Merge pull request #298 from scverse/fix/root-logger-level

Fix root logging level being set to INFO for all packages

Author: PauBadiaM

CHANGELOG.md

@@ -16,6 +16,9 @@ and this project adheres to [Semantic Versioning][].
 ### Changes
 - Refactored `ds.ensmbl_to_symbol` to reuse `_download` and fixed mirror fallback to actually switch between Ensembl mirrors
 
+### Bugfixes
+- Fixed `_log` setting the root logging level to INFO for all packages (#296)
+
 ## 2.1.4
 
 ### Changes

src/decoupler/_log.py

@@ -1,6 +1,10 @@
 import logging
 
-logging.basicConfig(level=logging.INFO, format="%(asctime)s | [%(levelname)s] %(message)s", datefmt="%Y-%m-%d %H:%M:%S")
+logger = logging.getLogger("decoupler")
+logger.setLevel(logging.INFO)
+_handler = logging.StreamHandler()
+_handler.setFormatter(logging.Formatter("%(asctime)s | [%(levelname)s] %(message)s", datefmt="%Y-%m-%d %H:%M:%S"))
+logger.addHandler(_handler)
 
 
 def _log(message: str, level: str = "info", verbose: bool = False) -> None:
@@ -19,6 +23,6 @@ def _log(message: str, level: str = "info", verbose: bool = False) -> None:
     level = level.lower()
     if verbose:
         if level == "warn":
-            logging.warning(message)
+            logger.warning(message)
         elif level == "info":
-            logging.info(message)
+            logger.info(message)

tests/ds/test_toy.py

@@ -45,7 +45,7 @@ def test_toy(
     verbose,
     caplog,
 ):
-    with caplog.at_level(logging.INFO):
+    with caplog.at_level(logging.INFO, logger="decoupler"):
         adata, net = dc.ds.toy(nobs=nobs, nvar=nvar, bval=bval, pstime=pstime, seed=seed, verbose=verbose)
     if verbose:
         assert len(caplog.text) > 0

tests/pp/test_net.py

@@ -24,7 +24,7 @@ def test_validate_net(
     verbose,
     caplog,
 ):
-    with caplog.at_level(logging.WARNING):
+    with caplog.at_level(logging.WARNING, logger="decoupler"):
         vnet = dc.pp.net._validate_net(net=net, verbose=verbose)
     assert caplog.text == ""
     assert net.shape == vnet.shape
@@ -34,7 +34,7 @@ def test_validate_net(
 
     net.drop(columns=["weight"], inplace=True)
     assert "weight" not in net.columns
-    with caplog.at_level(logging.WARNING):
+    with caplog.at_level(logging.WARNING, logger="decoupler"):
         vnet = dc.pp.net._validate_net(net=net, verbose=verbose)
     if verbose:
         assert len(caplog.text) > 0
@@ -119,7 +119,7 @@ def test_adjmat(
     caplog,
 ):
     features = adata.var_names
-    with caplog.at_level(logging.INFO):
+    with caplog.at_level(logging.INFO, logger="decoupler"):
         sources, targets, adjmat = dc.pp.adjmat(features=features, net=net, verbose=verbose)
     adjmat = adjmat.ravel()
     non_zero_adjmat = adjmat[adjmat != 0.0]
@@ -143,7 +143,7 @@ def test_idxmat(
     caplog,
 ):
     features = adata.var_names
-    with caplog.at_level(logging.INFO):
+    with caplog.at_level(logging.INFO, logger="decoupler"):
         sources, cnct, starts, offsets = dc.pp.idxmat(features=features, net=net, verbose=verbose)
     if verbose:
         assert len(caplog.text) > 0