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Update nwbinspector validation workflow #122

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merged 4 commits into from
Jan 8, 2025
Merged

Update nwbinspector validation workflow #122

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d567754
fail workflow if nwbinspector issues found
stephprince Jan 7, 2025
e1a89b8
update tests to avoid inspector violations
stephprince Jan 7, 2025
8305742
fix formatting
stephprince Jan 7, 2025
b75e9a8
update output file name
stephprince Jan 8, 2025
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6 changes: 5 additions & 1 deletion .github/workflows/tests.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -141,4 +141,8 @@ jobs:
run: |
python -m pip install --upgrade pip
python -m pip install nwbinspector
nwbinspector nwb_files --threshold BEST_PRACTICE_VIOLATION
nwbinspector nwb_files --threshold BEST_PRACTICE_VIOLATION --json-file-path out.json
if ! grep -q '"messages": \[\]' out.json; then
echo "NWBInspector found issues in the NWB files"
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It would be nice to also print the contents of the out.txt file to the command-line to make it easy to see the issues found in the GitHub Action directly. I would also rename out.txt to out.json

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@stephprince stephprince Jan 8, 2025 •
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It would be nice to also print the contents of the out.txt file to the command-line to make it easy to see the issues found in the GitHub Action directly.

The report summary should be printed out and formatted automatically by running nwbinspector (see the Install pynwb and run validation step here), in this action there are 0 issues found but otherwise it will print the issues in the GitHub Action.

I would also rename out.txt to out.json

Will do!

exit 1
fi
4 changes: 2 additions & 2 deletions tests/testNWBFile.cpp
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Expand Up @@ -50,7 +50,7 @@ TEST_CASE("createElectricalSeries", "[nwb]")

// write timeseries data
std::vector<float> mockData = {1.0f, 2.0f, 3.0f, 4.0f, 5.0f};
std::vector<double> mockTimestamps = {0.1, 0.2, 0.3, 0.4, 0.5};
std::vector<double> mockTimestamps = {0.1, 0.3, 0.4, 0.5, 0.8};
std::vector<SizeType> positionOffset = {0, 0};
std::vector<SizeType> dataShape = {mockData.size(), 0};

Expand Down Expand Up @@ -105,7 +105,7 @@ TEST_CASE("createMultipleEcephysDatasets", "[nwb]")

// write electrical series data
std::vector<float> mockData = {1.0f, 2.0f, 3.0f, 4.0f, 5.0f};
std::vector<double> mockTimestamps = {0.1, 0.2, 0.3, 0.4, 0.5};
std::vector<double> mockTimestamps = {0.1, 0.3, 0.4, 0.5, 0.8};
std::vector<SizeType> positionOffset = {0, 0};
std::vector<SizeType> dataShape = {mockData.size(), 0};

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14 changes: 11 additions & 3 deletions tests/testUtils.hpp
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Expand Up @@ -100,14 +100,22 @@ inline std::vector<std::vector<float>> getMockData2D(SizeType numSamples = 1000,
}

inline std::vector<double> getMockTimestamps(SizeType numSamples = 1000,
SizeType samplingRate = 30000)
SizeType samplingRate = 30000,
double maxOffset = 0.00001)
{
std::vector<double> mockTimestamps(numSamples);
double samplingPeriod = 1.0 / samplingRate;

std::random_device rd;
std::mt19937 rng(rd()); // random number generator
std::uniform_real_distribution<> dis(-maxOffset,
maxOffset); // range of floats

for (SizeType i = 0; i < numSamples; ++i) {
mockTimestamps[i] = i * samplingPeriod; // Each timestamp is the sample
// number times the sampling period
// Each timestamp is the sample number times the sampling period with an
// offset
double offset = dis(rng);
mockTimestamps[i] = i * samplingPeriod + offset;
}

return mockTimestamps;
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