Release peleffy 1.6.0

.gitattributes

@@ -1,2 +1,3 @@
 offPELE/_version.py export-subst
 *.py diff=python
+peleffy/_version.py export-subst

.github/workflows/conda.yml

@@ -9,8 +9,10 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-latest, macOS-latest]
-        python-version: [3.8, 3.9]
+        os: [ubuntu-latest, ]
+        python-version: [3.9, ]
+        #os: [ubuntu-latest, macOS-latest]  No need to make multiple releases anymore
+        #python-version: [3.8, 3.9]  No need to make multiple releases anymore
     name: Python ${{ matrix.python-version }} at ${{ matrix.os }}
     steps:
       - uses: actions/checkout@v4

devtools/conda/meta.yaml

@@ -18,16 +18,17 @@ requirements:
     - setuptools
 
   run:
-    - python
+    - python >=3.12
     - numpy
     - ipython
     - matplotlib
     - pytest
     - networkx
-    - rdkit
+    - rdkit >=2025.03.6
     - ambertools
-    - openff-toolkit==0.10.7
-    - openff-forcefields==2023.05.1
+    - openff-toolkit ==0.18.0
+    - openff-forcefields ==2026.01.0
+    - openff-nagl ==0.5.4
 
 about:
   home: https://github.com/martimunicoy/peleffy

devtools/envs/standard.yaml

@@ -3,7 +3,7 @@ channels:
   - conda-forge
 
 dependencies:
-  - python
+  - python=3.12
   - pip
   - flake8
   - pytest
@@ -12,7 +12,8 @@ dependencies:
   - coverage
   - ipython
   - ambertools
-  - rdkit
-  - openff-toolkit==0.10.7
-  - openff-forcefields==2023.05.1
+  - rdkit==2025.03.6
+  - openff-toolkit==0.18.0
+  - openff-forcefields==2026.01.0
+  - openff-nagl==0.5.4
 

docs/releasehistory.rst

@@ -7,11 +7,37 @@ Releases follow the ``major.minor.micro`` scheme recommended by `PEP440 <https:/
 * ``minor`` increments add features but do not break API compatibility
 * ``micro`` increments represent bugfix releases or improvements in documentation
 
+1.6.0 - Migration to Python 3.12, OpenFF upgrade and NAGL charge method
+------------------------------------------------------------------------
+
+This is a major release of peleffy that migrates the package to Python 3.12 and upgrades
+the OpenFF toolkit and force fields to their latest versions. It also introduces a new
+``OpenFF230ForceField`` class and the NAGL charge assignment method, which uses a Graph
+Convolutional Network (GCN) model to assign AM1-BCC charges directly from the molecular
+graph without requiring 3D conformers.
+
+New features
+""""""""""""
+- Migration to Python 3.12 and upgrade of all core dependencies (RDKit, OpenFF Toolkit, OpenFF Force Fields)
+- Upgrade of ``versioneer`` to v0.29 for full Python 3.12 compatibility
+- New ``OpenFF230ForceField`` class in ``peleffy.forcefield`` that uses ``openff_unconstrained-2.3.0.offxml`` as the underlying force field. This version is specifically designed to be used with NAGL charges and enforces their use as the only compatible charge method
+- New ``NAGLCalculator`` class in ``peleffy.forcefield.calculators`` that assigns partial charges using the OpenFF NAGL GCN model ``openff-gnn-am1bcc-1.0.0.pt`` via the OpenFF Toolkit's ``assign_partial_charges`` method. Charges are computed directly from the molecular graph and do not require 3D conformers
+- ``ForceFieldSelector`` now returns ``OpenFF230ForceField`` when ``openff_unconstrained-2.3.0.offxml`` is requested, separating it from other OpenFF versions
+- ``ChargeCalculatorSelector`` now includes ``nagl`` as an available charge method
+- ``setup.py`` updated with ``python_requires='>=3.12'`` and Python 3.12 classifier
+- ``devtools/conda/meta.yaml`` updated to reflect current dependency versions including ``openff-nagl``
+
+Bugfixes
+""""""""
+- Fixed ``SyntaxWarning: invalid escape sequence '\s'`` in ``versioneer.py`` v0.18 that appeared on Python 3.12
+- Fixed amide bond detection in rotamer library: the SMARTS pattern for rotatable bonds used ``[NH]`` which failed to exclude amide C–N bonds when explicit hydrogens were present (``[NH]`` requires implicit H count, but RDKit assigns explicit H atoms). Changed to ``[N]`` to correctly exclude any nitrogen bonded to a carbonyl from being part of a rotatable bond, regardless of hydrogen representation
+- Fixed ``ffld_server`` output handling: replaced ``-out_file`` flag with Python-level stdout redirection
+
 
 1.5.2 - Improvements for alchemistry
 ------------------------------------
 
-This is a minor release of peleffy that adds several improvements to the alchemistry module
+This is a minor release of peleffy that adds several improvements to the alchemistry module.
 
 New features
 """"""""""""

docs/usage.rst

@@ -201,7 +201,7 @@ It sets the method to compute the partial charges.
 
 - Flag: ``-c NAME``, ``--charge_method NAME``
 - Type: ``string``
-- Choices: one of [``gasteiger``, ``am1bcc``, ``OPLS``]
+- Choices: one of [``gasteiger``, ``am1bcc``, ``OPLS``, ``mulliken``, ``nagl``]
 - Default: ``am1bcc``
 - Example: the code below will calculate partial charges using 'gasteiger' method
 
@@ -256,4 +256,13 @@ It generates an Impact template that will be compatible with PELE's AMBER force
 
   .. code-block:: bash
 
-        $ python -m peleffy.main path/to/my_ligand.pdb --for_amber
+        $ python -m peleffy.main path/to/my_ligand.pdb --for_amber
+
+OpenFF 2.3.0
+------------
+Version 2.3.0 of OpenFF requires a specific charge method, which is NAGL. To select this charge method along with OpenFF-2.3.0 use the following command:
+
+  .. code-block:: bash
+
+        $ python -m peleffy.main path/to/my_ligand.pdb -f openff_unconstrained-2.3.0.offxml -c nagl
+

peleffy/__init__.py

@@ -1,3 +1,6 @@
 from ._version import get_versions
 __version__ = get_versions()['version']
 del get_versions
+
+from . import _version
+__version__ = _version.get_versions()['version']