From 9786f3b8de631272435e9b35c50a1ab9de81cbd0 Mon Sep 17 00:00:00 2001
From: Andrew White <white.d.andrew@gmail.com>
Date: Tue, 21 Nov 2023 10:23:23 -0800
Subject: [PATCH] Fixed eating paranthetical statements

---
 paperqa/types.py   | 7 ++++++-
 paperqa/version.py | 2 +-
 2 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/paperqa/types.py b/paperqa/types.py
index 41a907eaf..60f4c3c80 100644
--- a/paperqa/types.py
+++ b/paperqa/types.py
@@ -145,6 +145,7 @@ def markdown(self) -> Tuple[str, str]:
         index = 1
         for citation in iter_citations(self.answer):
             compound = ""
+            strip = True
             for c in citation.split(",;"):
                 c = c.strip("() ")
                 if c == "Extra background information":
@@ -157,17 +158,21 @@ def markdown(self) -> Tuple[str, str]:
                     self.get_citation(c)
                 except ValueError:
                     # not a citation
+                    strip = False
                     continue
                 refs[c] = index
                 compound += f"[^{index}]"
                 index += 1
-            output = output.replace(citation, compound)
+            if strip:
+                output = output.replace(citation, compound)
         formatted_refs = "\n".join(
             [
                 f"[^{i}]: [{self.get_citation(r)}]({extract_doi(self.get_citation(r))})"
                 for r, i in refs.items()
             ]
         )
+        # quick fix of space before period
+        output = output.replace(" .", ".")
         return output, formatted_refs
 
     def combine_with(self, other: "Answer") -> "Answer":
diff --git a/paperqa/version.py b/paperqa/version.py
index 641cc7839..d8c1804a3 100644
--- a/paperqa/version.py
+++ b/paperqa/version.py
@@ -1 +1 @@
-__version__ = "3.13.1"
+__version__ = "3.13.2"