Gradle plugin example

Signed-off-by: Tom Sellman <[email protected]>

Author: tom-seqera

Makefile

@@ -1,72 +1,21 @@
-
-config ?= compileClasspath
-
-ifdef module 
-mm = :${module}:
-else 
-mm = 
-endif 
+# Build the plugin
+assemble:
+	./gradlew assemble
 
 clean:
 	rm -rf .nextflow*
 	rm -rf work
 	rm -rf build
-	rm -rf plugins/*/build
 	./gradlew clean
 
-compile:
-	./gradlew :nextflow:exportClasspath compileGroovy
-	@echo "DONE `date`"
-
-
-check:
-	./gradlew check
-
-
-#
-# Show dependencies try `make deps config=runtime`, `make deps config=google`
-#
-deps:
-	./gradlew -q ${mm}dependencies --configuration ${config}
-
-deps-all:
-	./gradlew -q dependencyInsight --configuration ${config} --dependency ${module}
-
-#
-# Refresh SNAPSHOTs dependencies
-#
-refresh:
-	./gradlew --refresh-dependencies 
-
-#
-# Run all tests or selected ones
-#
+# Run plugin unit tests
 test:
-ifndef class
-	./gradlew ${mm}test
-else
-	./gradlew ${mm}test --tests ${class}
-endif
-
-assemble:
-	./gradlew assemble
-
-#
-# generate build zips under build/plugins
-# you can install the plugin copying manually these files to $HOME/.nextflow/plugins
-#
-buildPlugins:
-	./gradlew copyPluginZip
-
-#
-# Upload JAR artifacts to Maven Central
-#
-upload:
-	./gradlew upload
-
+	./gradlew test
 
-upload-plugins:
-	./gradlew plugins:upload
+# Install the plugin into local nextflow plugins dir
+install:
+	./gradlew install
 
-publish-index:
-	./gradlew plugins:publishIndex
+# Publish the plugin
+release:
+	./gradlew releasePlugin

README.md

@@ -1,114 +1,79 @@
-# nf-hello plugin 
- 
+# nf-hello plugin
+
 This project contains a simple Nextflow plugin called `nf-hello` which provides examples of different plugin extensions:
 
 - A custom trace observer that prints a message when the workflow starts and when the workflow completes
 - A custom channel factory called `reverse`
 - A custom operator called `goodbye`
 - A custom function called `randomString`
 
-NOTE: If you want to use this project as a starting point for a custom plugin, you must rename the `plugins/nf-hello` folder and update `settings.gradle` with your plugin name.
+NOTE: If you want to use this project as a starting point for a custom plugin, you must rename the `plugins/nf-hello`
+folder and update `settings.gradle` with your plugin name.
 
-See the [Nextflow documentation](https://nextflow.io/docs/latest/plugins.html) for more information about developing plugins.
+See the [Nextflow documentation](https://nextflow.io/docs/latest/plugins.html) for more information about developing
+plugins.
 
 ## Plugin structure
-                    
-- `settings.gradle`
-    
-    Gradle project settings. 
-
-- `plugins/nf-hello`
-    
-    The plugin implementation base directory.
-
-- `plugins/nf-hello/build.gradle` 
-    
-    Plugin Gradle build file. Project dependencies should be added here.
 
-- `plugins/nf-hello/src/resources/META-INF/MANIFEST.MF` 
-    
-    Manifest file defining the plugin attributes e.g. name, version, etc. The attribute `Plugin-Class` declares the plugin main class. This class should extend the base class `nextflow.plugin.BasePlugin` e.g. `nextflow.hello.HelloPlugin`.
+- `settings.gradle`
 
-- `plugins/nf-hello/src/resources/META-INF/extensions.idx`
-    
-    This file declares one or more extension classes provided by the plugin. Each line should contain the fully qualified name of a Java class that implements the `org.pf4j.ExtensionPoint` interface (or a sub-interface).
+  Gradle project settings.
 
-- `plugins/nf-hello/src/main` 
+- `src/main`
 
-    The plugin implementation sources.
+  The plugin implementation sources.
 
-- `plugins/nf-hello/src/test` 
+- `src/test`
 
-    The plugin unit tests. 
+  The plugin unit tests.
 
