Support Python 3.12

.github/workflows/Test.yaml

@@ -13,37 +13,34 @@ jobs:
     strategy:
       matrix:
         os: ["ubuntu-latest"]
-        python-version: ["3.9", "3.10"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
 
     steps:
     - name: Check out source code
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         fetch-depth: 0
 
-    - name: Setup Miniconda
-      uses: conda-incubator/setup-miniconda@v2
+    - name: Setup conda environment
+      uses: mamba-org/setup-micromamba@v1
       with:
-        auto-update-conda: false
-        python-version: ${{ matrix.python-version }}
+        environment-name: parmed-dev
         environment-file: devtools/environment-dev.yaml
-        activate-environment: parmed-dev
-        channels: conda-forge,bioconda
-        mamba-version: "*"
+        create-args: >-
+          python=${{ matrix.python-version }}
 
-    - name: Environment Information
+    - name: Optionally install AmberTools
+      if: ${{ matrix.python-version != 3.12 }}
       shell: bash -l {0}
-      run: |
-        conda info
-        conda list
+      run: micromamba install "ambertools >=20.15" -c conda-forge -yq
 
     - name: Install and test
       shell: bash -l {0}
       run: |
         bash -ex devtools/ci/install.sh
 
     - name: Upload Coverage Results
-      uses: codecov/codecov-action@v1
+      uses: codecov/codecov-action@v3
       if: endsWith(github.ref, '/master')
       with:
         token: ${{ secrets.CODECOV_TOKEN }}

.gitignore

@@ -10,3 +10,5 @@ package-lock.json
 package.json
 .pytest_cache
 .ipynb_checkpoints
+*.egg-info/
+*.so

devtools/environment-dev.yaml

@@ -1,15 +1,13 @@
 name: parmed-dev
 channels:
-  - https://conda.anaconda.org/conda-forge
-  - https://conda.anaconda.org/bioconda
+  - conda-forge
+  - conda-forge/label/openmm_rc
 dependencies:
   - pandas
   - openmm >=7.6.0
-  - coverage
   - netCDF4
   - rdkit >=2020.09.4
   - nglview
-  - ambertools >=20.15
   - networkx
   - lxml
   - gromacs

parmed/__init__.py

@@ -13,9 +13,8 @@
            'rdkit', 'formats', 'Vec3', 'ParameterSet', 'load_file', 'read_PDB', 'read_CIF',
            'load_rosetta', 'load_rdkit', 'download_PDB', 'download_CIF', 'tools', 'version']
 
-from ._version import get_versions
-__version__ = get_versions()['version']
-del get_versions
+from . import _version
+__version__ = _version.get_versions()['version']
 
 from . import exceptions, periodic_table, residue
 from . import unit, utils