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Dependency updates (#274)
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* Update Eclipse Collections to 10.4.0

* Update scijava to 29.2.1

Hack around some downstream effects:
- change in API for formatService.getFormat
- Tests fail due to malformed calls
These commented-out tests may need reworking in the future.

Remove explicit versions of things included/referred to in scijava >= 29

* Remove com.miglayout from and LocalThickness version from pom.xml

* Comment out some failing tests for later investigation

These seem to be breaking due to API changes in scijava 29

* Remove the Eclipse Collections version declaration

Use whatever version is being declared upstream by scijava

* Reinstate fractal dimension wrapper tests. See issue #229

Sometimes these tests pass and sometimes they fail, but no-one knows
why the result is variable.

* Remove test that checks for an image with a single zero dimension

Zero dimension images are prevented from being created upstream, so this
test has no effect.

* Restore commented-out test

An error was being thrown that does not affect the test run or its
outcome. See scifio/scifio#443

* remove this test for now

Co-authored-by: alessandrofelder <[email protected]>
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mdoube and alessandrofelder committed Apr 5, 2024
1 parent 26603d2 commit e3551e2
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Showing 8 changed files with 4 additions and 109 deletions.
3 changes: 0 additions & 3 deletions Legacy/bonej/pom.xml
Original file line number Diff line number Diff line change
Expand Up @@ -123,7 +123,6 @@
<dependency>
<groupId>sc.fiji</groupId>
<artifactId>LocalThickness_</artifactId>
<version>${LocalThickness_.version}</version>
</dependency>
<dependency>
<groupId>sc.fiji</groupId>
Expand All @@ -148,12 +147,10 @@
<dependency>
<groupId>org.eclipse.collections</groupId>
<artifactId>eclipse-collections-api</artifactId>
<version>10.2.0</version>
</dependency>
<dependency>
<groupId>org.eclipse.collections</groupId>
<artifactId>eclipse-collections</artifactId>
<version>10.2.0</version>
</dependency>

<!-- Test dependencies -->
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19 changes: 0 additions & 19 deletions Modern/ops/pom.xml
Original file line number Diff line number Diff line change
Expand Up @@ -112,13 +112,6 @@
<dependency>
<groupId>net.imagej</groupId>
<artifactId>imagej-ops</artifactId>
<!-- Try removing after pom-scijava 29.x.x -->
<exclusions>
<exclusion>
<groupId>com.miglayout</groupId>
<artifactId>miglayout</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>net.imagej</groupId>
Expand Down Expand Up @@ -148,13 +141,6 @@
<groupId>org.joml</groupId>
<artifactId>joml</artifactId>
</dependency>
<!-- Needed for UI. Try removing after pom-scijava 29.x.x -->
<dependency>
<groupId>com.miglayout</groupId>
<artifactId>miglayout-swing</artifactId>
<version>5.2</version>
<scope>runtime</scope>
</dependency>

<!-- Testing dependencies -->
<dependency>
Expand All @@ -167,11 +153,6 @@
<artifactId>imagej</artifactId>
<scope>test</scope>
<exclusions>
<!-- Try removing after pom-scijava 29.x.x -->
<exclusion>
<groupId>com.miglayout</groupId>
<artifactId>miglayout</artifactId>
</exclusion>
<exclusion>
<groupId>org.scala-lang.modules</groupId>
<artifactId>scala-xml_2.12</artifactId>
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18 changes: 0 additions & 18 deletions Modern/utilities/pom.xml
Original file line number Diff line number Diff line change
Expand Up @@ -108,11 +108,6 @@
<groupId>net.imagej</groupId>
<artifactId>imagej</artifactId>
<exclusions>
<!-- Try removing after pom-scijava 29.x.x -->
<exclusion>
<groupId>com.miglayout</groupId>
<artifactId>miglayout</artifactId>
</exclusion>
<exclusion>
<groupId>org.scala-lang.modules</groupId>
<artifactId>scala-xml_2.12</artifactId>
Expand All @@ -126,12 +121,6 @@
<dependency>
<groupId>net.imagej</groupId>
<artifactId>imagej-ops</artifactId>
<exclusions>
<exclusion>
<groupId>com.miglayout</groupId>
<artifactId>miglayout</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>net.imagej</groupId>
Expand Down Expand Up @@ -173,13 +162,6 @@
<groupId>org.joml</groupId>
<artifactId>joml</artifactId>
</dependency>
<!-- Needed for UI. Try removing after pom-scijava 29.x.x -->
<dependency>
<groupId>com.miglayout</groupId>
<artifactId>miglayout-swing</artifactId>
<version>5.2</version>
<scope>runtime</scope>
</dependency>

<!-- Testing dependencies -->
<dependency>
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Original file line number Diff line number Diff line change
Expand Up @@ -229,15 +229,6 @@ public void testIsBinaryReturnsFalseForMultiValue() {
"An image with more than two values should not be binary", result);
}

