refactor(code): Shorten data preparation

scoping_review.qmd

@@ -27,17 +27,6 @@ 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")
@@ -55,23 +44,15 @@ bib_sample = prep_data.bib_library_from_dir(WORKING_DATA)
 
 # load relevant studies
 from src import load_data
-raw_observations_df = load_data.from_yml(PROCESSED_DATA)
-
-# load zotero-based metadata: citations and uses
-zot_df = prep_data.bib_metadata_df(bib_sample)
-
-# Add WB country grouping definitions (income group, world region)
-df_country_groups = prep_data.country_groups_df(Path(f"{SUPPLEMENTARY_DATA}/wb-country-groupings.xlsx"))
 
 bib_df = prep_data.observations_with_metadata_df(
-    raw_observations = raw_observations_df,
-    study_metadata = zot_df,
-    country_groups = df_country_groups
+    raw_observations = load_data.from_yml(PROCESSED_DATA),
+    study_metadata = prep_data.bib_metadata_df(bib_sample),
+    country_groups = prep_data.country_groups_df(Path(f"{SUPPLEMENTARY_DATA}/wb-country-groupings.xlsx")),
 )
 raw_observations = None
 zot_df = None
 df_country_groups = None
-
 ```
 
 <!-- pagebreak to separate from TOC -->