diff --git a/peakdet/cli/run.py b/peakdet/cli/run.py
index a2d25e9..0c16fe4 100644
--- a/peakdet/cli/run.py
+++ b/peakdet/cli/run.py
@@ -142,14 +142,14 @@ def workflow(*, file_template, modality, fs, source='MRI', channel=1,
     """
 
     # 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 '
@@ -168,10 +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
@@ -183,7 +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),
diff --git a/peakdet/external.py b/peakdet/external.py
index 2ccb1aa..d0a274a 100644
--- a/peakdet/external.py
+++ b/peakdet/external.py
@@ -39,9 +39,9 @@ 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(',')
diff --git a/peakdet/io.py b/peakdet/io.py
index 439aac1..68a0d00 100644
--- a/peakdet/io.py
+++ b/peakdet/io.py
@@ -66,9 +66,9 @@ 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
@@ -81,7 +81,7 @@ 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
@@ -151,7 +151,7 @@ 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
@@ -197,9 +197,9 @@ 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)