Update Colab

notebooks/OpenFold.ipynb

@@ -101,11 +101,6 @@
         "\n",
         "      PATH=%env PATH\n",
         "      %env PATH=/opt/conda/bin:{PATH}\n",
-        "      %shell conda update -qy conda \\\n",
-        "          && conda install -qy -c conda-forge \\\n",
-        "            python=3.7 \\\n",
-        "            openmm=7.5.1 \\\n",
-        "            pdbfixer\n",
         "      pbar.update(80)\n",
         "\n",
         "      # Create a ramdisk to store a database chunk to make Jackhmmer run fast.\n",
@@ -148,7 +143,7 @@
         "      %shell git clone {GIT_REPO} openfold\n",
         "      pbar.update(8)\n",
         "      # Install the required versions of all dependencies.\n",
-        "      %shell pip3 install -r ./openfold/requirements.txt\n",
+        "      %shell conda env update -n base --file openfold/environment.yml\n",
         "      # Run setup.py to install only Openfold.\n",
         "      %shell pip3 install --no-dependencies ./openfold\n",
         "      pbar.update(10)\n",
@@ -171,13 +166,7 @@
         "      pbar.update(55)\n",
         "except subprocess.CalledProcessError:\n",
         "  print(captured)\n",
-        "  raise\n",
-        "\n",
-        "import jax\n",
-        "if jax.local_devices()[0].platform == 'tpu':\n",
-        "  raise RuntimeError('Colab TPU runtime not supported. Change it to GPU via Runtime -> Change Runtime Type -> Hardware accelerator -> GPU.')\n",
-        "elif jax.local_devices()[0].platform == 'cpu':\n",
-        "  raise RuntimeError('Colab CPU runtime not supported. Change it to GPU via Runtime -> Change Runtime Type -> Hardware accelerator -> GPU.')"
+        "  raise"
       ],
       "execution_count": null,
       "outputs": []