Merge branch 'papyrus_version' into 'dev'

Fix papyrus version inconsistently

See merge request cdd/QSPRpred!193

Author: LindeSchoenmaker

CHANGELOG.md

@@ -4,7 +4,7 @@ From v3.2.0 to v4.0.0
 
 ## Fixes
 
-None.
+- Add variable version to papyrus_filter for consistent version use.
 
 ## Changes
 

qsprpred/data/sources/papyrus/papyrus_class.py

@@ -132,6 +132,7 @@ def getData(
             raise ValueError(f"Output directory '{output_dir}' does not exist.")
         logger.debug(f"Filtering Papyrus for accession keys: {acc_keys}")
         data, path = papyrus_filter(
+            version=self.version,
             acc_key=acc_keys,
             quality=quality,
             out_dir=output_dir,

qsprpred/data/sources/papyrus/papyrus_filter.py

@@ -15,6 +15,7 @@
 
 
 def papyrus_filter(
+    version: str,
     acc_key: list[str],
     quality: str,
     out_dir: str,
@@ -31,6 +32,7 @@ def papyrus_filter(
     and outputs a .tsv file of all compounds fulfilling these requirements.
 
     Args:
+        version (str): Papyrus database version
         acc_key (list): list of UniProt accession keys
         quality (str): str with minimum quality of dataset to keep
         out_dir (str): path to the location of Papyrus data
@@ -59,7 +61,7 @@ def papyrus_filter(
     # read data
     logger.info(f"Reading data from {papyrus_dir}...")
     sample_data = read_papyrus(
-        is3d=stereo, chunksize=chunk_size, source_path=papyrus_dir, plusplus=plusplus
+        is3d=stereo, version=version, chunksize=chunk_size, source_path=papyrus_dir, plusplus=plusplus
     )
     logger.info("Read all data.")