From 6879b6b38f077289a95cd0e4d71a7fd59c35b822 Mon Sep 17 00:00:00 2001
From: Sebastian <sebastian.franz@iteratec.com>
Date: Thu, 4 Jan 2024 16:40:24 +0100
Subject: [PATCH] Removing deprecated references to bio_embeddings

---
 biotrainer/embedders/embedding_service.py | 2 +-
 examples/custom_embedder/README.md        | 2 +-
 examples/inference/predict.ipynb          | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/biotrainer/embedders/embedding_service.py b/biotrainer/embedders/embedding_service.py
index 52c1ae1f..e6aac452 100644
--- a/biotrainer/embedders/embedding_service.py
+++ b/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,
diff --git a/examples/custom_embedder/README.md b/examples/custom_embedder/README.md
index 02810e28..35332612 100644
--- a/examples/custom_embedder/README.md
+++ b/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
diff --git a/examples/inference/predict.ipynb b/examples/inference/predict.ipynb
index 2a6b33aa..15cda38f 100644
--- a/examples/inference/predict.ipynb
+++ b/examples/inference/predict.ipynb
@@ -144,7 +144,7 @@
     }
    ],
    "source": [
-    "from bio_embeddings.embed import OneHotEncodingEmbedder"
+    "from biotrainer.embedders import OneHotEncodingEmbedder"
    ]
   },
   {