diff --git a/showcase/OFE-color-horizontal.png b/showcase/OFE-color-horizontal.png new file mode 100644 index 0000000..f3ca65b Binary files /dev/null and b/showcase/OFE-color-horizontal.png differ diff --git a/showcase/openFE_logo3.png b/showcase/openFE_logo3.png deleted file mode 100644 index 698b475..0000000 Binary files a/showcase/openFE_logo3.png and /dev/null differ diff --git a/showcase/openfe_showcase.ipynb b/showcase/openfe_showcase.ipynb index c78dc35..9ca40ec 100644 --- a/showcase/openfe_showcase.ipynb +++ b/showcase/openfe_showcase.ipynb @@ -5,9 +5,9 @@ "id": "cb0d308b-8f50-4ac9-a8a3-550d8a2e3feb", "metadata": {}, "source": [ - " \n", + " \n", "\n", - "# The OpenFE Showcase: Relative Binding Free Energies in the TYK2 System" + "# OpenFE Showcase: Relative Binding Free Energies in the TYK2 System" ] }, { @@ -69,7 +69,7 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "id": "-jX9udRGehD3", "metadata": { "colab": { @@ -86,14 +86,17 @@ "# 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/v1.6.0/OpenFEforge-1.6.0-Linux-x86_64.sh\")" + " condacolab.install_from_url(\"https://github.com/OpenFreeEnergy/openfe/releases/download/v1.6.1/OpenFEforge-1.6.1-Linux-x86_64.sh\")" ] }, { "cell_type": "code", - "execution_count": 2, + "execution_count": null, "id": "dlCARZ2_fAI4", "metadata": { "colab": { @@ -108,12 +111,18 @@ "source": [ "# NBVAL_SKIP\n", "# Only run this cell if on google colab\n", + "# Colab will say the runtime crashed, but this is expected with `install_from_url`, and you should continue running the next cell\n", + "\n", "import os\n", "if \"COLAB_RELEASE_TAG\" in os.environ:\n", " import condacolab\n", " 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",