disable logging only for Timeloop instances, not the root logger; fixes

#175
saezlab · Jun 10, 2021 · 4eeda1f · 4eeda1f
1 parent ed6b0ba
commit 4eeda1f
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Showing 7 changed files with 13 additions and 13 deletions.
diff --git a/src/pypath/inputs/humap.py b/src/pypath/inputs/humap.py
@@ -77,6 +77,10 @@ def humap2_complexes(min_confidence = 0):
             for uniprot in l[2].split()
         )):
 
+            if not uniprots:
+
+                continue
+
             cplex = intera.Complex(
                 components = uniprots,
                 sources = 'hu.MAP2',

diff --git a/src/pypath/inputs/uniprot.py b/src/pypath/inputs/uniprot.py
@@ -26,8 +26,8 @@
 import datetime
 import collections
 import itertools
+
 import timeloop
-timeloop.app.logging.disable(level = 9999)
 
 import pypath.resources.urls as urls
 import pypath.share.curl as curl
@@ -171,6 +171,7 @@ def is_trembl(name, organism = 9606):
 
 
 _cleanup_timeloop = timeloop.Timeloop()
+_cleanup_timeloop.logger.setLevel(9999)
 
 @_cleanup_timeloop.job(
     interval = datetime.timedelta(

diff --git a/src/pypath/share/log.py b/src/pypath/share/log.py
@@ -27,9 +27,6 @@
 import datetime
 
 import timeloop
-# we use this for simple little tasks only
-# and don't want engage another logger
-timeloop.app.logging.disable(level=9999)
 
 import pypath.share.settings as settings
 
@@ -38,6 +35,7 @@
 
 
 _log_flush_timeloop = timeloop.Timeloop()
+_log_flush_timeloop.logger.setLevel(9999)
 
 
 def new_logger(name = None, logdir = None, verbosity = None, **kwargs):

diff --git a/src/pypath/utils/homology.py b/src/pypath/utils/homology.py
@@ -46,8 +46,8 @@
 import pypath.utils.taxonomy as taxonomy
 import pypath.share.cache as cache_mod
 
-timeloop.app.logging.disable(level = 9999)
 _homology_cleanup_timeloop = timeloop.Timeloop()
+_homology_cleanup_timeloop.logger.setLevel(9999)
 
 _logger = session_mod.Logger(name = 'homology')
 _log = _logger._log

diff --git a/src/pypath/utils/mapping.py b/src/pypath/utils/mapping.py
@@ -48,9 +48,6 @@
     import pickle
 
 import timeloop
-# we use this for simple little tasks only
-# and don't want engage another logger
-timeloop.app.logging.disable(level = 9999)
 
 # from pypath:
 import pypath.share.progress as progress
@@ -955,6 +952,7 @@ def __init__(
         )
 
         self._mapper_cleanup_timeloop = timeloop.Timeloop()
+        self._mapper_cleanup_timeloop.logger.setLevel(9999)
 
         for job in self._mapper_cleanup_timeloop.jobs:
 

diff --git a/src/pypath/utils/reflists.py b/src/pypath/utils/reflists.py
@@ -25,17 +25,14 @@
 import json
 import datetime
 import time
-import timeloop
 
 try:
     import cPickle as pickle
 
 except ImportError:
     import pickle
 
-# we use this for simple little tasks only
-# and don't want engage another logger
-timeloop.app.logging.disable(level = 9999)
+import timeloop
 
 import pypath.inputs.uniprot as uniprot_input
 import pypath.inputs.mirbase as mirbase_input
@@ -56,6 +53,7 @@
 
 
 _reflists_cleanup_timeloop = timeloop.Timeloop()
+_reflists_cleanup_timeloop.logger.setLevel(9999)
 
 
 class ReferenceListManager(session_mod.Logger):

diff --git a/src/pypath/utils/taxonomy.py b/src/pypath/utils/taxonomy.py
@@ -24,8 +24,8 @@
 
 import time
 import datetime
+
 import timeloop
-timeloop.app.logging.disable(level = 9999)
 
 import pypath.share.common as common
 import pypath.share.session as session
@@ -290,6 +290,7 @@ def uniprot_taxid(uniprot):
 
 
 _cleanup_timeloop = timeloop.Timeloop()
+_cleanup_timeloop.logger.setLevel(9999)
 
 @_cleanup_timeloop.job(
     interval = datetime.timedelta(