make EDF writer handle anonymized meas_date (#1479)

* make EDF writer handle anonymized meas_date

* indent

* test + coverage

* decorate

* pyproject.toml lint

* bump python versions

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* missed a few

* lint

* back to 3.13; 3.14 needs help

* changelog

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: drammock

.github/workflows/unit_tests.yml

@@ -51,7 +51,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        python-version: ["3.10", "3.13"]  # Oldest and newest supported versions
+        python-version: ["3.11", "3.13"]  # Oldest and newest supported versions
     steps:
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v6
@@ -129,22 +129,22 @@ jobs:
     #
     # 8 checks:
     # for each machine type (ubuntu, macos, windows):
-    # 3.10 / mne-stable / full / validator-stable
+    # 3.11 / mne-stable / full / validator-stable
     # 3.13 / mne-stable / full / validator-stable
     #
     # 4 additional checks with alternative MNE-Python and BIDS validator versions:
     # ubuntu / 3.13 / mne-main / full / validator-main -->  to test cutting edge of everything
-    # ubuntu / 3.10 / mne-prev / full / validator-stable --> to test last supported of everything
+    # ubuntu / 3.11 / mne-prev / full / validator-stable --> to test last supported of everything
     # ubuntu / 3.13 / mne-stable / minimal / validator-stable --> to test a minimal installation
-    # ubuntu / 3.12 / mne-stable / full / validator-main-schema --> to test next-gen BIDS validator
+    # ubuntu / 3.13 / mne-stable / full / validator-main-schema --> to test next-gen BIDS validator
     # macos-15-intel / 3.13 / mne-stable / full / validator-stable --> to test macos x86_64
     timeout-minutes: 60
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ["3.10", "3.13"]  # Oldest and newest supported versions
+        python-version: ["3.11", "3.13"]  # Oldest and newest supported versions
         mne-version: [mne-stable]
         mne-bids-install: [full]
         bids-validator-version: [validator-stable]
@@ -159,7 +159,7 @@ jobs:
             bids-validator-version: validator-main
           # Test previous MNE stable version
           - os: ubuntu-latest
-            python-version: "3.10"
+            python-version: "3.11"
             mne-version: mne-prev-stable
             mne-bids-install: full
             bids-validator-version: validator-stable
@@ -171,7 +171,7 @@ jobs:
             bids-validator-version: validator-stable
           # Test next gen BIDS schema validator
           - os: ubuntu-latest
-            python-version: "3.12"
+            python-version: "3.13"
             mne-version: mne-stable
             mne-bids-install: full
             bids-validator-version: validator-main-schema

doc/install.rst

@@ -32,7 +32,7 @@ Optional:
 We recommend installing ``mne-bids`` into an isolated Python environment,
 for example created via ``conda``
 (may be obtained through `miniconda <https://docs.conda.io/en/latest/miniconda.html>`_).
-We require that you **use Python 3.10 or higher**.
+We require that you **use Python 3.11 or higher**.
 You may choose to install ``mne-bids`` into your isolated Python environment
 `via pip <#installation-via-pip>`_ or
 `via conda <#installation-via-conda>`_.

doc/whats_new.rst

@@ -51,6 +51,7 @@ Detailed list of changes
 
 🛠 Requirements
 ^^^^^^^^^^^^^^^
+- MNE-BIDS now requires Python 3.11 or higher.
 - Including ``filelock`` as a dependency to handle atomic file writing and parallel processing support by `Bruno Aristimunha`_ (:gh:`1451`)
 
 - None yet
@@ -63,6 +64,7 @@ Detailed list of changes
 - Made the lock helpers skip reference counting when the optional ``filelock`` dependency is missing, preventing spurious ``AttributeError`` crashes during reads, by `Bruno Aristimunha`_ (:gh:`1469`)
 - Fixed a bug in :func:`mne_bids.read_raw_bids` that caused it to fail when reading BIDS datasets where the acquisition time was specified in local time rather than UTC only in Windows, by `Bruno Aristimunha`_ (:gh:`1452`)
 - Fixed bug in :func:`~mne_bids.write_raw_bids` where incorrect unit was sometimes written into ``channels.tsv`` file when converting data to BrainVision, EDF, or EEGLAB formats, by `Daniel McCloy`_ (:gh:`1475`)
+- Converting data to EDF format while also anonymizing it will now yield valid EDF files (with ``startdate`` set to 1985-01-01 00:00:00); the BIDS-compliant anonymized date will still be stored in ``scans.tsv`` file and restored to the in-memory Raw object when read using :func:`~mne_bids.read_raw_bids`, by `Daniel McCloy`_ (:gh:`1479`)
 