 ## Plugin classes
 
 - `HelloConfig`: shows how to handle options from the Nextflow configuration
 
-- `HelloExtension`: shows how to create custom channel factories, operators, and fuctions that can be included into pipeline scripts
+- `HelloExtension`: shows how to create custom channel factories, operators, and fuctions that can be included into
+  pipeline scripts
 
 - `HelloFactory` and `HelloObserver`: shows how to react to workflow events with custom behavior
 
 - `HelloPlugin`: the plugin entry point
 
-## Unit testing 
-
-To run your unit tests, run the following command in the project root directory (ie. where the file `settings.gradle` is located):
+## Building
 
+To compile and assemble the plugin, run the following command in the project root directory:
 ```bash
-./gradlew check
+make assemble
 ```
 
-## Testing and debugging
-
-To build and test the plugin during development, configure a local Nextflow build with the following steps:
+## Unit testing
 
-1. Clone the Nextflow repository in your computer into a sibling directory:
-    ```bash
-    git clone --depth 1 https://github.com/nextflow-io/nextflow ../nextflow
-    ```
-  
-2. Configure the plugin build to use the local Nextflow code:
-    ```bash
-    echo "includeBuild('../nextflow')" >> settings.gradle
-    ```
-  
-   (Make sure to not add it more than once!)
-
-3. Compile the plugin alongside the Nextflow code:
-    ```bash
-    make assemble
-    ```
-
-4. Run Nextflow with the plugin, using `./launch.sh` as a drop-in replacement for the `nextflow` command, and adding the option `-plugins nf-hello` to load the plugin:
-    ```bash
-    ./launch.sh run nextflow-io/hello -plugins nf-hello
-    ```
+To run your unit tests, run the following command in the project root directory:
+```bash
+make test
+```
 
-## Testing without Nextflow build
+## Testing with Nextflow
 
-The plugin can be tested without using a local Nextflow build using the following steps:
+The plugin can be tested without a local Nextflow installation:
 
-1. Build the plugin: `make buildPlugins`
-2. Copy `build/plugins/<your-plugin>` to `$HOME/.nextflow/plugins`
-3. Create a pipeline that uses your plugin and run it: `nextflow run ./my-pipeline-script.nf`
+1. Build and install the plugin to your local Nextflow installation: `make install`
+2. Create a pipeline that uses your plugin and run it: `nextflow run ./my-pipeline-script.nf`
 
 ## Package, upload, and publish
 
-The project should be hosted in a GitHub repository whose name matches the name of the plugin, that is the name of the directory in the `plugins` folder (e.g. `nf-hello`).
-
 Follow these steps to package, upload and publish the plugin:
 
-1. Create a file named `gradle.properties` in the project root containing the following attributes (this file should not be committed to Git):
+1. In `build.gradle` make sure that
+    * `github.repository` matches the repository of the plugin
+    * `github.indexUrl` points to your fork of the plugins index repository.
+
+2. Create a file named `$HOME/.gradle/gradle.properties`, where $HOME is your home directory. Add the following properties:
 
-   * `github_organization`: the GitHub organisation where the plugin repository is hosted.
-   * `github_username`: The GitHub username granting access to the plugin repository.
-   * `github_access_token`: The GitHub access token required to upload and commit changes to the plugin repository.
-   * `github_commit_email`: The email address associated with your GitHub account.
+    * `github_username`: The GitHub username granting access to the plugin repository.
+    * `github_access_token`: The GitHub access token required to upload and commit changes to the plugin repository.
+    * `github_commit_email`: The email address associated with your GitHub account.
 
-2. Use the following command to package and create a release for your plugin on GitHub:
-    ```bash
-    ./gradlew :plugins:nf-hello:upload
-    ```
+3. Use the following command to package and create a release for your plugin on GitHub: `make release`
 
-3. Create a pull request against [nextflow-io/plugins](https://github.com/nextflow-io/plugins/blob/main/plugins.json) to make the plugin accessible to Nextflow.
+4. Create a pull request against [nextflow-io/plugins](https://github.com/nextflow-io/plugins/blob/main/plugins.json) to
+   make the plugin accessible to Nextflow.

build.gradle

@@ -0,0 +1,30 @@
+plugins {
+    id 'io.nextflow.nextflow-plugin' version '0.0.1-alpha'
+}
+
+// plugin version
+version = '0.6.0'
+
+nextflowPlugin {
+    // minimum nextflow version
+    nextflowVersion = '24.11.0-edge'
+
+    // plugin metadata
+    provider = 'nextflow'
+    className = 'nextflow.hello.HelloPlugin'
+    extensionPoints = [
+        'nextflow.hello.HelloFactory',
+        'nextflow.hello.HelloExtension'
+    ]
+
+    publishing {
+        github {
+            repository = 'nextflow-io/nf-hello'
+            userName = project.findProperty('github_username')
+            authToken = project.findProperty('github_access_token')
+            email = project.findProperty('github_commit_email')
+
+            indexUrl = 'https://github.com/nextflow-io/plugins/blob/main/plugins.json'
+        }
+    }
+}

buildSrc/build.gradle

@@ -1,5 +1,7 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-8.4-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.10.2-bin.zip
+networkTimeout=10000
+validateDistributionUrl=true
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists