Protein mutation support in Neq Cycling Setup Unit

.github/workflows/ci.yaml

@@ -23,12 +23,11 @@ defaults:
 jobs:
   tests:
     runs-on: ${{ matrix.os }}-latest
-    name: "💻-${{matrix.os }} 🐍-${{ matrix.python-version }} - pydantic ${{matrix.pydantic}}"
+    name: "💻-${{matrix.os }} 🐍-${{ matrix.python-version }}"
     strategy:
       fail-fast: false
       matrix:
         os: ["ubuntu"]
-        pydantic: ["1", "2"]
         python-version:
           - "3.10"
           - "3.11"
@@ -53,7 +52,6 @@ jobs:
           cache-downloads: true
           create-args: >-
             python=${{ matrix.python-version }}
-            pydantic=${{ matrix.pydantic }}
           init-shell: bash
 
       - name: "Install"
@@ -82,12 +80,12 @@ jobs:
           # Set the OFE_SLOW_TESTS to True if running a Cron job
           OFE_SLOW_TESTS: ${{ fromJSON('{"false":"false","true":"true"}')[github.event_name != 'pull_request'] }}
         run: |
-              pytest -n auto -v --cov=feflow --cov-report=xml --durations=10
+              pytest -n logical -v --cov=feflow --cov-report=xml --durations=10
 
       - name: codecov
-        if: ${{ github.repository == 'choderalab/feflow'
+        if: ${{ github.repository == 'OpenFreeEnergy/feflow'
                 && github.event_name == 'pull_request' }}
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v4
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           file: coverage.xml

devtools/conda-envs/test_env.yaml

@@ -4,16 +4,16 @@ channels:
   - openeye
 dependencies:
     # Base depends
-  - gufe >=0.9.5
+  - gufe ~=1.7.1
   - numpy
-  - openfe >=0.15  # TODO: Remove once we don't depend on openfe
+  - openfe ~=1.7.0   # TODO: Remove once we don't depend on openfe
   - openff-units
   - openmm
   - openmmforcefields >=0.14.1  # TODO: remove when upstream deps fix this
-  - pymbar <4
-  - pydantic >=1.10.17
+  - openmmtools >=0.23.0
+  - pymbar ~=4.0
+  - pydantic >=1.10.17, <3
   - python
-
     # Testing (optional deps)
   - espaloma_charge  # To us Espaloma FF in tests
   - openeye-toolkits

docs/tutorials/protein-mutations-neq.ipynb

@@ -0,0 +1,49 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "47736a8f-7446-4600-b06d-4c8ffd05f66c",
+   "metadata": {},
+   "source": [
+    "TODO:\n",
+    "Add a tutorial here on how to use the protein-mutation capabilities in `FEFlow`.\n",
+    "\n",
+    "What should it have?\n",
+    "* How to mutate a protein from a PDB file with `pdbfixer`\n",
+    "* How to create the mapping between the WT and MUT\n",
+    "  * check mapping is correct (sanity check)\n",
+    "* Setting up the protocol\n",
+    "* Executing the protocol"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "fa00a848-79a2-46c3-a141-6e24ce0f7f4f",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.12.9"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}