autopep8 fixes

hubmapconsortium · Aug 9, 2023 · a7a021c · a7a021c
1 parent 60998fc
commit a7a021c
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Showing 4 changed files with 13 additions and 9 deletions.
diff --git a/src/portal_visualization/builders/anndata_builders.py b/src/portal_visualization/builders/anndata_builders.py
@@ -130,7 +130,8 @@ def get_conf_cells(self, marker=None):
  # print('TODO - Encoding Version 0.2.0 support')
 
  cell_set_obs.extend(RNA_SEQ_ANNDATA_FACTOR_PATHS)
- cell_set_obs_names.extend([f'Marker Gene {x}' for x in range(len(RNA_SEQ_ANNDATA_FACTORS))])
+ cell_set_obs_names.extend(
+ [f'Marker Gene {x}' for x in range(len(RNA_SEQ_ANNDATA_FACTORS))])
  dataset = vc.add_dataset(name=self._uuid).add_object(AnnDataWrapper(
  adata_url=adata_url,
  obs_feature_matrix_path="X",

diff --git a/src/portal_visualization/builders/scatterplot_builders.py b/src/portal_visualization/builders/scatterplot_builders.py
@@ -1,8 +1,6 @@
 from vitessce import (
  VitessceConfig,
  Component as cm,
- DataType as dt,
- FileType as ft,
 )
 
 
@@ -69,7 +67,6 @@ def __init__(self, entity, groups_token, assets_endpoint, **kwargs):
  {
  "rel_path": f"{SCRNA_SEQ_DIR}.cells.json",
  "file_type": "obsEmbedding.cells.json", # ft.OBS_EMBEDDING_CELLS_JSON
-
  "coordination_values": {
  "obsType": "cell",
  "embeddingType": "UMAP",

diff --git a/src/portal_visualization/builders/sprm_builders.py b/src/portal_visualization/builders/sprm_builders.py
@@ -242,7 +242,14 @@ def _setup_view_config_raster_cellsets_expression_segmentation(self, vc, dataset
  ).set_props(
  variablesLabelOverride="antigen", transpose=True)
 
- views = [description, layer_controller, spatial, cell_sets, gene_list, scatterplot, heatmap]
+ views = [
+ description,
+ layer_controller,
+ spatial,
+ cell_sets,
+ gene_list,
+ scatterplot,
+ heatmap]
 
  # Adding the obsLabelsType coordination here makes the tooltip not display any information for these factors
  # Seemingly due to name collision with obs sets, but removing the obs sets / using an empty list doesn't work

diff --git a/src/portal_visualization/utils.py b/src/portal_visualization/utils.py
@@ -79,17 +79,16 @@ def use_multiple_coordinations(vc, views, coordinationType, values):
  # Add the coordinations to the VC
  coordinations = vc.add_coordination(*[coordinationType for _ in values])
 
- # Set coordination values 
+ # Set coordination values
  for i, value in enumerate(values):
  coordinations[i].set_value(value)
 
  scopes = [str(l.c_scope) for l in coordinations]
- 
+
  custom_scope = VitessceConfigCoordinationScope(
  c_type=coordinationType, c_scope=scopes)
 
  for v in views:
  v.use_coordination(custom_scope)
-
- return vc
 
+ return vc