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deprecate the method _load_class_info #198

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merged 3 commits into from
Jan 24, 2024
Merged

deprecate the method _load_class_info #198

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76db23c
deprecate the method `_load_class_info`
CunliangGeng Dec 12, 2023
d085aec
add explicit attribute `self.chem_classes`
CunliangGeng Dec 20, 2023
b714bed
add explicit attribute `self. class_matches`
CunliangGeng Dec 20, 2023
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7 changes: 4 additions & 3 deletions src/nplinker/loader.py
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Original file line number Diff line number Diff line change
@@ -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
Expand Down Expand Up @@ -131,6 +132,8 @@ def __init__(self, config_data):
self.webapp_scoring_cutoff = self._config_webapp.get(
"tables_metcalf_threshold", self.TABLES_CUTOFF_DEFAULT
)
self.class_matches = None
self.chem_classes = None

logger.debug(
"DatasetLoader({}, {}, {})".format(self._root, self.dataset_id, self._remote_loading)
Expand Down Expand Up @@ -197,9 +200,6 @@ 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
Expand Down Expand Up @@ -519,6 +519,7 @@ 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.

Expand Down
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