Missing `optuna` dependency in `requirements.txt`

[althonos]

Hi @CyrilMa,

Having created a fresh uv environment and installed the dependencies in requirements.txt, trying to run the notebook is met with the following error:

---------------------------------------------------------------------------
ModuleNotFoundError                       Traceback (most recent call last)
Cell In[1], line 15
     12 from IPython.display import display
     14 sys.path.append("..")
---> 15 from proteomelm.ppi.model import prepare_ppi
     16 from notebooks_utils import *
     18 from proteomelm.ppi.model import EnhancedPPIModel

File ~/Code/ProteomeLM/notebooks/../proteomelm/ppi/__init__.py:19
      4 from .config import (
      5     DatasetConfig,
      6     ExperimentConfig,
   (...)     10     get_dscript_config
     11 )
     12 from .data_processing import (
     13     FastaProcessor,
     14     InteractionExtractor,
   (...)     17     create_extractor
     18 )
---> 19 from .feature_extraction import (
     20     PPIFeatureExtractor,
     21     FullProteomeExtractor
     22 )
     23 from .evaluation import (
     24     AttentionAnalyzer,
     25     PerformanceEvaluator
     26 )
     27 from .experiment_runner import (
     28     UnsupervisedExperimentRunner,
     29     SupervisedExperimentRunner,
     30     BatchExperimentRunner
     31 )

File ~/Code/ProteomeLM/notebooks/../proteomelm/ppi/feature_extraction.py:10
      7 from typing import Any, Dict, List, Optional, Tuple
      8 import torch
---> 10 from .model import prepare_ppi
     11 from .config import ExtractionConfig
     12 from .data_processing import InteractionExtractor

File ~/Code/ProteomeLM/notebooks/../proteomelm/ppi/model.py:17
     15 from sklearn.metrics import average_precision_score, roc_auc_score, classification_report
     16 import matplotlib.pyplot as plt
---> 17 import optuna
     19 from proteomelm.modeling_proteomelm import ProteomeLMForMaskedLM
     20 from proteomelm.utils.embedding import build_genome_esmc

ModuleNotFoundError: No module named 'optuna'

I guess optuna is missing, or the import optuna belongs to dead code that is never used otherwise in ProteomeLM?

Cheers!