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Merged
Yoshanuikabundi merged 5 commits into from
Mar 10, 2025
Merged

Use Py311 in examples environment #77

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eee2729
Use Py311 in examples environment
Yoshanuikabundi Feb 4, 2025
a7e6a5e
Remove parmed pin
Yoshanuikabundi Mar 7, 2025
04071a4
Merge branch 'main' into colab_py311
Yoshanuikabundi Mar 7, 2025
fec0f73
Pin torchdata <= 0.9.0
Yoshanuikabundi Mar 7, 2025
f7828f6
Make broken parmed example optional
Yoshanuikabundi Mar 7, 2025
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8 changes: 4 additions & 4 deletions devtools/conda-envs/examples_env.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@ channels:
- conda-forge
dependencies:
- pip
- python=3.10
- python=3.11
- jupyterlab>=4
- ipywidgets>=8
# Cookbook
Expand All @@ -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
4 changes: 3 additions & 1 deletion source/_ext/cookbook/globals_.py
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Expand Up @@ -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.

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2 changes: 1 addition & 1 deletion source/_ext/proc_examples.py
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Expand Up @@ -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,
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