fixed logging, added debug message indicates the test that run.

i removed the setup of the logging module from the core. It interferes
with the needs of the user of the lib (saqc). eg. Messages are double
printed or not at all.

>> It is strongly advised that you do not add any handlers other than
>> NullHandler to your library’s loggers. [...]
from https://docs.python.org/3/howto/logging.html

we might add a defalutLoggingSetup(log_level='INFO') function or similar in future,
to ease the setup the logging.

saqc/__main__.py

@@ -5,13 +5,16 @@ import click
 
 import numpy as np
 import pandas as pd
+import logging
 
-from saqc.core import SaQC, logger
+from saqc.core import SaQC
 from saqc.flagger import CategoricalFlagger
 from saqc.flagger.dmpflagger import DmpFlagger
 import dios
 
 
+logger = logging.getLogger("SaQC")
+
 FLAGGERS = {
     "numeric": CategoricalFlagger([-1, 0, 1]),
     "category": CategoricalFlagger(["NIL", "OK", "BAD"]),
@@ -19,6 +22,14 @@ FLAGGERS = {
 }
 
 
+def _setup_logging(loglvl):
+    logger.setLevel(loglvl)
+    handler = logging.StreamHandler()
+    formatter = logging.Formatter("[%(asctime)s][%(name)s][%(levelname)s]: %(message)s")
+    handler.setFormatter(formatter)
+    logger.addHandler(handler)
+
+
 @click.command()
 @click.option(
     "-c", "--config", type=click.Path(exists=True), required=True, help="path to the configuration file",
@@ -37,7 +48,7 @@ FLAGGERS = {
 @click.option("--fail/--no-fail", default=True, help="whether to stop the program run on errors")
 def main(config, data, flagger, outfile, nodata, log_level, fail):
 
-    logger.setLevel(log_level)
+    _setup_logging(log_level)
 
     data = pd.read_csv(data, index_col=0, parse_dates=True,)
     data = dios.DictOfSeries(data)

saqc/core/core.py

@@ -90,13 +90,6 @@ def _setup():
     pd.set_option("mode.chained_assignment", "warn")
     np.seterr(invalid="ignore")
 
-    # logging
-    logger.setLevel(logging.INFO)
-    handler = logging.StreamHandler()
-    formatter = logging.Formatter("[%(asctime)s][%(name)s][%(levelname)s]: %(message)s")
-    handler.setFormatter(formatter)
-    logger.addHandler(handler)
-
 
 _setup()
 
@@ -157,6 +150,7 @@ class SaQC:
         data, flagger = self._data, self._flagger
 
         for field, func in self._to_call:
+            logger.debug(f"processing: {field}, {func.__name__}, {func.kwargs}")
 
             try:
                 data_result, flagger_result = func(data=data, flagger=flagger, field=field)