Action to publish packages to mzio (#2285)

* add publish actions to upload packages in mzio repo

* update publish actions

* update publish actions

* publish locally for testing

use
./gradlew convention-plugins:java-convention:publish
for convention plugins

* update action to publish convention plugins

* update publish task names

* make publish tasks publish on github

* add centralised publishing config

* update package names

* review

.github/workflows/gradle_release.yml

@@ -42,5 +42,3 @@ jobs:
           prerelease: true
           title: "Release build"
           files: build/*/*
-
-

.github/workflows/push_stable_packages.yml

@@ -0,0 +1,38 @@
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+# GitHub recommends pinning actions to a commit SHA.
+# To get a newer version, you will need to update the SHA.
+# You can also reference a tag or branch, but the action may change without warning.
+
+name: Publish packages to GitHub Packages
+on:
+  workflow_dispatch
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-java@v4
+        with:
+          java-version: '22.0.1'
+          distribution: 'temurin'
+      - name: Setup Gradle
+        uses: gradle/actions/setup-gradle@af1da67850ed9a4cedd57bfd976089dd991e2582 # v4.0.0
+
+      - name: Publish mzmine packages
+        run: ./gradlew publish
+        env:
+          PUBLISH_PACKAGE_USERNAME: ${{ secrets.PUBLISH_PACKAGE_USERNAME }}
+          PUBLISH_PACKAGE_TOKEN: ${{ secrets.PUBLISH_PACKAGE_TOKEN }}
+      - name: Publish convention plugins
+        run: ./gradlew convention-plugins:java-convention:publish
+        env:
+          PUBLISH_PACKAGE_USERNAME: ${{ secrets.PUBLISH_PACKAGE_USERNAME }}
+          PUBLISH_PACKAGE_TOKEN: ${{ secrets.PUBLISH_PACKAGE_TOKEN }}

build.gradle.kts

@@ -0,0 +1,40 @@
+plugins {
+    `maven-publish`
+}
+
+// list of sub projects that create a java library
+val publishingSubProjects = listOf(
+    "convention-plugins",
+    "java-convention",
+    "javafx-framework",
+    "mzmine-community",
+    "taskcontroller",
+    "utils"
+)
+
+
+subprojects {
+    // this variable is set by running .\gradlew publish with the command line argument -Pmziorepo=true
+    val pushOnline: Boolean = project.findProperty("mziorepo")?.toString()?.toBoolean() ?: false
+    if(name in publishingSubProjects) {
+        apply(plugin = "maven-publish")
+
+        publishing {
+            repositories {
+                if (pushOnline) {
+                    maven {
+                        url = uri("https://maven.pkg.github.com/mzio-gmbh/mzio_mzmine")
+                        credentials {
+                            username = System.getenv("PUBLISH_PACKAGE_USERNAME")
+                            password = System.getenv("PUBLISH_PACKAGE_TOKEN")
+                        }
+                    }
+                } else {
+                    maven {
+                        url = uri(layout.projectDirectory.dir("../local-repo/"))
+                    }
+                }
+            }
+        }
+    }
+}

convention-plugins/README.MD

@@ -10,4 +10,9 @@ https://docs.gradle.org/current/samples/sample_building_java_applications_multi_
 
 https://docs.gradle.org/current/samples/sample_convention_plugins.html
 
-https://docs.gradle.org/current/samples/sample_sharing_convention_plugins_with_build_logic.html
+https://docs.gradle.org/current/samples/sample_sharing_convention_plugins_with_build_logic.html
+
+
+## Version
+
+The version of this project is bound to the mzmine community version.

convention-plugins/java-convention/build.gradle.kts

@@ -1,11 +1,62 @@
 plugins {
     `kotlin-dsl`
+    id("maven-publish")
+    alias(libs.plugins.semver)
 }
 
+semver {
+    properties = "../../mzmine-community/src/main/resources/mzmineversion.properties"
+}
+
+// this variable is set by running .\gradlew publish with the command line argument -Pmziorepo=true
+val pushOnline: Boolean = project.findProperty("mziorepo")?.toString()?.toBoolean() ?: false
+
+
 kotlin {
     jvmToolchain(21)
 }
 
 dependencies {
     implementation(libs.javafx.plugin)
 }
+
+afterEvaluate {
+    // the repositories must be set in the afterEvaluate block, because the semver plugin will
+    // not be initialised otherwise. The convention plugin version is bound to the mzmine community version.
+    publishing {
+        repositories {
+            if (pushOnline) {
+                maven {
+                    url = uri("https://maven.pkg.github.com/mzio-gmbh/mzio_mzmine")
+                    credentials {
+                        username = System.getenv("PUBLISH_PACKAGE_USERNAME")
+                        password = System.getenv("PUBLISH_PACKAGE_TOKEN")
+                    }
+                }
+            } else {
+                maven {
+                    url = uri(layout.projectDirectory.dir("../../local-repo/"))
+                }
+            }
+        }
+        publications {
+            register<MavenPublication>("publish-convention-plugins") {
+                from(components["java"])
+                pom {
+                    group = "io.github.mzmine"
+                    artifactId = "convention-plugins"
+                    name = "mzmine-community convention-plugins"
+                    description = "mzmine-community convention plugins"
+                    url = "https://github.com/mzmine/mzmine"
+                    version = semver.version
+                    developers {
+                        developer {
+                            id = "mzmine"
+                            name = "mzmine"
+                        }
+                    }
+                }
+            }
+        }
+    }
+}

