Merge pull request #311 from OpenFreeEnergy/cinnabar-update

update for new cinnabar API

Author: jthorton

cookbook/cinnabar_absolute.ipynb

@@ -8,7 +8,7 @@ dependencies:
   - nbval
   - nglview
   - notebook
-  - numpy <2.4.0  # https://github.com/OpenFreeEnergy/cinnabar/issues/198
+  - numpy
   - pip
   - pytest
   - pytest-cov
@@ -17,4 +17,5 @@ dependencies:
   - openfe==1.11.0
   - openff-interchange-base != 0.5.1  # https://github.com/openforcefield/openff-interchange/issues/1450
   - pip:
-    - git+https://github.com/OpenFreeEnergy/openfe_analysis@main # Use coda-forge v0.5 after ne wopenfe release releases pins on openfe-analysis
+    - git+https://github.com/OpenFreeEnergy/openfe_analysis@main # Use conda-forge v0.5 after new openfe release updates pins on openfe-analysis
+    - git+https://github.com/OpenFreeEnergy/cinnabar@main # Use conda-forge v0.6.0 after new openfe release updates pins on cinnabar

environment.yaml

@@ -37,7 +37,7 @@
      "text": [
       "  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current\n",
       "                                 Dload  Upload   Total   Spent    Left  Speed\n",
-      "100 12.7M  100 12.7M    0     0   604k      0  0:00:21  0:00:21 --:--:--  693k\n",
+      "100 12.7M  100 12.7M    0     0  2951k      0  0:00:04  0:00:04 --:--:-- 2951k\n",
       "Archive:  septop_results.zip\n",
       "  inflating: septop_results/pre_openfe_v1.11/results_2/rbfe_1_7b.json  \n",
       "  inflating: septop_results/pre_openfe_v1.11/results_2/rbfe_7a_7b.json  \n",
@@ -403,8 +403,8 @@
     "        m = Measurement(\n",
     "            labelA=ligA,\n",
     "            labelB=ligB,\n",
-    "            DG=DDGbind * unit.kilocalorie_per_mole,\n",
-    "            uncertainty=bind_unc * unit.kilocalorie_per_mole,\n",
+    "            DG=float(DDGbind) * unit.kilocalorie_per_mole,\n",
+    "            uncertainty=float(bind_unc) * unit.kilocalorie_per_mole,\n",
     "            computational=True,\n",
     "        )\n",
     "        fe_results.append(m)\n",
@@ -492,7 +492,25 @@
    "execution_count": 11,
    "id": "3b81c26b-4e3d-4bca-bfb1-4f72c75ec1bf",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/Users/joshua/mambaforge/envs/openfe_dev/lib/python3.12/site-packages/openmoltools/utils.py:9: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.\n",
+      "  from pkg_resources import resource_filename\n",
+      "/Users/joshua/mambaforge/envs/openfe_dev/lib/python3.12/site-packages/Bio/Application/__init__.py:39: BiopythonDeprecationWarning: The Bio.Application modules and modules relying on it have been deprecated.\n",
+      "\n",
+      "Due to the on going maintenance burden of keeping command line application\n",
+      "wrappers up to date, we have decided to deprecate and eventually remove these\n",
+      "modules.\n",
+      "\n",
+      "We instead now recommend building your command line and invoking it directly\n",
+      "with the subprocess module.\n",
+      "  warnings.warn(\n"
+     ]
+    }
+   ],
    "source": [
     "# Specify paths to result directories\n",
     "results_dir = [pathlib.Path(\"septop_results/current/\")]\n",
@@ -1145,7 +1163,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "openfe_dev",
    "language": "python",
    "name": "python3"
   },
@@ -1159,7 +1177,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.13.13"
+   "version": "3.12.9"
   },
   "widgets": {
    "application/vnd.jupyter.widget-state+json": {