From e6dacd8cc7bf1a00bb82e7304cdb04159dc9bf8f Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Tue, 20 Oct 2026 14:37:43 +0200 Subject: [PATCH 1/7] Open for development --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 6ce271e..388da51 100644 --- a/pom.xml +++ b/pom.xml @@ -5,7 +5,7 @@ nanojava Java library extending the Chemistry Development Kit with functionality for nanomaterials. NanoJava - 2.0.7 + 2.0.8-SNAPSHOT https://github.com/enanomapper/nanojava From 80117259f5da8ad5aee2032d1de978a4cf5cbfd1 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Tue, 20 Oct 2026 14:42:19 +0200 Subject: [PATCH 2/7] CDK 2.13 --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 388da51..3b3a678 100644 --- a/pom.xml +++ b/pom.xml @@ -48,7 +48,7 @@ - 2.12 + 2.13 5.13.3 UTF-8 11 From 036d235ed4179fe839d680096c9bfba2d17ea1eb Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Tue, 20 Oct 2026 14:43:02 +0200 Subject: [PATCH 3/7] CMLXOM 4.19 --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 3b3a678..75a60f2 100644 --- a/pom.xml +++ b/pom.xml @@ -71,7 +71,7 @@ org.blueobelisk cmlxom - 4.17 + 4.19 org.openscience.cdk From 8b1c9e2b6990eae760290bbe574b2946f7129157 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Tue, 20 Oct 2026 14:43:22 +0200 Subject: [PATCH 4/7] jQUDT 1.5.4 --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 75a60f2..85aeec2 100644 --- a/pom.xml +++ b/pom.xml @@ -106,7 +106,7 @@ com.github.egonw jqudt - 1.5.2 + 1.5.4 com.github.stefanbirkner From eeeb1c6d5851a81a7e53dfcd82d99ba3b18cca9f Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Tue, 20 Oct 2026 14:53:17 +0200 Subject: [PATCH 5/7] Report JUnit results --- .github/workflows/maven.yml | 14 +++++++++++++- 1 file changed, 13 insertions(+), 1 deletion(-) diff --git a/.github/workflows/maven.yml b/.github/workflows/maven.yml index 1eb1017..0a7c64e 100644 --- a/.github/workflows/maven.yml +++ b/.github/workflows/maven.yml @@ -6,6 +6,11 @@ on: pull_request: branches: [ main ] +permissions: + contents: read + checks: write + pull-requests: write + jobs: build: runs-on: ubuntu-latest @@ -23,7 +28,14 @@ jobs: java-version: ${{ matrix.java }} - name: Build with Maven run: mvn clean install -Dgpg.skip -Dmaven.javadoc.skip=true - - name: push JaCoCo stats to codecov.io + - name: Publish Test Report + id: report + uses: mikepenz/action-junit-report@v6 + if: success() || failure() # always run even if the previous step fails + with: + report_paths: '**/target/surefire-reports/TEST-*.xml' + comment: true + - name: Push JaCoCo stats to codecov.io uses: codecov/codecov-action@v3 env: CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} From 2b488dac5b7712b6b09cd94f03772db3d4e946c7 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Tue, 20 Oct 2026 14:55:09 +0200 Subject: [PATCH 6/7] Release 2.0.8 --- CITATION.cff | 4 ++-- README.md | 4 ++-- pom.xml | 2 +- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index e528983..9ffcbf0 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -11,7 +11,7 @@ authors: given-names: Ammar orcid: https://orcid.org/0000-0002-8399-8990 title: NanoJava -version: 2.0.7 -date-released: 2026-05-18 +version: 2.0.8 +date-released: 2026-10-20 doi: 10.5281/zenodo.6984324 url: "https://github.com/enanomapper/nanojava" diff --git a/README.md b/README.md index 180e1d4..b50dd4d 100644 --- a/README.md +++ b/README.md @@ -53,11 +53,11 @@ If you do not have Docker or if it is an overhead for your use case, you can bun 4. Now, you will have the standalone jar file in the "target" folder named: - nanojava-2.0.7-jar-with-dependencies.jar + nanojava-2.0.8-jar-with-dependencies.jar 5. The JAR file is used in the same way as the Docker image in the "Usage" section with replacing: - "docker run" with "java -jar nanojava-2.0.7-jar-with-dependencies.jar" + "docker run" with "java -jar nanojava-2.0.8-jar-with-dependencies.jar" and make sure you provide the absolute paths for your files in this case. diff --git a/pom.xml b/pom.xml index 85aeec2..37bcf46 100644 --- a/pom.xml +++ b/pom.xml @@ -5,7 +5,7 @@ nanojava Java library extending the Chemistry Development Kit with functionality for nanomaterials. NanoJava - 2.0.8-SNAPSHOT + 2.0.8 https://github.com/enanomapper/nanojava From 258b0277c9e52aa487dfc16f2b7725bde6bba48d Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Tue, 20 Oct 2026 15:03:43 +0200 Subject: [PATCH 7/7] Some action version updates --- .github/workflows/maven.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/maven.yml b/.github/workflows/maven.yml index 0a7c64e..0847f49 100644 --- a/.github/workflows/maven.yml +++ b/.github/workflows/maven.yml @@ -20,9 +20,9 @@ jobs: name: Java ${{ matrix.java }} steps: - - uses: actions/checkout@v6 + - uses: actions/checkout@v7 - name: Set up Java - uses: actions/setup-java@v5 + uses: actions/setup-java@v6 with: distribution: temurin java-version: ${{ matrix.java }} @@ -36,6 +36,6 @@ jobs: report_paths: '**/target/surefire-reports/TEST-*.xml' comment: true - name: Push JaCoCo stats to codecov.io - uses: codecov/codecov-action@v3 + uses: codecov/codecov-action@v7 env: CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}