Merge branch 'master' into fix-release-docker

.dvc/config

@@ -3,3 +3,5 @@
     remote = aws
 ['remote "aws"']
     url = s3://ml-storage-dvc/grobid-superconductors/
+    version_aware = true
+    region = eu-central-1

.github/workflows/ci-build-release.yml

@@ -2,14 +2,14 @@ name: Build release
 
 on:
   push:
-    branches: 
+    branches:
       - main
       - master
     tags:
       - 'v*'
   pull_request:
     branches: [ main ]
-    
+
 concurrency:
   group: docker
   cancel-in-progress: true
@@ -19,17 +19,26 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v1
-      - name: Set up JDK 11
-        uses: actions/setup-java@v1
+      - uses: actions/checkout@v3
+      - name: Set up JDK 17
+        uses: actions/setup-java@v4
         with:
-          java-version: 1.11
+          java-version: '17.0.10+7'
+          distribution: 'temurin'
+          cache: 'gradle'
       - name: Build with Gradle
         run: ./gradlew build -x test
 
       - name: Test with Gradle Jacoco and Coveralls
         run: ./gradlew test jacocoTestReport coveralls --no-daemon
 
+      - name: Coveralls GitHub Action
+        uses: coverallsapp/github-action@v2
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          format: jacoco
+
+
   docker-build:
     needs: [build]
     runs-on: ubuntu-latest
@@ -50,6 +59,8 @@ jobs:
           fi
           echo "TAGS=${TAGS}"
           echo ::set-output name=tags::${TAGS}
+      - name: Create more disk space
+        run: sudo rm -rf /usr/share/dotnet && sudo rm -rf /opt/ghc && sudo rm -rf "/usr/local/share/boost" && sudo rm -rf "$AGENT_TOOLSDIRECTORY"
       - uses: actions/checkout@v2
       - name: Build and push
         id: docker_build

.github/workflows/ci-build-unstable.yml

@@ -12,34 +12,49 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v1
-    - name: Set up JDK 11
-      uses: actions/setup-java@v1
+    - uses: actions/checkout@v4
+    - name: Set up JDK 17
+      uses: actions/setup-java@v4
       with:
-        java-version: 1.11
+        java-version: '17.0.10+7'
+        distribution: 'temurin'
+        cache: 'gradle'
     - name: Build with Gradle
       run: ./gradlew build -x test
 
     - name: Test with Gradle Jacoco and Coveralls
       run: ./gradlew test jacocoTestReport coveralls --no-daemon
 
-#    - name: Coveralls GitHub Action
-#      uses: coverallsapp/[email protected]
-#      with:
-#        github-token: ${{ secrets.GITHUB_TOKEN }}
+    - name: Coveralls GitHub Action
+      uses: coverallsapp/github-action@v2
+      with:
+        github-token: ${{ secrets.GITHUB_TOKEN }}
+        format: jacoco
 
-  docker-build:
-    needs: [build]
 
-    runs-on: self-hosted
+  docker-build:
+    needs: [ build ]
+    runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v2
-      - name: set up proxy http
-        run: echo -e "systemProp.http.proxyHost=wwwout.nims.go.jp\nsystemProp.http.proxyPort=8888\nsystemProp.http.nonProxyHosts=*.nims.go.jp,localhost\n\nsystemProp.https.proxyHost=wwwout.nims.go.jp\nsystemProp.https.proxyPort=8888\nsystemProp.https.nonProxyHosts=*.nims.go.jp,localhost" >> gradle.properties
-      - name: check result proxy
-        run: cat gradle.properties
-      - name: Build the Docker image
-        run: docker build . --file Dockerfile --tag lfoppiano/grobid-superconductors:latest
-      - name: Cleanup older than 24h images and containers
-        run: docker system prune --filter "until=24h" --force
+      - name: Create more disk space
+        run: |
+            sudo rm -rf /usr/share/dotnet 
+            sudo rm -rf /opt/ghc 
+            sudo rm -rf "/usr/local/share/boost" 
+            sudo rm -rf "$AGENT_TOOLSDIRECTORY"
+            sudo rm -rf /opt/hostedtoolcache
+      - uses: actions/checkout@v4
+      - name: Build and push
+        id: docker_build
+        uses: mr-smithers-excellent/docker-build-push@v6
+        with:
+          dockerfile: Dockerfile
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+          image: lfoppiano/grobid-superconductors
+          registry: docker.io
+          pushImage: ${{ github.event_name != 'pull_request' }}
+          tags: latest-develop
+      - name: Image digest
+        run: echo ${{ steps.docker_build.outputs.digest }}

