Update workflows for README badges

.github/workflows/build.yml

@@ -5,35 +5,110 @@ on: [push]
 jobs:
   build:
     runs-on: ubuntu-latest
-    
+
     steps:
 
     - name: Checkout the repo
-      uses: actions/checkout@v2
-    
+      uses: actions/checkout@v4
+
     - name: Set up JDK 1.8
-      uses: actions/setup-java@v1
+      uses: actions/setup-java@v3
       with:
-        java-version: 1.8
-
-    - name: Cache Gradle packages
-      uses: actions/cache@v2
+        java-version: '8'
+        distribution: 'corretto'
+
+    - name: Validate Gradle wrapper
+      uses: gradle/wrapper-validation-action@v1
+
+    - name: Setup Gradle
+      uses: gradle/gradle-build-action@v2
+
+    - name: Run Gradle build
+      run: |
+        ./gradlew build
+        rm build/reports/jacoco/test/html/jacoco-sessions.html
+
+    - name: Publish coverage report
+      if: ${{ github.ref == 'refs/heads/main' || github.ref == 'refs/heads/develop' }}
+      uses: JamesIves/github-pages-deploy-action@v4
       with:
-        path: ~/.gradle/caches
-        key: ${{ runner.os }}-gradle-${{ hashFiles('**/*.gradle') }}
-        restore-keys: ${{ runner.os }}-gradle
-
-    - name: Grant execute permission for gradlew
+        branch: gh-pages
+        folder: build/reports/jacoco/test/html
+        target-folder: _coverage
+
+    - name: Extract coverage percent
+      if: ${{ github.ref == 'refs/heads/main' || github.ref == 'refs/heads/develop' }}
       run: |
-        chmod +x gradlew
-    
-    - name: Test with Gradle
+        echo "COVERAGE=$(grep -oP '>\K([0-9]+)(?=%)' build/reports/jacoco/test/html/index.html | head -n 1)" >> $GITHUB_ENV
+
+    - name: Generate coverage badge
+      if: ${{ github.ref == 'refs/heads/main' || github.ref == 'refs/heads/develop' }}
+      uses: knightdave/[email protected]
+      with:
+        file: docs/_badges/coverage.svg
+        label: coverage
+        value: ${{ env.COVERAGE }}
+        value_format: "%d%%"
+        anybadge_args: 50=red 60=orange 80=yellow 100=green
+        template: docs/_badges/template.svg
+        overwrite: true
+
+    - name: Publish badge
+      if: ${{ github.ref == 'refs/heads/main' || github.ref == 'refs/heads/develop' }}
+      uses: JamesIves/github-pages-deploy-action@v4
+      with:
+        branch: gh-pages
+        folder: docs/_badges
+        target-folder: _badges
+        clean: false
+
+  result:
+    if: ${{ always() }}
+
+    runs-on: ubuntu-latest
+
+    needs: [build]
+
+    steps:
+
+    - name: Checkout the repo
+      uses: actions/checkout@v4
+
+    - name: Get build result
       run: |
-        ./gradlew test
-    
-    - name: Upload coverage to Codecov  
-      uses: codecov/codecov-action@v2
+        if [[ ${{ needs.build.result }} == "success" || ${{ needs.build.result }} == "skipped" ]]; then
+          exit 0
+        else
+          exit 1
+        fi
+
+    - name: Generate passing badge
+      if: success()
+      uses: knightdave/[email protected]
+      with:
+        file: docs/_badges/build.svg
+        label: build
+        value: passing
+        color: green
+        template: docs/_badges/template.svg
+        overwrite: true
+
+    - name: Generate failing badge
+      if: failure()
+      uses: knightdave/[email protected]
+      with:
+        file: docs/_badges/build.svg
+        label: build
+        value: failing
+        color: red
+        template: docs/_badges/template.svg
+        overwrite: true
+
+    - name: Publish badge
+      if: success() || failure()
+      uses: JamesIves/github-pages-deploy-action@v4
       with:
-        token: ${{ secrets.CODECOV_TOKEN }}
-        file: ./build/reports/jacoco/test/jacocoTestReport.xml
-        verbose: true
+        branch: gh-pages
+        folder: docs/_badges
+        target-folder: _badges
+        clean: false

.github/workflows/documentation.yml

@@ -3,7 +3,8 @@ name: documentation
 on:
   push:
     branches:
-      - master
+      - main
+      - develop
 
 jobs:
   documentation:
@@ -12,40 +13,83 @@ jobs:
     steps:
 
     - name: Checkout the repo
-      uses: actions/checkout@v2
-      with:
-        persist-credentials: false
-        fetch-depth: 0
+      uses: actions/checkout@v4
 
     - name: Set up JDK 1.8
-      uses: actions/setup-java@v1
+      uses: actions/setup-java@v3
       with:
-        java-version: 1.8
-
-    - name: Cache Gradle packages
-      uses: actions/cache@v2
+        java-version: '8'
+        distribution: 'corretto'
+
+    - name: Validate Gradle wrapper
+      uses: gradle/wrapper-validation-action@v1
+
+    - name: Setup Gradle
+      uses: gradle/gradle-build-action@v2
+
+    - name: Generate javadoc
+      run: ./gradlew javadoc
+
+    - name: Publish docs
+      uses: JamesIves/github-pages-deploy-action@v4
       with:
-        path: ~/.gradle/caches
-        key: ${{ runner.os }}-gradle-${{ hashFiles('**/*.gradle') }}
-        restore-keys: ${{ runner.os }}-gradle
-
-    - name: Grant execute permission for gradlew
-      run: |
-        chmod +x gradlew
-    
-    - name: Generate documentation with Gradle
-      run: |
-        ./gradlew javadoc
+        branch: gh-pages
+        folder: docs/javadoc
+        clean-exclude: |
+          _badges
+          _coverage
 
