From 6cdc0488971b6a61cc9ea3d5c67baa73924a46ee Mon Sep 17 00:00:00 2001
From: Gerd Duscher <50049264+gduscher@users.noreply.github.com>
Date: Sat, 27 Jan 2024 17:55:50 -0500
Subject: [PATCH] crystal tool now compatible

---
 notebooks/0_pyTEMlib.ipynb  |  7 ++++---
 pyTEMlib/crystal_tools.py   | 11 +----------
 tests/test_crystal_tools.py |  2 +-
 3 files changed, 6 insertions(+), 14 deletions(-)

diff --git a/notebooks/0_pyTEMlib.ipynb b/notebooks/0_pyTEMlib.ipynb
index b1db0d7b..45b69b36 100644
--- a/notebooks/0_pyTEMlib.ipynb
+++ b/notebooks/0_pyTEMlib.ipynb
@@ -36,10 +36,11 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
    "outputs": [],
-   "source": []
+   "source": [],
+   "metadata": {
+    "collapsed": false
+   }
   }
  ],
  "metadata": {
diff --git a/pyTEMlib/crystal_tools.py b/pyTEMlib/crystal_tools.py
index 318aaedb..42303432 100644
--- a/pyTEMlib/crystal_tools.py
+++ b/pyTEMlib/crystal_tools.py
@@ -283,16 +283,7 @@ def ball_and_stick(atoms, extend=1, max_bond_length=0.):
     neighbor_list.update(super_cell)
     bond_matrix = neighbor_list.get_connectivity_matrix()
 
-    del_double = []
-    for (k, s) in bond_matrix.keys():
-        if k > s:
-            del_double.append((k, s))
-    del_double.sort(reverse=False)
-    for key in del_double:
-        # Todo: why is ther a key error
-        # bond_matrix.pop(key)
-        pass
-
+    bond_matrix = np.triu(bond_matrix.toarray())
     if super_cell.info is None:
         super_cell.info = {}
     super_cell.info['plot_cell'] = {'bond_matrix': bond_matrix, 'corner_vectors': corner_vectors,
diff --git a/tests/test_crystal_tools.py b/tests/test_crystal_tools.py
index 2dcdd317..4a414c6a 100644
--- a/tests/test_crystal_tools.py
+++ b/tests/test_crystal_tools.py
@@ -43,7 +43,7 @@ def test_ball_and_stick(self):
                          [0, 0, 0, 0, 0, 0, 0, 0, 1],
                          [0, 0, 0, 0, 0, 0, 0, 0, 1],
                          [0, 0, 0, 0, 0, 0, 0, 0, 0]]
-        # np.testing.assert_allclose(cell_2_plot.info['plot_cell']['bond_matrix'].toarray(), bonds_desired)
+        np.testing.assert_allclose(cell_2_plot.info['plot_cell']['bond_matrix'], bonds_desired)
 
     def test_from_dictionary(self):
         tags = {'unit_cell': np.array([[4.05, 0, 0], [0, 4.05, 0], [0, 0, 4.05]]),