Integrate Loguru

peakdet/__init__.py

@@ -12,7 +12,11 @@
                                 interpolate_physio, peakfind_physio,
                                 plot_physio, reject_peaks)
 from peakdet.physio import (Physio)
+from loguru import logger
 
 from ._version import get_versions
 __version__ = get_versions()['version']
-del get_versions
+del get_versions
+
+# TODO: Loguru does not detect the module's name
+logger.disable("")

peakdet/cli/run.py

@@ -2,11 +2,11 @@
 import glob
 import os
 import sys
-import warnings
 import matplotlib
 matplotlib.use('WXAgg')
 from gooey import Gooey, GooeyParser
 import peakdet
+from loguru import logger
 
 TARGET = 'pythonw' if sys.platform == 'darwin' else 'python'
 TARGET += ' -u ' + os.path.abspath(__file__)
@@ -105,9 +105,10 @@ def get_parser():
     return parser
 
 
+@logger.catch
 def workflow(*, file_template, modality, fs, source='MRI', channel=1,
              output='peakdet.csv', savehistory=True, noedit=False, thresh=0.2,
-             measurements=ATTR_CONV.keys()):
+             measurements=ATTR_CONV.keys(), verbose=True):
     """
     Basic workflow for physiological data
 
@@ -138,16 +139,17 @@ def workflow(*, file_template, modality, fs, source='MRI', channel=1,
         Which HRV-related measurements to save from data. See ``peakdet.HRV``
         for available measurements. Default: all available measurements.
     """
-
+    logger.remove(0)
+    logger.add(sys.stderr, backtrace=verbose, diagnose=verbose)
     # output file
-    print('OUTPUT FILE:\t\t{}\n'.format(output))
+    logger.info('OUTPUT FILE:\t\t{}\n'.format(output))
     # grab files from file template
-    print('FILE TEMPLATE:\t{}\n'.format(file_template))
+    logger.info('FILE TEMPLATE:\t{}\n'.format(file_template))
     files = glob.glob(file_template, recursive=True)
 
     # convert measurements to peakdet.HRV attribute friendly names
     try:
-        print('REQUESTED MEASUREMENTS: {}\n'.format(', '.join(measurements)))
+        logger.info('REQUESTED MEASUREMENTS: {}\n'.format(', '.join(measurements)))
     except TypeError:
         raise TypeError('It looks like you didn\'t select any of the options '
                         'specifying desired output measurements. Please '
@@ -166,10 +168,10 @@ def workflow(*, file_template, modality, fs, source='MRI', channel=1,
         # requested on command line, warn and use existing measurements so
         # as not to totally fork up existing file
         if eheader != head:
-            warnings.warn('Desired output file already exists and requested '
-                          'measurements do not match with measurements in '
-                          'existing output file. Using the pre-existing '
-                          'measurements, instead.')
+            logger.warning('Desired output file already exists and requested '
+                           'measurements do not match with measurements in '
+                           'existing output file. Using the pre-existing '
+                           'measurements, instead.')
             measurements = [f.strip() for f in eheader.split(',')[1:]]
         head = ''
     # if output file doesn't exist, nbd
@@ -181,7 +183,7 @@ def workflow(*, file_template, modality, fs, source='MRI', channel=1,
         # iterate through all files and do peak detection with manual editing
         for fname in files:
             fname = os.path.relpath(fname)
-            print('Currently processing {}'.format(fname))
+            logger.info('Currently processing {}'.format(fname))
 
             # if we want to save history, this is the output name it would take
             outname = os.path.join(os.path.dirname(fname),
@@ -225,6 +227,7 @@ def workflow(*, file_template, modality, fs, source='MRI', channel=1,
 
 
 def main():
+    logger.enable("")
     opts = get_parser().parse_args()
     workflow(**vars(opts))
 

peakdet/external.py

@@ -3,9 +3,9 @@
 Functions for interacting with physiological data acquired by external packages
 """
 
-import warnings
 import numpy as np
 from peakdet import physio, utils
+from loguru import logger
 
 
 @utils.make_operation(exclude=[])
@@ -38,9 +38,9 @@ def load_rtpeaks(fname, channel, fs):
     """
 
     if fname.startswith('/'):
-        warnings.warn('Provided file seems to be an absolute path. In order '
-                      'to ensure full reproducibility it is recommended that '
-                      'a relative path is provided.')
+        logger.warning('Provided file seems to be an absolute path. In order '
+                       'to ensure full reproducibility it is recommended that '
+                       'a relative path is provided.')
 
