[MRG] change utils.logger.warning -> utils.warn (#9434)

* change utils.logger.warning -> utils.warn

* fix flake

* revert fixes for mne/fixes.py, due to circular import

* FIX: Revert

* DOC: Give reason

Co-authored-by: Eric Larson <larson.eric.d@gmail.com>

mne/gui/_coreg_gui.py

@@ -90,7 +90,7 @@
 from ..coreg import fit_matched_points, scale_mri, _find_fiducials_files
 from ..viz.backends._pysurfer_mayavi import _toggle_mlab_render
 from ..viz._3d import _get_3d_option
-from ..utils import logger, set_config, _pl
+from ..utils import logger, set_config, _pl, warn
 from ._fiducials_gui import MRIHeadWithFiducialsModel, FiducialsPanel
 from ._file_traits import trans_wildcard, DigSource, SubjectSelectorPanel
 from ._viewer import (HeadViewController, PointObject, SurfaceObject,
@@ -895,7 +895,7 @@ def close(self, info, is_ok):
             try:
                 info.object.save_config(size=size)
             except Exception as exc:
-                warnings.warn("Error saving GUI configuration:\n%s" % (exc,))
+                warn("Error saving GUI configuration:\n%s" % (exc,))
             return True
 
 

mne/io/brainvision/brainvision.py

@@ -484,8 +484,8 @@ def _get_vhdr_info(vhdr_fname, eog, misc, scale):
         try:
             n_samples = cfg.getint(cinfostr, 'DataPoints')
         except configparser.NoOptionError:
-            logger.warning('No info on DataPoints found. Inferring number of '
-                           'samples from the data file size.')
+            warn('No info on DataPoints found. Inferring number of '
+                 'samples from the data file size.')
             with open(data_fname, 'rb') as fid:
                 fid.seek(0, 2)
                 n_bytes = fid.tell()

mne/io/kit/kit.py

@@ -512,7 +512,7 @@ def get_kit_info(rawfile, allow_unknown_format, standardize_names=None,
             version_string = "V%iR%03i" % (version, revision)
             if allow_unknown_format:
                 unsupported_format = True
-                logger.warning("Force loading KIT format %s", version_string)
+                warn("Force loading KIT format %s", version_string)
             else:
                 raise UnsupportedKITFormat(
                     version_string,

mne/utils/misc.py

@@ -123,7 +123,7 @@ def run_subprocess(command, return_code=False, verbose=None, *args, **kwargs):
     # non-blocking adapted from https://stackoverflow.com/questions/375427/non-blocking-read-on-a-subprocess-pipe-in-python#4896288  # noqa: E501
     out_q = Queue()
     err_q = Queue()
-    with running_subprocess(command, *args, **kwargs) as p:
+    with running_subprocess(command, *args, **kwargs) as p, p.stdout, p.stderr:
         out_t = Thread(target=_enqueue_output, args=(p.stdout, out_q))
         err_t = Thread(target=_enqueue_output, args=(p.stderr, err_q))
         out_t.daemon = True
@@ -149,12 +149,16 @@ def run_subprocess(command, return_code=False, verbose=None, *args, **kwargs):
                     break
                 else:
                     err = err.decode('utf-8')
+                    # Leave this as logger.warning rather than warn(...) to
+                    # mirror the logger.info above for stdout. This function
+                    # is basically just a version of subprocess.call, and
+                    # shouldn't emit Python warnings due to stderr outputs
+                    # (the calling function can check for stderr output and
+                    # emit a warning if it wants).
                     logger.warning(err)
                     all_err += err
             if do_break:
                 break
-    p.stdout.close()
-    p.stderr.close()
     output = (all_out, all_err)
 
     if return_code: