microscopepony · rleigh-codelibre · Apr 30, 2018 · Mar 22, 2018 · Mar 22, 2018 · Apr 9, 2018
diff --git a/.gitignore b/.gitignore
@@ -1,2 +1,3 @@
 .DS_Store
 target
+.idea
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
@@ -0,0 +1,22 @@
+stages:
+  - build
+  - test
+
+build-package:
+  stage: build
+  tags:
+    - matlab-R2017b
+  script:
+    - mvn install
+  artifacts:
+    paths:
+      - target/*.zip
+      - target/*.tar.gz
+
+test-package:
+  stage: test
+  tags:
+    - matlab-R2017b
+  script:
+    - PATH=/usr/local/MATLAB/R2017b/bin:$PATH
+    - mvn -P test-matlab
diff --git a/pom.xml b/pom.xml
@@ -7,11 +7,11 @@
 
   <groupId>ome</groupId>
   <artifactId>bio-formats-matlab</artifactId>
-  <version>5.8.1-SNAPSHOT</version>
+  <version>5.8.2</version>
   <packaging>pom</packaging>
 
-  <name>Bio-Formats bundle collection</name>
-  <description>Create matlab of Bio-Formats jars and tools for distribution.</description>
+  <name>Bio-Formats matlab package</name>
+  <description>Create matlab package of Bio-Formats jars and tools for distribution.</description>
   <url>https://www.openmicroscopy.org/bio-formats</url>
   <inceptionYear>2005</inceptionYear>
 
@@ -23,10 +23,13 @@
          When possible, we advise using the relevant groupId and version
          properties for your dependencies rather than hardcoding them. -->
 
+    <test.output.dir>${basedir}/target/matlab-test-results</test.output.dir>
+    <test.output>${test.output.dir}/report.xml</test.output>
+
     <date>${maven.build.timestamp}</date>
     <year>2018</year>
     <project.rootdir>${basedir}</project.rootdir>
-    <bioformats.version>5.8.1-SNAPSHOT</bioformats.version>
+    <bioformats.version>5.8.2</bioformats.version>
     <bio-formats_package.version>${bioformats.version}</bio-formats_package.version>
     <imagej1.version>1.48s</imagej1.version>
     <log4j.version>1.2.17</log4j.version>
@@ -51,7 +54,7 @@
       <plugin>
         <groupId>org.apache.maven.plugins</groupId>
         <artifactId>maven-enforcer-plugin</artifactId>
-        <version>3.0.0-M1</version>
+        <version>3.0.0-M2</version>
         <executions>
           <execution>
             <id>enforce-maven</id>
@@ -70,12 +73,7 @@
       </plugin>
       <plugin>
         <artifactId>maven-clean-plugin</artifactId>
-        <version>3.0.0</version>
-      </plugin>
-
-      <plugin>
-        <artifactId>maven-dependency-plugin</artifactId>
-        <version>3.0.2</version>
+        <version>3.1.0</version>
       </plugin>
 
       <plugin>
@@ -90,7 +88,7 @@
 
       <plugin>
         <artifactId>maven-plugin-plugin</artifactId>
-        <version>3.5.1</version>
+        <version>3.5.2</version>
       </plugin>
 
       <plugin>
@@ -107,7 +105,12 @@
 
       <plugin>
         <artifactId>maven-resources-plugin</artifactId>
-        <version>3.0.2</version>
+        <version>3.1.0</version>
+      </plugin>
+
+      <plugin>
+        <artifactId>maven-site-plugin</artifactId>
+        <version>3.7.1</version>
       </plugin>
 
       <plugin>
@@ -136,6 +139,7 @@
       <plugin>
         <groupId>org.apache.maven.plugins</groupId>
         <artifactId>maven-dependency-plugin</artifactId>
+        <version>3.1.1</version>
         <executions>
           <execution>
             <id>unpack-ome-xml</id>
@@ -289,7 +293,7 @@
           <plugin>
             <groupId>org.apache.maven.plugins</groupId>
             <artifactId>maven-dependency-plugin</artifactId>
-            <version>3.0.2</version>
+            <version>3.1.1</version>
             <executions>
               <execution>
                 <id>unpack</id>
@@ -312,6 +316,26 @@
               </execution>
             </executions>
           </plugin>
+          <plugin>
+            <groupId>org.apache.maven.plugins</groupId>
+            <artifactId>maven-antrun-plugin</artifactId>
+            <version>1.8</version>
+            <executions>
+              <execution>
+                <id>create-test-output-dir</id>
+                <phase>test</phase>
+                <configuration>
+                  <tasks>
+                    <delete dir="${test.output.dir}"/>
+                    <mkdir dir="${test.output.dir}"/>
+                  </tasks>
+                </configuration>
+                <goals>
+                  <goal>run</goal>
+                </goals>
+              </execution>
+            </executions>
+          </plugin>
           <plugin>
             <groupId>org.codehaus.mojo</groupId>
             <artifactId>exec-maven-plugin</artifactId>
@@ -329,13 +353,13 @@
               <executable>matlab</executable>
               <workingDirectory>${java.io.tmpdir}</workingDirectory>
               <environmentVariables>
-                <MATLABPATH>${project.build.directory}/test-matlab/bio-formats-matlab-${project.version}</MATLABPATH>
+                <MATLABPATH>${project.build.directory}/test-matlab/bio-formats-matlab-${project.version}${path.separator}${basedir}/test</MATLABPATH>
               </environmentVariables>
               <arguments>
                 <argument>-nodesktop</argument>
                 <argument>-nosplash</argument>
                 <argument>-r</argument>
-                <argument>runtests ${project.rootdir}/test</argument>
+                <argument>runbfxunit ${test.output}</argument>
               </arguments>
             </configuration>
           </plugin>

