Merge branch 'main' into from_binder_to_colab

Author: atravitz

.pre-commit-config.yaml

@@ -5,11 +5,11 @@ ci:
 
 files: (^notebooks)
 repos:
-  - repo: https://github.com/psf/black
-    rev: 25.1.0
+  - repo: https://github.com/psf/black-pre-commit-mirror
+    rev: 25.9.0
     hooks:
       - id: black
-  - repo: https://github.com/psf/black
-    rev: 25.1.0
+  - repo: https://github.com/psf/black-pre-commit-mirror
+    rev: 25.9.0
     hooks:
       - id: black-jupyter

showcase/OFE-color-horizontal.png

@@ -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"
    ]
   },
   {
@@ -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",