Merge pull request #10 from BIOP/qp0.6.0

Migration to QuPath-0.6.0

Author: Rdornier

.github/workflows/build.yml

@@ -0,0 +1,26 @@
+name: Run gradle build
+
+on:
+  pull_request:
+    branches:
+      - "main"
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+jobs:
+  prepare:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Grant execute permission for gradlew
+        run: chmod +x gradlew
+      - name: Upload workspace
+        uses: actions/upload-artifact@v4
+        with:
+          name: workspace
+          path: .
+  build:
+    needs: prepare
+    uses: qupath/actions/.github/workflows/gradle.yml@main

.github/workflows/github_release.yml

@@ -0,0 +1,10 @@
+name: Make draft release
+
+on:
+  workflow_dispatch:
+
+jobs:
+  build:
+    permissions:
+      contents: write
+    uses: qupath/actions/.github/workflows/github-release.yml@main

.github/workflows/gradle.yml

@@ -0,0 +1,55 @@
+name: Publish to SciJava Maven (Root)
+
+on:
+  workflow_dispatch:
+  workflow_call:
+    inputs:
+      release:
+        required: false
+        type: boolean
+        default: false
+
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-java@v4
+        with:
+          java-version: '21'
+          distribution: 'temurin'
+
+      - name: Setup Gradle
+        uses: gradle/actions/setup-gradle@v4
+
+      - name: Add release flag if input variable is set
+        if: ${{ inputs.release }}
+        shell: bash
+        run: |
+          echo "RELEASE_FLAG='-Prelease'" >> $GITHUB_ENV
+
+      - name: Publish release
+        if: ${{ inputs.release }}
+        shell: bash
+        run: |
+          ./gradlew publish -Ptoolchain=21 -Prelease ${{ inputs.gradle-args }}
+        env:
+          MAVEN_USER: ${{ secrets.MAVEN_USER }}
+          MAVEN_PASS: ${{ secrets.MAVEN_PASS }}
+
+      - name: Publish snapshot
+        if: ${{ inputs.release == false }}
+        shell: bash
+        run: |
+          ./gradlew publish -Ptoolchain=21 ${{ inputs.gradle-args }}
+        env:
+          MAVEN_USER: ${{ secrets.MAVEN_USER }}
+          MAVEN_PASS: ${{ secrets.MAVEN_PASS }}
+
+      - uses: actions/upload-artifact@v4
+        if: ${{ inputs.release }}
+        with:
+          name: ${{ github.event.repository.name }}-release-jar
+          path: build/libs
+          retention-days: 7

.github/workflows/maven.yml

@@ -4,18 +4,9 @@ on:
   workflow_dispatch:
 
 jobs:
-  publish:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-java@v2
-        with:
-          java-version: '17'
-          distribution: 'adopt-hotspot'
-      - name: Grant execute permission for gradlew
-        run: chmod +x gradlew
-      - name: Publish package
-        run: ./gradlew publish -P toolchain=17 -P release=true
-        env:
-          MAVEN_USER: ${{ secrets.MAVEN_USER }}
-          MAVEN_PASS: ${{ secrets.MAVEN_PASS }}
+  build:
+    name: Publish release
+    uses: ./.github/workflows/maven.yml
+    secrets: inherit
+    with:
+      release: true

.github/workflows/publish-release.yml

@@ -4,25 +4,7 @@ on:
   workflow_dispatch:
 
 jobs:
-  publish:
-
-    runs-on: ubuntu-latest
-
-    steps:
-      - uses: actions/checkout@v3
-      - name: Set up JDK 17
-        uses: actions/setup-java@v3
-        with:
-          java-version: '17'
-          distribution: 'temurin'
-      - name: Make gradlew executable
-        run: chmod +x ./gradlew
-      - name: Validate Gradle wrapper
-        uses: gradle/wrapper-validation-action@v1
-      - name: Publish snapshot
-        uses: gradle/gradle-build-action@v2.4.2
-        with:
-          arguments: publish
-        env:
-          MAVEN_USER: ${{ secrets.MAVEN_USER }}
-          MAVEN_PASS: ${{ secrets.MAVEN_PASS }}
+  build:
+    name: Publish snapshot
+    uses: ./.github/workflows/maven.yml
+    secrets: inherit

.github/workflows/publish-snapshot.yml

@@ -0,0 +1,33 @@
+name: Update gradle version
+
+on:
+  workflow_dispatch:
+    inputs:
+      gradle-version:
+        description: Gradle version
+        default: latest
+        type: string
+        required: false
+
+jobs:
+  update:
+    env:
+      GH_TOKEN: ${{ github.token }}
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash
+    steps:
+      - uses: actions/checkout@v4
+      - name: Update gradlew
+        run: |
+          ./gradlew wrapper --gradle-version ${{ inputs.gradle-version }}
+      - name: Commit and push
+        run: |
+          git config user.name "github-actions[bot]"
+          git config user.email "github-actions[bot]@users.noreply.github.com"
+          git checkout -b gradle-update
+          git add .
+          git commit --allow-empty -m "Update gradle via qupath/actions/.github/workflows/update-gradle.yml"
+          git push -u origin gradle-update
+          gh pr create --title "Update gradle via actions" --body "$(./gradlew --version)"

