seems scout is working

oktoberfest/predict/koina.py

@@ -586,7 +586,6 @@ def __predict_async(self, data: Dict[str, np.ndarray], debug=False) -> Dict[str,
 
                 unfinished_tasks = new_unfinished_tasks
                 pbar.refresh()
-
         return self.__handle_results(infer_results, debug)
 
     def __handle_results(

oktoberfest/predict/predict.py

@@ -87,17 +87,16 @@ def _prepare_alignment_df(
     :param xl: if true, select the top 50 spectra for cross-linked peptide
     :return: a library that is modified according to the description above
     """
-    top_n = 1000 if not xl else 50
+    top_n = 1000 if not xl else 20
     hcd_targets = library.obs.query("(FRAGMENTATION == 'HCD') & ~REVERSE")
     hcd_targets = hcd_targets.sort_values(by="SCORE", ascending=False)
     if group_by_charge:
         hcd_targets = hcd_targets.groupby("PRECURSOR_CHARGE")
     top_hcd_targets = hcd_targets.head(top_n)
-
+    top_n= len(top_hcd_targets)
     alignment_library = library[top_hcd_targets.index]
     alignment_library = Spectra(anndata.concat([alignment_library for _ in range(*ce_range)]))
     alignment_library.obs.reset_index(inplace=True)
-
     alignment_library.obs["ORIG_COLLISION_ENERGY"] = alignment_library.obs["COLLISION_ENERGY"]
     alignment_library.obs["COLLISION_ENERGY"] = np.repeat(range(*ce_range), top_n)
 

oktoberfest/runner.py

@@ -142,7 +142,7 @@ def _annotate_and_get_library(spectra_file: Path, config: Config, tims_meta_file
 def _get_best_ce(library: Spectra, spectra_file: Path, config: Config):
     results_dir = config.output / "results"
     results_dir.mkdir(exist_ok=True)
-    if (library.obs["FRAGMENTATION"] == "HCD").any():
+    if ((library.obs["FRAGMENTATION"] == "HCD") & (library.obs["REVERSE"] == False)).any():
         server_kwargs = {
             "server_url": config.prediction_server,
             "ssl": config.ssl,