diff --git a/devtools/conda-envs/examples_env.yml b/devtools/conda-envs/examples_env.yml index 8d287c8b1..26dab57f3 100644 --- a/devtools/conda-envs/examples_env.yml +++ b/devtools/conda-envs/examples_env.yml @@ -3,7 +3,7 @@ channels: - conda-forge dependencies: - pip - - python=3.10 + - python=3.11 - jupyterlab>=4 - ipywidgets>=8 # Cookbook @@ -23,8 +23,8 @@ dependencies: - lammps - rich - jax - - parmed <4 + - parmed - nglview ~=3.0.6 - psi4 - # New versions of torchdata require new versions of PyTorch which are not supported by DGL - - torchdata<=0.10.0 + # torchdata.datapipes was removed in 0.10.0 + - torchdata<=0.9.0 diff --git a/source/_ext/cookbook/globals_.py b/source/_ext/cookbook/globals_.py index d0b274c7d..f3c071021 100644 --- a/source/_ext/cookbook/globals_.py +++ b/source/_ext/cookbook/globals_.py @@ -92,7 +92,9 @@ """ # ".*/experimental/.*", -OPTIONAL_NOTEBOOKS: list[str] = list() +OPTIONAL_NOTEBOOKS: list[str] = [ + "openforcefield/openff-toolkit/external/swap_amber_parameters/swap_existing_ligand_parameters.ipynb", +] """ Notebooks whose execution failure will not cause notebook processing to fail. diff --git a/source/_ext/proc_examples.py b/source/_ext/proc_examples.py index 6c30b3b45..88a181d23 100644 --- a/source/_ext/proc_examples.py +++ b/source/_ext/proc_examples.py @@ -163,7 +163,7 @@ def create_colab_notebook(src: Path, cache_branch: str): cell_type="code", source=[ "# Execute this cell to make this notebook's dependencies available", - "!pip install -U https://github.com/conda-incubator/condacolab/archive/cuda-version-12.tar.gz", + "!pip install -q condacolab", "import condacolab", "condacolab.install()", *wget_files,