Merge remote-tracking branch 'origin/develop' into slf4j-api_2

.classpath-template

@@ -6,8 +6,6 @@
         <classpathentry kind="src" path="components/formats-bsd/src"/>
         <classpathentry kind="src" path="components/formats-gpl/build/src"/>
         <classpathentry kind="src" path="components/formats-gpl/src"/>
-        <classpathentry kind="src" path="components/stubs/lwf-stubs/build/src"/>
-        <classpathentry kind="src" path="components/stubs/lwf-stubs/src"/>
         <classpathentry kind="src" path="components/test-suite/build/src"/>
         <classpathentry kind="src" path="components/test-suite/src"/>
         <classpathentry kind="src" path="components/formats-api/test"/>

.github/workflows/ant.yml

@@ -11,7 +11,7 @@ jobs:
         os: [ubuntu-latest, windows-latest]
     runs-on: ${{ matrix.os }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: Set up JDK ${{ matrix.java }}
         uses: actions/setup-java@v3
         with:
@@ -23,7 +23,7 @@ jobs:
             ant docs
       - name: Upload artifacts
         # upload just one set of artifacts for easier PR review
-        if: matrix.os == 'ubuntu-latest' && matrix.java == '1.8'
+        if: matrix.os == 'ubuntu-latest' && matrix.java == '8'
         uses: actions/upload-artifact@v3
         with:
           path: artifacts/

.github/workflows/maven.yml

@@ -19,7 +19,7 @@ jobs:
     env:
       maven_commands: install # default is install
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: Set up JDK ${{ matrix.java }}
         uses: actions/setup-java@v3
         with:
@@ -28,12 +28,45 @@ jobs:
           cache: 'maven'
       - name: Build
         run: mvn ${{ env.maven_commands }}
-  deploy:
+  deploy_snapshots:
     if: ${{ github.ref == 'refs/heads/develop' && github.repository_owner == 'ome' }}
     needs: build
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
+      - name: Retrieve version
+        id: get_version
+        run: |
+          VERSION=$( mvn help:evaluate -Dexpression=project.version -q -DforceStdout )
+          echo "version=$VERSION" >> $GITHUB_OUTPUT
+      - name: Set server
+        id: set_server
+        run: |
+          if [[ ${{ steps.get_version.outputs.version }} =~ 'SNAPSHOT' ]]; then
+              echo server='ome.snapshots' >> $GITHUB_OUTPUT
+            else
+              echo server='ome.releases' >> $GITHUB_OUTPUT
+          fi
+      - name: Set up Repository
+        uses: actions/setup-java@v3
+        with:
+          java-version: 8
+          distribution: 'zulu'
+          server-id: ${{ steps.set_server.outputs.server }}
+          server-username: MAVEN_USERNAME
+          server-password: MAVEN_PASSWORD
+      - name: Deploy SNAPSHOT
+        if: ${{ steps.set_server.outputs.server == 'ome.snapshots' }}
+        run: mvn deploy
+        env:
+          MAVEN_USERNAME: ${{ secrets.CI_DEPLOY_USER }}
+          MAVEN_PASSWORD: ${{ secrets.CI_DEPLOY_PASS }}
+  deploy_tags:
+    if: startsWith(github.ref, 'refs/tags') && github.repository_owner == 'ome'
+    needs: build
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
       - name: Retrieve version
         id: get_version
         run: |
@@ -45,7 +78,7 @@ jobs:
           if [[ ${{ steps.get_version.outputs.version }} =~ 'SNAPSHOT' ]]; then
             echo server='ome.snapshots' >> $GITHUB_OUTPUT
           else
-            echo server='ome.staging' >> $GITHUB_OUTPUT
+            echo server='ome.releases' >> $GITHUB_OUTPUT
           fi
       - name: Set up Repository
         uses: actions/setup-java@v3
@@ -55,7 +88,8 @@ jobs:
           server-id: ${{ steps.set_server.outputs.server }}
           server-username: MAVEN_USERNAME
           server-password: MAVEN_PASSWORD
-      - name: Deploy SNAPSHOT
+      - name: Deploy Tags
+        if: ${{ steps.set_server.outputs.server == 'ome.releases' }}
         run: mvn deploy
         env:
           MAVEN_USERNAME: ${{ secrets.CI_DEPLOY_USER }}

