[WIP] Integrate Loguru

phys2denoise/metrics/cardiac.py

@@ -1,5 +1,6 @@
 """Denoising metrics for cardio recordings."""
 import numpy as np
+from loguru import logger
 
 from .. import references
 from ..due import due
@@ -8,6 +9,7 @@
 from .utils import convolve_and_rescale
 
 
+@logger.catch
 def _cardiac_metrics(card, peaks, samplerate, metric, window=6, central_measure="mean"):
     """
     Compute cardiac metrics.

phys2denoise/metrics/utils.py

@@ -2,13 +2,11 @@
 import logging
 
 import numpy as np
+from loguru import logger
 from numpy.lib.stride_tricks import sliding_window_view as swv
 from scipy.interpolate import interp1d
 from scipy.stats import zscore
 
-LGR = logging.getLogger(__name__)
-LGR.setLevel(logging.INFO)
-
 
 def print_metric_call(metric, args):
     """
@@ -33,7 +31,7 @@ def print_metric_call(metric, args):
 
     msg = f"{msg}\n"
 
-    LGR.info(msg)
+    logger.info(msg)
 
 
 def mirrorpad_1d(arr, buffer=250):
@@ -58,7 +56,7 @@ def mirrorpad_1d(arr, buffer=250):
         post_mirror = np.take(mirror, idx, axis=0)
     except IndexError:
         len(arr)
-        LGR.warning(
+        logger.warning(
             f"Requested buffer size ({buffer}) is longer than input array length "
             f"({len(arr)}). Fixing buffer size to array length."
         )

phys2denoise/workflow.py

@@ -18,6 +18,7 @@
 
 import numpy as np
 import pandas as pd
+from loguru import logger
 
 from phys2denoise.cli.run import _get_parser
 from phys2denoise.metrics.cardiac import crf
@@ -32,8 +33,8 @@
 from . import __version__
 from .due import Doi, due
 
-LGR = logging.getLogger(__name__)
-LGR.setLevel(logging.INFO)
+# LGR = logging.getLogger(__name__)
+# LGR.setLevel(logging.INFO)
 
 
 def save_bash_call(outdir):
@@ -59,6 +60,7 @@ def save_bash_call(outdir):
     f.close()
 
 
+@logger.catch
 def select_input_args(metric, metric_args):
     """
     Retrieve required args for metric from a dictionary of possible arguments.
@@ -112,6 +114,7 @@ def select_input_args(metric, metric_args):
     version=__version__,
     cite_module=True,
 )
+@logger.catch
 def phys2denoise(
     filename,
     outdir=".",
@@ -182,8 +185,10 @@ def phys2denoise(
         )
 
     version_number = __version__
-    LGR.info(f"Currently running phys2denoise version {version_number}")
-    LGR.info(f"Input file is {filename}")
+    # LGR.info(f"Currently running phys2denoise version {version_number}")
+    # LGR.info(f"Input file is {filename}")
+    logger.info(f"Currently running phys2denoise version {version_number}")
+    logger.info(f"Input file is {filename}")
 
     # Check options to make them internally coherent pt. II
     # #!# This can probably be done while parsing?

setup.cfg

@@ -53,10 +53,13 @@ test =
     coverage
 devtools =
     pre-commit
+logger =
+    loguru
 dev =
     %(devtools)s
     %(doc)s
     %(test)s
+    %(logger)s
 
 [options.entry_points]
 console_scripts =