fix(script): Suppress bibtex warning on import

When first importing bibtex entries, if there are e.g. double entries,
the library gives an 'unsuppressable' warning which will always
appear in the manuscript otherwise. This simply ensures no warning
is displayed by turning off logging for the duration of their use.

scoping_review.qmd

@@ -27,6 +27,17 @@ import seaborn as sns
 from tabulate import tabulate
 import bibtexparser
 
+from contextlib import contextmanager
+import logging
+@contextmanager
+def all_logging_disabled(highest_level=logging.CRITICAL):
+    previous_level = logging.root.manager.disable
+    logging.disable(highest_level)
+    try:
+        yield
+    finally:
+        logging.disable(previous_level)
+
 sns.set_style("whitegrid")
 
 DATA_DIR=Path("./02-data")
@@ -39,12 +50,14 @@ bib_string=""
 for partial_bib in RAW_DATA.glob("**/*.bib"):
     with open(partial_bib) as f:
         bib_string+="\n".join(f.readlines())
+with all_logging_disabled():
     bib_sample_raw_db = bibtexparser.parse_string(bib_string)
 
 bib_string=""
 for partial_bib in WORKING_DATA.glob("**/*.bib"):
     with open(partial_bib) as f:
         bib_string+="\n".join(f.readlines())
+with all_logging_disabled():
     bib_sample = bibtexparser.parse_string(bib_string)
 
 # load relevant studies