Fix NDHistogram iteration bug in DpEngine (.items() → .iteritems() / _hist_array) and add Python 3 conda environment file

Cluster/DpEngine.py

@@ -76,7 +76,15 @@ def __init__(self, data, N_iter, Pi_k, use_fixed=False, co_assign_flag=False, ig
         if N_iter == 0:
             return None
 
-        mut_iter = iter(data.items())
+        # NDHistogram has .iteritems(), not .items()
+        if hasattr(data, "items"):
+            mut_iter = iter(data.items())
+        elif hasattr(data, "iteritems"):
+            mut_iter = data.iteritems()
+        # elif hasattr(data, "_hist_array"):
+        #     mut_iter = ((i, v) for i, v in enumerate(data._hist_array))
+        else:
+            raise TypeError("Unsupported data type for DpEngine: {}".format(type(data)))
         s_cluster = DP_cluster(self, DP_item(next(mut_iter)[0], self))
 
         for label, mut_hist in mut_iter:
@@ -242,8 +250,13 @@ def tree_cluster_DP(self, co_assign, K, clonal_threshold=0.95, var_loc=None, DP_
         # Flatten for TSNE and summary.
         log_data_flattened = []
 
-        for label, mutation in self.data.items():
-            log_data_flattened.append(mutation.flatten())
+        # NDHistogram has .iteritems(), not .items()
+        if hasattr(self.data, "items"):
+            for label, mutation in self.data.items():
+                log_data_flattened.append(mutation.flatten())
+        elif hasattr(self.data, "iteritems"):
+            for label, mutation in self.data.iteritems():
+                log_data_flattened.append(mutation.flatten())
 
         '''Normalize for TSNE'''
 

envs/phylogicndt_py3.yml

@@ -0,0 +1,24 @@
+name: phylogicndt_py3
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python=3.9
+  - pip
+  - setuptools
+  - wheel
+  # scientific stack from conda
+  - numpy=1.24.2
+  - scipy=1.10.1
+  - pandas=1.5.3
+  - matplotlib=3.6.3
+  - seaborn=0.12.2
+  - scikit-learn=1.3.0
+  - networkx=2.8.8
+  - intervaltree=2.1.0
+  - graphviz
+  - python-graphviz
+  # optional R support
+  - r-base=4.3
+  - pip:
+      - sselogsumexp @ git+https://github.com/rmcgibbo/logsumexp.git