add check for missing timezone.

.pre-commit-config.yaml

@@ -11,8 +11,7 @@ repos:
     -   id: black
 
 - repo: https://github.com/codespell-project/codespell
-  # Configuration for codespell is in pyproject.toml
-  rev: v2.2.6
+  rev: v2.3.0
   hooks:
   - id: codespell
     additional_dependencies:

CHANGELOG.md

@@ -1,4 +1,9 @@
-# Upcoming
+# Upcoming (0.5.0)
+
+
+### New Checks
+
+* Add: `check_session_start_time_contains_time_zone` [#458](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/458).
 
 # v0.4.35
 

docs/best_practices/nwbfile_metadata.rst

@@ -19,21 +19,26 @@ objects in the :ref:`nwb-schema:sec-NWBFile` is the ``timestamps_reference_time`
 ``session_start_time``, but when writing multiple NWBFiles that are all designed to align to the same time reference,
 the ``timestamp_reference_time`` used across all of the NWBFiles may be set separately from the ``session_start_time``.
 
-All time-related data in the NWBFile should be synchronized to the ``timestamps_reference_time`` so that future users
-are able to understand the timing of all events contained within the NWBFile.
+All time-related data in the ``NWBFile`` should be synchronized to the ``timestamps_reference_time`` so that future users
+are able to understand the timing of all events contained within the ``NWBFile``.
 
 The ``timestamps_reference_time`` should also be the earliest timestamp in the file, giving all other time references
 a positive value relative to that. There should be no time references which are negative.
 
 Given the importance of this field within an :ref:`nwb-schema:sec-NWBFile`, is it critical that it be set to a proper
 value. Default values should generally not be used for this field. If the true date is unknown, use your
-best guess. If the exact start time is unknown, then it is fine to simply set it to midnight on that date.
+best guess. If working with human participants and such data is protected information, use the date 1900-01-01.
+
+**New in PyNWB 2.7.0, released May 2, 2024:**
+
+The ``session_start_time`` is no longer required to have a timezone offset. This information is now optional, but recommended. If the timezone offset is not provided, it should **not** be assumed to be UTC.
 
 
 Check functions: :py:meth:`~nwbinspector.checks.nwbfile_metadata.check_session_start_time_old_date`,
 :py:meth:`~nwbinspector.checks.nwbfile_metadata.check_session_start_time_future_date`,
 :py:meth:`~nwbinspector.checks.time_series.check_timestamp_of_the_first_sample_is_not_negative`
-:py:meth:`~nwbinspector.checks.tables.check_table_time_columns_are_not_negative`
+:py:meth:`~nwbinspector.checks.tables.check_table_time_columns_are_not_negative`,
+:py:meth:`~nwbinspector.checks.nwbfile_metadata.check_session_start_time_contains_time_zone`,
 
 
 

pyproject.toml

@@ -22,8 +22,7 @@ extend-exclude = '''
 '''
 
 [tool.codespell]
-# Ref: https://github.com/codespell-project/codespell#using-a-config-file
 skip = '.git*,*.pdf,*.css'
 check-hidden = true
 # ignore-regex = ''
-# ignore-words-list = ''
+ignore-words-list = 'assertin'

src/nwbinspector/checks/nwbfile_metadata.py

@@ -1,7 +1,7 @@
 """Check functions that examine general NWBFile metadata."""
 
 import re
-from datetime import datetime
+from datetime import datetime, date
 
 from isodate import parse_duration, Duration
 from pynwb import NWBFile, ProcessingModule
@@ -36,6 +36,22 @@ def check_session_start_time_old_date(nwbfile: NWBFile):
         )
 
