 'git+https://gitlab.com/ase/ase'
+
+      - name: Reinstall pymongo
+        run: |
+          # Reinstall pymongo to fix compatibility issue https://github.com/hyperopt/hyperopt/issues/547
+          micromamba run -n pymatgen uv pip uninstall bson
+          micromamba run -n pymatgen uv pip install pymongo
 
       - name: pytest split ${{ matrix.split }}
         run: |
-          pytest --splits 10 --group ${{ matrix.split }} --durations-path tests/files/.pytest-split-durations tests
+          micromamba run -n pymatgen pytest --splits 10 --group ${{ matrix.split }} --durations-path tests/files/.pytest-split-durations tests

pymatgen/io/babel.py

@@ -182,14 +182,14 @@ def rotor_conformer(self, *rotor_args, algo: str = "WeightedRotorSearch", forcef
         else:
             self.add_hydrogen()
 
-        ff = openbabel.OBForceField_FindType(forcefield)
+        ff = openbabel.OBForceField.FindType(forcefield)
         if ff == 0:
             warnings.warn(
                 f"This input {forcefield=} is not supported "
                 "in openbabel. The forcefield will be reset as "
                 "default 'mmff94' for now."
             )
-            ff = openbabel.OBForceField_FindType("mmff94")
+            ff = openbabel.OBForceField.FindType("mmff94")
 
         try:
             rotor_search = getattr(ff, algo)
@@ -264,10 +264,10 @@ def confab_conformers(
         else:
             self.add_hydrogen()
 
-        ff = openbabel.OBForceField_FindType(forcefield)
+        ff = openbabel.OBForceField.FindType(forcefield)
         if ff == 0:
             print(f"Could not find {forcefield=} in openbabel, the forcefield will be reset as default 'mmff94'")
-            ff = openbabel.OBForceField_FindType("mmff94")
+            ff = openbabel.OBForceField.FindType("mmff94")
 
         if freeze_atoms:
             print(f"{len(freeze_atoms)} atoms will be freezed")
@@ -346,8 +346,8 @@ def from_molecule_graph(cls, mol: MoleculeGraph) -> Self:
         """
         return cls(mol.molecule)
 
-    @needs_openbabel
     @classmethod
+    @needs_openbabel
     def from_str(cls, string_data: str, file_format: str = "xyz") -> Self:
         """
         Uses OpenBabel to read a molecule from a string in all supported