Merge remote-tracking branch 'upstream/main' into visualize-fixes

devtools/conda-envs/beta_rc_env.yaml

@@ -1,4 +1,4 @@
-name: test
+name: openff-toolkit-beta-rc-test
 channels:
   - conda-forge/label/openmm_rc
   - openeye/label/rc
@@ -7,7 +7,6 @@ channels:
 dependencies:
     # Base depends
   - python
-  - pydantic =1
   - packaging
   - numpy
   - networkx
@@ -19,6 +18,7 @@ dependencies:
   - openff-forcefields >=2023.05.1
   - smirnoff99Frosst
   - openff-units =0.2.0
+  - openff-amber-ff-ports
   - openff-utilities >=0.1.5
   - openff-interchange-base >=0.3.10
   - openff-nagl-base ==0.3.0
@@ -37,11 +37,14 @@ dependencies:
   - bson
   - msgpack-python
   - qcelemental
-  - qcportal >=0.15
+  - qcportal >=0.15, <0.50.0a0
   - qcengine
+  - nglview
   - mdtraj
   - nbval
   - mypy
+  - typing_extensions
+  - pydantic =1
   - pip:
     - types-setuptools
     - types-toml

devtools/conda-envs/openeye-examples.yaml

@@ -19,7 +19,7 @@ dependencies:
   - openff-amber-ff-ports >=0.0.3
   - openff-units =0.2.0
   - openff-utilities >=0.1.5
-  - openff-interchange-base >=0.3.10
+  - openff-interchange-base ==0.3.14
   - openff-nagl-base ==0.3.0
   - openff-nagl-models ==0.1.0
   - typing_extensions

devtools/conda-envs/rdkit-examples.yaml

@@ -18,7 +18,7 @@ dependencies:
   - openff-amber-ff-ports >=0.0.3
   - openff-units =0.2.0
   - openff-utilities >=0.1.5
-  - openff-interchange-base >=0.3.10
+  - openff-interchange-base ==0.3.14
   - openff-nagl-base ==0.3.0
   - openff-nagl-models ==0.1.0
   - typing_extensions

docs/releasehistory.md

@@ -14,16 +14,17 @@ Releases follow the `major.minor.micro` scheme recommended by [PEP440](https://w
 
 ### Bugfixes
 
-### New features
-
-### Improved documentation and warnings
+- [PR #1740](https://github.com/openforcefield/openff-toolkit/pull/1740): Updates for Mypy 1.6.
 
-## Current development
+### New features
 
-- [PR #1747](https://github.com/openforcefield/openff-toolkit/pull/1747): Warns if a SMILES with full atom mappings is passed to `Molecule.from_smiles`, which does not use the atom map for atom ordering (`Molecule.from_mapped_smiles` does).
 - [PR #1731](https://github.com/openforcefield/openff-toolkit/pull/1731): Support SMIRNOFF vdW version 0.5.
 - [PR #1751](https://github.com/openforcefield/openff-toolkit/pull/1751): Improve visualization API docs and support multiple bonds in `Topology.visualize()`
 
+### Improved documentation and warnings
+
+- [PR #1747](https://github.com/openforcefield/openff-toolkit/pull/1747): Warns if a SMILES with full atom mappings is passed to `Moleucle.from_smiles`, which does not use the atom map for atom ordering (`Molecule.from_mapped_smiles` does).
+
 ## 0.14.4
 
