From 8196808c7cf441ed4f8323704a39f515a6874cf5 Mon Sep 17 00:00:00 2001
From: Ben Dichter <ben.dichter@gmail.com>
Date: Fri, 3 May 2024 11:51:44 -0500
Subject: [PATCH 01/10] add check for missing timezone. Also add best practice
 docs and tests for check

---
 docs/best_practices/nwbfile_metadata.rst    | 13 +++++++++----
 src/nwbinspector/checks/nwbfile_metadata.py | 18 +++++++++++++++++-
 tests/unit_tests/test_nwbfile_metadata.py   | 21 ++++++++++++++++++++-
 3 files changed, 46 insertions(+), 6 deletions(-)

diff --git a/docs/best_practices/nwbfile_metadata.rst b/docs/best_practices/nwbfile_metadata.rst
index 5e897ce7e..1f47af16b 100644
--- a/docs/best_practices/nwbfile_metadata.rst
+++ b/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`,
 
 
 
diff --git a/src/nwbinspector/checks/nwbfile_metadata.py b/src/nwbinspector/checks/nwbfile_metadata.py
index a5fbae66e..852d66ef9 100644
--- a/src/nwbinspector/checks/nwbfile_metadata.py
+++ b/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 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):
     """
diff --git a/tests/unit_tests/test_nwbfile_metadata.py b/tests/unit_tests/test_nwbfile_metadata.py
index d86140965..b8350e8a6 100644
--- a/tests/unit_tests/test_nwbfile_metadata.py
+++ b/tests/unit_tests/test_nwbfile_metadata.py
@@ -1,5 +1,5 @@
 from uuid import uuid4
-from datetime import datetime, timezone
+from datetime import datetime, timezone, date
 
 from pynwb import NWBFile, ProcessingModule
 from pynwb.file import Subject
@@ -23,6 +23,7 @@
     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 +57,24 @@ def test_check_session_start_time_future_date_pass():
     assert check_session_start_time_future_date(nwbfile) is None
 
 
+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
+
+
+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="",

From a9ace70d50b658164bec8543d269acae89c2a314 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 3 May 2024 16:53:12 +0000
Subject: [PATCH 02/10] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/nwbinspector/checks/nwbfile_metadata.py | 4 +---
 tests/unit_tests/test_nwbfile_metadata.py   | 6 +++++-
 2 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/src/nwbinspector/checks/nwbfile_metadata.py b/src/nwbinspector/checks/nwbfile_metadata.py
index 852d66ef9..a29a91cc7 100644
--- a/src/nwbinspector/checks/nwbfile_metadata.py
+++ b/src/nwbinspector/checks/nwbfile_metadata.py
@@ -46,9 +46,7 @@ def check_session_start_time_contains_time_zone(nwbfile: NWBFile):
     session_start_time = nwbfile.session_start_time
     if session_start_time.tzinfo is None:
         return InspectorMessage(
-            message=(
-                f"The session_start_time ({session_start_time}) does not contain a time zone."
-            )
+            message=(f"The session_start_time ({session_start_time}) does not contain a time zone.")
         )
 
 
diff --git a/tests/unit_tests/test_nwbfile_metadata.py b/tests/unit_tests/test_nwbfile_metadata.py
index b8350e8a6..45a01b7f5 100644
--- a/tests/unit_tests/test_nwbfile_metadata.py
+++ b/tests/unit_tests/test_nwbfile_metadata.py
@@ -58,7 +58,11 @@ def test_check_session_start_time_future_date_pass():
 
 
 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))
+    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
 
 

From 4f67b29324236daf636cea9d52167ea90d139d94 Mon Sep 17 00:00:00 2001
From: Ben Dichter <ben.dichter@gmail.com>
Date: Fri, 3 May 2024 12:55:40 -0400
Subject: [PATCH 03/10] Update CHANGELOG.md

---
 CHANGELOG.md | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9cb11a883..60307f39f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,10 @@
 # Upcoming
 
+
+### New Checks
+
+* Add check for missing timezone for `session_start_time` [#458](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/458).
+
 # v0.4.35
 
 ### Fixes

From 283ebab63821b73e8c24fb0e8b43b6aba05065f0 Mon Sep 17 00:00:00 2001
From: Ben Dichter <ben.dichter@gmail.com>
Date: Fri, 3 May 2024 12:55:55 -0400
Subject: [PATCH 04/10] Update CHANGELOG.md

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 60307f39f..43157115d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,4 +1,4 @@
-# Upcoming
+# Upcoming (0.5.0)
 
 
 ### New Checks

From 5a5b2293176b3115aeb575516d7203de0d06403c Mon Sep 17 00:00:00 2001
From: Ben Dichter <ben.dichter@gmail.com>
Date: Fri, 3 May 2024 12:56:57 -0400
Subject: [PATCH 05/10] Update CHANGELOG.md

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 43157115d..cb21d3e42 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,7 +3,7 @@
 
 ### New Checks
 
-* Add check for missing timezone for `session_start_time` [#458](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/458).
+* Add: `check_session_start_time_contains_time_zone` [#458](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/458).
 
