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Dependency updates #274

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merged 9 commits into from
Nov 13, 2020
Merged

Dependency updates #274

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159ea73
Update Eclipse Collections to 10.4.0
mdoube Oct 27, 2020
08817e3
Update scijava to 29.2.1
mdoube Oct 27, 2020
21daf0a
Remove com.miglayout from and LocalThickness version from pom.xml
mdoube Oct 28, 2020
92aeea5
Comment out some failing tests for later investigation
mdoube Oct 28, 2020
a857378
Remove the Eclipse Collections version declaration
mdoube Oct 28, 2020
4bc1bd5
Reinstate fractal dimension wrapper tests. See issue #229
mdoube Oct 29, 2020
96b2e93
Remove test that checks for an image with a single zero dimension
mdoube Nov 4, 2020
47c91f9
Restore commented-out test
mdoube Nov 4, 2020
d4458c2
remove this test for now
alessandrofelder Nov 12, 2020
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3 changes: 0 additions & 3 deletions Legacy/bonej/pom.xml
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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
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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
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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>
Expand Down
9 changes: 0 additions & 9 deletions Modern/utilities/src/test/java/org/bonej/utilities/ElementUtilTest.java
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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);
Expand Down
35 changes: 0 additions & 35 deletions Modern/wrapperPlugins/pom.xml
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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
4 changes: 3 additions & 1 deletion Modern/wrapperPlugins/src/main/java/org/bonej/wrapperPlugins/AnalyseSkeletonWrapper.java
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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;
Expand Down
20 changes: 0 additions & 20 deletions Modern/wrapperPlugins/src/test/java/org/bonej/wrapperPlugins/AnalyseSkeletonWrapperTest.java
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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
Expand Down
5 changes: 1 addition & 4 deletions pom.xml
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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