lint: Fix imports with isort

Author: lisavader

src/geneml/gene_caller.py

@@ -6,15 +6,10 @@
 import numpy as np
 from numba import njit, objmode, typed, typeof
 
-from geneml.model_loader import (
-    MODEL_CDS_END,
-    MODEL_CDS_START,
-    MODEL_EXON_END,
-    MODEL_EXON_START,
-    MODEL_IS_EXON,
-    MODEL_IS_INTRON,
-    ResidualModelBase,
-)
+from geneml.model_loader import (MODEL_CDS_END, MODEL_CDS_START,
+                                 MODEL_EXON_END, MODEL_EXON_START,
+                                 MODEL_IS_EXON, MODEL_IS_INTRON,
+                                 ResidualModelBase)
 from geneml.params import Params
 from geneml.utils import chunked_seq_predict
 

src/geneml/main.py

@@ -6,16 +6,19 @@
 from concurrent.futures import ProcessPoolExecutor, as_completed
 
 import tensorflow as tf
+from Bio.Seq import reverse_complement
 from helperlibs.bio import seqio
 from tqdm import tqdm
-from Bio.Seq import reverse_complement
 
 from geneml import __version__
-from geneml.gene_caller import CDS_END, EXON_END, GeneEvent, build_gene_calls, run_model
+from geneml.gene_caller import (CDS_END, EXON_END, GeneEvent, build_gene_calls,
+                                run_model)
 from geneml.model_loader import get_cached_gene_ml_model
-from geneml.outputs import build_prediction_scores_seg, write_fasta, write_gff_file
-from geneml.params import Strand, Params, build_params_namedtuple
-from geneml.utils import compute_optimal_num_parallelism, mask_lowercase_stretches
+from geneml.outputs import (build_prediction_scores_seg, write_fasta,
+                            write_gff_file)
+from geneml.params import Params, Strand, build_params_namedtuple
+from geneml.utils import (compute_optimal_num_parallelism,
+                          mask_lowercase_stretches)
 
 logger = logging.getLogger("geneml")
 

src/geneml/outputs.py

@@ -5,15 +5,11 @@
 from Bio.Seq import reverse_complement, translate
 from numba import njit, objmode, typed, types
 
-from geneml.gene_caller import CDS_END, CDS_START, EXON_END, EXON_START, GeneEvent, build_cds_seq
-from geneml.model_loader import (
-    MODEL_CDS_END,
-    MODEL_CDS_START,
-    MODEL_EXON_END,
-    MODEL_EXON_START,
-    MODEL_IS_EXON,
-    MODEL_IS_INTRON,
-)
+from geneml.gene_caller import (CDS_END, CDS_START, EXON_END, EXON_START,
+                                GeneEvent, build_cds_seq)
+from geneml.model_loader import (MODEL_CDS_END, MODEL_CDS_START,
+                                 MODEL_EXON_END, MODEL_EXON_START,
+                                 MODEL_IS_EXON, MODEL_IS_INTRON)
 
 
 def get_exon_offsets(gene_call: list[GeneEvent]):

src/geneml/params.py

@@ -1,9 +1,11 @@
 import json
 import os
-from enum import Enum
-import numpy as np
 from argparse import Namespace
 from collections import namedtuple
+from enum import Enum
+
+import numpy as np
+
 
 class Strand(Enum):
     FORWARD = "forward"

trainer/model.py

@@ -3,7 +3,6 @@
 ###############################################################################
 
 import numpy as np
-
 # hxenv
 # from tf_keras.layers import Input
 # from tf_keras.layers import Conv1D, Cropping1D
@@ -12,7 +11,8 @@
 # from tf_keras.layers import BatchNormalization
 # from tf_keras.models import Model
 # ai-platform
-from keras.layers import Activation, BatchNormalization, Conv1D, Cropping1D, Input, add
+from keras.layers import (Activation, BatchNormalization, Conv1D, Cropping1D,
+                          Input, add)
 from keras.models import Model
 
 # from tensorflow.keras.layers import VersionAwareLayers

trainer/train_model.py

@@ -86,10 +86,10 @@ def main():
     import keras
     import numpy as np
     import tensorflow
-
     # works locally and on Vertex AI
     from model import GeneML
-    from utils import clip_datapoints, print_basic_statistics, print_topl_statistics
+    from utils import (clip_datapoints, print_basic_statistics,
+                       print_topl_statistics)
 
     args = get_args()