added debug logging

ms2rescore/core.py

@@ -55,10 +55,14 @@ def rescore(configuration: Dict, psm_list: Optional[PSMList] = None) -> None:
     )
 
     # TODO: avoid hard coding feature generators in some way
-    rt_required = "deeplc" in config["feature_generators"] and None in psm_list["retention_time"]
-    im_required = ("ionmob" or "im2deep" in config["feature_generators"]) and None in psm_list[
-        "ion_mobility"
-    ]
+    rt_required = ("deeplc" in config["feature_generators"]) and (
+        None in psm_list["retention_time"]
+    )
+    im_required = ("ionmob" or "im2deep" in config["feature_generators"]) and (
+        None in psm_list["ion_mobility"]
+    )
+    logger.debug(f"RT required: {rt_required}, IM required: {im_required}")
+
     if rt_required or im_required:
         logger.info("Parsing missing retention time and/or ion mobility values from spectra...")
         get_missing_values(config, psm_list, missing_rt=rt_required, missing_im=im_required)

pyproject.toml

@@ -35,7 +35,7 @@ dependencies = [
     "numpy>=1.16.0",
     "pandas>=1.0",
     "rich>=12",
-    "pyteomics>=4.1.0",
+    "pyteomics>=4.1.0, <4.7",
     "lxml>=4.5",
     "ms2pip>=4.0.0-dev5",
     "click>=7",