Small simplification to progress monitoring within plot_njt (#643)

* begin njt refactoring

* refactor plot_njt

* fix docs

* tweak

* add tests

* fix nan comparisons

* poetry update

* consistent color for NA

* fix karyotype categorical

* fix warning

* fix haplotype networks

* simplify progress

* add example

Author: alimanfoo

malariagen_data/anoph/distance.py

@@ -363,26 +363,18 @@ def _njt(
         )
         D = squareform(dist)
 
-        # Progress doesn't mix well with debug logging.
-        show_progress = self._show_progress and not self._debug
-
         # anjl supports passing in a progress bar function to get progress on the
         # neighbour-joining iterations.
-        if show_progress:
-            progress = self._tqdm_class
-            progress_options = dict(
-                desc="Construct neighbour-joining tree", leave=False
-            )
-        else:
-            progress = None
-            progress_options = dict()
+        progress_options = dict(desc="Construct neighbour-joining tree", leave=False)
 
         # Decide which algorithm to use and run the neighbour-joining.
         if algorithm == "rapid":
-            Z = anjl.rapid_nj(D=D, progress=progress, progress_options=progress_options)
+            Z = anjl.rapid_nj(
+                D=D, progress=self._progress, progress_options=progress_options
+            )
         else:
             Z = anjl.canonical_nj(
-                D=D, progress=progress, progress_options=progress_options
+                D=D, progress=self._progress, progress_options=progress_options
             )
 
         return dict(

notebooks/plot_njt.ipynb

@@ -266,6 +266,23 @@
     ")"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "18fde26a-339a-44a1-a91f-425f22ed96d1",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "ag3.plot_njt(\n",
+    "    region=\"3L:15,000,000-15,100,000\",\n",
+    "    sample_sets=\"3.0\",\n",
+    "    n_snps=1_000,\n",
+    "    color=\"taxon\",\n",
+    "    metric=\"euclidean\",\n",
+    "    algorithm=\"canonical\",\n",
+    ")"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,