-    - name: Commit documentation changes
+    - name: Extract project version
       run: |
-        git add -f docs/
-        git config --local user.email "[email protected]"
-        git config --local user.name "GitHub Action"
-        git commit -m "Automated documentation updates"
-        
-    - name: Push changes
-      uses: ad-m/github-push-action@master
+        echo "VERSION=$(grep -oP 'version = "\K([0-9\.]+)(?=")' build.gradle)" >> $GITHUB_ENV
+
+    - name: Generate version badge
+      uses: knightdave/[email protected]
+      with:
+        file: docs/_badges/version.svg
+        label: version
+        value: v${{ env.VERSION }}
+        color: teal
+        template: docs/_badges/template.svg
+        overwrite: true
+
+    - name: Generate license badge
+      uses: knightdave/[email protected]
+      with:
+        file: docs/_badges/license.svg
+        label: license
+        value: BSD-3-Clause
+        color: yellowgreen
+        template: docs/_badges/template.svg
+        overwrite: true
+
+    - name: Generate passing badge
+      if: success()
+      uses: knightdave/[email protected]
+      with:
+        file: docs/_badges/documentation.svg
+        label: docs
+        value: passing
+        color: green
+        template: docs/_badges/template.svg
+        overwrite: true
+
+    - name: Generate failing badge
+      if: failure()
+      uses: knightdave/[email protected]
+      with:
+        file: docs/_badges/documentation.svg
+        label: docs
+        value: failing
+        color: red
+        template: docs/_badges/template.svg
+        overwrite: true
+
+    - name: Publish badge
+      if: success() || failure()
+      uses: JamesIves/github-pages-deploy-action@v4
       with:
-        github_token: ${{ secrets.GITHUB_TOKEN }}
-        branch: ${{ github.ref }}
+        branch: gh-pages
+        folder: docs/_badges
+        target-folder: _badges
+        clean: false

.github/workflows/lint.yml

@@ -15,9 +15,40 @@ jobs:
         fetch-depth: 0
 
     - name: Lint code base
-      uses: dbelyaev/action-checkstyle@master
+      uses: dbelyaev/action-checkstyle@v0.9.5
       with:
         github_token: ${{ secrets.GITHUB_TOKEN }}
         reporter: github-check
         checkstyle_config: .github/config/checks.xml
         fail_on_error: true
+
+    - name: Generate passing badge
+      if: success()
+      uses: knightdave/[email protected]
+      with:
+        file: docs/_badges/lint.svg
+        label: lint
+        value: passing
+        color: green
+        template: docs/_badges/template.svg
+        overwrite: true
+
+    - name: Generate failing badge
+      if: failure()
+      uses: knightdave/[email protected]
+      with:
+        file: docs/_badges/lint.svg
+        label: lint
+        value: failing
+        color: red
+        template: docs/_badges/template.svg
+        overwrite: true
+
+    - name: Publish badge
+      if: success() || failure()
+      uses: JamesIves/github-pages-deploy-action@v4
+      with:
+        branch: gh-pages
+        folder: docs/_badges
+        target-folder: _badges
+        clean: false

.gitignore

@@ -8,7 +8,7 @@
 bin/
 lib/
 build/
-docs/
+docs/javadoc
 working/
 .DS_Store
 MANIFEST.MF

README.md

@@ -2,9 +2,11 @@
 
 ## Agent-based model of heterogeneous cell populations in dynamic microenvironments
 
-[![Build Status](https://github.com/bagherilab/ARCADE/workflows/build/badge.svg)](https://github.com/bagherilab/ARCADE/actions?query=workflow%3Abuild)
-[![Documentation](https://github.com/bagherilab/ARCADE/workflows/documentation/badge.svg)](https://bagherilab.github.io/ARCADE/javadoc/overview-summary.html)
-[![Codecov](https://img.shields.io/codecov/c/gh/bagherilab/ARCADE/v3.1)](https://codecov.io/gh/bagherilab/ARCADE)
-[![Lint Status](https://github.com/bagherilab/ARCADE/workflows/lint/badge.svg)](https://github.com/bagherilab/ARCADE/actions?query=workflow%3Alint)
+[![Build status](https://bagherilab.github.io/ARCADE/_badges/build.svg)](https://github.com/bagherilab/ARCADE/actions?query=workflow%3Abuild)
+[![Lint status](https://bagherilab.github.io/ARCADE/_badges/lint.svg)](https://github.com/bagherilab/ARCADE/actions?query=workflow%3Alint)
+[![Documentation](https://bagherilab.github.io/ARCADE/_badges/documentation.svg)](https://bagherilab.github.io/ARCADE/)
+[![Coverage](https://bagherilab.github.io/ARCADE/_badges/coverage.svg)](https://bagherilab.github.io/ARCADE/_coverage/)
+![Version](https://bagherilab.github.io/ARCADE/_badges/version.svg)
+[![License](https://bagherilab.github.io/ARCADE/_badges/license.svg)](https://github.com/bagherilab/ARCADE/blob/develop/LICENSE)
 
 ARCADE v2 is licensed under GPL 3. ARCADE v3+ is licensed under BSD 3-Clause.

build.gradle

@@ -3,7 +3,7 @@ plugins {
     id "jacoco"
 }
 
-version = "3.1"
+version = "3.1.1"
 sourceCompatibility = 1.8
 
 repositories {