From c5e5b7e205c98fea2dd1750060ac0488f1d41d6a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Se=C3=A1n=20Kavanagh?=
 <51478689+kavanase@users.noreply.github.com>
Date: Mon, 25 Apr 2022 12:30:37 +0100
Subject: [PATCH 1/2] Fix `substituting_specie` assignment for substitutions

---
 defect_finder/BDM.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/defect_finder/BDM.py b/defect_finder/BDM.py
index 7551926e..9ab852fd 100644
--- a/defect_finder/BDM.py
+++ b/defect_finder/BDM.py
@@ -72,9 +72,13 @@ def calc_number_electrons(
         substituting_specie = str(defect_dict['site_specie'])
         site_specie = 'Vac' # Consider an interstitial as the interstitial atom substituting a vacant position
     
-    elif defect_dict['defect_type'] in ['antisite', 'substitution']:
+    elif defect_dict['defect_type'] == 'antisite':
         site_specie = str(defect_dict['site_specie'])
         substituting_specie = defect_dict['substituting_specie']
+    
+    elif defect_dict['defect_type'] == 'substitution':
+        site_specie = str(defect_dict['site_specie'])
+        substituting_specie = defect_dict['substitution_specie']
         
     num_electrons = - ( oxidation_states[substituting_specie] - oxidation_states[site_specie] ) 
     # print( f"Number of missing/extra electrons of defect {defect['name']}: ", num_electrons )   

From d5863f4bb4db342fc63de1cd9b9e48e99de9aaee Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Se=C3=A1n=20Kavanagh?=
 <51478689+kavanase@users.noreply.github.com>
Date: Mon, 6 Jun 2022 14:34:23 +0100
Subject: [PATCH 2/2] Update test workflow to explicitly test output plots

---
 .github/workflows/build_and_test.yml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/build_and_test.yml b/.github/workflows/build_and_test.yml
index ecc7301b..c7362158 100644
--- a/.github/workflows/build_and_test.yml
+++ b/.github/workflows/build_and_test.yml
@@ -39,4 +39,7 @@ jobs:
           pip install -e .[tests]
 
       - name: Test
-        run: pytest
+        run:  |
+          pytest
+          pytest tests/test_shakenbreak.py --mpl  # test output plots
+