feat(xml-jats): parse XML JATS documents (#967)

* chore(xml-jats): separate authors and affiliations

In XML PubMed (JATS) backend, convert authors and affiliations as they
are typically rendered on PDFs.

Signed-off-by: Cesar Berrospi Ramis <75900930+ceberam@users.noreply.github.com>

* fix(xml-jats): replace new line character by a space

Instead of removing new line character from text, replace it by a space character.

Signed-off-by: Cesar Berrospi Ramis <75900930+ceberam@users.noreply.github.com>

* feat(xml-jats): improve existing parser and extend features

Partially support lists, respect reading order, parse more sections, support equations, better text formatting.

Signed-off-by: Cesar Berrospi Ramis <75900930+ceberam@users.noreply.github.com>

* chore(xml-jats): rename PubMed objects to JATS

Signed-off-by: Cesar Berrospi Ramis <75900930+ceberam@users.noreply.github.com>

---------

Signed-off-by: Cesar Berrospi Ramis <75900930+ceberam@users.noreply.github.com>

tests/test_backend_jats.py

@@ -0,0 +1,73 @@
+import json
+import os
+from io import BytesIO
+from pathlib import Path
+
+from docling_core.types.doc import DoclingDocument
+
+from docling.datamodel.base_models import DocumentStream, InputFormat
+from docling.datamodel.document import ConversionResult
+from docling.document_converter import DocumentConverter
+
+GENERATE = False
+
+
+def get_pubmed_paths():
+    directory = Path(os.path.dirname(__file__) + f"/data/pubmed/")
+    xml_files = sorted(directory.rglob("*.xml"))
+    return xml_files
+
+
+def get_converter():
+    converter = DocumentConverter(allowed_formats=[InputFormat.XML_JATS])
+    return converter
+
+
+def verify_export(pred_text: str, gtfile: str):
+    if not os.path.exists(gtfile) or GENERATE:
+        with open(gtfile, "w") as fw:
+            fw.write(pred_text)
+        return True
+    else:
+        with open(gtfile, "r") as fr:
+            true_text = fr.read()
+        assert pred_text == true_text, f"pred_text!=true_text for {gtfile}"
+        return pred_text == true_text
+
+
+def test_e2e_pubmed_conversions(use_stream=False):
+    pubmed_paths = get_pubmed_paths()
+    converter = get_converter()
+
+    for pubmed_path in pubmed_paths:
+        gt_path = (
+            pubmed_path.parent.parent / "groundtruth" / "docling_v2" / pubmed_path.name
+        )
+        if use_stream:
+            buf = BytesIO(pubmed_path.open("rb").read())
+            stream = DocumentStream(name=pubmed_path.name, stream=buf)
+            conv_result: ConversionResult = converter.convert(stream)
+        else:
+            conv_result: ConversionResult = converter.convert(pubmed_path)
+        doc: DoclingDocument = conv_result.document
+
+        pred_md: str = doc.export_to_markdown()
+        assert verify_export(pred_md, str(gt_path) + ".md"), "export to md"
+
+        pred_itxt: str = doc._export_to_indented_text(
+            max_text_len=70, explicit_tables=False
+        )
+        assert verify_export(
+            pred_itxt, str(gt_path) + ".itxt"
+        ), "export to indented-text"
+
+        pred_json: str = json.dumps(doc.export_to_dict(), indent=2)
+        assert verify_export(pred_json, str(gt_path) + ".json"), "export to json"
+
+
+def test_e2e_pubmed_conversions_stream():
+    test_e2e_pubmed_conversions(use_stream=True)
+
+
+def test_e2e_pubmed_conversions_no_stream():
+    test_e2e_pubmed_conversions(use_stream=False)