Convert citation to formatted_citation usage where necessary

paperqa/agents/helpers.py

@@ -93,7 +93,7 @@ def table_formatter(
             try:
                 display_name = cast(Docs, obj).texts[0].doc.title  # type: ignore[attr-defined]
             except AttributeError:
-                display_name = cast(Docs, obj).texts[0].doc.citation
+                display_name = cast(Docs, obj).texts[0].doc.formatted_citation
             table.add_row(display_name[:max_chars_per_column], filename)
         return table
     raise NotImplementedError(

paperqa/core.py

@@ -64,7 +64,7 @@ async def map_fxn_summary(
     # needed empties for failures/skips
     llm_result = LLMResult(model="", date="")
     extras: dict[str, Any] = {}
-    citation = text.name + ": " + text.doc.citation
+    citation = text.name + ": " + text.doc.formatted_citation
     success = False
 
     if prompt_runner:

paperqa/docs.py

@@ -609,7 +609,7 @@ async def aget_evidence(
                         prompt_runner=prompt_runner,
                         extra_prompt_data={
                             "summary_length": answer_config.evidence_summary_length,
-                            "citation": f"{m.name}: {m.doc.citation}",
+                            "citation": f"{m.name}: {m.doc.formatted_citation}",
                         },
                         parser=llm_parse_json if prompt_config.use_json else None,
                         callbacks=callbacks,
@@ -715,7 +715,7 @@ async def aquery(  # noqa: PLR0912
             context_inner_prompt.format(
                 name=c.text.name,
                 text=c.context,
-                citation=c.text.doc.citation,
+                citation=c.text.doc.formatted_citation,
                 **(c.model_extra or {}),
             )
             for c in filtered_contexts
@@ -756,7 +756,7 @@ async def aquery(  # noqa: PLR0912
             answer_text = answer_text.replace(prompt_config.EXAMPLE_CITATION, "")
         for c in filtered_contexts:
             name = c.text.name
-            citation = c.text.doc.citation
+            citation = c.text.doc.formatted_citation
             # do check for whole key (so we don't catch Callahan2019a with Callahan2019)
             if name_in_text(name, answer_text):
                 bib[name] = citation

paperqa/types.py

@@ -129,6 +129,11 @@ class Doc(Embeddable):
     def __hash__(self) -> int:
         return hash((self.docname, self.dockey))
 
+    @computed_field  # type: ignore[prop-decorator]
+    @property
+    def formatted_citation(self) -> str:
+        return self.citation
+
 
 class Text(Embeddable):
     text: str
@@ -607,8 +612,9 @@ def __getitem__(self, item: str):
         except AttributeError:
             return self.other[item]
 
+    @computed_field  # type: ignore[prop-decorator]
     @property
-    def formatted_citation(self) -> str:
+    def formatted_citation(self) -> str | None:  # type: ignore[override]
 
         if self.is_retracted:
             base_message = "**RETRACTED ARTICLE**"
@@ -620,15 +626,9 @@ def formatted_citation(self) -> str:
             )
             return f"{base_message} {citation_message} {retract_info}"
 
-        if (
-            self.citation is None  # type: ignore[redundant-expr]
-            or self.citation_count is None
-            or self.source_quality is None
-        ):
-            raise ValueError(
-                "Citation, citationCount, and sourceQuality are not set -- do you need"
-                " to call `hydrate`?"
-            )
+        if self.citation_count is None or self.source_quality is None:
+            logger.warning("citation_count and source_quality are not set.")
+            return self.citation
 
         if self.source_quality_message:
             return (