Removing deprecated references to bio_embeddings

biotrainer/embedders/embedding_service.py

@@ -14,7 +14,7 @@
 from ..protocols import Protocol
 from ..utilities import read_FASTA
 
-# Defines if reduced embeddings from bio_embeddings should be used.
+# Defines if reduced embeddings should be used.
 # Reduced means that the per-residue embeddings are reduced to a per-sequence embedding
 _REQUIRES_REDUCED_EMBEDDINGS = {
     Protocol.residue_to_class: False,

examples/custom_embedder/README.md

@@ -1,6 +1,6 @@
 # custom_embedder example
 
-The examples in this folder show how to use a custom embedder that is not included in *bio_embeddings*.
+The examples in this folder show how to use a custom embedder that is not included in *biotrainer*.
 
 **Example models**:
 1. [ESM-2](https://github.com/facebookresearch/esm) large model from

examples/inference/predict.ipynb

@@ -144,7 +144,7 @@
     }
    ],
    "source": [
-    "from bio_embeddings.embed import OneHotEncodingEmbedder"
+    "from biotrainer.embedders import OneHotEncodingEmbedder"
    ]
   },
   {