.github/workflows/update-gradle.yml

@@ -8,7 +8,7 @@ Zenodo DOI: [![DOI](https://zenodo.org/badge/417468733.svg)](https://doi.org/10.
 This repo adds some support to use [Spotiflow](https://github.com/weigertlab/spotiflow) within QuPath through a Python virtual environment.
 
 > [!WARNING]
-> This extension is developed for QuPath 0.5.x
+> This extension is developed for QuPath 0.6.x
 
 
 # Citing
@@ -24,13 +24,14 @@ As this code is neither novel nor entirely original, there is no linked publicat
 ## Code authorship
 **Author**: Rémy Dornier (1)
 
-**Contributors**: Olivier Burri (1), Nicolas Chiaruttini (1), Romain Guiet (1)
+**Contributors**: Albert Dominguez Mantes (2), Olivier Burri (1), Nicolas Chiaruttini (1), Romain Guiet (1)
 
 This code heavily mirrors functions and design implemented in [QuPath Cellpose](https://github.com/BIOP/qupath-extension-cellpose).
 
 **Affiliations**
 
 (1) EPFL BioImaging and Optics Platform (BIOP)
+(2) EPFL Weigert Lab
 
 ### If you use this extension, you should cite the following publications
 
@@ -92,11 +93,27 @@ On macOS or Linux:
 where `{HOME}` will be the location of your home directory, typically `/Users/user-name/` on macOS or `/home/user-name/` on Linux.
 
 ## Step 2: Install the QuPath Spotiflow extension
+### On QuPath 0.6.x
 
-Download the latest `qupath-extension-spotiflow-[version].jar` file from [releases](https://github.com/biop/qupath-extension-spotiflow/releases) and unzip it into your `extensions` directory. 
+- Open QuPath
+- Go under `Extensions -> Manage extensions`
+- Expand the `QuPath-BIOP catalog`
 
-If your extensions directory is unset, drag & drop `qupath-extension-spotiflow-[version].jar` onto the main QuPath window. You'll be prompted to select a QuPath user directory.
-The extension will then be copied to a location inside that directory.
+> Note: if you don't have the **QuPath-BIOP-catalog** installed, please follow the [catalog installation steps](https://github.com/BIOP/qupath-biop-catalog?tab=readme-ov-file#installation)
+
+- Search for `QuPath Spotiflow extension` and click on the green button
+- Select the latest version
+- Click on `Install`
+
+> Note: If you need to update the extension, click on the ⚙️ button and select the latest version to install.
+
+### On QuPath 0.5.x
+
+Download the latest `qupath-extension-spotiflow-[version].jar` file from [releases](https://github.com/biop/qupath-extension-spotiflow/releases) and copy it into your extensions directory.
+
+If your extensions directory is unset, drag & drop `qupath-extension-spotiflow-[version].jar` onto the main QuPath window. 
+You'll be prompted to select a QuPath user directory. The extension will then be copied to a location inside that directory.
+You finally need to restart QuPath.
 
 <!--
 To copy `run-cellpose-qc.py`, go to Extensions > Installed Extensions and click on "Open Extensions Directory". You can place the `run-cellpose-qc.py` in the same folder.
@@ -147,7 +164,7 @@ Running Spotiflow is done via a script and is very similar to the excellent [QuP
 
 You can find a template in QuPath in
 
-`Extensions > Spotiflow > Spotiflow detection script template`
+`Extensions > Spotiflow > Spotiflow detection template`
 
 Or you can download the [Spotiflow_detection_template.groovy](src/main/resources/scripts/Spotiflow_detection_template.groovy) script from this repo and open it in the QuPath script editor.  
 
@@ -156,7 +173,7 @@ Or you can download the [Spotiflow_detection_template.groovy](src/main/resources
 
 ### Getting all available arguments
 
-All builder options that are implemented are documented [in the Javadoc](https://biop.github.io/qupath-extension-spotiflow/).
+All builder options that are implemented are documented [in the Javadoc](https://biop.github.io/qupath-extension-spotiflow/qupath/ext/biop/spotiflow/SpotiflowBuilder.html).
 You can pass additional options to `spotiflow` by adding `.addParameter()` before the `.build()` line. 
 
 To get the available additional arguments, call the help from the `spotiflow` object using `spotiflow.helpPredict()`