[MRG] Switch to mne python verbose decorator

.mailmap

@@ -4,6 +4,7 @@ Alex Rockhill <[email protected]> <[email protected]>
 Alex Rockhill <[email protected]> <[email protected]>
 Alexandre Gramfort <[email protected]>
 Alexandre Gramfort <[email protected]> <[email protected]>
+Bruno Aristimunha <[email protected]>
 Ariel Rokem <[email protected]>
 Chris Holdgraf <[email protected]>
 Chris Holdgraf <[email protected]> <[email protected]>

doc/authors.rst

@@ -9,6 +9,7 @@
 .. _Arne Gottwald: https://github.com/waldie11
 .. _Austin Hurst: https://github.com/a-hurst
 .. _Berk Gerçek: https://github.com/berkgercek
+.. _Bruno Aristimunha: https://github.com/bruAristimunha
 .. _Bruno Hebling Vieira: https://github.com/bhvieira
 .. _Chris Holdgraf: https://bids.berkeley.edu/people/chris-holdgraf
 .. _Christian O'Reilly: https://github.com/christian-oreilly

doc/whats_new.rst

@@ -21,7 +21,7 @@ The following authors contributed for the first time. Thank you so much! 🤩
 
 * `Julius Welzel`_
 * `Alex Lopez Marquez`_
-
+* `Bruno Aristimunha`_
 
 The following authors had contributed before. Thank you for sticking around! 🤘
 
@@ -36,6 +36,7 @@ Detailed list of changes
 
 - :func:`mne_bids.write_raw_bids()` has a new parameter `electrodes_tsv_task` which allows adding the `task` entity to the `electrodes.tsv` filepath, by `Alex Lopez Marquez`_ (:gh:`1424`)
 - Extended the configuration to recognise `motion` as a valid BIDS datatype by `Julius Welzel`_ (:gh:`1430`)
+- Better control of verbosity in several functions, by `Bruno Aristimunha`_ (:gh:`1449`)
 
 🧐 API and behavior changes
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -51,13 +52,13 @@ Detailed list of changes
 ^^^^^^^^^^^^
 
 - Fixed a bug that modified the name and help message of some of the available commands, by `Alex Lopez Marquez`_ (:gh:`1441`)
-- Updated MEG/iEEG writers to satisfy the stricter checks in the latest BIDS validator releases: BTi/4D run folders now retain their ``.pdf`` suffix (falling back to the legacy naming when an older validator is detected), KIT marker files encode the run via the ``acq`` entity instead of ``run``, datasets lacking iEEG montages receive placeholder ``electrodes.tsv``/``coordsystem.json`` files, and the ``AssociatedEmptyRoom`` entry stores dataset-relative paths  by `Bruno Aritimunha`_ (:gh:`1449`)
+- Updated MEG/iEEG writers to satisfy the stricter checks in the latest BIDS validator releases: BTi/4D run folders now retain their ``.pdf`` suffix (falling back to the legacy naming when an older validator is detected), KIT marker files encode the run via the ``acq`` entity instead of ``run``, datasets lacking iEEG montages receive placeholder ``electrodes.tsv``/``coordsystem.json`` files, and the ``AssociatedEmptyRoom`` entry stores dataset-relative paths  by `Bruno Aristimunha`_ (:gh:`1449`)
 
 ⚕️ Code health
 ^^^^^^^^^^^^^^
 
 - Made :func:`mne_bids.copyfiles.copyfile_brainvision` output more meaningful error messages when encountering problematic files, by `Stefan Appelhoff`_ (:gh:`1444`)
-- Raised the minimum ``edfio`` requirement to ``0.4.10``,  eeglabio to ``0.1.0``  by `Bruno Aritimunha`_ (:gh:`1449`)
-- Relaxed EDF padding warnings in the test suite to accommodate upstream changes by `Bruno Aritimunha`_ (:gh:`1449`)
+- Raised the minimum ``edfio`` requirement to ``0.4.10``,  eeglabio to ``0.1.0``  by `Bruno Aristimunha`_ (:gh:`1449`)
+- Relaxed EDF padding warnings in the test suite to accommodate upstream changes by `Bruno Aristimunha`_ (:gh:`1449`)
 