     with open(fname, 'r') as src:
         header = src.readline().strip().split(',')

peakdet/io.py

@@ -5,9 +5,9 @@
 
 import json
 import os.path as op
-import warnings
 import numpy as np
 from peakdet import physio, utils
+from loguru import logger
 
 EXPECTED = ['data', 'fs', 'history', 'metadata']
 
@@ -64,9 +64,9 @@ def load_physio(data, *, fs=None, dtype=None, history=None,
     # if we got a numpy array, load that into a Physio object
     elif isinstance(data, np.ndarray):
         if history is None:
-            warnings.warn('Loading data from a numpy array without providing a'
-                          'history will render reproducibility functions '
-                          'useless! Continuing anyways.')
+            logger.warning('Loading data from a numpy array without providing a'
+                           'history will render reproducibility functions '
+                           'useless! Continuing anyways.')
         phys = physio.Physio(np.asarray(data, dtype=dtype), fs=fs,
                              history=history)
     # create a new Physio object out of a provided Physio object
@@ -79,7 +79,7 @@ def load_physio(data, *, fs=None, dtype=None, history=None,
     # reset sampling rate, as requested
     if fs is not None and fs != phys.fs:
         if not np.isnan(phys.fs):
-            warnings.warn('Provided sampling rate does not match loaded rate. '
+            logger.warning('Provided sampling rate does not match loaded rate. '
                           'Resetting loaded sampling rate {} to provided {}'
                           .format(phys.fs, fs))
         phys._fs = fs
@@ -148,7 +148,7 @@ def load_history(file, verbose=False):
     data = None
     for (func, kwargs) in history:
         if verbose:
-            print('Rerunning {}'.format(func))
+            logger.info('Rerunning {}'.format(func))
         # loading functions don't have `data` input because it should be the
         # first thing in `history` (when the data was originally loaded!).
         # for safety, check if `data` is None; someone could have potentially
@@ -194,9 +194,9 @@ def save_history(file, data):
 
     data = check_physio(data)
     if len(data.history) == 0:
-        warnings.warn('History of provided Physio object is empty. Saving '
-                      'anyway, but reloading this file will result in an '
-                      'error.')
+        logger.warning('History of provided Physio object is empty. Saving '
+                       'anyway, but reloading this file will result in an '
+                       'error.')
     file += '.json' if not file.endswith('.json') else ''
     with open(file, 'w') as dest:
         json.dump(data.history, dest, indent=4)

peakdet/operations.py

@@ -8,7 +8,6 @@
 from scipy import interpolate, signal
 from peakdet import editor, utils
 
-
 @utils.make_operation()
 def filter_physio(data, cutoffs, method, *, order=3):
     """

peakdet/physio.py

@@ -6,7 +6,6 @@
 import numpy as np
 
 
-
 class Physio():
     """
     Class to hold physiological data and relevant information
@@ -40,7 +39,6 @@ class Physio():
     suppdata : :obj:`numpy.ndarray`
         Secondary physiological waveform
     """
-
     def __init__(self, data, fs=None, history=None, metadata=None, suppdata=None):
         self._data = np.asarray(data).squeeze()
         if self.data.ndim > 1:

peakdet/utils.py

@@ -8,6 +8,8 @@
 import inspect
 import numpy as np
 from peakdet import physio
+from loguru import logger
+import sys
 
 
 def make_operation(*, exclude=None):
@@ -225,3 +227,11 @@ def check_troughs(data, peaks, troughs=None):
         all_troughs[f] = idx
 
     return all_troughs
+
+def enable_logger(diagnose=True, backtrace=True):
+    """
+    Toggles the use of the module's logger and configures it
+    """
+    logger.enable("")
+    logger.remove(0)
+    logger.add(sys.stderr, backtrace=backtrace, diagnose=diagnose)

requirements.txt

@@ -1,3 +1,4 @@
 matplotlib
 numpy
 scipy
+loguru

setup.cfg

@@ -57,11 +57,14 @@ test =
     pytest-cov
     %(style)s
     %(nk)s
+logger = 
+    loguru
 all =
     %(doc)s
     %(duecredit)s
     %(style)s
     %(test)s
+    %(logger)s
 
 
 [options.package_data]