More robust citation lookups (#210)

* Added ; to allowed delimiters for citations * Add check now that it is a citation, since things like (in year 2020) were triggering
Future-House · Nov 20, 2023 · 30e9989 · 30e9989
1 parent def3640
commit 30e9989
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Showing 3 changed files with 12 additions and 5 deletions.
diff --git a/paperqa/types.py b/paperqa/types.py
@@ -145,13 +145,19 @@ def markdown(self) -> Tuple[str, str]:
         index = 1
         for citation in iter_citations(self.answer):
             compound = ""
-            for c in citation.split(","):
+            for c in citation.split(",;"):
                 c = c.strip("() ")
                 if c == "Extra background information":
                     continue
                 if c in refs:
                     compound += f"[^{refs[c]}]"
                     continue
+                # check if it is a citation
+                try:
+                    self.get_citation(c)
+                except ValueError:
+                    # not a citation
+                    continue
                 refs[c] = index
                 compound += f"[^{index}]"
                 index += 1

diff --git a/paperqa/version.py b/paperqa/version.py
@@ -1 +1 @@
-__version__ = "3.13.0"
+__version__ = "3.13.1"
diff --git a/tests/test_paperqa.py b/tests/test_paperqa.py
@@ -49,14 +49,15 @@ def test_iter_citations():
         "time. For instance, the effectiveness of COVID-19 vaccines against severe "
         "COVID-19 declined to 64% after 121 days, compared to around 90% initially "
         "(Chemaitelly2022WaningEO, Foo2019Bar). Despite this, vaccines still provide "
-        "significant protection against severe outcomes."
+        "significant protection against severe outcomes (Bar2000Foo pg 1-3; Far2000 pg 2-5)."
     )
     ref = [
         "(Dorabawila2022EffectivenessOT)",
         "(Bernal2021EffectivenessOC pg. 1-3)",
         "(Thompson2021EffectivenessOC pg. 3-5, Goo2031Foo pg. 3-4)",
         "(Marfé2021EffectivenessOC)",
         "(Chemaitelly2022WaningEO, Foo2019Bar)",
+        "(Bar2000Foo pg 1-3; Far2000 pg 2-5)",
     ]
     assert list(iter_citations(text)) == ref
 
@@ -130,13 +131,13 @@ def test_markdown():
     answer = Answer(
         question="What was Fredic's greatest accomplishment?",
         answer="Frederick Bates's greatest accomplishment was his role in resolving land disputes "
-        "and his service as governor of Missouri (Wiki2023 chunk 1).",
+        "and his service as governor of Missouri (Wiki2023 chunk 1). It is said (in 2010) that foo.",
         contexts=[
             Context(
                 context="",
                 text=Text(
                     text="Frederick Bates's greatest accomplishment was his role in resolving land disputes "
-                    "and his service as governor of Missouri (Wiki2023 chunk 1).",
+                    "and his service as governor of Missouri.",
                     name="Wiki2023 chunk 1",
                     doc=Doc(
                         name="Wiki2023",