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Merged
atravitz merged 6 commits into from
Oct 7, 2025
Merged

bump to 1.6.1 #231

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8f76c7b
update logo
atravitz Oct 3, 2025
39d2725
bump to v1.6.1
atravitz Oct 3, 2025
98c6166
fix image
atravitz Oct 3, 2025
fc8bdaa
adding workarounds for colab bugs
atravitz Oct 7, 2025
e9a2525
add comment for clarity
atravitz Oct 7, 2025
bf29f24
Merge branch 'main' into bump_to_1.6.1
atravitz Oct 7, 2025
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19 changes: 14 additions & 5 deletions showcase/openfe_showcase.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -5,9 +5,9 @@
"id": "cb0d308b-8f50-4ac9-a8a3-550d8a2e3feb",
"metadata": {},
"source": [
"<img src=\"openFE_logo3.png\" width=\"100\"> \n",
"<img src=\"OFE-color-horizontal.png\" width=\"300\"> \n",
"\n",
"# The OpenFE Showcase: Relative Binding Free Energies in the TYK2 System"
"# OpenFE Showcase: Relative Binding Free Energies in the TYK2 System"
]
},
{
Expand Down Expand Up @@ -69,7 +69,7 @@
},
{
"cell_type": "code",
"execution_count": 1,
"execution_count": null,
"id": "-jX9udRGehD3",
"metadata": {
"colab": {
Expand All @@ -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": {
Expand All @@ -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",
Expand Down
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