Add time series duration check and corresponding tests #627
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stephprince
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Oct 9, 2025
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stephprince
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Added my review, could you also add a CHANGELOG entry?
| return None | ||
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| @register_check(importance=Importance.CRITICAL, neurodata_type=TimeSeries) |
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Should this be critical or a best practice violation?
tests/unit_tests/test_time_series.py
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| def test_check_rate_not_below_threshold_fail_period_like_value(): | ||
| """Test detection when period was likely used instead of rate.""" | ||
| # If someone uses 2.0 thinking it's a 2 second period, the rate should be 0.5 Hz | ||
| period_value = 2.0 | ||
| time_series = pynwb.TimeSeries( | ||
| name="test_time_series", | ||
| unit="test_units", | ||
| data=np.zeros(shape=100), | ||
| starting_time=0.0, | ||
| rate=period_value, | ||
| ) | ||
| result = check_rate_not_below_threshold(time_series) | ||
| # Should pass with default threshold since 2.0 > 0.01 | ||
| assert result is None | ||
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| # But should fail with a custom threshold | ||
| result = check_rate_not_below_threshold(time_series, low_rate_threshold=5.0) | ||
| assert result is not None |
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Suggested change
| def test_check_rate_not_below_threshold_fail_period_like_value(): | |
| """Test detection when period was likely used instead of rate.""" | |
| # If someone uses 2.0 thinking it's a 2 second period, the rate should be 0.5 Hz | |
| period_value = 2.0 | |
| time_series = pynwb.TimeSeries( | |
| name="test_time_series", | |
| unit="test_units", | |
| data=np.zeros(shape=100), | |
| starting_time=0.0, | |
| rate=period_value, | |
| ) | |
| result = check_rate_not_below_threshold(time_series) | |
| # Should pass with default threshold since 2.0 > 0.01 | |
| assert result is None | |
| # But should fail with a custom threshold | |
| result = check_rate_not_below_threshold(time_series, low_rate_threshold=5.0) | |
| assert result is not None |
I think this test covers the same behavior as the test above and below?
tests/unit_tests/test_time_series.py
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| result = check_time_series_duration(time_series) | ||
| assert result is not None | ||
| assert "long_time_series" in result.message | ||
| assert "exceeds the threshold" in result.message | ||
| assert result.importance == Importance.BEST_PRACTICE_SUGGESTION |
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Can you update these to be checked against the full inspector message? Similarly in the other tests.
e.g. check_time_series_duration(time_series) == InspectorMessage(...
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| one_year = 31557600.0 | ||
| rate = 1.0 # 1 Hz | ||
| num_samples = int(one_year + 1000) # More than 1 year worth of samples | ||
| time_series = pynwb.TimeSeries( | ||
| name="long_time_series", | ||
| unit="test_units", | ||
| data=np.zeros(shape=num_samples), | ||
| starting_time=0.0, | ||
| rate=rate, | ||
| ) |
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We might want to avoid creating a large array here just for tests, could lower the rate instead to minimize the number of samples
| """ | ||
| Check if the TimeSeries duration is longer than the specified threshold. | ||
| The default threshold is 1 year (31,557,600 seconds = 365.25 days). |
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Is there a reason for the year long threshold? I imagine anything longer than a month or two could be worth flagging since it is a best practice suggestion.
Co-authored-by: Steph Prince <[email protected]>
Co-authored-by: Steph Prince <[email protected]>
Co-authored-by: Steph Prince <[email protected]>
Co-authored-by: Steph Prince <[email protected]>
for more information, see https://pre-commit.ci
Co-authored-by: Steph Prince <[email protected]>
for more information, see https://pre-commit.ci
Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## dev #627 +/- ##
==========================================
+ Coverage 73.03% 76.91% +3.88%
==========================================
Files 47 47
Lines 1587 1616 +29
==========================================
+ Hits 1159 1243 +84
+ Misses 428 373 -55
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