From d461150da7cbb3aa709b96d2bb8f79f4de448a3e Mon Sep 17 00:00:00 2001 From: Michael Doube Date: Mon, 13 Oct 2025 17:57:04 +0200 Subject: [PATCH 01/17] use bonej-plus 0.0.12-SNAPSHOT --- Modern/wrapperPlugins/pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Modern/wrapperPlugins/pom.xml b/Modern/wrapperPlugins/pom.xml index 762b6a77..3672217c 100644 --- a/Modern/wrapperPlugins/pom.xml +++ b/Modern/wrapperPlugins/pom.xml @@ -127,7 +127,7 @@ org.bonej bonej-plus - 0.0.11 + 0.0.12-SNAPSHOT From fa688ff96446a7c8c31e6d178f76ebe0347fad72 Mon Sep 17 00:00:00 2001 From: mdoube Date: Mon, 3 Nov 2025 22:24:25 +0100 Subject: [PATCH 02/17] Use BeanCounter from its own package --- .../main/java/org/bonej/wrapperPlugins/GPUCheckerWrapper.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Modern/wrapperPlugins/src/main/java/org/bonej/wrapperPlugins/GPUCheckerWrapper.java b/Modern/wrapperPlugins/src/main/java/org/bonej/wrapperPlugins/GPUCheckerWrapper.java index 9ab4464b..e494f94e 100644 --- a/Modern/wrapperPlugins/src/main/java/org/bonej/wrapperPlugins/GPUCheckerWrapper.java +++ b/Modern/wrapperPlugins/src/main/java/org/bonej/wrapperPlugins/GPUCheckerWrapper.java @@ -31,8 +31,6 @@ import java.awt.Checkbox; import java.util.List; -import org.bonej.plus.BeanCounter; -import org.bonej.plus.BeanCounterPlugin; import org.bonej.plus.DeviceCheck; import org.bonej.plus.Regulator; import org.bonej.plus.Utilities; @@ -40,6 +38,8 @@ import org.scijava.command.Command; import org.scijava.plugin.Plugin; +import ch.beancounter.BeanCounter; +import ch.beancounter.BeanCounterPlugin; import ij.IJ; import ij.Prefs; import ij.gui.GenericDialog; From be2c72ad52871c183bab075ea401af4e6e530557 Mon Sep 17 00:00:00 2001 From: mdoube Date: Mon, 3 Nov 2025 23:16:23 +0100 Subject: [PATCH 03/17] Get beancounter from the github repo for SNAPSHOTs --- .github/workflows/build-pr.yml | 7 ++++++- pom.xml | 9 ++++++++- 2 files changed, 14 insertions(+), 2 deletions(-) diff --git a/.github/workflows/build-pr.yml b/.github/workflows/build-pr.yml index 968ab7b0..3e5c660e 100644 --- a/.github/workflows/build-pr.yml +++ b/.github/workflows/build-pr.yml @@ -25,6 +25,7 @@ jobs: rm -rf ~/.m2/repository/com/github/* rm -rf ~/.m2/repository/io/github/* rm -rf ~/.m2/repository/org/bonej/* + rm -rf ~/.m2/repository/ch/beancounter/* - name: Cache Maven packages uses: actions/cache@v3 @@ -37,7 +38,11 @@ jobs: - name: Set up Maven settings uses: s4u/maven-settings-action@v2 with: - servers: '[{"id": "github", "username": "${{ github.actor }}", "password": "${{ secrets.BONEJ_PLUS_REPO }}"}]' + servers: > + [ + {"id": "github-bonej-plus", "username": "${{ github.actor }}", "password": "${{ secrets.BONEJ_PLUS_REPO }}"}, + {"id": "github-beancounter", "username": "${{ github.actor }}", "password": "${{ secrets.BONEJ_PLUS_REPO }}"} + ] githubServer: false - name: Set up CI environment diff --git a/pom.xml b/pom.xml index 25f5176e..eac14174 100644 --- a/pom.xml +++ b/pom.xml @@ -129,10 +129,17 @@ false - github + github-bonej-plus https://maven.pkg.github.com/bonej-org/bonej-plus false true + + github-beancounter + https://maven.pkg.github.com/bonej-org/beancounter + false + true + + From 53a7ef6612179b09f8fbd68a5f00ec3225833857 Mon Sep 17 00:00:00 2001 