Merge pull request #302 from jkmckenna/0.3.2

0.3.2

Author: jkmckenna

pyproject.toml

@@ -147,6 +147,7 @@ torch = [
 all = [
     # cluster
     "fastcluster",
+    "igraph"
     "leidenalg",
 
     # informatics
@@ -172,6 +173,7 @@ all = [
     "omegaconf",
     "scikit-learn>=1.0.2",
     "shap",
+    "tensorly",
     "torch>=1.9.0",
     "wandb",
 

src/smftools/_version.py

@@ -1,3 +1,3 @@
 from __future__ import annotations
 
-__version__ = "0.3.1"
+__version__ = "0.3.2"

src/smftools/cli/hmm_adata.py

@@ -1068,9 +1068,7 @@ def hmm_adata_core(
                 cmap_a=cfg.clustermap_cmap_a,
                 min_quality=cfg.read_quality_filter_thresholds[0],
                 min_length=cfg.read_len_filter_thresholds[0],
-                min_mapped_length_to_reference_length_ratio=cfg.read_len_to_ref_ratio_filter_thresholds[
-                    0
-                ],
+                min_mapped_length_to_reference_length_ratio=cfg.read_len_to_ref_ratio_filter_thresholds[0],
                 min_position_valid_fraction=1 - cfg.position_max_nan_threshold,
                 demux_types=cfg.clustermap_demux_types_to_plot,
                 save_path=hmm_cluster_save_dir,
@@ -1124,9 +1122,7 @@ def hmm_adata_core(
                 cmap_a=cfg.clustermap_cmap_a,
                 min_quality=cfg.read_quality_filter_thresholds[0],
                 min_length=cfg.read_len_filter_thresholds[0],
-                min_mapped_length_to_reference_length_ratio=cfg.read_len_to_ref_ratio_filter_thresholds[
-                    0
-                ],
+                min_mapped_length_to_reference_length_ratio=cfg.read_len_to_ref_ratio_filter_thresholds[0],
                 min_position_valid_fraction=1 - cfg.position_max_nan_threshold,
                 demux_types=cfg.clustermap_demux_types_to_plot,
                 save_path=hmm_cluster_save_dir,