 :doc:`Find out what was new in previous releases <whats_new_previous_releases>`

mne_bids/copyfiles.py

@@ -410,7 +410,7 @@ def copyfile_brainvision(vhdr_src, vhdr_dest, anonymize=None, verbose=None):
                 fout.write(line)
 
     if anonymize is not None:
-        raw = read_raw_brainvision(vhdr_src, preload=False, verbose=0)
+        raw = read_raw_brainvision(vhdr_src, preload=False, verbose=verbose)
         daysback, keep_his, _ = _check_anonymize(anonymize, raw, ".vhdr")
         raw.info = anonymize_info(raw.info, daysback=daysback, keep_his=keep_his)
         _anonymize_brainvision(fname_dest + ".vhdr", date=raw.info["meas_date"])
@@ -423,7 +423,8 @@ def copyfile_brainvision(vhdr_src, vhdr_dest, anonymize=None, verbose=None):
         logger.info("Anonymized all dates in VHDR and VMRK.")
 
 
-def copyfile_edf(src, dest, anonymize=None):
+@verbose
+def copyfile_edf(src, dest, anonymize=None, verbose=None):
     """Copy an EDF, EDF+, or BDF file to a new location, optionally anonymize.
 
     .. warning:: EDF/EDF+/BDF files contain two fields for recording dates:
@@ -505,9 +506,9 @@ def copyfile_edf(src, dest, anonymize=None):
     # Anonymize EDF/BDF data, if requested
     if anonymize is not None:
         if ext_src in [".bdf", ".BDF"]:
-            raw = read_raw_bdf(dest, preload=False, verbose=0)
+            raw = read_raw_bdf(dest, preload=False, verbose=verbose)
         elif ext_src in [".edf", ".EDF"]:
-            raw = read_raw_edf(dest, preload=False, verbose=0)
+            raw = read_raw_edf(dest, preload=False, verbose=verbose)
         else:
             raise ValueError(f"Unsupported file type ({ext_src})")
 

mne_bids/dig.py

@@ -207,6 +207,7 @@ def _write_electrodes_tsv(raw, fname, datatype, overwrite=False):
     _write_tsv(fname, data, overwrite=True)
 
 
+@verbose
 def _write_optodes_tsv(raw, fname, overwrite=False, verbose=True):
     """Create a optodes.tsv file and save it.
 

mne_bids/inspect.py

@@ -124,7 +124,11 @@ def inspect_dataset(
 _global_vars = dict(raw_fig=None, dialog_fig=None, mne_close_key=None)
 
 
-def _inspect_raw(*, bids_path, l_freq, h_freq, find_flat, show_annotations):
+# do you think we should expose the verbose of this functions?
+@verbose
+def _inspect_raw(
+    *, bids_path, l_freq, h_freq, find_flat, show_annotations, verbose=None
+):
     """Raw data inspection."""
     # Delay the import
     import matplotlib

mne_bids/read.py

@@ -35,13 +35,15 @@
 from mne_bids.utils import _get_ch_type_mapping, _import_nibabel, verbose, warn
 
 
+@verbose
 def _read_raw(
     raw_path,
     electrode=None,
     hsp=None,
     hpi=None,
     allow_maxshield=False,
     config_path=None,
+    verbose=None,
     **kwargs,
 ):
     """Read a raw file into MNE, making inferences based on extension."""
@@ -50,7 +52,13 @@ def _read_raw(
     # KIT systems
     if ext in [".con", ".sqd"]:
         raw = io.read_raw_kit(
-            raw_path, elp=electrode, hsp=hsp, mrk=hpi, preload=False, **kwargs
+            raw_path,
+            elp=electrode,
+            hsp=hsp,
+            mrk=hpi,
+            preload=False,
+            verbose=verbose,
+            **kwargs,
         )
 