 ⚕️ Code health
 ^^^^^^^^^^^^^^

examples/convert_empty_room.py

@@ -29,7 +29,7 @@
 # Let us first import mne_bids.
 
 import shutil
-from datetime import datetime, timezone
+from datetime import UTC, datetime
 
 import mne
 from mne.datasets import sample
@@ -98,7 +98,7 @@
 for date in dates:
     er_bids_path.update(session=date)
     er_meas_date = datetime.strptime(date, "%Y%m%d")
-    er_raw.set_meas_date(er_meas_date.replace(tzinfo=timezone.utc))
+    er_raw.set_meas_date(er_meas_date.replace(tzinfo=UTC))
     write_raw_bids(er_raw, er_bids_path, overwrite=True)
 
 # %%

mne_bids/read.py

@@ -6,7 +6,7 @@
 import json
 import os
 import re
-from datetime import datetime, timedelta, timezone
+from datetime import UTC, datetime, timedelta
 from difflib import get_close_matches
 from pathlib import Path
 
@@ -417,14 +417,14 @@ def _handle_scans_reading(scans_fname, raw, bids_path):
 
         if acq_time_is_utc:
             # Enforce setting timezone to UTC without additonal conversion
-            acq_time = acq_time.replace(tzinfo=timezone.utc)
+            acq_time = acq_time.replace(tzinfo=UTC)
         else:
             # Convert time offset to UTC
             if acq_time.tzinfo is None:
                 # Windows needs an explicit local tz for naive, pre-epoch times.
-                local_tz = datetime.now().astimezone().tzinfo or timezone.utc
+                local_tz = datetime.now().astimezone().tzinfo or UTC
                 acq_time = acq_time.replace(tzinfo=local_tz)
-            acq_time = acq_time.astimezone(timezone.utc)
+            acq_time = acq_time.astimezone(UTC)
 
         logger.debug(f"Loaded {scans_fname} scans file to set acq_time as {acq_time}.")
         # First set measurement date to None and then call call anonymize() to

mne_bids/tests/test_path.py

@@ -8,7 +8,7 @@
 import shutil
 import shutil as sh
 import timeit
-from datetime import datetime, timezone
+from datetime import UTC, datetime
 from pathlib import Path
 
 import mne
@@ -1435,7 +1435,7 @@ def test_find_empty_room(return_bids_test_dir, tmp_path):
     for date in dates:
         er_bids_path.update(session=date)
         er_meas_date = datetime.strptime(date, "%Y%m%d")
-        er_meas_date = er_meas_date.replace(tzinfo=timezone.utc)
+        er_meas_date = er_meas_date.replace(tzinfo=UTC)
         er_raw.set_meas_date(er_meas_date)
         write_raw_bids(er_raw, er_bids_path, verbose=False)
 
@@ -1460,8 +1460,8 @@ def test_find_empty_room(return_bids_test_dir, tmp_path):
     bids_root = tmp_path / "associated-empty-room"
     bids_root.mkdir()
     raw = _read_raw_fif(raw_fname)
-    meas_date = datetime(year=2020, month=1, day=10, tzinfo=timezone.utc)
-    er_date = datetime(year=2010, month=1, day=1, tzinfo=timezone.utc)
+    meas_date = datetime(year=2020, month=1, day=10, tzinfo=UTC)
+    er_date = datetime(year=2010, month=1, day=1, tzinfo=UTC)
     raw.set_meas_date(meas_date)
 
     er_raw_matching_date = er_raw.copy().set_meas_date(meas_date)
@@ -1543,7 +1543,7 @@ def test_find_emptyroom_ties(tmp_path):
     )
     er_dir = er_dir_path.mkdir().directory
 
-    meas_date = datetime.strptime(session, "%Y%m%d").replace(tzinfo=timezone.utc)
+    meas_date = datetime.strptime(session, "%Y%m%d").replace(tzinfo=UTC)
 
     raw = _read_raw_fif(raw_fname)
 

mne_bids/tests/test_read.py

@@ -13,7 +13,7 @@
 import shutil as sh
 from collections import OrderedDict
 from contextlib import nullcontext
-from datetime import date, datetime, timezone
+from datetime import UTC, date, datetime
 from pathlib import Path
 
