Remove sed patch for jax 0.4

sokrypton · Dec 28, 2023 · 4e9714a · 4e9714a
1 parent 5fd3a84
commit 4e9714a
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diff --git a/AlphaFold2.ipynb b/AlphaFold2.ipynb
@@ -149,8 +149,6 @@
         "  os.system(\"pip install -q --no-warn-conflicts 'colabfold[alphafold-minus-jax] @ git+https://github.com/sokrypton/ColabFold'\")\n",
         "  os.system(\"ln -s /usr/local/lib/python3.*/dist-packages/colabfold colabfold\")\n",
         "  os.system(\"ln -s /usr/local/lib/python3.*/dist-packages/alphafold alphafold\")\n",
-        "  # patch for jax > 0.3.25\n",
-        "  os.system(\"sed -i 's/weights = jax.nn.softmax(logits)/logits=jnp.clip(logits,-1e8,1e8);weights=jax.nn.softmax(logits)/g' alphafold/model/modules.py\")\n",
         "  os.system(\"touch COLABFOLD_READY\")\n",
         "\n",
         "if USE_AMBER or USE_TEMPLATES:\n",

diff --git a/batch/AlphaFold2_batch.ipynb b/batch/AlphaFold2_batch.ipynb
@@ -130,7 +130,6 @@
         "  pip install -q --no-warn-conflicts \"colabfold[alphafold-minus-jax] @ git+https://github.com/sokrypton/ColabFold\"\n",
         "  ln -s /usr/local/lib/python3.*/dist-packages/colabfold colabfold\n",
         "  ln -s /usr/local/lib/python3.*/dist-packages/alphafold alphafold\n",
-        "  sed -i 's/weights = jax.nn.softmax(logits)/logits=jnp.clip(logits,-1e8,1e8);weights=jax.nn.softmax(logits)/g' alphafold/model/modules.py\n",
         "  touch COLABFOLD_READY\n",
         "fi\n",
         "\n",