Formatting

vamb/__main__.py

@@ -771,9 +771,11 @@ def cluster_and_write_files(
             print(
                 str(i + 1),
                 None if cluster.radius is None else round(cluster.radius, 3),
-                None
-                if cluster.observed_pvr is None
-                else round(cluster.observed_pvr, 2),
+                (
+                    None
+                    if cluster.observed_pvr is None
+                    else round(cluster.observed_pvr, 2)
+                ),
                 cluster.kind_str,
                 sum(sequence_lens[i] for i in cluster.members),
                 len(cluster.members),

vamb/aamb_encode.py

@@ -1,6 +1,5 @@
 """Adversarial autoencoders (AAE) for metagenomics binning, this files contains the implementation of the AAE"""
 
-
 import numpy as np
 from math import log, isfinite
 import time

vamb/semisupervised_encode.py

@@ -1,6 +1,5 @@
 """Semisupervised multimodal VAEs for metagenomics binning, this files contains the implementation of the VAEVAE for MMSEQ predictions"""
 
-
 __cmd_doc__ = """Encode depths and TNF using a VAE to latent representation"""
 
 import numpy as _np

vamb/taxvamb_encode.py

@@ -1,6 +1,5 @@
 """Hierarchical loss for the labels suggested in https://arxiv.org/abs/2210.10929"""
 
-
 __cmd_doc__ = """Hierarchical loss for the labels"""
 
 

workflow_avamb/src/rip_bins.py

@@ -183,9 +183,9 @@ def remove_meaningless_edges_from_pairs(
                     contig_length,
                 )
                 print("Cluster ripped because of a meaningless edge ", cluster_updated)
-                clusters_changed_but_not_intersecting_contigs[
-                    cluster_updated
-                ] = cluster_contigs[cluster_updated]
+                clusters_changed_but_not_intersecting_contigs[cluster_updated] = (
+                    cluster_contigs[cluster_updated]
+                )
 
     components: list[set[str]] = list()
     for component in nx.connected_components(graph_clusters):
@@ -295,9 +295,9 @@ def make_all_components_pair(
                     contig_length,
                 )
                 print("Cluster ripped because of a pairing component ", cluster_updated)
-                clusters_changed_but_not_intersecting_contigs[
-                    cluster_updated
-                ] = cluster_contigs[cluster_updated]
+                clusters_changed_but_not_intersecting_contigs[cluster_updated] = (
+                    cluster_contigs[cluster_updated]
+                )
                 component_len = max(
                     [
                         len(nx.node_connected_component(graph_clusters, node_i))