From da603081f9af30b5f12f67b1c4626d692d51c130 Mon Sep 17 00:00:00 2001 From: Zeming Lin Date: Wed, 27 May 2026 12:28:12 +0000 Subject: [PATCH] Pin tutorial pip-install lines + ESM3_README to commit SHA --- README.md | 4 ++-- _assets/ESM3_README.md | 4 ++-- cookbook/local/open_generate.ipynb | 2 +- cookbook/tutorials/embed.ipynb | 5 +++-- cookbook/tutorials/esm3_generate.ipynb | 2 +- cookbook/tutorials/esm3_guided_generation.ipynb | 2 +- cookbook/tutorials/esmc_layer_sweep.ipynb | 2 +- cookbook/tutorials/esmc_mutation_scoring.ipynb | 2 +- cookbook/tutorials/esmfold2.ipynb | 2 +- cookbook/tutorials/esmprotein.ipynb | 2 +- cookbook/tutorials/gfp_design.ipynb | 2 +- 11 files changed, 15 insertions(+), 14 deletions(-) diff --git a/README.md b/README.md index 9ca668c..2066ca0 100644 --- a/README.md +++ b/README.md @@ -97,7 +97,7 @@ Note that our API migrated from forge.evolutionaryscale.ai to [biohub.ai](https: To get started with ESM, install the python library using `pip`: ``` -pip install "esm @ git+https://github.com/Biohub/esm.git@c94ed8d763bbd7088b296949e5b401e8ea12073a" +pip install esm@git+https://github.com/Biohub/esm.git@c94ed8d ``` Then import the necessary libraries and instantiate your desired model. @@ -221,7 +221,7 @@ with open("1mht_pred.cif", "w") as f: Install the `esm` Python package ``` -pip install "esm @ git+https://github.com/Biohub/esm.git@c94ed8d763bbd7088b296949e5b401e8ea12073a" +pip install esm@git+https://github.com/Biohub/esm.git@c94ed8d ``` Import the necessary libraries. diff --git a/_assets/ESM3_README.md b/_assets/ESM3_README.md index 2e6421e..66796e9 100644 --- a/_assets/ESM3_README.md +++ b/_assets/ESM3_README.md @@ -34,7 +34,7 @@ The code for ESM3 is available from Github and weights for esm3-sm-open-v1 is av First install the python library using `pip`: ``` -pip install esm +pip install esm@git+https://github.com/Biohub/esm.git@c94ed8d ``` Then import the necessary libraries and instantiate your model. Use your token from the [Biohub platform](https://biohub.ai") @@ -54,7 +54,7 @@ The following code demonstrates how to run ESM3 locally and generate a simple se First install the python library using `pip`: ``` -pip install esm +pip install esm@git+https://github.com/Biohub/esm.git@c94ed8d ``` Then import the necessary libraries for your model. diff --git a/cookbook/local/open_generate.ipynb b/cookbook/local/open_generate.ipynb index b9dd9a8..189a2f3 100644 --- a/cookbook/local/open_generate.ipynb +++ b/cookbook/local/open_generate.ipynb @@ -32,7 +32,7 @@ "outputs": [], "source": [ "%set_env TOKENIZERS_PARALLELISM=false\n", - "!pip install esm\n", + "!pip install esm@git+https://github.com/Biohub/esm.git@c94ed8d\n", "import numpy as np\n", "import torch\n", "\n", diff --git a/cookbook/tutorials/embed.ipynb b/cookbook/tutorials/embed.ipynb index 769024e..523461a 100644 --- a/cookbook/tutorials/embed.ipynb +++ b/cookbook/tutorials/embed.ipynb @@ -23,8 +23,9 @@ "outputs": [], "source": [ "# If you are working in colab, uncomment these lines to install dependencies\n", - "# ! pip install esm\n", - "# ! pip install matplotlib" + "# ! pip install esm@git+https://github.com/Biohub/esm.git@c94ed8d\n", + "# ! pip install matplotlib\n", + "# ! pip install seaborn\n" ] }, { diff --git a/cookbook/tutorials/esm3_generate.ipynb b/cookbook/tutorials/esm3_generate.ipynb index 