.github/workflows/ci-integration-manual.yml

@@ -0,0 +1,32 @@
+name: Run integration tests manually
+
+on:
+  push:
+    branches:
+      - master
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout grobid home
+      uses: actions/checkout@v4
+      with:
+        repository: kermitt2/grobid
+        path: ./grobid
+    - name: Checkout grobid-superconductors
+      uses: actions/checkout@v4
+      with:
+        path: ./grobid/grobid-superconductors
+    - name: Set up JDK 17
+      uses: actions/setup-java@v4
+      with:
+        java-version: '17.0.10+7'
+        distribution: 'temurin'
+        cache: 'gradle'
+    - name: Build and run integration tests
+      working-directory: ./grobid/grobid-superconductors
+      run: ./gradlew copyModels integration --no-daemon
+

.java-version

@@ -1 +1 @@
-11.0
+17.0

CITATION.cff

@@ -0,0 +1,54 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+authors:
+- family-names: "Foppiano"
+  given-names: "Luca"
+  orcid: "https://orcid.org/0000-0002-6114-6164"
+- family-names: "de Castro"
+  given-names: "Pedro Baptista"
+  orcid: "https://orcid.org/0000-0001-8673-2840"
+- family-names: "Ortiz Suarez"
+  given-names: "Pedro"
+  orcid: "https://orcid.org/0000-0003-0343-8852"
+- family-names: "Terashima"
+  given-names: "Kensei"
+  orcid: "https://orcid.org/0000-0003-0375-3043"
+- family-names: "Takano"
+  given-names: "Yoshihiko"
+  orcid: "https://orcid.org/0000-0002-1541-6928"
+- family-names: "Ishii"
+  given-names: "Masashi"
+  orcid: "https://orcid.org/0000-0003-0357-2832"
+title: "grobid-superconductors"
+version: 2.0.4
+url: "https://github.com/lfoppiano/grobid-superconductors"
+preferred-citation:
+  type: article
+  authors:
+  - family-names: "Foppiano"
+    given-names: "Luca"
+    orcid: "https://orcid.org/0000-0002-6114-6164"
+  - family-names: "de Castro"
+    given-names: "Pedro Baptista"
+    orcid: "https://orcid.org/0000-0001-8673-2840"
+  - family-names: "Ortiz Suarez"
+    given-names: "Pedro"
+    orcid: "https://orcid.org/0000-0003-0343-8852"
+  - family-names: "Terashima"
+    given-names: "Kensei"
+    orcid: "https://orcid.org/0000-0003-0375-3043"
+  - family-names: "Takano"
+    given-names: "Yoshihiko"
+    orcid: "https://orcid.org/0000-0002-1541-6928"
+  - family-names: "Ishii"
+    given-names: "Masashi"
+    orcid: "https://orcid.org/0000-0003-0357-2832"
+  doi: "10.1080/27660400.2022.2153633"
+  journal: " Science and Technology of Advanced Materials: Methods"
+  month: 1
+#   start: 1 # First page number
+#   end: 10 # Last page number
+  title: "Automatic extraction of materials and properties from superconductors scientific literature"
+  issue: 1
+  volume: 3
+  year: 2023