From 42793a85240d342a07efe0a5cd3a1834581d62e1 Mon Sep 17 00:00:00 2001 From: Cunliang Geng Date: Tue, 12 Dec 2023 14:57:47 +0100 Subject: [PATCH] deprecate the method `_load_class_info` To refactor the following when dealing with annotations: - running of CANOPUS to predict chemical classes - loading chemical classes to annotate spectra and moleclar families --- src/nplinker/loader.py | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/src/nplinker/loader.py b/src/nplinker/loader.py index 2645a4e3..c3db6281 100644 --- a/src/nplinker/loader.py +++ b/src/nplinker/loader.py @@ -1,6 +1,7 @@ import glob import os from pathlib import Path +from deprecated import deprecated from nplinker.class_info.chem_classes import ChemClassPredictions from nplinker.class_info.class_matches import ClassMatches from nplinker.class_info.runcanopus import run_canopus @@ -197,9 +198,6 @@ def load(self): if not self._load_genomics(): return False - if not self._load_class_info(): - return False - self._load_optional() # Restrict strain list to only relevant strains (those that are present @@ -519,6 +517,7 @@ def _run_bigscape(self): self.bigscape_dir = find_bigscape_dir(self.bigscape_dir) + @deprecated(reason="To be refactored. It was used in the `self.load` method before.") def _load_class_info(self): """Load class match info (based on mibig) and chemical class predictions.