fix: rename geb to dgeb

README.md

@@ -1,71 +1,69 @@
-<h1 align="center">Genomic Embedding Benchmark</h1>
+<h1 align="center">Diverse Genomic Embedding Benchmark</h1>
 
 <p align="center">
-    <a href="https://github.com/tattabio/geb/releases">
-        <img alt="GitHub release" src="https://img.shields.io/github/v/release/tattabio/geb.svg">
+    <a href="https://github.com/tattabio/dgeb/releases">
+        <img alt="GitHub release" src="https://img.shields.io/github/v/release/tattabio/dgeb.svg">
     </a>
     <a href="">
         <img alt="arXiv URL" src="">
     </a>
-    <a href="https://github.com/tattabio/geb/blob/main/LICENSE">
-        <img alt="License" src="https://img.shields.io/github/license/tattabio/geb.svg">
+    <a href="https://github.com/tattabio/dgeb/blob/main/LICENSE">
+        <img alt="License" src="https://img.shields.io/github/license/tattabio/dgeb.svg">
     </a>
-    <a href="https://pepy.tech/project/geb">
-        <img alt="Downloads" src="https://static.pepy.tech/personalized-badge/geb?period=total&units=international_system&left_color=grey&right_color=orange&left_text=Downloads">
+    <a href="https://pepy.tech/project/dgeb">
+        <img alt="Downloads" src="https://static.pepy.tech/personalized-badge/dgeb?period=total&units=international_system&left_color=grey&right_color=orange&left_text=Downloads">
     </a>
 </p>
 
 <h4 align="center">
     <p>
         <a href="#installation">Installation</a> |
         <a href="#usage">Usage</a> |
-        <a href="https://huggingface.co/spaces/GEB">Leaderboard</a> |
+        <a href="https://huggingface.co/spaces/dgeb">Leaderboard</a> |
         <a href="#documentation">Documentation</a> |
         <a href="#citing">Citing</a>
     <p>
 </h4>
 
 <h3 align="center">
-    <a href="https://huggingface.co/spaces/GEB"><img style="float: middle; padding: 10px 10px 10px 10px;" width="100" height="100" src="./docs/images/tatta_logo.png" /></a>
+    <a href="https://huggingface.co/spaces/dgeb"><img style="float: middle; padding: 10px 10px 10px 10px;" width="100" height="100" src="./docs/images/tatta_logo.png" /></a>
 </h3>
 
 ## Installation
 
 TODO(joshua):
+
 ```bash
-pip install geb
+pip install dgeb
 ```
 
 ## Usage
 
-- Using the python script (see [run_geb.py](https://github.com/tattabio/geb/blob/main/run_geb.py)):
+- Using the python script (see [run_dgeb.py](https://github.com/tattabio/geb/blob/main/run_geb.py)):
 
 ```bash
-python run_geb.py --model facebook/esm2_t6_8M_UR50D
+python run_dgeb.py --model facebook/esm2_t6_8M_UR50D
 ```
 
-
 - Using the python API:
 
 ```py
-import geb
+import dgeb
 
-model = geb.get_model("facebook/esm2_t6_8M_UR50D")
-tasks = geb.get_tasks_by_modality(geb.Modality.PROTEIN)
-evaluation = geb.GEB(tasks=tasks)
+model = dgeb.get_model("facebook/esm2_t6_8M_UR50D")
+tasks = dgeb.get_tasks_by_modality(geb.Modality.PROTEIN)
+evaluation = dgeb.DGEB(tasks=tasks)
 evaluation.run(model, output_folder="results")
 ```
 
-
 ### Using a custom model
 
-Custom models should be wrapped with the `geb.models.BioSeqTransformer` abstract class, and specify the modality, number of layers, and embedding dimension. See see [models.py](https://github.com/tattabio/geb/blob/main/geb/models.py) for additional examples on custom model loading and inference.
-
+Custom models should be wrapped with the `dgeb.models.BioSeqTransformer` abstract class, and specify the modality, number of layers, and embedding dimension. See see [models.py](https://github.com/tattabio/geb/blob/main/geb/models.py) for additional examples on custom model loading and inference.
 
 ```python
-import geb
-from geb.models import BioSeqTransformer
-from geb.modality import Modality
+import dgeb
+from dgeb.models import BioSeqTransformer
+from dgeb.modality import Modality
 
 class MyModel(BioSeqTransformer):
 
@@ -83,38 +81,38 @@ class MyModel(BioSeqTransformer):
 
 
 model = MyModel()
-tasks = geb.get_tasks_by_modality(model.modality)
+tasks = dgeb.get_tasks_by_modality(model.modality)
 evaluation = MTEB(tasks=tasks)
 evaluation.run(model)
 ```
 
 ### Evaluating on a custom dataset
 
-TODO(andre): Update this section 
+TODO(andre): Update this section
 
 To evaluate on a custom task, you can run the following code on your custom task.
 
 ```python
-import geb
-from geb.tasks import AbsTask
+import dgeb
+from dgeb.tasks import AbsTask
 
 class MyCustomTask(AbsTask):
     def run(
         self, model: BioSeqTransformer, layers: Optional[List[int]] = None
     ) -> TaskResult:
         pass
 
-model = geb.models.ESM("facebook/esm2_t6_8M_UR50D")
-evaluation = geb.GEB(tasks=[MyCustomTask()])
+model = dgeb.models.ESM("facebook/esm2_t6_8M_UR50D")
+evaluation = dgeb.DGEB(tasks=[MyCustomTask()])
 evaluation.run(model)
 ```
 
 </details>
 
 ## Citing
 
-GEB was introduced in "[GEB: Genomic Embedding Benchmark]()", feel free to cite:
+dgeb was introduced in "[DGEB: Diverse Genomic Embedding Benchmark]()", feel free to cite:
 
 TODO(andre): bibtex
 
-For works that have used GEB for benchmarking, you can find them on the [leaderboard](https://huggingface.co/spaces/tattabio/GEB/leaderboard).
+For works that have used dgeb for benchmarking, you can find them on the [leaderboard](https://huggingface.co/spaces/tattabio/DGEB/leaderboard).

plot_benchmarks.py

@@ -10,8 +10,8 @@
 import pandas as pd
 import seaborn as sns
 
-from geb.geb import get_all_tasks, get_output_folder, get_tasks_by_name
-from geb.tasks.tasks import TaskResult
+from dgeb.geb import get_all_tasks, get_output_folder, get_tasks_by_name
+from dgeb.tasks.tasks import TaskResult
 
 ALL_TASKS = [task.metadata.id for task in get_all_tasks()]