 ### Behavior changes

examples/toolkit_showcase/toolkit_showcase.ipynb

@@ -24,7 +24,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "e672c065e0d74f328356d436a29dbdcd",
+       "model_id": "dbedbca72b0640ae8b55d1dbc6516b12",
        "version_major": 2,
        "version_minor": 0
       },
@@ -120,7 +120,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "69e31d0f9d8045248800b26c75cc2091",
+       "model_id": "f159325d10c74fd481cc10b659eb78f4",
        "version_major": 2,
        "version_minor": 0
       },
@@ -474,7 +474,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "d2b270558a934ee5b8762aac0568ae3e",
+       "model_id": "d0837281d578488f93a96c9ad5a5c4d0",
        "version_major": 2,
        "version_minor": 0
       },
@@ -616,8 +616,14 @@
     "# Under the hood, this creates *OpenMM* `System` and `Topology` objects, then combines them together\n",
     "simulation = interchange.to_openmm_simulation(integrator=integrator)\n",
     "\n",
-    "# Add a reporter to record the structure every 10 steps\n",
-    "dcd_reporter = openmm.app.DCDReporter(\"trajectory.dcd\", 10)\n",
+    "# Add a reporter to record the structure every 100 steps, 1000 if using a CUDA-enabled GPU\n",
+    "try:\n",
+    "    openmm.Platform.getPlatformByName(\"CUDA\")\n",
+    "    stride = 1000\n",
+    "except openmm.OpenMMException:\n",
+    "    stride = 100\n",
+    "\n",
+    "dcd_reporter = openmm.app.DCDReporter(file=\"trajectory.dcd\", reportInterval=stride)\n",
     "simulation.reporters.append(dcd_reporter)"
    ]
   },
@@ -639,8 +645,8 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Original state has energy -192996.94 kJ/mol with maximum force 149492.33 kJ/(mol nm)\n",
-      "Minimized state has energy -404672.44 kJ/mol with maximum force 2368.55 kJ/(mol nm)\n"
+      "Original state has energy -190024.66 kJ/mol with maximum force 149324.54 kJ/(mol nm)\n",
+      "Minimized state has energy -405397.28 kJ/mol with maximum force 2557.75 kJ/(mol nm)\n"
      ]
     }
    ],
@@ -742,17 +748,19 @@
   {
    "cell_type": "code",
    "execution_count": 15,
-   "metadata": {},
+   "metadata": {
+    "scrolled": true
+   },
    "outputs": [
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "4ad956ce9c7c4d668806de6370f4b9a8",
+       "model_id": "668303a97a5440a9b8c89c5d0dc29ac6",
        "version_major": 2,
        "version_minor": 0
       },
       "text/plain": [
-       "NGLWidget(max_frame=345)"
+       "NGLWidget(max_frame=78)"
       ]
      },
      "metadata": {},
@@ -774,7 +782,7 @@
    "metadata": {},
    "source": [
     "<div class=\"alert alert-info\" style=\"max-width: 700px; margin-left: auto; margin-right: auto;\">\n",
-    "ℹ️ MDTraj is a great library for analysis. Check out the <a href=https://mdtraj.org/1.9.4/api/generated/mdtraj.Trajectory.html>docs</a> for the <code>Trajectory</code> object you just created, as well as their <a href=https://mdtraj.org/1.9.4/analysis.html>analysis functions</a>, and see if you can compute something interesting. Its real superpower is that it provides the coordinates of the trajectory as a <a href=https://numpy.org/doc/stable/reference/generated/numpy.array.html>NumPy array</a>, so if you're really keen try computing something directly from <code>mdt_traj.xyz</code>\n",
+    "ℹ️ MDTraj is a great library for analysis. Check out the <a href=https://mdtraj.org/1.9.4/api/generated/mdtraj.Trajectory.html>docs</a> for the <code>Trajectory</code> object you just created, as well as their <a href=https://mdtraj.org/1.9.4/analysis.html>analysis functions</a>, and see if you can compute something interesting. Its real superpower is that it provides the coordinates of the trajectory as a <a href=https://numpy.org/doc/stable/reference/generated/numpy.array.html>NumPy array</a>, so if you're really keen try computing something directly from <code>trajectory.xyz</code>\n",
     "</div>"
    ]
   },
@@ -818,7 +826,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.18"
+   "version": "3.11.6"
   },
   "widgets": {
    "application/vnd.jupyter.widget-state+json": {