86fba03..c391f3a 100644 --- a/cookbook/tutorials/esm3_generate.ipynb +++ b/cookbook/tutorials/esm3_generate.ipynb @@ -31,7 +31,7 @@ "source": [ "%set_env TOKENIZERS_PARALLELISM=false\n", "# If you are working in colab, uncomment these lines to install dependencies\n", - "# !pip install esm\n", + "# !pip install esm@git+https://github.com/Biohub/esm.git@c94ed8d\n", "# !pip install py3Dmol\n", "\n", "import numpy as np\n", diff --git a/cookbook/tutorials/esm3_guided_generation.ipynb b/cookbook/tutorials/esm3_guided_generation.ipynb index d2f0698..59364b2 100644 --- a/cookbook/tutorials/esm3_guided_generation.ipynb +++ b/cookbook/tutorials/esm3_guided_generation.ipynb @@ -38,7 +38,7 @@ "outputs": [], "source": [ "# # If you are working in colab, uncomment these lines to install dependencies\n", - "# !pip install esm\n", + "# !pip install esm@git+https://github.com/Biohub/esm.git@c94ed8d\n", "# !pip install py3dmol" ] }, diff --git a/cookbook/tutorials/esmc_layer_sweep.ipynb b/cookbook/tutorials/esmc_layer_sweep.ipynb index 757b4a9..e495e82 100644 --- a/cookbook/tutorials/esmc_layer_sweep.ipynb +++ b/cookbook/tutorials/esmc_layer_sweep.ipynb @@ -73,7 +73,7 @@ "outputs": [], "source": [ "# If you are working in colab, uncomment these lines to install dependencies\n", - "# !pip install esm" + "# !pip install esm@git+https://github.com/Biohub/esm.git@c94ed8d" ] }, { diff --git a/cookbook/tutorials/esmc_mutation_scoring.ipynb b/cookbook/tutorials/esmc_mutation_scoring.ipynb index ff73787..4b91205 100644 --- a/cookbook/tutorials/esmc_mutation_scoring.ipynb +++ b/cookbook/tutorials/esmc_mutation_scoring.ipynb @@ -77,7 +77,7 @@ "outputs": [], "source": [ "# If you are working in colab, uncomment these lines to install dependencies\n", - "# !pip install esm\n", + "# !pip install esm@git+https://github.com/Biohub/esm.git@c94ed8d\n", "# !pip install py3dmol" ] }, diff --git a/cookbook/tutorials/esmfold2.ipynb b/cookbook/tutorials/esmfold2.ipynb index 615b72e..ccb382e 100644 --- a/cookbook/tutorials/esmfold2.ipynb +++ b/cookbook/tutorials/esmfold2.ipynb @@ -57,7 +57,7 @@ "outputs": [], "source": [ "# If you are working in colab, uncomment these lines to install dependencies\n", - "# !pip install esm\n", + "# !pip install esm@git+https://github.com/Biohub/esm.git@c94ed8d\n", "# !pip install py3dmol" ] }, diff --git a/cookbook/tutorials/esmprotein.ipynb b/cookbook/tutorials/esmprotein.ipynb index 5f81fb1..d68a1c8 100644 --- a/cookbook/tutorials/esmprotein.ipynb +++ b/cookbook/tutorials/esmprotein.ipynb @@ -52,7 +52,7 @@ "outputs": [], "source": [ "# If you are working in colab, uncomment these lines to install dependencies\n", - "# ! pip install esm\n", + "# ! pip install esm@git+https://github.com/Biohub/esm.git@c94ed8d\n", "# ! pip install py3Dmol\n", "# ! pip install matplotlib\n", "# ! pip install dna-features-viewer" diff --git a/cookbook/tutorials/gfp_design.ipynb b/cookbook/tutorials/gfp_design.ipynb index 384f53d..9dc7a7d 100644 --- a/cookbook/tutorials/gfp_design.ipynb +++ b/cookbook/tutorials/gfp_design.ipynb @@ -41,7 +41,7 @@ "outputs": [], "source": [ "# If you are working in colab, uncomment these lines to install dependencies\n", - "# !pip install esm\n", + "# !pip install esm@git+https://github.com/Biohub/esm.git@c94ed8d\n", "# !pip install py3Dmol\n", "\n", "from IPython.display import clear_output\n",