.github/workflows/release.yml

@@ -9,7 +9,7 @@ jobs:
     name: Release artifacts
     runs-on: ubuntu-20.04
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: Set up JDK
         uses: actions/setup-java@v3
         with:

.mailmap

@@ -1,12 +1,69 @@
+Aaron Avery <[email protected]> <[email protected]>
+Abraham Sorber <[email protected]> <[email protected]>
+Aleksandra Tarkowska <[email protected]> <[email protected]>
+Alex Herbert <[email protected]> aherbert <[email protected]>
+Alexandr Virodov <[email protected]> <[email protected]>
+Andreas Knab <[email protected]> <[email protected]>
+Andrew Patterson <[email protected]> Andrew J Patterson <[email protected]>
 Andrew Patterson <[email protected]> <[email protected]>
+Balaji Ramalingam <[email protected]> bramalingam <[email protected]>
+Brian Long <[email protected]> berl <[email protected]>
+Brian Long <[email protected]> <[email protected]>
+Brian Loranger <[email protected]> <[email protected]>
 Chris Allan <[email protected]> <[email protected]>
 Chris Allan <[email protected]> <[email protected]>
+Christian Niedworok <[email protected]> cniedwor <[email protected]>
+Christian Sachs <[email protected]> <[email protected]>
+Christian Sachs <[email protected]> <[email protected]>
+Claire McQuin <[email protected]> mcquin <[email protected]>
+Colin Blackburn <[email protected]> <[email protected]>
+Colin Blackburn <[email protected]> <[email protected]>
 Curtis Rueden <[email protected]> <unknown@unknown>
-Jean-Marie Burel <[email protected]>
+Constanze Wendtland <[email protected]> 
+Constanze Wendtland <[email protected]> <[email protected]>
+David Gault <[email protected]> dgault <[email protected]>
+David Pinto <[email protected]> <[email protected]>
+Donald MacDonald <[email protected]> <[email protected]>
+Eliana Andreica <[email protected]> dinelia <[email protected]>
+Eliana Andreica <[email protected]> ANDREICA Eliana <[email protected]>
+Helen Flynn <[email protected]> <[email protected]>
+Ian Munro <[email protected]> imunro <[email protected]>
+Ilya Parmon <[email protected]> Parm0n <[email protected]>
+Jan Eglinger <[email protected]> <[email protected]>
+Jean-Marie Burel <[email protected]> jburel <[email protected]>
+Jean-Marie Burel <[email protected]> jean-marie burel <[email protected]>
+Jean-Yves Tinevez <[email protected]> <[email protected]>
+Jeremy Muhlich <[email protected]> <[email protected]>
+Jim Crowe <[email protected]> redcrow <[email protected]>
+Johan Herz <[email protected]> <[email protected]>
 Johannes Schindelin <[email protected]> <[email protected]>
-Josh Moore <[email protected]> <[email protected]>
-Kristin Briney <[email protected]>
+Josh Moore <[email protected]> <[email protected]>
+Josh Moore <[email protected]> <[email protected]>
+Kristian Kjaergaard <[email protected]> kkjaergaard <[email protected]>
+Kristin Briney <[email protected]> Kristin <[email protected]>
+Mark Carroll <[email protected]> <[email protected]>
 Mark Hiner <[email protected]> <[email protected]>
+Mark Kittisopikul <[email protected]> <[email protected]>
+Matthieu Moisse <[email protected]> mmoisse <[email protected]>
 Melissa Linkert <[email protected]> <[email protected]>
-Premysl Fiala <[email protected]>
+Nicholas Chiaruttini <[email protected]> <[email protected]>
+Nicola Papp <[email protected]> nicola <[email protected]>
+Nils Gladitz <[email protected]> <[email protected]>
+Paul van Schayck <[email protected]> pvc-local <[email protected]>
+Peter Bankhead <[email protected]> Pete <[email protected]>
+Premysl Fiala <[email protected]> PremyslFiala <[email protected]>
+Premysl Fiala <[email protected]> Premysl.Fiala <[email protected]>
+Richard Myers <[email protected]> <[email protected]>
+Richard Myers <[email protected]> <[email protected]>
 Roger Leigh <[email protected]> <[email protected]>
+Roger Leigh <[email protected]> <[email protected]>
+Roger Leigh <[email protected]> <[email protected]>
+Sébastien Besson <[email protected]> <[email protected]>
+Shaquille Louisa <[email protected]> <118732057+ShaquilleLouisa-LambertInstruments@users.noreply.github.com>
+Simone Leo <[email protected]> <[email protected]>
+Stefan Helfrich <[email protected]> <[email protected]>
+Stefan Helfrich <[email protected]> <[email protected]>
+Stephan Wagner-Conrad <[email protected]> <[email protected]>
+Tomas Farago <[email protected]> <[email protected]>
+Wim Pomp <[email protected]> <[email protected]>
+Zachary Connerty-Marin <[email protected]> zacsimile <[email protected]>

build.xml

@@ -16,8 +16,7 @@ Bio-Formats
     JAR file:      bio-formats.jar
     Path:          components/bio-formats
     Project deps:  Formats Common, OME-XML Java library, JAI Image I/O Tools,
-                   MDB Tools (Java port), Apache Jakarta POI,
-                   Luratech LuraWave stubs
+                   MDB Tools (Java port), Apache Jakarta POI
     Library deps:  JGoodies Forms, Logback, NetCDF,
                    Simple Logging Facade for Java API, TestNG
     Optional:      Xalan Serializer, Xalan
@@ -76,21 +75,6 @@ JAI Image I/O Tools
                    This component will be removed once our changes have been
                    added to the official JAI CVS repository.
 
-===============================================================================
-The following components are stubs of third party projects:
-
-Luratech LuraWave stubs
-    Stub of proprietary Java API to handle Luratech LWF compression
-    -=-
-    JAR file:      lwf-stubs.jar
-    Path:          components/stubs/lwf-stubs
-    Project deps:  (none)
-    Optional:      (none)
-    License:       BSD
-    Project URL:   http://www.luratech.com/
-    Notes:         required to compile Bio-Formats's support for Luratech LWF
-                   compression for the Opera Flex format
-
 ===============================================================================
 The following external dependencies (in the jar folder) may be required:
 Ant-Contrib
@@ -142,7 +126,7 @@ Logback
     License:   EPL v1.0 and LGPL 2.1
 
 Native library loader
-    JAR file:  native-lib-loader-2.0.2.jar
+    JAR file:  native-lib-loader-2.4.0.jar
     URL:       http://github.com/scijava/native-lib-loader
     Notes:     required for loading native libraries
     License:   BSD

components/bio-formats-plugins/pom.xml

@@ -8,7 +8,7 @@
   <parent>
     <groupId>ome</groupId>
     <artifactId>pom-bio-formats</artifactId>
-    <version>6.12.1-SNAPSHOT</version>
+    <version>7.1.0-SNAPSHOT</version>
     <relativePath>../..</relativePath>
   </parent>
 

components/bio-formats-plugins/src/loci/plugins/config/ConfigWindow.java

@@ -218,7 +218,6 @@ public ConfigWindow() {
     //   + upgrade button for "ImageJ" just launches ImageJ upgrade plugin
     // - can install native libs by downloading installer from its web site
     //   + QuickTime for Java
-    //   + Nikon ND2 plugin
     //   + ImageIO Tools
 
     libInfo.add(makeLabel("Path", false));
@@ -375,18 +374,6 @@ public void run() {
     // Ant replaces date token with datestamp of the build
     if (bfVersion.equals("@" + "date" + "@")) bfVersion = "Internal build";
 
-    String qtVersion = null;
-    try {
-      Class<?> qtToolsClass = Class.forName("loci.formats.gui.LegacyQTTools");
-      Object qtTools = qtToolsClass.newInstance();
-      Method getQTVersion = qtToolsClass.getMethod("getQTVersion");
-      qtVersion = (String) getQTVersion.invoke(qtTools);
-    }
-    catch (Throwable t) {
-      log.println("Could not determine QuickTime version:");
-      t.printStackTrace(log);
-    }
-
     String clibIIOVersion = null;
     try {
       Class<?> jpegSpi = Class.forName(
@@ -428,7 +415,6 @@ public void run() {
     HashMap<String, String> versions = new HashMap<String, String>();
     versions.put("javaVersion", javaVersion);
     versions.put("bfVersion", bfVersion);
-    if (qtVersion != null) versions.put("qtVersion", qtVersion);
     if (clibIIOVersion != null) versions.put("clibIIOVersion", clibIIOVersion);
     if (matlabVersion != null) versions.put("matlabVersion", matlabVersion);