Merge branch 'main' into sideload_examples

.github/workflows/ci.yaml

@@ -23,19 +23,24 @@ defaults:
 
 jobs:
   tests:
-    runs-on: ${{ matrix.OS }}-latest
-    name: "tests"
+    runs-on: ${{ matrix.os }}-latest
+    name: "💻-${{matrix.os }} 🐍-${{ matrix.python-version }} 🗃️${{ matrix.pydantic-version }}"
     strategy:
       fail-fast: false
       matrix:
-        os: ['ubuntu']
+        os: ["ubuntu"]
+        pydantic-version: [">1"]
         python-version:
           - "3.9"
           - "3.10"
           - "3.11"
         include:
-          - os: 'macos'
+          - os: "macos"
             python-version: "3.11"
+            pydantic-version: ">1"
+          - os: "ubuntu"
+            python-version: "3.11"
+            pydantic-version: "<2"
 
     steps:
       - uses: actions/checkout@v3
@@ -52,6 +57,7 @@ jobs:
           cache-downloads: true
           extra-specs: |
             python==${{ matrix.python-version }}
+            pydantic=${{ matrix.pydantic-version }}
 
       - name: "Install GUFE from main@HEAD"
         run: python -m pip install --no-deps git+https://github.com/OpenFreeEnergy/gufe@main

docs/tutorials/index.rst

@@ -13,7 +13,7 @@ Relative Free Energies CLI tutorial
 
 The :any:`Relative Free Energies with the OpenFE CLI <rbfe_cli_tutorial>`
 tutorial walks users through how to use the OpenFE command line to calculate
-relative hydration free energies from a small set of benzene modifications.
+relative binding free energies of various ligands against the TYK2 target.
 
 Associated with it is also a :any:`notebook <rbfe_python_tutorial>`
 for how to achieve the same outcomes using the Python API.

environment.yml

@@ -11,7 +11,7 @@ dependencies:
   - pytest-xdist
   - pytest-cov
   - pytest-rerunfailures
-  - pydantic <2
+  - pydantic >1
   - coverage
   - cinnabar ==0.3.0
   - openff-toolkit>=0.13.0

openfe/protocols/openmm_rfe/equil_rfe_settings.py

@@ -26,7 +26,7 @@ from openfe.protocols.openmm_utils.omm_settings import (
 try:
     from pydantic.v1 import validator
 except ImportError:
-    from pydantic import validator
+    from pydantic import validator  # type: ignore[assignment]
 
 
 class AlchemicalSettings(SettingsBaseModel):

openfe/protocols/openmm_utils/omm_settings.py

@@ -22,7 +22,7 @@ from gufe.settings import (
 try:
     from pydantic.v1 import validator
 except ImportError:
-    from pydantic import validator
+    from pydantic import validator  # type: ignore[assignment]
 
 class SystemSettings(SettingsBaseModel):
     """Settings describing the simulation system settings."""