refactor: Remove AnnotatedDocument class

The AnnotatedDocument class was, essentially, a simple tuple of a document
and a list of annotations. While not bad in a vacuum, it is unwieldy and
passing this around instead of a document, annotations, or both where
necessary is more restrictive and frankly unnecessary.

This commit removes the data class and any instances of its use. Instead,
we now pass the individual components around to anything that needs them.
This also frees us up to pass only annotations around for example.

We also do not iterate through the selected papis documents to work on
in each exporter anymore (since we only pass a single document), but
in the main function itself. This leads to less duplication and makes
the overall run function the overall single source of iteration through
selected documents. Everything else only knows about a single document -
the one it is operating on - which seems much neater.

For now, it does not change much, but should make later work on extra
exporters or extractors easier.

papis_extract/__init__.py

@@ -7,7 +7,8 @@ import papis.notes
 import papis.strings
 from papis.document import Document
 
-from papis_extract import extractor, exporter
+from papis_extract import exporter, extractor
+from papis_extract.annotation import Annotation
 from papis_extract.formatter import Formatter, formatters
 
 logger = papis.logging.get_logger(__name__)
@@ -44,7 +45,7 @@ papis.config.register_default_settings(DEFAULT_OPTIONS)
     "--template",
     "-t",
     type=click.Choice(
-        ["markdown", "markdown-setext", "markdown-atx", "count", "csv"],
+        list(formatters.keys()),
         case_sensitive=False,
     ),
     help="Choose an output template to format annotations with.",
@@ -85,27 +86,34 @@ def main(
         logger.warning(papis.strings.no_documents_retrieved_message)
         return
 
-    formatter = formatters[template]
+    formatter = formatters.get(template)
 
     run(documents, edit=manual, write=write, git=git, formatter=formatter, force=force)
 
 
 def run(
     documents: list[Document],
-    formatter: Formatter,
+    formatter: Formatter | None,
     edit: bool = False,
     write: bool = False,
     git: bool = False,
     force: bool = False,
 ) -> None:
-    annotated_docs = extractor.start(documents)
-    if write:
-        exporter.to_notes(
-            formatter=formatter,
-            annotated_docs=annotated_docs,
-            edit=edit,
-            git=git,
-            force=force,
-        )
-    else:
-        exporter.to_stdout(formatter=formatter, annotated_docs=annotated_docs)
+    for doc in documents:
+        annotations: list[Annotation] = extractor.start(doc)
+
+        if write:
+            exporter.to_notes(
+                formatter=formatter or formatters["markdown-atx"],
+                document=doc,
+                annotations=annotations,
+                edit=edit,
+                git=git,
+                force=force,
+            )
+        else:
+            exporter.to_stdout(
+                formatter=formatter or formatters["markdown"],
+                document=doc,
+                annotations=annotations,
+            )