 import mne
@@ -108,7 +108,7 @@ def _make_parallel_raw(subject, *, seed=None):
     info = mne.create_info(["MEG0113"], 100, ch_types="mag")
     data = rng.standard_normal((1, 100)) * 1e-12
     raw = mne.io.RawArray(data, info)
-    raw.set_meas_date(datetime(2020, 1, 1, tzinfo=timezone.utc))
+    raw.set_meas_date(datetime(2020, 1, 1, tzinfo=UTC))
     raw.info["line_freq"] = 60
     raw.info["subject_info"] = {
         "his_id": subject,
@@ -802,7 +802,7 @@ def test_handle_scans_reading(tmp_path):
     scans_tsv = _from_tsv(scans_path)
     acq_time_str = scans_tsv["acq_time"][0]
     acq_time = datetime.strptime(acq_time_str, "%Y-%m-%dT%H:%M:%S.%fZ")
-    acq_time = acq_time.replace(tzinfo=timezone.utc)
+    acq_time = acq_time.replace(tzinfo=UTC)
     new_acq_time = acq_time_str.split(".")[0] + "Z"
     assert acq_time == raw_01.info["meas_date"]
     scans_tsv["acq_time"][0] = new_acq_time
@@ -813,7 +813,7 @@ def test_handle_scans_reading(tmp_path):
     raw_02 = read_raw_bids(bids_path)
     new_acq_time = new_acq_time.replace("Z", ".0Z")
     new_acq_time = datetime.strptime(new_acq_time, "%Y-%m-%dT%H:%M:%S.%fZ")
-    new_acq_time = new_acq_time.replace(tzinfo=timezone.utc)
+    new_acq_time = new_acq_time.replace(tzinfo=UTC)
     assert raw_02.info["meas_date"] == new_acq_time
     assert new_acq_time != raw_01.info["meas_date"]
 
@@ -833,7 +833,7 @@ def test_handle_scans_reading(tmp_path):
         # from the original date and the same as the newly altered date
         raw_03 = read_raw_bids(bids_path)
         new_acq_time = datetime.strptime(new_acq_time_str, date_format)
-        assert raw_03.info["meas_date"] == new_acq_time.astimezone(timezone.utc)
+        assert raw_03.info["meas_date"] == new_acq_time.astimezone(UTC)
 
     # Regression for naive, pre-epoch acquisition times (Windows bug GH-1399)
     pre_epoch_str = "1950-06-15T13:45:30"
@@ -842,10 +842,8 @@ def test_handle_scans_reading(tmp_path):
 
     raw_pre_epoch = read_raw_bids(bids_path)
     pre_epoch_naive = datetime.strptime(pre_epoch_str, "%Y-%m-%dT%H:%M:%S")
-    local_tz = datetime.now().astimezone().tzinfo or timezone.utc
-    expected_pre_epoch = pre_epoch_naive.replace(tzinfo=local_tz).astimezone(
-        timezone.utc
-    )
+    local_tz = datetime.now().astimezone().tzinfo or UTC
+    expected_pre_epoch = pre_epoch_naive.replace(tzinfo=local_tz).astimezone(UTC)
     assert raw_pre_epoch.info["meas_date"] == expected_pre_epoch
     if raw_pre_epoch.annotations.orig_time is not None:
         assert raw_pre_epoch.annotations.orig_time == expected_pre_epoch

mne_bids/tests/test_write.py

@@ -15,7 +15,7 @@
 import time
 import warnings
 from concurrent.futures import ProcessPoolExecutor
-from datetime import date, datetime, timedelta, timezone
+from datetime import UTC, date, datetime, timedelta
 from glob import glob
 from pathlib import Path
 
@@ -24,7 +24,7 @@
 import pandas as pd
 import pytest
 from mne.datasets import testing
-from mne.io import anonymize_info
+from mne.io import anonymize_info, read_raw_edf
 from mne.io.constants import FIFF
 from mne.io.kit.kit import get_kit_info
 from mne.utils import check_version
@@ -115,7 +115,7 @@ def _make_parallel_raw(subject, *, seed=None):
     info = mne.create_info(["MEG0113"], 100, ch_types="mag")
     data = rng.standard_normal((1, 100)) * 1e-12
     raw = mne.io.RawArray(data, info, verbose=False)
-    raw.set_meas_date(datetime(2020, 1, 1, tzinfo=timezone.utc))
+    raw.set_meas_date(datetime(2020, 1, 1, tzinfo=UTC))
     raw.info["line_freq"] = 60
     raw.info["subject_info"] = {
         "his_id": subject,
@@ -267,7 +267,7 @@ def test_write_participants(_bids_validate, tmp_path):
     raw = _read_raw_fif(raw_fname)
 