javafx-framework/build.gradle.kts

@@ -1,6 +1,33 @@
+/*
+ * Copyright (c) 2004-2024 The mzmine Development Team
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
 plugins {
     id("io.github.mzmine.java-library-conv")
     id("io.github.mzmine.javafx-conv")
+    id("maven-publish")
+    alias(libs.plugins.semver)
 }
 
 repositories {
@@ -16,4 +43,34 @@ dependencies {
     implementation("io.mzio:memory-management:1.0.0")
     implementation("io.mzio:taskcontroller:1.0.0")
     implementation(libs.guava)
-}
+}
+
+semver {
+    properties = "../mzmine-community/src/main/resources/mzmineversion.properties"
+}
+
+afterEvaluate {
+    // the repositories must be set in the afterEvaluate block, because the semver plugin will
+    // not be initialised otherwise. The version of this library is bound to the mzmine community version.
+    publishing {
+        publications {
+            register<MavenPublication>("publish-javafx-framework") {
+                from(components["java"])
+                pom {
+                    group = "io.github.mzmine"
+                    artifactId = "javafx-framework"
+                    name = "mzmine-javafx-framework"
+                    description = "mzmine-community java fx framework"
+                    url = "https://github.com/mzmine/mzmine"
+                    version = semver.version
+                    developers {
+                        developer {
+                            id = "mzmine"
+                            name = "mzmine"
+                        }
+                    }
+                }
+            }
+        }
+    }
+}

mzmine-community/build.gradle

@@ -45,6 +45,9 @@ plugins {
     // https://github.com/ethauvin/semver-gradle
     alias(libs.plugins.semver)
     alias(libs.plugins.licensereport)
+
+    id("maven-publish")
+    id("version-catalog")
 }
 
 // save version to main resources
@@ -53,7 +56,14 @@ plugins {
 // version with -beta is currently not supported by jpackage (maybe windows --app-version)
 // java.lang.IllegalArgumentException: "Version [3.0.0-beta] contains invalid component [0-beta]"
 semver {
-    properties = "src/main/resources/mzmineversion.properties"
+    def versionFile = getLayout().getProjectDirectory().dir("src/main/resources").file("mzmineversion.properties").getAsFile()
+    properties = versionFile.toString()
+}
+
+catalog {
+    versionCatalog {
+        from(files("$rootDir/gradle/libs.versions.toml"))
+    }
 }
 
 // version is now in version.properties
@@ -611,3 +621,36 @@ tasks.compileJava.dependsOn(checkLicense, copyLicenseInformationToResources, cop
 // copying must be finished before packaging
 tasks.processResources.dependsOn(copyLicenseInformationToResources, copyLicenseInformationToBuild)
 tasks.processResources.dependsOn(copyLicenseInformationToResources, copyLicenseInformationToBuild)
+
+
+// make sure the publish action is run after the semver plugin has been evaluated,
+// otherwise the version will always be 1.0.0
+afterEvaluate {
+    publishing {
+        publications {
+            register("mzmine-community-package", MavenPublication) {
+                from(components["java"])
+                pom {
+                    name = "mzmine-community"
+                    description = "mzmine-community"
+                    artifactId = "mzmine-community"
+                    url = "https://github.com/mzmine/mzmine"
+                    version = semver.version
+                    developers {
+                        developer {
+                            id = "mzmine"
+                            name = "mzmine"
+                        }
+                    }
+                }
+            }
+
+            register("versionCatalog", MavenPublication) {
+                from(components["versionCatalog"])
+                version = semver.version
+                artifactId = 'mzmine-community-version-catalog'
+                // This is important so the published artifact registers as a .toml file, rather than a library
+            }
+        }
+    }
+}

settings.gradle.kts

@@ -20,4 +20,4 @@ include(
     "javafx-framework",
     "config",
 )
-//includeBuild("convention-plugins")
+//includeBuild("convention-plugins")

taskcontroller/build.gradle.kts

@@ -1,6 +1,33 @@
+/*
+ * Copyright (c) 2004-2024 The mzmine Development Team
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
 plugins {
     id("io.github.mzmine.java-library-conv")
     id("io.github.mzmine.javafx-conv")
+    id("maven-publish")
+    alias(libs.plugins.semver)
 }
 
 repositories {
@@ -13,4 +40,34 @@ dependencies {
     implementation("io.mzio:memory-management:1.0.0")
     implementation(project(":utils"))
     implementation(libs.guava)
-}
+}
+
+semver {
+    properties = "../mzmine-community/src/main/resources/mzmineversion.properties"
+}
+
+afterEvaluate {
+    // the repositories must be set in the afterEvaluate block, because the semver plugin will
+    // not be initialised otherwise. The version of this library is bound to the mzmine community version.
+    publishing {
+        publications {
+            register<MavenPublication>("publish-task-controller") {
+                from(components["java"])
+                pom {
+                    group = "io.github.mzmine"
+                    artifactId = "taskcontroller"
+                    name = "mzmine-community-task-controller"
+                    description = "mzmine-community task controller"
+                    url = "https://github.com/mzmine/mzmine"
+                    version = semver.version
+                    developers {
+                        developer {
+                            id = "mzmine"
+                            name = "mzmine"
+                        }
+                    }
+                }
+            }
+        }
+    }
+}