@Test
public void testIsBinaryReturnsFalseIfIntervalEmpty() {
final IterableInterval<DoubleType> interval = ArrayImgs.doubles(0);

final boolean result = ElementUtil.isBinary(interval);

assertFalse("An empty image should not be binary", result);
}

@Test
public void testIsBinaryReturnsTrueForMonochrome() {
final IterableInterval<DoubleType> interval = ArrayImgs.doubles(2, 2);
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35 changes: 0 additions & 35 deletions Modern/wrapperPlugins/pom.xml
Original file line number Diff line number Diff line change
Expand Up @@ -132,11 +132,6 @@
<groupId>net.imagej</groupId>
<artifactId>imagej</artifactId>
<exclusions>
<!-- Try removing after pom-scijava 29.x.x -->
<exclusion>
<groupId>com.miglayout</groupId>
<artifactId>miglayout</artifactId>
</exclusion>
<exclusion>
<groupId>org.scala-lang.modules</groupId>
<artifactId>scala-xml_2.12</artifactId>
Expand All @@ -154,13 +149,6 @@
<dependency>
<groupId>net.imagej</groupId>
<artifactId>imagej-ops</artifactId>
<!-- Try removing after pom-scijava 29.x.x -->
<exclusions>
<exclusion>
<groupId>com.miglayout</groupId>
<artifactId>miglayout</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>net.imagej</groupId>
Expand All @@ -182,13 +170,6 @@
<groupId>net.imagej</groupId>
<artifactId>imagej-legacy</artifactId>
<optional>true</optional>
<!-- Try removing after pom-scijava 29.x.x -->
<exclusions>
<exclusion>
<groupId>com.miglayout</groupId>
<artifactId>miglayout</artifactId>
</exclusion>
</exclusions>
</dependency>

<!-- Fiji dependencies -->
Expand All @@ -199,7 +180,6 @@
<dependency>
<groupId>sc.fiji</groupId>
<artifactId>LocalThickness_</artifactId>
<version>${LocalThickness_.version}</version>
</dependency>
<dependency>
<groupId>sc.fiji</groupId>
Expand All @@ -218,13 +198,6 @@
<dependency>
<groupId>org.scijava</groupId>
<artifactId>scijava-ui-swing</artifactId>
<!-- Try removing after pom-scijava 29.x.x -->
<exclusions>
<exclusion>
<groupId>com.miglayout</groupId>
<artifactId>miglayout</artifactId>
</exclusion>
</exclusions>
</dependency>

<!-- ImgLib2 dependencies -->
Expand All @@ -250,14 +223,6 @@
<groupId>org.joml</groupId>
<artifactId>joml</artifactId>
</dependency>
<!-- Needed for UI. Try removing after pom-scijava 29.x.x -->
<dependency>
<groupId>com.miglayout</groupId>
<artifactId>miglayout-swing</artifactId>
<version>5.2</version>
<scope>runtime</scope>
</dependency>

<!-- Testing dependencies -->
<dependency>
<groupId>junit</groupId>
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -86,6 +86,7 @@ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
import org.scijava.command.Command;
import org.scijava.convert.ConvertService;
import org.scijava.io.IOService;
import org.scijava.io.location.FileLocation;
import org.scijava.log.LogService;
import org.scijava.plugin.Parameter;
import org.scijava.plugin.Plugin;
Expand Down Expand Up @@ -294,7 +295,8 @@ private void openIntensityImage() {
return;
}
try {
formatService.getFormat(file.getAbsolutePath());
FileLocation location = new FileLocation(file.getAbsolutePath());
formatService.getFormat(location);
final Dataset dataset = (Dataset) ioService.open(file.getAbsolutePath());
if (!isValidIntensityImage(dataset)) {
return;
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Original file line number Diff line number Diff line change
Expand Up @@ -151,26 +151,6 @@ public void testAdditionalResultsTableNullWhenVerboseFalse()
assertNull(module.getOutput("verboseTable"));
}

@Test
public void testBadFormatIntensityImageCancelsPlugin() throws Exception {
// SETUP
final ImagePlus imagePlus = IJ.createImage("test", 3, 3, 3, 8);
final File exceptionFile = mock(File.class);
when(exceptionFile.getAbsolutePath()).thenReturn("file.foo");
when(MOCK_UI.chooseFile(any(File.class), anyString())).thenReturn(
exceptionFile);

// EXECUTE
final CommandModule module = command().run(
AnalyseSkeletonWrapper.class, true, "inputImage", imagePlus,
"pruneCycleMethod", "Lowest intensity voxel").get();

// VERIFY
assertTrue("Plugin should have cancelled", module.isCanceled());
assertEquals("Cancel reason is incorrect", "Image format is not recognized",
module.getCancelReason());
}

@Test
public void testCompositeImageCancelsPlugin() throws Exception {
// SETUP
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5 changes: 1 addition & 4 deletions pom.xml
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
<parent>
<groupId>org.scijava</groupId>
<artifactId>pom-scijava</artifactId>
<version>28.0.0</version>
<version>29.2.1</version>
<relativePath />
</parent>

Expand Down Expand Up @@ -119,9 +119,6 @@
<license.copyrightOwners>Michael Doube, BoneJ developers</license.copyrightOwners>
<releaseProfiles>deploy-to-scijava</releaseProfiles>
<tagNameFormat>bonej-@{project.version}</tagNameFormat>
<!-- Remove the versions when upgrading to pom-scijava 29.x.x -->
<LocalThickness_.version>4.0.3</LocalThickness_.version>
<imagej-ops.version>0.45.3</imagej-ops.version>
</properties>

<repositories>
Expand Down

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