Merge pull request #99 from openforcefield/offtk-0-16-9

Update examples_env.yml for OFFTK 0.16.9

Author: Yoshanuikabundi

devtools/conda-envs/examples_env.yml

@@ -2,6 +2,12 @@ name: openff-docs-examples
 channels:
   - conda-forge
 dependencies:
+  # Examples
+  - openff-toolkit-examples>=0.16.9
+  - openff-interchange ~=0.4.2
+  - openff-nagl
+  # openff-fragmenter
+  # Runtime
   - pip
   - python=3.11
   - jupyterlab>=4
@@ -12,11 +18,7 @@ dependencies:
   - nbformat
   - requests
   - packaging
-  # Examples
-  - openff-toolkit-examples>=0.16.8
-  - openff-interchange ~=0.4.2
-  - openff-nagl
-  # - openff-fragmenter
+  # Other deps
   - openff-qcsubmit
   - openmmforcefields ~=0.14.2
   - gromacs >=2021=nompi*
@@ -26,15 +28,11 @@ dependencies:
   - parmed
   - nglview ~=3.0.6
   - psi4
-  # openff-nagl optional training deps
-  - pyarrow
-  - dgl
-  - openff-recharge
-  # torchdata.datapipes was removed in 0.10.0
-  - torchdata<=0.9.0
   # NAGL training dependencies
   # hopefully will be replaced by openff-nagl-training in future
   - pyarrow
   - openff-recharge
   - dask-jobqueue
   - dgl
+  # torchdata.datapipes was removed in 0.10.0
+  - torchdata<=0.9.0

source/_ext/cookbook/globals_.py

@@ -92,9 +92,7 @@
 """
 
 # ".*/experimental/.*",
-OPTIONAL_NOTEBOOKS: list[str] = [
-    "openforcefield/openff-toolkit/external/swap_amber_parameters/swap_existing_ligand_parameters.ipynb",
-]
+OPTIONAL_NOTEBOOKS: list[str] = []
 """
 Notebooks whose execution failure will not cause notebook processing to fail.