From eba7f4ca75eab8c8905700cef3049e7785e1f851 Mon Sep 17 00:00:00 2001
From: Benjamin Morgan <benmorgan2@gmail.com>
Date: Wed, 7 Jul 2021 17:12:26 +0000
Subject: [PATCH] Converted Site.probabilities to return a dict.

---
 pyscses/site.py    | 15 +++++++++++++++
 tests/test_site.py |  4 ++++
 2 files changed, 19 insertions(+)

diff --git a/pyscses/site.py b/pyscses/site.py
index c126a73..13e33fd 100644
--- a/pyscses/site.py
+++ b/pyscses/site.py
@@ -6,6 +6,7 @@
 from pyscses.defect_species import DefectSpecies
 from typing import List, Optional, Dict
 from pyscses.defect_at_site import DefectAtSite
+import warnings
 
 class LabelError(Exception):
     pass
@@ -180,6 +181,20 @@ def probabilities(self,
     def probabilities_as_list(self,
                               phi: float,
                               temp: float) -> List[float]:
+        """Calculates the probabilities of this site being occupied by each defect species.
+
+        Legacy interface that returns a list of site-occupation probabilities
+        in the same order as `Site.defects`.
+
+            Args:
+            phi (float): Electrostatic potential at this site in Volts.
+            temp (float): Temperature in Kelvin.
+
+        Returns:
+            list(float): Probabilities of site occupation for each defect species.
+
+        """
+        warnings.warn("Site.probabilities_as_list() is deprecated and targetted for removal. Please use Site.probabilities() instead.", DeprecationWarning)
         probabilities_dict = self.probabilities(phi=phi, temp=temp)
         return [probabilities_dict[d.label] for d in self.defects]
 
diff --git a/tests/test_site.py b/tests/test_site.py
index c1dc99d..7df00be 100644
--- a/tests/test_site.py
+++ b/tests/test_site.py
@@ -183,6 +183,10 @@ def test_probabilities_two(self):
                                                  temp=298.0),
                          {'A': exp_A, 'B': exp_B})
 
+    def test_probabilites_as_list(self):
+        self.site.probabilities = Mock(return_value={'E': 0.1, 'D': 0.2})
+        self.site.probabilities_as_list(phi=1.0, temp=298.0)
+
 
 if __name__ == '__main__':
     unittest.main()