n5, imglib2, multiview-reconstruction bumps

[bogovicj]

Still waiting on JaneliaSciComp/multiview-reconstruction#98

But update n5 artifacts with tests that fail during smelt (due to unmet prerequisites), these tests are now skipped.

• Updated imglib2-realtransform and imglib2-algororithm (suggested by @tpietzsch )
• Updated multiview-simulation (suggested by @StephanPreibisch )
• Updated imglib2-labelmultisets (suggested by @cmhulbert )

[ctrueden]

@bogovicj Thanks. I rolled these version bumps into the pombast branch I'm working on as 0b2c9bc. Running a fresh mega-melt now...

[ctrueden]

@bogovicj Still waiting for the n5-universe smelt to finish, but already I've seen how the tests are behaving now:

n5-universe test log

[INFO] -------------------------------------------------------
[INFO]  T E S T S
[INFO] -------------------------------------------------------
[INFO] Running org.janelia.saalfeldlab.n5.universe.translation.TranslatedN5Tests
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.022 s -- in org.janelia.saalfeldlab.n5.universe.translation.TranslatedN5Tests
[INFO] Running org.janelia.saalfeldlab.n5.universe.metadata.MetadataUtilsTest
[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s -- in org.janelia.saalfeldlab.n5.universe.metadata.MetadataUtilsTest
[INFO] Running org.janelia.saalfeldlab.n5.universe.metadata.AxisMetadataTests
Optional[org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalMultiscaleMetadata@360fe828]
org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalSpatialMetadata@52c3f893
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.010 s -- in org.janelia.saalfeldlab.n5.universe.metadata.AxisMetadataTests
[INFO] Running org.janelia.saalfeldlab.n5.universe.metadata.GenericMetadataParserTest
[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.047 s -- in org.janelia.saalfeldlab.n5.universe.metadata.GenericMetadataParserTest
[INFO] Running org.janelia.saalfeldlab.n5.universe.metadata.TransformTests
[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.049 s -- in org.janelia.saalfeldlab.n5.universe.metadata.TransformTests
[INFO] Running org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v04.NgffAxisTests
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.139 s -- in org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v04.NgffAxisTests
[INFO] Running org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v04.BuildMultiscaleTest
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s -- in org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v04.BuildMultiscaleTest
[INFO] Running org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v04.UnitTest
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s -- in org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v04.UnitTest
[INFO] Running org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v04.CoordinateTransformParsingTest
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 s -- in org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v04.CoordinateTransformParsingTest
[INFO] Running org.janelia.saalfeldlab.n5.universe.metadata.MetadataTests
[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0 s -- in org.janelia.saalfeldlab.n5.universe.metadata.MetadataTests
[INFO] Running org.janelia.saalfeldlab.n5.universe.metadata.NgffTests
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s -- in org.janelia.saalfeldlab.n5.universe.metadata.NgffTests
[INFO] Running org.janelia.saalfeldlab.n5.universe.metadata.TranslationTests
[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.201 s -- in org.janelia.saalfeldlab.n5.universe.metadata.TranslationTests
[INFO] Running org.janelia.saalfeldlab.n5.universe.IdentityTranslatedN5Tests
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.033 s -- in org.janelia.saalfeldlab.n5.universe.IdentityTranslatedN5Tests
[INFO] Running org.janelia.saalfeldlab.n5.universe.storage.n5.N5StorageTests
[WARNING] Tests run: 115, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 843.5 s -- in org.janelia.saalfeldlab.n5.universe.storage.n5.N5StorageTests
[INFO] Running org.janelia.saalfeldlab.n5.universe.storage.n5.N5FileSystemTest
[WARNING] Tests run: 38, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.578 s -- in org.janelia.saalfeldlab.n5.universe.storage.n5.N5FileSystemTest
[INFO] Running org.janelia.saalfeldlab.n5.universe.storage.n5.N5HttpFactoryTest
[WARNING] Tests run: 38, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 832.3 s -- in org.janelia.saalfeldlab.n5.universe.storage.n5.N5HttpFactoryTest
[INFO] Running org.janelia.saalfeldlab.n5.universe.storage.n5.N5AmazonS3FactoryTest$N5AmazonS3MockTest
[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 6.756 s -- in org.janelia.saalfeldlab.n5.universe.storage.n5.N5AmazonS3FactoryTest$N5AmazonS3MockTest
[INFO] Running org.janelia.saalfeldlab.n5.universe.storage.n5.N5GoogleCloudFactoryTest$N5GoogleCloudMockTest
[WARNING] Tests run: 38, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 2.207 s -- in org.janelia.saalfeldlab.n5.universe.storage.n5.N5GoogleCloudFactoryTest$N5GoogleCloudMockTest
[INFO] Running org.janelia.saalfeldlab.n5.universe.storage.zarr.ZarrStorageTests
[WARNING] Tests run: 293, Failures: 0, Errors: 0, Skipped: 61, Time elapsed: 1753 s -- in org.janelia.saalfeldlab.n5.universe.storage.zarr.ZarrStorageTests
[INFO] Running org.janelia.saalfeldlab.n5.universe.storage.zarr.zarr3.Zarr3GoogleCloudFactoryTest$ZarrGoogleCloudMockTest
[WARNING] Tests run: 47, Failures: 0, Errors: 0, Skipped: 12, Time elapsed: 2.412 s -- in org.janelia.saalfeldlab.n5.universe.storage.zarr.zarr3.Zarr3GoogleCloudFactoryTest$ZarrGoogleCloudMockTest
[INFO] Running org.janelia.saalfeldlab.n5.universe.storage.zarr.zarr3.Zarr3AmazonS3FactoryTest$ZarrAmazonS3MockTest
[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 6.757 s -- in org.janelia.saalfeldlab.n5.universe.storage.zarr.zarr3.Zarr3AmazonS3FactoryTest$ZarrAmazonS3MockTest
[INFO] Running org.janelia.saalfeldlab.n5.universe.storage.zarr.zarr3.Zarr3FileSystemTest
[WARNING] Tests run: 47, Failures: 0, Errors: 0, Skipped: 12, Time elapsed: 0.246 s -- in org.janelia.saalfeldlab.n5.universe.storage.zarr.zarr3.Zarr3FileSystemTest
[INFO] Running org.janelia.saalfeldlab.n5.universe.storage.zarr.zarr3.Zarr3HttpFactoryTest
[WARNING] Tests run: 47, Failures: 0, Errors: 0, Skipped: 11, Time elapsed: 785.5 s -- in org.janelia.saalfeldlab.n5.universe.storage.zarr.zarr3.Zarr3HttpFactoryTest
[INFO] Running org.janelia.saalfeldlab.n5.universe.storage.zarr.zarr2.Zarr2GoogleCloudFactoryTest$ZarrGoogleCloudMockTest
[WARNING] Tests run: 50, Failures: 0, Errors: 0, Skipped: 8, Time elapsed: 3.473 s -- in org.janelia.saalfeldlab.n5.universe.storage.zarr.zarr2.Zarr2GoogleCloudFactoryTest$ZarrGoogleCloudMockTest
[INFO] Running org.janelia.saalfeldlab.n5.universe.storage.zarr.zarr2.Zarr2FileSystemTest
[WARNING] Tests run: 50, Failures: 0, Errors: 0, Skipped: 8, Time elapsed: 0.295 s -- in org.janelia.saalfeldlab.n5.universe.storage.zarr.zarr2.Zarr2FileSystemTest
[INFO] Running org.janelia.saalfeldlab.n5.universe.storage.zarr.zarr2.Zarr2HttpFactoryTest
[WARNING] Tests run: 50, Failures: 0, Errors: 0, Skipped: 8, Time elapsed: 947.2 s -- in org.janelia.saalfeldlab.n5.universe.storage.zarr.zarr2.Zarr2HttpFactoryTest
[INFO] Running org.janelia.saalfeldlab.n5.universe.storage.zarr.zarr2.Zarr2AmazonS3FactoryTest$ZarrAmazonS3MockTest
[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 6.756 s -- in org.janelia.saalfeldlab.n5.universe.storage.zarr.zarr2.Zarr2AmazonS3FactoryTest$ZarrAmazonS3MockTest
[INFO] Running org.janelia.saalfeldlab.n5.universe.N5TreeNodeTest
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s -- in org.janelia.saalfeldlab.n5.universe.N5TreeNodeTest
[INFO] Running org.janelia.saalfeldlab.n5.universe.options.N5FactoryOptionsTest
[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s -- in org.janelia.saalfeldlab.n5.universe.options.N5FactoryOptionsTest
[INFO] Running org.janelia.saalfeldlab.n5.universe.N5FactoryTests
[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.332 s -- in org.janelia.saalfeldlab.n5.universe.N5FactoryTests
[INFO] 
[INFO] Results:
[INFO] 
[WARNING] Tests run: 803, Failures: 0, Errors: 0, Skipped: 72

