Transformers MolFeat notebook (#11)

** TODO:**
- [x] Add the actual requirements 
- [x] Polish model + fine tuning cells + text
- [x] Check the visualisations / interaction are working as expect on
PaperSpace
- [x] Fix `Run
trilom/file-changes-action@a6ca26c;
Error: undefined` error

---------

Co-authored-by: Alexandre Payot <[email protected]>

.gradient/notebook-tests.yaml

@@ -247,3 +247,11 @@ packed-bert-single-label-classification:
   notebook:
     file: packedBERT_single_label_text_classification.ipynb
     timeout: 10000
+
+#MolFeat Transformer
+molfeat:
+  location: ../molfeat
+  generated: true
+  notebook:
+    file: transformers_molfeat_finetune.ipynb
+    timeout: 1000

dolly2-instruction-following/api/pipeline.py

@@ -95,13 +95,14 @@ def __init__(
         tokenizer: Optional[AutoTokenizer] = None,
         prompt_format: Optional[str] = None,
         end_key: Optional[str] = None,
+        task=None,
         **kwargs,
     ) -> None:
         if sequence_length is not None:
             config.model.sequence_length = sequence_length
         if micro_batch_size is not None:
             config.execution.micro_batch_size = micro_batch_size
-
+        self.task = "text-generation"
         logging.info(f"Creating session")
         session: popxl.Session = inference(config)
         if isinstance(hf_dolly_checkpoint, str):

molfeat/requirements.txt

@@ -0,0 +1,13 @@
+ipywidgets==8.0.6
+awscli==1.27.76
+matplotlib==3.7.1
+molfeat==0.8.8
+transformers==4.28.1
+tabulate==0.9.0
+seaborn==0.12.2
+stmol
+rdkit==2023.3.1
+py3Dmol==2.0.1.post1
+torchinfo==1.7.2
+numpy
+examples-utils[common] @ git+https://github.com/graphcore/examples-utils@latest_stable