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Merged
atravitz merged 3 commits into from
Oct 24, 2025
Merged

add torchvision and datetime workarounds to all notebooks using colab #253

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9a7907c
add torchvision and datetime workarounds to all notebooks using colab
atravitz Oct 24, 2025
ba254eb
execute septop notebook
atravitz Oct 24, 2025
8f3fa4c
fix deprecation warning
atravitz Oct 24, 2025
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7 changes: 7 additions & 0 deletions abfe_tutorial/abfe_tutorial.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -45,6 +45,9 @@
"# Only run this cell if on google colab\n",
"import os\n",
"if \"COLAB_RELEASE_TAG\" in os.environ:\n",
" # fix for colab's torchvision causing issues\n",
" !rm -r /usr/local/lib/python3.12/dist-packages/torchvision\n",
" \n",
" !pip install -q condacolab\n",
" import condacolab\n",
" condacolab.install_from_url(\"https://github.com/OpenFreeEnergy/openfe/releases/download/v1.7.0/OpenFEforge-1.7.0-Linux-x86_64.sh\")"
Expand All @@ -65,6 +68,10 @@
" import locale\n",
" locale.getpreferredencoding = lambda: \"UTF-8\"\n",
" !mkdir inputs && cd inputs && openfe fetch rbfe-tutorial\n",
" # quick fix for https://github.com/conda-incubator/condacolab/issues/75\n",
" # if deprecation warnings persist, rerun this cell\n",
" import warnings\n",
" warnings.filterwarnings(action=\"ignore\", message=r\"datetime.datetime.utcnow\") \n",
" for _ in range(3):\n",
" # Sometimes we have to re-run the check\n",
" try:\n",
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7 changes: 7 additions & 0 deletions ahfe_tutorial/ahfe_tutorial.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -45,6 +45,9 @@
"# Only run this cell if on google colab\n",
"import os\n",
"if \"COLAB_RELEASE_TAG\" in os.environ:\n",
" # fix for colab's torchvision causing issues\n",
" !rm -r /usr/local/lib/python3.12/dist-packages/torchvision\n",
" \n",
" !pip install -q condacolab\n",
" import condacolab\n",
" condacolab.install_from_url(\"https://github.com/OpenFreeEnergy/openfe/releases/download/v1.7.0/OpenFEforge-1.7.0-Linux-x86_64.sh\")"
Expand All @@ -65,6 +68,10 @@
" import locale\n",
" locale.getpreferredencoding = lambda: \"UTF-8\"\n",
" !mkdir inputs && cd inputs && openfe fetch rbfe-tutorial\n",
" # quick fix for https://github.com/conda-incubator/condacolab/issues/75\n",
" # if deprecation warnings persist, rerun this cell\n",
" import warnings\n",
" warnings.filterwarnings(action=\"ignore\", message=r\"datetime.datetime.utcnow\") \n",
" for _ in range(3):\n",
" # Sometimes we have to re-run the check\n",
" try:\n",
Expand Down
11 changes: 9 additions & 2 deletions openmm_md/plain_md.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -78,7 +78,7 @@
},
{
"cell_type": "code",
"execution_count": 1,
"execution_count": null,
"id": "6559bc05",
"metadata": {},
"outputs": [],
Expand All @@ -87,14 +87,17 @@
"# Only run this cell if on google colab\n",
"import os\n",
"if \"COLAB_RELEASE_TAG\" in os.environ:\n",
" # fix for colab's torchvision causing issues\n",
" !rm -r /usr/local/lib/python3.12/dist-packages/torchvision\n",
" \n",
" !pip install -q condacolab\n",
" import condacolab\n",
" condacolab.install_from_url(\"https://github.com/OpenFreeEnergy/openfe/releases/download/v1.7.0/OpenFEforge-1.7.0-Linux-x86_64.sh\")"
]
},
{
"cell_type": "code",
"execution_count": 2,
"execution_count": null,
"id": "eb1368ca",
"metadata": {},
"outputs": [],
Expand All @@ -107,6 +110,10 @@
" import locale\n",
" locale.getpreferredencoding = lambda: \"UTF-8\"\n",
" !mkdir inputs && cd inputs && openfe fetch rbfe-tutorial\n",
" # quick fix for https://github.com/conda-incubator/condacolab/issues/75\n",
" # if deprecation warnings persist, rerun this cell\n",
" import warnings\n",
" warnings.filterwarnings(action=\"ignore\", message=r\"datetime.datetime.utcnow\") \n",
" for _ in range(3):\n",
" # Sometimes we have to re-run the check\n",
" try:\n",
Expand Down
14 changes: 8 additions & 6 deletions openmm_rbfe/OpenFE_showcase_1_RBFE_of_T4lysozyme.ipynb
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73 changes: 73 additions & 0 deletions openmm_septop/ligand_network.graphml
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102 changes: 43 additions & 59 deletions openmm_septop/septop_tutorial.ipynb
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7 changes: 7 additions & 0 deletions plotting_rbfes_with_cinnabar/PlottingFreeEnergiesUsingCinnabar.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -31,6 +31,9 @@
"# Only run this cell if on google colab\n",
"import os\n",
"if \"COLAB_RELEASE_TAG\" in os.environ:\n",
" # fix for colab's torchvision causing issues\n",
" !rm -r /usr/local/lib/python3.12/dist-packages/torchvision\n",
" \n",
" !pip install -q condacolab\n",
" import condacolab\n",
" condacolab.install_from_url(\"https://github.com/OpenFreeEnergy/openfe/releases/download/v1.7.0/OpenFEforge-1.7.0-Linux-x86_64.sh\")"
Expand All @@ -51,6 +54,10 @@
" import locale\n",
" locale.getpreferredencoding = lambda: \"UTF-8\"\n",
" !mkdir inputs && cd inputs && openfe fetch rbfe-tutorial\n",
" # quick fix for https://github.com/conda-incubator/condacolab/issues/75\n",
" # if deprecation warnings persist, rerun this cell\n",
" import warnings\n",
" warnings.filterwarnings(action=\"ignore\", message=r\"datetime.datetime.utcnow\") \n",
" for _ in range(3):\n",
" # Sometimes we have to re-run the check\n",
" try:\n",
Expand Down
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