     # add fake participants data
-    raw.set_meas_date(datetime(year=1994, month=1, day=26, tzinfo=timezone.utc))
+    raw.set_meas_date(datetime(year=1994, month=1, day=26, tzinfo=UTC))
     birthday = (1993, 1, 26)
     birthday = date(*birthday)
     raw.info["subject_info"] = {
@@ -478,10 +478,10 @@ def test_stamp_to_dt():
     """Test conversions of meas_date to datetime objects."""
     meas_date = (1346981585, 835782)
     meas_datetime = _stamp_to_dt(meas_date)
-    assert meas_datetime == datetime(2012, 9, 7, 1, 33, 5, 835782, tzinfo=timezone.utc)
+    assert meas_datetime == datetime(2012, 9, 7, 1, 33, 5, 835782, tzinfo=UTC)
     meas_date = (1346981585,)
     meas_datetime = _stamp_to_dt(meas_date)
-    assert meas_datetime == datetime(2012, 9, 7, 1, 33, 5, 0, tzinfo=timezone.utc)
+    assert meas_datetime == datetime(2012, 9, 7, 1, 33, 5, 0, tzinfo=UTC)
 
 
 @testing.requires_testing_data
@@ -688,7 +688,7 @@ def test_fif(_bids_validate, tmp_path):
     raw = _read_raw_fif(raw_fname)
     meas_date = raw.info["meas_date"]
     if not isinstance(meas_date, datetime):
-        meas_date = datetime.fromtimestamp(meas_date[0], tz=timezone.utc)
+        meas_date = datetime.fromtimestamp(meas_date[0], tz=UTC)
     er_date = meas_date.strftime("%Y%m%d")
     er_bids_path = BIDSPath(
         subject="emptyroom", session=er_date, task="noise", root=bids_root
@@ -3457,6 +3457,43 @@ def test_convert_eeg_formats(dir_name, fmt, fname, reader, tmp_path):
     assert_array_almost_equal(raw.get_data(), raw2.get_data()[:, :orig_len], decimal=6)
 
 
+@testing.requires_testing_data
+def test_anonymize_and_convert_to_edf(tmp_path):
+    """Test anonymization if converting to EDF (different codepath than EDF → EDF)."""
+    bids_root = tmp_path / "EDF"
+    raw_fname = data_path / "NihonKohden" / "MB0400FU.EEG"
+    bids_path = _bids_path.copy().update(root=bids_root, datatype="eeg")
+    raw = _read_raw_nihon(raw_fname)
+
+    with (
+        pytest.warns(RuntimeWarning, match="limits `startdate` to dates after 1985"),
+        pytest.warns(RuntimeWarning, match="Converting data files to EDF format"),
+    ):
+        bids_output_path = write_raw_bids(
+            raw=raw,
+            format="EDF",
+            bids_path=bids_path,
+            overwrite=True,
+            verbose=False,
+            anonymize=dict(daysback=41234),
+        )
+    # make sure the written EDF file is valid
+    direct_read = read_raw_edf(bids_output_path.fpath)
+    assert direct_read.info["meas_date"] == datetime(1985, 1, 1, tzinfo=UTC)
+    # make sure MNE-BIDS replaced the 1985-1-1 date with the date from scans.tsv
+    bids_read = read_raw_bids(bids_output_path)
+    bids_output_path.update(
+        suffix="scans",
+        extension=".tsv",
+        task=None,
+        acquisition=None,
+        run=None,
+        datatype=None,
+    )
+    scans = _from_tsv(bids_output_path.fpath)
+    assert bids_read.info["meas_date"] == datetime.fromisoformat(scans["acq_time"][0])
+
+
 @pytest.mark.parametrize("dir_name, fmt, fname, reader", test_converteeg_data)
 @pytest.mark.filterwarnings(
     warning_str["channel_unit_changed"],
@@ -3699,7 +3736,7 @@ def test_write_associated_emptyroom(_bids_validate, tmp_path, empty_room_dtype):
     bids_root = tmp_path / "bids1"
     raw_fname = data_path / "MEG" / "sample" / "sample_audvis_trunc_raw.fif"
     raw = _read_raw_fif(raw_fname)
-    meas_date = datetime(year=2020, month=1, day=10, tzinfo=timezone.utc)
+    meas_date = datetime(year=2020, month=1, day=10, tzinfo=UTC)
 
     if empty_room_dtype == "BIDSPath":
         # First write "empty-room" data

mne_bids/utils.py

@@ -6,7 +6,7 @@
 import json
 import os
 import re
-from datetime import date, datetime, timedelta, timezone
+from datetime import UTC, date, datetime, timedelta
 from pathlib import Path
 
 import numpy as np
@@ -469,7 +469,7 @@ def _stamp_to_dt(utc_stamp):
     stamp = [int(s) for s in utc_stamp]
     if len(stamp) == 1:  # In case there is no microseconds information
         stamp.append(0)
-    return datetime.fromtimestamp(0, tz=timezone.utc) + timedelta(
+    return datetime.fromtimestamp(0, tz=UTC) + timedelta(
         0, stamp[0], stamp[1]
     )  # day, sec, μs