fix(repo): Rename all references to data and output dir

src/extract/load_data.py

@@ -9,7 +9,7 @@ try:
 except ModuleNotFoundError:
     import yml as yaml  # for directly running the package
 
-DEFAULT_YAML_PATH = Path("02-data/processed")
+DEFAULT_YAML_PATH = Path("data/processed")
 
 
 def to_tsv(studies: list[dict]) -> str:

src/globals.py

@@ -3,7 +3,7 @@ import os
 
 PROJECT_DIR=Path(os.getenv("QUARTO_PROJECT_DIR", "."))
 
-DATA_DIR=PROJECT_DIR.joinpath("02-data")
+DATA_DIR=PROJECT_DIR.joinpath("data")
 
 RAW_DATA=DATA_DIR.joinpath("raw")
 WORKING_DATA=DATA_DIR.joinpath("intermediate")

src/model/prisma.py

@@ -33,7 +33,7 @@ del bib_sample, bib_sample_raw_db
 if __name__ == "__main__":
     nr = PrismaNumbers()
 
-    # FIXME use 02-data/supplementary undeduplciated counts to get database starting and snowballing counts
+    # FIXME use data/supplementary undeduplciated counts to get database starting and snowballing counts
     outp = f"""
     flowchart TD;
         search_db["Records identified through database searching (n={nr.nr_database_query_raw})"] --> starting_sample;