From: mdoube Date: Mon, 3 Nov 2025 23:36:28 +0100 Subject: [PATCH 04/17] Try again with different credentials --- .github/workflows/build-pr.yml | 31 ++++++++++++++++++------------- 1 file changed, 18 insertions(+), 13 deletions(-) diff --git a/.github/workflows/build-pr.yml b/.github/workflows/build-pr.yml index 3e5c660e..4990bec0 100644 --- a/.github/workflows/build-pr.yml +++ b/.github/workflows/build-pr.yml @@ -8,15 +8,30 @@ on: jobs: build: runs-on: ubuntu-latest + permissions: + contents: read + packages: read steps: - uses: actions/checkout@v4 - - name: Set up Java + - name: Set up Java for bonej-plus uses: actions/setup-java@v4 with: - java-version: '8' - distribution: 'zulu' + java-version: '11' + distribution: 'zulu' + server-id: github-bonej-plus + server-username: GITHUB_ACTOR + server-password: ${{ secrets.BONEJ_PLUS_REPO }} + - name: Set up Java for beancounter repo + uses: actions/setup-java@v4 + with: + java-version: '11' + distribution: 'zulu' + server-id: github-beancounter + server-username: GITHUB_ACTOR + server-password: ${{ secrets.BONEJ_PLUS_REPO }} + # Needed if the cache is out of whack and needs to be totally refreshed # - name: Clear Maven cache # run: rm -rf ~/.m2/repository/* @@ -35,16 +50,6 @@ jobs: key: ${{ runner.os }}-m2-${{ hashFiles('**/pom.xml') }}-${{ github.run_id }} restore-keys: ${{ runner.os }}-m2 - - name: Set up Maven settings - uses: s4u/maven-settings-action@v2 - with: - servers: > - [ - {"id": "github-bonej-plus", "username": "${{ github.actor }}", "password": "${{ secrets.BONEJ_PLUS_REPO }}"}, - {"id": "github-beancounter", "username": "${{ github.actor }}", "password": "${{ secrets.BONEJ_PLUS_REPO }}"} - ] - githubServer: false - - name: Set up CI environment run: .github/setup.sh From a3ff11b56efde18e654c6cde8845c7ac163b5024 Mon Sep 17 00:00:00 2001 From: mdoube Date: Mon, 3 Nov 2025 23:51:42 +0100 Subject: [PATCH 05/17] Try again with a different username --- .github/workflows/build-pr.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/build-pr.yml b/.github/workflows/build-pr.yml index 4990bec0..e80fd8d0 100644 --- a/.github/workflows/build-pr.yml +++ b/.github/workflows/build-pr.yml @@ -20,7 +20,7 @@ jobs: java-version: '11' distribution: 'zulu' server-id: github-bonej-plus - server-username: GITHUB_ACTOR + server-username: ${{ secrets.PAT_USERNAME }} server-password: ${{ secrets.BONEJ_PLUS_REPO }} - name: Set up Java for beancounter repo @@ -29,7 +29,7 @@ jobs: java-version: '11' distribution: 'zulu' server-id: github-beancounter - server-username: GITHUB_ACTOR + server-username: ${{ secrets.PAT_USERNAME }} server-password: ${{ secrets.BONEJ_PLUS_REPO }} # Needed if the cache is out of whack and needs to be totally refreshed From a568c691d825e17b2392a7651038261fd2fbdfee Mon Sep 17 00:00:00 2001 From: mdoube Date: Tue, 4 Nov 2025 10:05:19 +0100 Subject: [PATCH 06/17] Revert "Try again with a different username" This reverts commit a3ff11b56efde18e654c6cde8845c7ac163b5024. --- .github/workflows/build-pr.