From cc7d74761cf1e01b903894b6a3947bb57636575d Mon Sep 17 00:00:00 2001
From: "Ankur Sinha (Ankur Sinha Gmail)" <sanjay.ankur@gmail.com>
Date: Tue, 7 Nov 2023 16:59:14 +0000
Subject: [PATCH] feat(connectivity-plots): move matrix plot to new sub-module

---
 pyneuroml/plot/Connectivity.py | 35 ++++++++++++++++++++++++++++++++++
 pyneuroml/pynml.py             | 17 ++---------------
 2 files changed, 37 insertions(+), 15 deletions(-)
 create mode 100644 pyneuroml/plot/Connectivity.py

diff --git a/pyneuroml/plot/Connectivity.py b/pyneuroml/plot/Connectivity.py
new file mode 100644
index 000000000..e2878c889
--- /dev/null
+++ b/pyneuroml/plot/Connectivity.py
@@ -0,0 +1,35 @@
+#!/usr/bin/env python3
+"""
+Connectivity plotting methods
+
+File: pyneuroml/plot/Connectivity.py
+
+Copyright 2023 NeuroML contributors
+"""
+
+import logging
+
+logger = logging.getLogger(__name__)
+logger.setLevel(logging.INFO)
+
+
+def plot_connectivity_matrix(filename, level):
+    """Plot a connectivity matrix
+
+    :param filename: name of NeuroML file
+    :type filename: str
+    :param level: level at which to plot
+    :type level: int
+    """
+    from neuromllite.MatrixHandler import MatrixHandler
+    from neuroml.hdf5.NeuroMLXMLParser import NeuroMLXMLParser
+
+    logger.info("Converting %s to matrix form, level %i" % (filename, level))
+
+    handler = MatrixHandler(level=level, nl_network=None)
+
+    currParser = NeuroMLXMLParser(handler)
+    currParser.parse(filename)
+    handler.finalise_document()
+
+    logger.info("Done with MatrixHandler...")
diff --git a/pyneuroml/pynml.py b/pyneuroml/pynml.py
index 703e54022..82603364f 100644
--- a/pyneuroml/pynml.py
+++ b/pyneuroml/pynml.py
@@ -2312,23 +2312,10 @@ def evaluate_arguments(args):
             exit_on_fail = True
         elif args.matrix:
             confirm_neuroml_file(f)
-            from neuromllite.MatrixHandler import MatrixHandler
-
             level = int(args.matrix[0])
+            from pyneuroml.plot.Connectivity import plot_connectivity_matrix
 
-            logger.info("Converting %s to matrix form, level %i" % (f, level))
-
-            from neuroml.hdf5.NeuroMLXMLParser import NeuroMLXMLParser
-
-            handler = MatrixHandler(level=level, nl_network=None)
-
-            currParser = NeuroMLXMLParser(handler)
-
-            currParser.parse(f)
-
-            handler.finalise_document()
-
-            logger.info("Done with MatrixHandler...")
+            plot_connectivity_matrix(f, level)
 
             exit(0)
         elif args.validate: