[pre-commit.ci] auto fixes from pre-commit.com hooks

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barcodebert/bzsl/feature_extraction/__init__.py

@@ -1,3 +1,7 @@
-from .utils import extract_clean_barcode_list, extract_clean_barcode_list_for_aligned, extract_dna_features
+from .utils import (
+    extract_clean_barcode_list,
+    extract_clean_barcode_list_for_aligned,
+    extract_dna_features,
+)
 
 __all__ = ["extract_clean_barcode_list", "extract_clean_barcode_list_for_aligned", "extract_dna_features"]

barcodebert/bzsl/genus_species/main.py

@@ -6,7 +6,11 @@
 import numpy as np
 import torch
 
-from barcodebert.bzsl.genus_species.bayesian_classifier import BayesianClassifier, apply_pca, calculate_priors
+from barcodebert.bzsl.genus_species.bayesian_classifier import (
+    BayesianClassifier,
+    apply_pca,
+    calculate_priors,
+)
 from barcodebert.bzsl.genus_species.dataset import get_data_splits, load_data
 
 

barcodebert/bzsl/models/dnabert/tokenization_utils.py

@@ -26,7 +26,13 @@
 
 from tokenizers.implementations import BaseTokenizer
 
-from .file_utils import cached_path, hf_bucket_url, is_remote_url, is_tf_available, is_torch_available
+from .file_utils import (
+    cached_path,
+    hf_bucket_url,
+    is_remote_url,
+    is_tf_available,
+    is_torch_available,
+)
 
 if is_tf_available():
     import tensorflow as tf

barcodebert/bzsl/surrogate_species/bayesian_model.py

@@ -6,7 +6,11 @@
 from scipy.spatial.distance import cdist
 from scipy.special import gammaln
 
-from barcodebert.bzsl.surrogate_species.utils import DataLoader, apply_pca, perf_calc_acc
+from barcodebert.bzsl.surrogate_species.utils import (
+    DataLoader,
+    apply_pca,
+    perf_calc_acc,
+)
 
 
 class Model:

baselines/cnn/1D_CNN_supervised.py

@@ -7,7 +7,6 @@
 import torch.optim as optim
 from torch.utils.data import DataLoader
 
-
 data_folder = "/h/pmillana/projects/BarcodeBERT_soft_penalty/data"
 train = pd.read_csv(f"{data_folder}/supervised_train.csv")
 test = pd.read_csv(f"{data_folder}/supervised_test.csv")

baselines/models/dnabert2.py

@@ -19,7 +19,13 @@
 from transformers.modeling_outputs import MaskedLMOutput, SequenceClassifierOutput
 from transformers.models.bert.modeling_bert import BertPreTrainedModel
 
-from .dnabert2_padding import index_first_axis, index_put_first_axis, pad_input, unpad_input, unpad_input_only
+from .dnabert2_padding import (
+    index_first_axis,
+    index_put_first_axis,
+    pad_input,
+    unpad_input,
+    unpad_input_only,
+)
 
 try:
     from .flash_attn_triton import flash_attn_qkvpacked_func