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/build-pr.yml b/.github/workflows/build-pr.yml index e80fd8d0..4990bec0 100644 --- a/.github/workflows/build-pr.yml +++ b/.github/workflows/build-pr.yml @@ -20,7 +20,7 @@ jobs: java-version: '11' distribution: 'zulu' server-id: github-bonej-plus - server-username: ${{ secrets.PAT_USERNAME }} + server-username: GITHUB_ACTOR server-password: ${{ secrets.BONEJ_PLUS_REPO }} - name: Set up Java for beancounter repo @@ -29,7 +29,7 @@ jobs: java-version: '11' distribution: 'zulu' server-id: github-beancounter - server-username: ${{ secrets.PAT_USERNAME }} + server-username: GITHUB_ACTOR server-password: ${{ secrets.BONEJ_PLUS_REPO }} # Needed if the cache is out of whack and needs to be totally refreshed From 31d147c7a40a0019951241dcfa1fa785c14178f3 Mon Sep 17 00:00:00 2001 From: mdoube Date: Tue, 4 Nov 2025 10:05:28 +0100 Subject: [PATCH 07/17] Revert "Try again with different credentials" This reverts commit 53a7ef6612179b09f8fbd68a5f00ec3225833857. --- .github/workflows/build-pr.yml | 31 +++++++++++++------------------ 1 file changed, 13 insertions(+), 18 deletions(-) diff --git a/.github/workflows/build-pr.yml b/.github/workflows/build-pr.yml index 4990bec0..3e5c660e 100644 --- a/.github/workflows/build-pr.yml +++ b/.github/workflows/build-pr.yml @@ -8,30 +8,15 @@ on: jobs: build: runs-on: ubuntu-latest - permissions: - contents: read - packages: read steps: - uses: actions/checkout@v4 - - name: Set up Java for bonej-plus + - name: Set up Java uses: actions/setup-java@v4 with: - java-version: '11' - distribution: 'zulu' - server-id: github-bonej-plus - server-username: GITHUB_ACTOR - server-password: ${{ secrets.BONEJ_PLUS_REPO }} + java-version: '8' + distribution: 'zulu' - - name: Set up Java for beancounter repo - uses: actions/setup-java@v4 - with: - java-version: '11' - distribution: 'zulu' - server-id: github-beancounter - server-username: GITHUB_ACTOR - server-password: ${{ secrets.BONEJ_PLUS_REPO }} - # Needed if the cache is out of whack and needs to be totally refreshed # - name: Clear Maven cache # run: rm -rf ~/.m2/repository/* @@ -50,6 +35,16 @@ jobs: key: ${{ runner.os }}-m2-${{ hashFiles('**/pom.xml') }}-${{ github.run_id }} restore-keys: ${{ runner.os }}-m2 + - name: Set up Maven settings + uses: s4u/maven-settings-action@v2 + with: + servers: > + [ + {"id": "github-bonej-plus", "username": "${{ github.actor }}", "password": "${{ secrets.BONEJ_PLUS_REPO }}"}, + {"id": "github-beancounter", "username": "${{ github.actor }}", "password": "${{ secrets.BONEJ_PLUS_REPO }}"} + ] + githubServer: false + - name: Set up CI environment run: .github/setup.sh From 81422e07127c8dd53336855ed667b192def9f397 Mon Sep 17 00:00:00 2001 From: mdoube Date: Tue, 4 Nov 2025 10:09:26 +0100 Subject: [PATCH 08/17] Roll back and try again step by step --- .github/workflows/build-pr.yml | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/.github/workflows/build-pr.yml b/.github/workflows/build-pr.yml index 3e5c660e..75b1fb12 100644 --- a/.github/workflows/build-pr.yml +++ b/.github/workflows/build-pr.yml @@ -38,11 +38,8 @@ jobs: - name: Set up Maven settings uses: s4u/maven-settings-action@v2 with: - servers: > - [ - {"id": "github-bonej-plus", "username": "${{ github.actor }}", "password": "${{ secrets.BONEJ_PLUS_REPO }}"}, - {"id": "github-beancounter", "username": "${{ github.actor }}", "password": "${{ secrets.BONEJ_PLUS_REPO }}"} - ] + servers: '[{"id": "github-bonej-plus", "username": "${{ github.actor }}", "password": "${{ secrets.BONEJ_PLUS_REPO }}"}]' +# ,{"id": "github-beancounter", "username": "${{ github.actor }}", "password": "${{ secrets.BONEJ_PLUS_REPO }}"} githubServer: false - name: Set up CI environment From 63df3520a15fd707e61b35b9d74c983e6333f9fb Mon Sep 17 00:00:00 2001 From: mdoube Date: Tue, 4 Nov 2025 10:31:12 +0100 Subject: [PATCH 09/17] Try adding beancounter server credentials --- .github/workflows/build-pr.yml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.github/workflows/build-pr.yml b/.github/workflows/build-pr.yml index 75b1fb12..cbc14ed3 100644 --- a/.github/workflows/build-pr.yml +++ b/.github/workflows/build-pr.yml @@ -38,8 +38,7 @@ jobs: - name: Set up Maven settings uses: s4u/maven-settings-action@v2 with: - servers: '[{"id": "github-bonej-plus", "username": "${{ github.actor }}", "password": "${{ secrets.BONEJ_PLUS_REPO }}"}]' -# ,{"id": "github-beancounter", "username": "${{ github.actor }}", "password": "${{ secrets.BONEJ_PLUS_REPO }}"} + servers: '[{"id": "github-bonej-plus", "username": "${{ github.actor }}", "password": "${{ secrets.BONEJ_PLUS_REPO }}"},{"id": "github-beancounter", "username": "${{ github.actor }}", "password": "${{ secrets.BONEJ_PLUS_REPO }}"}]' githubServer: false - name: Set up CI environment From 691efca3927d0c0e1f94c178f6508d3ec0c4f294 Mon Sep 17 00:00:00 2001 From: mdoube Date: Tue, 4 Nov 2025 10:44:57 +0100 Subject: [PATCH 10/17] Explicitly add beancouter as a dependency --- Modern/wrapperPlugins/pom.xml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/Modern/wrapperPlugins/pom.xml b/Modern/wrapperPlugins/pom.xml index 3672217c..b08bbd48 100644 --- a/Modern/wrapperPlugins/pom.xml +++ b/Modern/wrapperPlugins/pom.xml @@ -129,6 +129,11 @@ bonej-plus 0.0.12-SNAPSHOT + + ch.beancounter + beancounter + 0.0.1-SNAPSHOT + From f25553640eb34e130b7718f7a66007f23a013d30 Mon Sep 17 00:00:00 2001 From: mdoube Date: Tue, 4 Nov 2025 15:38:03 +0100 Subject: [PATCH 11/17] Remove the GPU Checker It belongs in bonej-plus and created problems being included here. --- .../wrapperPlugins/GPUCheckerWrapper.java | 142 ------------------ 1 file changed, 142 deletions(-) delete mode 100644 Modern/wrapperPlugins/src/main/java/org/bonej/wrapperPlugins/GPUCheckerWrapper.java diff --git a/Modern/wrapperPlugins/src/main/java/org/bonej/wrapperPlugins/GPUCheckerWrapper.java b/Modern/wrapperPlugins/src/main/java/org/bonej/wrapperPlugins/GPUCheckerWrapper.java deleted file mode 100644 index e494f94e..00000000 --- a/Modern/wrapperPlugins/src/main/java/org/bonej/wrapperPlugins/GPUCheckerWrapper.java +++ /dev/null @@ -1,142 +0,0 @@ -/*- - * #%L - * High-level BoneJ2 commands. - * %% - * Copyright (C) 2015 - 2025 Michael Doube, BoneJ developers - * %% - * Redistribution and use in source and binary forms, with or without - * modification, are permitted provided that the following conditions are met: - * - * 1. Redistributions of source code must retain the above copyright notice, - * this list of conditions and the following disclaimer. - * 2. Redistributions in binary form must reproduce the above copyright notice, - * this list of conditions and the following disclaimer in the documentation - * and/or other materials provided with