 
+@register_check(importance=Importance.BEST_PRACTICE_SUGGESTION, neurodata_type=NWBFile)
+def check_session_start_time_contains_time_zone(nwbfile: NWBFile):
+    """
+    Check if the session_start_time contains a time zone.
+
+    Best Practice: :ref:`best_practice_global_time_reference`
+    """
+    session_start_time = nwbfile.session_start_time
+    if isinstance(session_start_time, date):
+        return
+    if session_start_time.tzinfo is None:
+        return InspectorMessage(
+            message=(f"The session_start_time ({session_start_time}) does not contain a time zone.")
+        )
+
+
 @register_check(importance=Importance.CRITICAL, neurodata_type=NWBFile)
 def check_session_start_time_future_date(nwbfile: NWBFile):
     """
@@ -44,8 +60,19 @@ def check_session_start_time_future_date(nwbfile: NWBFile):
     Best Practice: :ref:`best_practice_global_time_reference`
     """
     session_start_time = nwbfile.session_start_time
+
+    if isinstance(session_start_time, date):
+        current_date = date.today()
+        if session_start_time > current_date:
+            return InspectorMessage(
+                message=(
+                    f"The session_start_time ({session_start_time}) is set to a future date. "
+                    "Please ensure that the session_start_time is set to the correct date and time."
+                )
+            )
+
     current_time = datetime.now()
-    if session_start_time.tzinfo is not None:
+    if isinstance(session_start_time, datetime) and session_start_time.tzinfo is not None:
         current_time = current_time.astimezone()
     if session_start_time >= current_time:
         return InspectorMessage(

tests/unit_tests/test_nwbfile_metadata.py

@@ -1,6 +1,8 @@
 from uuid import uuid4
-from datetime import datetime, timezone
+from datetime import datetime, timezone, date
 
+import pynwb
+import pytest
 from pynwb import NWBFile, ProcessingModule
 from pynwb.file import Subject
 
@@ -23,6 +25,7 @@
     check_processing_module_name,
     check_session_start_time_old_date,
     check_session_start_time_future_date,
+    check_session_start_time_contains_time_zone,
     PROCESSING_MODULE_CONFIG,
 )
 from nwbinspector.tools import make_minimal_nwbfile
@@ -56,6 +59,40 @@ def test_check_session_start_time_future_date_pass():
     assert check_session_start_time_future_date(nwbfile) is None
 
 
+@pytest.mark.skipif(pynwb.__version__ < "2.7.0", reason="Feature not supported in pynwb < 2.7.0")
+def test_check_session_start_time_contains_time_zone_pass():
+    nwbfile = NWBFile(
+        session_description="",
+        identifier=str(uuid4()),
+        session_start_time=datetime(2010, 1, 1, 0, 0, 0, 0, timezone.utc),
+    )
+    assert check_session_start_time_contains_time_zone(nwbfile) is None
+
+
+@pytest.mark.skipif(pynwb.__version__ < "2.7.0", reason="Feature not supported in pynwb < 2.7.0")
+def test_check_session_start_time_is_date_contains_time_zone_pass():
+    nwbfile = NWBFile(
+        session_description="",
+        identifier=str(uuid4()),
+        session_start_time=date(2010, 1, 1),
+    )
+    assert check_session_start_time_contains_time_zone(nwbfile) is None
+
+
+@pytest.mark.skipif(pynwb.__version__ < "2.7.0", reason="Feature not supported in pynwb < 2.7.0")
+def test_check_session_start_time_contains_time_zone_fail():
+    session_start_time = datetime(2010, 1, 1, 0, 0, 0, 0)
+    nwbfile = NWBFile(session_description="", identifier=str(uuid4()), session_start_time=session_start_time)
+    assert check_session_start_time_contains_time_zone(nwbfile) == InspectorMessage(
+        message=f"The session_start_time ({session_start_time}) does not contain a time zone.",
+        importance=Importance.BEST_PRACTICE_SUGGESTION,
+        check_function_name="check_session_start_time_contains_time_zone",
+        object_type="NWBFile",
+        object_name="root",
+        location="/",
+    )
+
+
 def test_check_session_start_time_future_date_fail():
     nwbfile = NWBFile(
         session_description="",