The TL;DR is that even with the new test skipping logic, some of the tests take an extremely long time to finish. Here are they ones >10s, sorted by time taken:

[WARNING] Tests run: 293, Failures: 0, Errors: 0, Skipped: 61, Time elapsed: 1753 s -- in org.janelia.saalfeldlab.n5.universe.storage.zarr.ZarrStorageTests
[WARNING] Tests run: 50, Failures: 0, Errors: 0, Skipped: 8, Time elapsed: 947.2 s -- in org.janelia.saalfeldlab.n5.universe.storage.zarr.zarr2.Zarr2HttpFactoryTest
[WARNING] Tests run: 115, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 843.5 s -- in org.janelia.saalfeldlab.n5.universe.storage.n5.N5StorageTests
[WARNING] Tests run: 38, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 832.3 s -- in org.janelia.saalfeldlab.n5.universe.storage.n5.N5HttpFactoryTest
[WARNING] Tests run: 47, Failures: 0, Errors: 0, Skipped: 11, Time elapsed: 785.5 s -- in org.janelia.saalfeldlab.n5.universe.storage.zarr.zarr3.Zarr3HttpFactoryTest

So the timeouts must be happening before the test-skipping decision is made...

For now, I will configure pombast to skip the above problematic tests. If you later improve things further, we can re-enable any adjusted tests then.