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add torchvision and datetime workarounds to all notebooks using colab (#253)
* add torchvision and datetime workarounds to all notebooks using colab * execute septop notebook * fix deprecation warning
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7 files changed

+154
-67
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7 files changed

+154
-67
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‎abfe_tutorial/abfe_tutorial.ipynb‎

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"# Only run this cell if on google colab\n",
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"import os\n",
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"if \"COLAB_RELEASE_TAG\" in os.environ:\n",
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" # fix for colab's torchvision causing issues\n",
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" !rm -r /usr/local/lib/python3.12/dist-packages/torchvision\n",
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" \n",
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" !pip install -q condacolab\n",
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" import condacolab\n",
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" condacolab.install_from_url(\"https://github.com/OpenFreeEnergy/openfe/releases/download/v1.7.0/OpenFEforge-1.7.0-Linux-x86_64.sh\")"
@@ -65,6 +68,10 @@
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" import locale\n",
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" locale.getpreferredencoding = lambda: \"UTF-8\"\n",
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" !mkdir inputs && cd inputs && openfe fetch rbfe-tutorial\n",
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" # quick fix for https://github.com/conda-incubator/condacolab/issues/75\n",
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" # if deprecation warnings persist, rerun this cell\n",
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" import warnings\n",
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" warnings.filterwarnings(action=\"ignore\", message=r\"datetime.datetime.utcnow\") \n",
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" for _ in range(3):\n",
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" # Sometimes we have to re-run the check\n",
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" try:\n",

‎ahfe_tutorial/ahfe_tutorial.ipynb‎

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"# Only run this cell if on google colab\n",
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"import os\n",
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"if \"COLAB_RELEASE_TAG\" in os.environ:\n",
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" # fix for colab's torchvision causing issues\n",
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" !rm -r /usr/local/lib/python3.12/dist-packages/torchvision\n",
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" \n",
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" !pip install -q condacolab\n",
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" import condacolab\n",
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" condacolab.install_from_url(\"https://github.com/OpenFreeEnergy/openfe/releases/download/v1.7.0/OpenFEforge-1.7.0-Linux-x86_64.sh\")"
@@ -65,6 +68,10 @@
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" import locale\n",
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" locale.getpreferredencoding = lambda: \"UTF-8\"\n",
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" !mkdir inputs && cd inputs && openfe fetch rbfe-tutorial\n",
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" # quick fix for https://github.com/conda-incubator/condacolab/issues/75\n",
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" # if deprecation warnings persist, rerun this cell\n",
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" import warnings\n",
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" warnings.filterwarnings(action=\"ignore\", message=r\"datetime.datetime.utcnow\") \n",
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" for _ in range(3):\n",
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" # Sometimes we have to re-run the check\n",
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" try:\n",

‎openmm_md/plain_md.ipynb‎

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},
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{
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"cell_type": "code",
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"execution_count": 1,
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"execution_count": null,
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"id": "6559bc05",
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"metadata": {},
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"outputs": [],
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"# Only run this cell if on google colab\n",
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"import os\n",
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"if \"COLAB_RELEASE_TAG\" in os.environ:\n",
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" # fix for colab's torchvision causing issues\n",
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" !rm -r /usr/local/lib/python3.12/dist-packages/torchvision\n",
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" \n",
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" !pip install -q condacolab\n",
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" import condacolab\n",
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" condacolab.install_from_url(\"https://github.com/OpenFreeEnergy/openfe/releases/download/v1.7.0/OpenFEforge-1.7.0-Linux-x86_64.sh\")"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 2,
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"execution_count": null,
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"id": "eb1368ca",
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"metadata": {},
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"outputs": [],
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" import locale\n",
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" locale.getpreferredencoding = lambda: \"UTF-8\"\n",
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" !mkdir inputs && cd inputs && openfe fetch rbfe-tutorial\n",
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" # quick fix for https://github.com/conda-incubator/condacolab/issues/75\n",
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" # if deprecation warnings persist, rerun this cell\n",
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" import warnings\n",
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" warnings.filterwarnings(action=\"ignore\", message=r\"datetime.datetime.utcnow\") \n",
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" for _ in range(3):\n",
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" # Sometimes we have to re-run the check\n",
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" try:\n",

‎openmm_rbfe/OpenFE_showcase_1_RBFE_of_T4lysozyme.ipynb‎

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‎openmm_septop/ligand_network.graphml‎

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‎openmm_septop/septop_tutorial.ipynb‎

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‎plotting_rbfes_with_cinnabar/PlottingFreeEnergiesUsingCinnabar.ipynb‎

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"# Only run this cell if on google colab\n",
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"import os\n",
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"if \"COLAB_RELEASE_TAG\" in os.environ:\n",
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" # fix for colab's torchvision causing issues\n",
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" !rm -r /usr/local/lib/python3.12/dist-packages/torchvision\n",
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" \n",
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" !pip install -q condacolab\n",
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" import condacolab\n",
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" condacolab.install_from_url(\"https://github.com/OpenFreeEnergy/openfe/releases/download/v1.7.0/OpenFEforge-1.7.0-Linux-x86_64.sh\")"
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" import locale\n",
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" locale.getpreferredencoding = lambda: \"UTF-8\"\n",
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" !mkdir inputs && cd inputs && openfe fetch rbfe-tutorial\n",
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" # quick fix for https://github.com/conda-incubator/condacolab/issues/75\n",
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" # if deprecation warnings persist, rerun this cell\n",
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" import warnings\n",
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" warnings.filterwarnings(action=\"ignore\", message=r\"datetime.datetime.utcnow\") \n",
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" for _ in range(3):\n",
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" # Sometimes we have to re-run the check\n",
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" try:\n",

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