Fix Bibtex rendering in reports

pyproject.toml

@@ -28,6 +28,8 @@ dependencies = [
     "nilearn>=0.7",
     "numpy>=1.16",
     "pandas>=2.0",
+    "pybtex",
+    "pybtex-apa-style",
     "scikit-learn>=0.21",
     "scipy>=1.2.0",
     "threadpoolctl",
@@ -48,6 +50,7 @@ doc = [
     "sphinx-argparse",
     "sphinxcontrib-bibtex",
 ]
+
 tests = [
     "codecov",
     "coverage",

tedana/reporting/html_report.py

@@ -8,13 +8,26 @@
 import pandas as pd
 from bokeh import __version__ as bokehversion
 from bokeh import embed, layouts, models
+from pybtex.database.input import bibtex
 
 from tedana import __version__
 from tedana.io import load_json
 from tedana.reporting import dynamic_figures as df
 
 LGR = logging.getLogger("GENERAL")
 
+from pybtex.plugin import find_plugin
+
+APA = find_plugin("pybtex.style.formatting", "apa")()
+HTML = find_plugin("pybtex.backends", "html")()
+
+
+def _bib2html(bibliography):
+    parser = bibtex.Parser()
+    bibliography = parser.parse_file(bibliography)
+    formatted_bib = APA.format_bibliography(bibliography)
+    return "<br>".join(entry.text.render(HTML) for entry in formatted_bib)
+
 
 def _generate_buttons(out_dir, io_generator):
     resource_path = Path(__file__).resolve().parent.joinpath("data", "html")
@@ -85,6 +98,9 @@ def _update_template_bokeh(bokeh_id, info_table, about, prefix, references, boke
     # Initial carpet plot (default one)
     initial_carpet = f"./figures/{prefix}carpet_optcom.svg"
 
+    # Convert bibtex to html
+    references = _bib2html(references)
+
     body_template_name = "report_body_template.html"
     body_template_path = resource_path.joinpath(body_template_name)
     with open(str(body_template_path)) as body_file:
@@ -273,8 +289,7 @@ def get_elbow_val(elbow_prefix):
     with open(opj(io_generator.out_dir, f"{io_generator.prefix}report.txt"), "r+") as f:
         about = f.read()
 
-    with open(opj(io_generator.out_dir, f"{io_generator.prefix}references.bib")) as f:
-        references = f.read()
+    references = opj(io_generator.out_dir, f"{io_generator.prefix}references.bib")
 
     # Read info table
     data_descr_path = io_generator.get_name("data description json")