the distribution. - * - * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" - * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE - * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE - * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE - * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR - * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF - * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS - * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN - * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) - * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE - * POSSIBILITY OF SUCH DAMAGE. - * #L% - */ -package org.bonej.wrapperPlugins; - -import java.awt.Checkbox; -import java.util.List; - -import org.bonej.plus.DeviceCheck; -import org.bonej.plus.Regulator; -import org.bonej.plus.Utilities; -import org.jocl.cl_device_id; -import org.scijava.command.Command; -import org.scijava.plugin.Plugin; - -import ch.beancounter.BeanCounter; -import ch.beancounter.BeanCounterPlugin; -import ij.IJ; -import ij.Prefs; -import ij.gui.GenericDialog; - -@Plugin(type = Command.class, menuPath = "Plugins>BoneJ>Plus>Check GPUs") -public class GPUCheckerWrapper extends BoneJCommand { - - final static String PREF_BASE = "BoneJ."; - - @Override - public void run() { - if (Regulator.getInstance().isLocked()) { - IJ.showMessage("BoneJ+", "A plugin is already running."); - return; - } - - //check balance, if empty then give the opportunity to top up - if (BeanCounter.getInstance().getBalance() <= 0) { - - (new BeanCounterPlugin()).run(); - - //balance not topped up, quit. - if (BeanCounter.getInstance().getBalance() <= 0) - return; - } - - String[] platformNames = DeviceCheck.getPlatformNames(DeviceCheck.getPlatformIds()); - for (int p = 0; p < platformNames.length; p++) - System.out.println("Found platform: "+platformNames[p]); - cl_device_id[][] devices = DeviceCheck.getAllDeviceIds(); - String[][] deviceNames = DeviceCheck.getDeviceNames(devices); - boolean[][] isCompliant = DeviceCheck.getCompliance(devices); - - //clear Prefs of old deviceName and useDevice entries - //around 10 platforms in existence I think, but may need to be updated - //to handle severely Frankensteinish hardware configurations - for (int pl = 0; pl < 20; pl++) { - int d = 0; - int noDeviceFoundCount = 0; - while (noDeviceFoundCount < 10) { - //if either deviceName or useDevice entry is present, this device was recorded in prefs - if (Prefs.get(PREF_BASE+"deviceName["+pl+":"+d+"]", null) != null || - Prefs.get(PREF_BASE+"useDevice["+pl+":"+d+"]", null) != null) { - - System.out.println("Found a device listed in the prefs at "+pl+":"+d); - - //setting to null removes the key and the value - Prefs.set(PREF_BASE+"deviceName["+pl+":"+d+"]", null); - Prefs.set(PREF_BASE+"useDevice["+pl+":"+d+"]", null); - //reset the counter - loop will keep going for 10 empty devices after the last hit - noDeviceFoundCount = 0; - } else { -// System.out.println("No device listed in the prefs at "+pl+":"+d); - noDeviceFoundCount++; - } - d++; - } - } - - - GenericDialog gd = new GenericDialog("Select GPUs"); - for (int p = 0; p < platformNames.length; p++) { - gd.addMessage("Platform "+p+": "+platformNames[p]); - if (devices[p].length == 0) { - gd.addMessage("No devices on this platform"); - continue; - } - for (int d = 0; d < devices[p].length; d++) { - //log in Prefs the name of each device - Prefs.set(PREF_BASE+"deviceName["+p+":"+d+"]", deviceNames[p][d]); - //default to use all compliant devices - gd.addCheckbox("Device_"+p+"-"+d+": "+ deviceNames[p][d], isCompliant[p][d]); - } - } - - List checkboxes = gd.getCheckboxes(); - int i = 0; - for (int p = 0; p < platformNames.length; p++) { - for (int d = 0; d < devices[p].length; d++) { - Checkbox checkbox = (Checkbox) checkboxes.get(i); - checkbox.setEnabled(isCompliant[p][d]); - if (!isCompliant[p][d]) - checkbox.setState(false); - i++; - } - } - - gd.showDialog(); - - for (int p = 0; p < platformNames.length; p++) { - for (int d = 0; d < devices[p].length; d++) { - Prefs.set(PREF_BASE+"useDevice["+p+":"+d+"]", gd.getNextBoolean()); - } - } - - //reset and clear any singleton classes that might be floating about - //note that multiple calls may lead to VRAM leak on NVIDIA cards, which don't let go of resources well - Utilities.purgeAll(); - } -} From 921e4e781fdbd337f274a64eeb037dc962d0c236 Mon Sep 17 00:00:00 2001 From: mdoube Date: Tue, 4 Nov 2025 21:06:16 +0100 Subject: [PATCH 12/17] Remove explicit beancounter dependency Should be brought in transitively via bonej-plus --- Modern/wrapperPlugins/pom.xml | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/Modern/wrapperPlugins/pom.xml b/Modern/wrapperPlugins/pom.xml index b08bbd48..b4be7b83 100644 --- a/Modern/wrapperPlugins/pom.xml +++ b/Modern/wrapperPlugins/pom.xml @@ -129,12 +129,7 @@ bonej-plus 0.0.12-SNAPSHOT - - ch.beancounter - beancounter - 0.0.1-SNAPSHOT - - + net.imagej From 828b8e79f535a344d41fdfa21d372ab62ecee830 Mon Sep 17 00:00:00 2001 From: mdoube Date: Fri, 21 Nov 2025 19:38:12 +0100 Subject: [PATCH 13/17] remove dependency on bonej-plus This created a circular dependency which breaks the Maven dependency model. --- Modern/wrapperPlugins/pom.xml | 5 ----- 1 file changed, 5 deletions(-) diff --git a/Modern/wrapperPlugins/pom.xml b/Modern/wrapperPlugins/pom.xml index b4be7b83..63cd76b3 100644 --- a/Modern/wrapperPlugins/pom.xml +++ b/Modern/wrapperPlugins/pom.xml @@ -124,11 +124,6 @@ org.bonej bonej-ops - - org.bonej - bonej-plus - 0.0.12-SNAPSHOT - From debb0010695311606220b72f37323f19f1bb9a68 Mon Sep 17 00:00:00 2001 From: mdoube Date: Tue, 25 Nov 2025 11:25:43 +0100 Subject: [PATCH 14/17] use mockito 5.20.0 4.11 was complaining about Java >20 Caused by: java.lang.IllegalArgumentException: Java 21 (65) is not supported by the current version of Byte Buddy which officially supports Java 20 (64) - update Byte Buddy or set net.bytebuddy.experimental as a VM property at net.bytebuddy.utility.OpenedClassReader.of(OpenedClassReader.java:96) --- Legacy/util/pom.xml | 2 ++ Modern/utilities/pom.xml | 2 ++ Modern/wrapperPlugins/pom.xml | 2 ++ 3 files changed, 6 insertions(+) diff --git a/Legacy/util/pom.xml b/Legacy/util/pom.xml index b877fc0f..f7cccd3e 100644 --- a/Legacy/util/pom.xml +++ b/Legacy/util/pom.xml @@ -120,6 +120,8 @@ org.mockito mockito-core + + 5.20.0 test diff --git a/Modern/utilities/pom.xml b/Modern/utilities/pom.xml index a389b488..ded7c537 100644 --- a/Modern/utilities/pom.xml +++ b/Modern/utilities/pom.xml @@ -172,6 +172,8 @@ org.mockito mockito-core + + 5.20.0 test diff --git a/Modern/wrapperPlugins/pom.xml b/Modern/wrapperPlugins/pom.xml index 63cd76b3..98a8f722 100644 --- a/Modern/wrapperPlugins/pom.xml +++ b/Modern/wrapperPlugins/pom.xml @@ -240,6 +240,8 @@ org.mockito mockito-core + + 5.20.0 test From 73a0b5d6cb5a9489a6bbdf72509caabb032696b7 Mon Sep 17 00:00:00 2001 From: mdoube Date: Tue, 25 Nov 2025 12:51:49 +0100 Subject: [PATCH 15/17] Build with Java 21 limited to 8 compatibility --- .github/workflows/build-main.yml | 4 ++-- .github/workflows/build-pr.yml | 4 ++-- pom.xml | 17 +++++++++++++++++ 3 files changed, 21 insertions(+), 4 deletions(-) diff --git a/.github/workflows/build-main.yml b/.github/workflows/build-main.yml index c0227994..ac37c251 100644 --- a/.github/workflows/build-main.yml +++ b/.github/workflows/build-main.yml @@ -16,8 +16,8 @@ jobs: - name: Set up Java uses: actions/setup-java@v4 with: - java-version: '8' - distribution: 'zulu' + java-version: '21' + distribution: 'temurin' - name: Cache Maven packages uses: actions/cache@v3 diff --git a/.github/workflows/build-pr.yml b/.github/workflows/build-pr.yml index cbc14ed3..9aec9ea3 100644 --- a/.github/workflows/build-pr.yml +++ b/.github/workflows/build-pr.yml @@ -14,8 +14,8 @@ jobs: - name: Set up Java uses: actions/setup-java@v4 with: - java-version: '8' - distribution: 'zulu' + java-version: '21' + distribution: 'temurin' # Needed if the cache is out of whack and needs to be totally refreshed # - name: Clear Maven cache diff --git a/pom.xml b/pom.xml index eac14174..4b6bc46c 100644 --- a/pom.xml +++ b/pom.xml @@ -119,7 +119,24 @@ Michael Doube, BoneJ developers sign,deploy-to-scijava bonej-@{project.version} + 8 + + + + + + org.apache.maven.plugins + maven-compiler-plugin + 3.14.0 + + ${maven.compiler.release} + + + + + + From 91c681e0d3254da6a196b67d7157484ce92c3b52 Mon Sep 17 00:00:00 2001 From: mdoube Date: Tue, 25 Nov 2025 13:09:28 +0100 Subject: [PATCH 16/17] remove bonej-plus and beancounter repos They are not dependencies so no need to include the repo address. --- pom.xml | 15 +-------------- 1 file changed, 1 insertion(+), 14 deletions(-) diff --git a/pom.xml b/pom.xml index 4b6bc46c..17e63cf8 100644 --- a/pom.xml +++ b/pom.xml @@ -144,19 +144,6 @@ https://maven.scijava.org/content/groups/public true false - - - github-bonej-plus - https://maven.pkg.github.com/bonej-org/bonej-plus - false - true - - - github-beancounter - https://maven.pkg.github.com/bonej-org/beancounter - false - true - - + From 91555de215275e053f499bf2e7969d38beee9be2 Mon Sep 17 00:00:00 2001 From: mdoube Date: Tue, 25 Nov 2025 13:10:58 +0100 Subject: [PATCH 17/17] Revert "remove bonej-plus and beancounter repos" This reverts commit 91c681e0d3254da6a196b67d7157484ce92c3b52. --- pom.xml | 15 ++++++++++++++- 1 file changed, 14 insertions(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 17e63cf8..4b6bc46c 100644 --- a/pom.xml +++ b/pom.xml @@ -144,6 +144,19 @@ https://maven.scijava.org/content/groups/public true false - + + + github-bonej-plus + https://maven.pkg.github.com/bonej-org/bonej-plus + false + true + + + github-beancounter + https://maven.pkg.github.com/bonej-org/beancounter + false + true + +