     # BTi systems
@@ -60,15 +68,16 @@ def _read_raw(
             config_fname=config_path,
             head_shape_fname=hsp,
             preload=False,
+            verbose=verbose,
             **kwargs,
         )
 
     elif ext == ".fif":
-        raw = reader[ext](raw_path, allow_maxshield, **kwargs)
+        raw = reader[ext](raw_path, allow_maxshield, verbose=verbose, **kwargs)
 
     elif ext in [".ds", ".vhdr", ".set", ".edf", ".bdf", ".EDF", ".snirf", ".cdt"]:
         raw_path = Path(raw_path)
-        raw = reader[ext](raw_path, **kwargs)
+        raw = reader[ext](raw_path, verbose=verbose, **kwargs)
 
     # MEF and NWB are allowed, but not yet implemented
     elif ext in [".mef", ".nwb"]:
@@ -1048,6 +1057,7 @@ def read_raw_bids(
         hsp=None,
         hpi=None,
         config_path=config_path,
+        verbose=verbose,
         **extra_params,
     )
 

mne_bids/tests/test_read.py

@@ -5,6 +5,7 @@
 
 import contextlib
 import json
+import logging
 import os
 import os.path as op
 import re
@@ -1368,6 +1369,24 @@ def test_ignore_exclude_param(tmp_path):
     assert ch_name in raw.ch_names
 
 
+@testing.requires_testing_data
+def test_read_raw_bids_respects_verbose(tmp_path, caplog):
+    """Ensure ``verbose=False`` suppresses info-level logging."""
+    bids_path = _bids_path.copy().update(root=tmp_path, datatype="meg")
+    raw = _read_raw_fif(raw_fname, verbose=False)
+    write_raw_bids(raw, bids_path=bids_path, overwrite=True, verbose=False)
+
+    caplog.set_level("INFO", logger="mne")
+    read_raw_bids(bids_path=bids_path, verbose=False)
+
+    info_logs = [
+        record
+        for record in caplog.records
+        if record.levelno <= logging.INFO and record.name.startswith("mne")
+    ]
+    assert not info_logs
+
+
 @pytest.mark.filterwarnings(warning_str["channel_unit_changed"])
 @testing.requires_testing_data
 def test_channels_tsv_raw_mismatch(tmp_path):

mne_bids/tests/test_verbose.py

@@ -0,0 +1,56 @@
+"""Testing utilities for the MNE BIDS verbosity."""
+
+# Authors: The MNE-BIDS developers
+# SPDX-License-Identifier: BSD-3-Clause
+
+import importlib
+import inspect
+import pkgutil
+
+import mne_bids
+
+
+def _iter_modules():
+    # include top-level package module
+    yield importlib.import_module("mne_bids")
+    for module_info in pkgutil.walk_packages(
+        mne_bids.__path__, mne_bids.__name__ + "."
+    ):
+        yield importlib.import_module(module_info.name)
+
+
+def _has_verbose_param(obj):
+    try:
+        signature = inspect.signature(obj)
+    except (TypeError, ValueError):
+        return False
+    return "verbose" in signature.parameters
+
+
+def _is_verbose_decorated(obj):
+    source = getattr(obj, "__source__", "")
+    return "_use_log_level_" in source
+
+
+def _iter_functions_and_methods(module):
+    for name, obj in inspect.getmembers(module, inspect.isfunction):
+        if obj.__module__ != module.__name__:
+            continue
+        yield f"{module.__name__}.{name}", obj
+    for name, cls in inspect.getmembers(module, inspect.isclass):
+        if cls.__module__ != module.__name__:
+            continue
+        for method_name, method in inspect.getmembers(cls, inspect.isfunction):
+            if method.__module__ != module.__name__:
+                continue
+            yield f"{module.__name__}.{cls.__name__}.{method_name}", method
+
+
+def test_functions_with_verbose_are_decorated():
+    """Test that all functions with a verbose parameter are decorated."""
+    missing = []
+    for module in _iter_modules():
+        for qualname, obj in _iter_functions_and_methods(module):
+            if _has_verbose_param(obj) and not _is_verbose_decorated(obj):
+                missing.append(qualname)
+    assert not missing, f"Missing @verbose decorator: {missing}"