Pin tutorial pip-install lines + ESM3_README to commit SHA (#307)

Co-authored-by: Zeming Lin <zlin@biohub.org>

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.

_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.

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",

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"
    ]
   },
   {

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",

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"
    ]
   },

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"
    ]
   },
   {

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"
    ]
   },

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"
    ]
   },

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"

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",