- reformatted the 6 files identified ifor CI/CD check (black formatter). Resolves the formatting failures.

Author: BenjaminIsaac0111

scripts/inspect_outputs.py

@@ -4,7 +4,10 @@
 import argparse
 import numpy as np
 from spatial_transcript_former.models import SpatialTranscriptFormer
-from spatial_transcript_former.recipes.hest.utils import get_sample_ids, setup_dataloaders
+from spatial_transcript_former.recipes.hest.utils import (
+    get_sample_ids,
+    setup_dataloaders,
+)
 
 
 class Args:

scripts/inspect_sample.py

@@ -5,7 +5,10 @@
 
 # Add src to path
 sys.path.append(os.path.abspath("src"))
-from spatial_transcript_former.recipes.hest.io import get_hest_data_dir, load_h5ad_metadata
+from spatial_transcript_former.recipes.hest.io import (
+    get_hest_data_dir,
+    load_h5ad_metadata,
+)
 from spatial_transcript_former.config import get_config
 from spatial_transcript_former.data.pathways import (
     download_msigdb_gmt,

src/spatial_transcript_former/recipes/hest/build_vocab.py

@@ -11,7 +11,10 @@
 
 # Add src to path
 sys.path.append(os.path.abspath("src"))
-from spatial_transcript_former.recipes.hest.io import get_hest_data_dir, load_h5ad_metadata
+from spatial_transcript_former.recipes.hest.io import (
+    get_hest_data_dir,
+    load_h5ad_metadata,
+)
 from spatial_transcript_former.config import get_config
 from spatial_transcript_former.data.pathways import (
     download_msigdb_gmt,

src/spatial_transcript_former/train.py

@@ -24,7 +24,10 @@
 from spatial_transcript_former.training.engine import train_one_epoch, validate
 from spatial_transcript_former.training.experiment_logger import ExperimentLogger
 from spatial_transcript_former.visualization import run_inference_plot
-from spatial_transcript_former.recipes.hest.utils import get_sample_ids, setup_dataloaders
+from spatial_transcript_former.recipes.hest.utils import (
+    get_sample_ids,
+    setup_dataloaders,
+)
 
 from spatial_transcript_former.training.arguments import parse_args
 from spatial_transcript_former.training.builder import setup_model, setup_criterion

tests/test_data_integrity.py

@@ -3,7 +3,10 @@
 import torch
 import numpy as np
 import h5py
-from spatial_transcript_former.recipes.hest.io import get_hest_data_dir, load_h5ad_metadata
+from spatial_transcript_former.recipes.hest.io import (
+    get_hest_data_dir,
+    load_h5ad_metadata,
+)
 from spatial_transcript_former.recipes.hest.dataset import load_global_genes
 from spatial_transcript_former.data.pathways import (
     download_msigdb_gmt,

tests/test_dataset_mocks.py

@@ -2,7 +2,10 @@
 import numpy as np
 import pytest
 from unittest.mock import MagicMock, patch
-from spatial_transcript_former.recipes.hest.dataset import HEST_Dataset, HEST_FeatureDataset
+from spatial_transcript_former.recipes.hest.dataset import (
+    HEST_Dataset,
+    HEST_FeatureDataset,
+)
 
 
 @pytest.fixture