fix links

Author: markgeejw

mise.dev.toml

@@ -4,3 +4,4 @@ _.python.venv = ".pixi/envs/dev"
 
 [tools]
 dprint = "latest"
+pandoc = "latest"

mise.toml

@@ -3,4 +3,4 @@ pandoc = "latest"
 pixi = "latest"
 
 [env]
-# _.python.venv = ".pixi/envs/default"
+_.python.venv = ".pixi/envs/default"

source/python-api/api-reference/embedding.rst

@@ -3,7 +3,7 @@ openprotein.embeddings
 
 Create embeddings for your protein sequences using open-source and proprietary models!
 
-Note that for PoET Models, you will also need to utilize our :doc:`align <align>`. workflow.
+Note that for PoET Models, you will also need to utilize our :doc:`align <align>` workflow.
 
 Interface 
 ---------

source/python-api/foundation-models/SVD-embeddings.ipynb

@@ -207,7 +207,7 @@
       "source": [
         "## Next steps\n",
         "\n",
-        "For more information, visit the [Embeddings API](https://docs.openprotein.ai/api-python/embedding.html) reference."
+        "For more information, visit the [Embeddings API](../api-reference/embedding.html) reference."
       ]
     }
   ],

source/python-api/foundation-models/attention-maps.ipynb

@@ -180,7 +180,7 @@
       "source": [
         "## Next steps\n",
         "\n",
-        "For more information, visit the [Embeddings API](https://docs.openprotein.ai/api-python/embedding.html) reference."
+        "For more information, visit the [Embeddings API](../api-reference/embedding.html) reference."
       ]
     }
   ],

source/python-api/foundation-models/logits.ipynb

@@ -397,7 +397,7 @@
       "source": [
         "## Next steps\n",
         "\n",
-        "For more information, visit the [Embeddings API](https://docs.openprotein.ai/api-python/embedding.html) reference."
+        "For more information, visit the [Embeddings API](../api-reference/embedding.html) reference."
       ]
     }
   ],

source/python-api/poet/creating-MSA.ipynb

@@ -222,11 +222,11 @@
       "source": [
         "## Next steps\n",
         "\n",
-        "Learn more about the MSAs on our [MSA API](https://docs.openprotein.ai/api-python/align.html) page.\n",
+        "Learn more about the MSAs on our [MSA API](../api-reference/align.html#openprotein.align.AlignAPI.create_msa) page.\n",
         "\n",
-        "You can use your MSA to create a prompt and start generating, scoring, and analyzing sequences with our state-of-the-art PoET model. See [Creating a prompt](https://colab.research.google.com/drive/1BTuPVz4B5jLNvnsEXSJhSjBrOEWJ_ygj?usp=drive_link) for instructions.\n",
+        "You can use your MSA to create a prompt and start generating, scoring, and analyzing sequences with our state-of-the-art PoET model. See [Creating a prompt](./creating-prompt.ipynb) for instructions.\n",
         "\n",
-        "You can also use your MSA with our structure prediction tool to visualize the 3D structure of sequence. See [Structure prediction](https://docs.openprotein.ai/api-python/demos/fold_demo.html) for more information."
+        "You can also use your MSA with our structure prediction tool to visualize the 3D structure of sequence. See [Using AlphaFold2](../structure-prediction/Using_AlphaFold2.html) for more information."
       ]
     }
   ],

source/python-api/poet/scoring-sequences.ipynb

@@ -16,7 +16,7 @@
         "\n",
         "## What you need before getting started\n",
         "\n",
-        "You need a previously generated multiple sequence alignment (MSA) and a prompt. See [Creating an MSA](https://colab.research.google.com/drive/1uoX7g6CBYU_PQzh5mEI6WAR8MbVDLq9A#scrollTo=kB3_IJ-HZh-g) and [Creating a prompt](https://colab.research.google.com/drive/1BTuPVz4B5jLNvnsEXSJhSjBrOEWJ_ygj#scrollTo=XnXhgmXVbMxD) for more information.\n",
+        "You need a previously generated multiple sequence alignment (MSA) and a prompt. See [Creating an MSA](./creating-MSA.ipynb) and [Creating a prompt](./creating-prompt.ipynb) for more information.\n",
         "\n",
         "## Scoring your sequences\n",
         "\n",
@@ -129,7 +129,7 @@
       "source": [
         "## Next steps\n",
         "\n",
-        "Learn more about the `score` function in our [PoET API](https://docs.openprotein.ai/api-python/embedding.html#openprotein.api.embedding.PoETModel.score) page.\n",
+        "Learn more about the `score` function in our [PoET Model API](../api-reference/embedding.html#openprotein.embeddings.PoETModel.score) page.\n",
         "\n",
         "Now that you have a list of sequence variants of interest, you can use the PoET model to perform a [single site analysis] to score all single substitution variants of your parent sequence conditioned on the prompt. See [Using PoET single site analysis](https://colab.research.google.com/drive/1iWZkoQtQxbLoxrzhUeHFTNO5TtWoMIvX?usp=drive_link) for more information."
       ]

source/python-api/poet/single-site-analysis.ipynb

@@ -10,11 +10,11 @@
         "\n",
         "This tutorial shows you how to perform a single site analysis using PoET, which scores all single substitution variants of an input sequence with a given prompt. Use this as a starting point to design single mutant or combinatorial variant libraries and predict the strength of protein activity.\n",
         "\n",
-        "Find more information about the PoET model on our [PoET API](https://docs.openprotein.ai/api-python/embedding.html#openprotein.api.embedding.PoETModel) page.\n",
+        "Find more information about the PoET model on our [PoET model API](../api-reference/embedding.html#openprotein.embeddings.PoETModel) page.\n",
         "\n",
         "## What you need before getting started\n",
         "\n",
-        "You need a prompt and a multiple sequence alignment (MSA). For more information, see [Creating a multiple sequence alignment](https://colab.research.google.com/drive/1uoX7g6CBYU_PQzh5mEI6WAR8MbVDLq9A?usp=drive_link) and [Creating a prompt](https://colab.research.google.com/drive/1BTuPVz4B5jLNvnsEXSJhSjBrOEWJ_ygj?usp=drive_link)."
+        "You need a prompt and a multiple sequence alignment (MSA). For more information, see [Creating a multiple sequence alignment](./creating-MSA.ipynb) and [Creating a prompt](./creating-prompt.ipynb)."
       ]
     },
     {
@@ -36,7 +36,6 @@
       },
       "outputs": [],
       "source": [
-        "\n",
         "poet = session.embedding.get_model(\"poet\")\n",
         "sspjob = poet.single_site(prompt=prompt, sequence=\"MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQRVEDAFYTLVREIRQYRLKKISKEEKTPGCVKIKKCIIM\".encode())"
       ]