diff --git a/test/ReaderTest.m b/test/ReaderTest.m
@@ -26,7 +26,7 @@
 % 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
 
 classdef ReaderTest < TestBfMatlab
-    
+
     properties
         reader
         sizeX
@@ -35,14 +35,9 @@
         sizeC
         sizeT
     end
-
-    methods
-        function self = ReaderTest(name)
-            self = self@TestBfMatlab(name);
-        end
-
-        function setUp(self)
-            setUp@TestBfMatlab(self)
+
+    methods (TestMethodSetup)
+        function ReaderTestSetUp(self)
             javaaddpath(self.jarPath);
             self.reader = loci.formats.in.FakeReader();
             self.sizeX = self.reader.DEFAULT_SIZE_X;
@@ -53,13 +48,14 @@ function setUp(self)
             loci.common.DebugTools.setRootLevel('ERROR');
             import ome.units.UNITS.*;
         end
-
-        function tearDown(self)
+    end
+
+    methods (TestMethodTeardown)
+        function ReaderTestTearDown(self)
             if ~isempty(self.reader),
                 self.reader.close();
                 self.reader = [];
             end
-            tearDown@TestBfMatlab(self)
         end
     end
 end
diff --git a/test/TestBfCheckJavaMemory.m b/test/TestBfCheckJavaMemory.m
@@ -26,48 +26,46 @@
 % 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
 
 classdef TestBfCheckJavaMemory < TestBfMatlab
-    
+
     properties
         minMemory
         warning_id = ''
     end
-    
+
     methods
-        function self = TestBfCheckJavaMemory(name)
-            self = self@TestBfMatlab(name);
-        end
-
         % Dimension size tests
         function runJavaMemoryCheck(self)
             lastwarn('');
             bfCheckJavaMemory(self.minMemory)
             [last_warning_msg, last_warning_id] = lastwarn;
-            assertEqual(last_warning_id, self.warning_id);
+            self.assertEqual(last_warning_id, self.warning_id);
             lastwarn('');
         end
-
+    end
+
+    methods (Test)
         function testZero(self)
             self.minMemory = 0;
             self.runJavaMemoryCheck()
         end
-        
+
         function testMaxMemory(self)
             self.minMemory = self.getRuntime();
             self.runJavaMemoryCheck()
         end
-        
+
         function testLowMemory(self)
             self.minMemory = round(self.getRuntime() + 100);
             self.warning_id = 'BF:lowJavaMemory';
             self.runJavaMemoryCheck()
         end
     end
+
     methods(Static)
-
         function memory = getRuntime()
             runtime = java.lang.Runtime.getRuntime();
             memory = runtime.maxMemory() / (1024 * 1024);
         end
     end
-    
+
 end
diff --git a/test/TestBfCheckJavaPath.m b/test/TestBfCheckJavaPath.m
@@ -27,39 +27,37 @@
 
 
 classdef TestBfCheckJavaPath < TestBfMatlab
-    
+
     properties
         status
         version
         maxTime = .1
     end
-
-    methods
-        function self = TestBfCheckJavaPath(name)
-            self = self@TestBfMatlab(name);
-        end
-
+
+    methods (Test)
         function testDefault(self)
+            javaaddpath(self.jarPath);
             self.status = bfCheckJavaPath();
-            assertTrue(self.status);
+            self.assertTrue(self.status);
         end
-        
+
         function testAutoloadBioformats(self)
+            javaaddpath(self.jarPath);
             self.status = bfCheckJavaPath(true);
-            assertTrue(self.status);
+            self.assertTrue(self.status);
         end
-        
+
         function testNoAutoloadBioformats(self)
             isStatic = ismember(self.jarPath,...
                 javaclasspath('-static'));
             self.status = bfCheckJavaPath(false);
             if isStatic
-                assertTrue(self.status);
+                self.assertTrue(self.status);
             else
-                assertFalse(self.status);
+                self.assertFalse(self.status);
             end
         end
-        
+
         function testPerformance(self)
             nCounts = 10;
             times = zeros(nCounts);
@@ -68,27 +66,28 @@ function testPerformance(self)
                 bfCheckJavaPath();
                 times(i) = toc;
             end
-            
+
             % First call should be the longest as the Bio-Formats JAR file is
             % added to the javaclasspath
-            assertTrue(times(1) > times(2));
+            self.assertTrue(times(1) > times(2));
             % Second call should still be longer than all the following
             % ones. Profiling reveals some amount of time is spent while
             % computing javaclasspath.local_get_static_path
-            assertTrue(all(times(2) > times(3:end)));
+            self.assertTrue(all(times(2) > times(3:end)));
             % From the third call and onwards, javaclasspath and thus
             % bfCheckJavaPath should return fast
-            assertTrue(mean(times(3:end)) < self.maxTime);
+            self.assertTrue(mean(times(3:end)) < self.maxTime);
         end
-        
+
         function testJavaMethod(self)
+            javaaddpath(self.jarPath);
             self.status = bfCheckJavaPath(true);
             version = char(loci.formats.FormatTools.VERSION);
             [self.status self.version]= bfCheckJavaPath(false);
-            assertEqual(self.version,version);
+            self.assertEqual(self.version,version);
             if (exist ('OCTAVE_VERSION', 'builtin'))
                 version = char(java_get('loci.formats.FormatTools', 'VERSION'));
-                assertEqual( self.version, version);
+                self.assertEqual( self.version, version);
             end
         end
     end