 # v0.4.35
 

From 7a28782b798df68858f2172b4b25ea062cf64296 Mon Sep 17 00:00:00 2001
From: Ben Dichter <ben.dichter@gmail.com>
Date: Fri, 3 May 2024 13:42:00 -0500
Subject: [PATCH 06/10] add skip for earlier versions of pynwb

---
 tests/unit_tests/test_nwbfile_metadata.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/tests/unit_tests/test_nwbfile_metadata.py b/tests/unit_tests/test_nwbfile_metadata.py
index b8350e8a6..dac4b7fcb 100644
--- a/tests/unit_tests/test_nwbfile_metadata.py
+++ b/tests/unit_tests/test_nwbfile_metadata.py
@@ -1,6 +1,8 @@
 from uuid import uuid4
-from datetime import datetime, timezone, date
+from datetime import datetime, timezone
 
+import pynwb
+import pytest
 from pynwb import NWBFile, ProcessingModule
 from pynwb.file import Subject
 
@@ -57,11 +59,13 @@ 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_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)

From 8b5300670952d8d0978e9e94d5c19513f514dc99 Mon Sep 17 00:00:00 2001
From: Ben Dichter <ben.dichter@gmail.com>
Date: Fri, 3 May 2024 17:58:23 -0500
Subject: [PATCH 07/10] add handling of date to time zone check

---
 src/nwbinspector/checks/nwbfile_metadata.py | 15 ++++++++++++++-
 tests/unit_tests/test_nwbfile_metadata.py   | 12 +++++++++++-
 2 files changed, 25 insertions(+), 2 deletions(-)

diff --git a/src/nwbinspector/checks/nwbfile_metadata.py b/src/nwbinspector/checks/nwbfile_metadata.py
index a29a91cc7..bdebbdfe8 100644
--- a/src/nwbinspector/checks/nwbfile_metadata.py
+++ b/src/nwbinspector/checks/nwbfile_metadata.py
@@ -44,6 +44,8 @@ def check_session_start_time_contains_time_zone(nwbfile: NWBFile):
     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.")
@@ -58,8 +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(
diff --git a/tests/unit_tests/test_nwbfile_metadata.py b/tests/unit_tests/test_nwbfile_metadata.py
index 8b58015ba..9a7d72c2e 100644
--- a/tests/unit_tests/test_nwbfile_metadata.py
+++ b/tests/unit_tests/test_nwbfile_metadata.py
@@ -1,5 +1,5 @@
 from uuid import uuid4
-from datetime import datetime, timezone
+from datetime import datetime, timezone, date
 
 import pynwb
 import pytest
@@ -69,6 +69,16 @@ def test_check_session_start_time_contains_time_zone_pass():
     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)

From bf54b4d777f67e068cf4ab412affa333c534632f Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Fri, 24 May 2024 08:59:22 -0400
Subject: [PATCH 08/10] ignore assertin for codespell

---
 pyproject.toml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 2b3b8638f..0bd4542e7 100644
--- a/pyproject.toml
+++ b/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'

From d5a14d31b7062acdc01b18998c075668fa076048 Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Fri, 24 May 2024 09:04:11 -0400
Subject: [PATCH 09/10] remove codespell workflow

---
 .github/workflows/codespell.yml | 23 -----------------------
 1 file changed, 23 deletions(-)
 delete mode 100644 .github/workflows/codespell.yml

diff --git a/.github/workflows/codespell.yml b/.github/workflows/codespell.yml
deleted file mode 100644
index a7e91c56e..000000000
--- a/.github/workflows/codespell.yml
+++ /dev/null
@@ -1,23 +0,0 @@
-# Codespell configuration is within pyproject.toml
----
-name: Codespell
-
-on:
-  push:
-    branches: [dev]
-  pull_request:
-    branches: [dev]
-
-permissions:
-  contents: read
-
-jobs:
-  codespell:
-    name: Check for spelling errors
-    runs-on: ubuntu-latest
-
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v4
-      - name: Codespell
-        uses: codespell-project/actions-codespell@v2

From bf5c91217c14ab182d33334f7e5fdafcc942ebb5 Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Fri, 24 May 2024 09:05:31 -0400
Subject: [PATCH 10/10] bump version in pre-commit

---
 .pre-commit-config.yaml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 2a2336f35..ffeb26674 100644
--- a/.pre-commit-config.yaml
+++ b/.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: