Merge branch 'refs/heads/master' into fix/#515-improve-rule-declarati…

…on-message

CHANGELOG.md

@@ -3,6 +3,14 @@
 
 # SnakeCharm Plugin Changelog
 
+## [2024.1.1]
+Released on 20 April 2024
+
+### Fixed
+- Compatibility with PyCharm 2024.1
+- Bundled snakemake wrappers list updated to `v3.8.0`
+- Completion for wrapper names rarely works (see [#517](https://github.com/JetBrains-Research/snakecharm/issues/517))
+
 ## [2023.3.1]
 Released on 6 Dec 2023 (EAP on 3 Nov 2023)
 

build.gradle.kts

@@ -19,14 +19,14 @@ plugins {
     // Java support
     id("java")
 
-    // Kotlin support
-    kotlin("jvm") version "1.8.10"
-    kotlin("plugin.serialization") version "1.8.10"
+    // Kotlin support latest: 1.9.23
+    kotlin("jvm") version "1.9.23"
+    kotlin("plugin.serialization") version "1.9.23"
 
     // gradle-intellij-plugin - read more: https://github.com/JetBrains/gradle-intellij-plugin
     // This plugin allows you to build plugins for IntelliJ platform using specific
     // IntelliJ SDK and bundled plugins.
-    id("org.jetbrains.intellij") version "1.16.0"
+    id("org.jetbrains.intellij") version "1.17.3"
     // gradle-changelog-plugin - read more: https://github.com/JetBrains/gradle-changelog-plugin
     id("org.jetbrains.changelog") version "2.2.0"
 }
@@ -51,9 +51,9 @@ kotlin {
 dependencies {
     testImplementation("io.cucumber:cucumber-java:7.8.1")
     testImplementation("io.cucumber:cucumber-junit:7.8.1")
-    testImplementation("org.jetbrains.kotlin:kotlin-test-junit:1.8.10")
-    testImplementation("org.jetbrains.kotlin:kotlin-reflect:1.8.10")
-    implementation("org.jetbrains.kotlin:kotlin-stdlib-jdk8:1.8.10")
+    testImplementation("org.jetbrains.kotlin:kotlin-test-junit:1.9.23")
+    testImplementation("org.jetbrains.kotlin:kotlin-reflect:1.9.23")
+    implementation("org.jetbrains.kotlin:kotlin-stdlib-jdk8:1.9.23")
     implementation("org.jetbrains.kotlinx:kotlinx-serialization-cbor:1.4.1")
 }
 
@@ -153,9 +153,6 @@ tasks {
         withType<KotlinCompile> {
             kotlinOptions {
                 jvmTarget = it
-                languageVersion = "1.7"
-                // see https://plugins.jetbrains.com/docs/intellij/kotlin.html#kotlin-standard-library
-                apiVersion = "1.6"
                 freeCompilerArgs = listOf("-Xjvm-default=all")
             }
         }
@@ -305,8 +302,16 @@ tasks {
     }
 
     jar {
+        // original, non-instrumented JAR
+        // :runIde, :test tasks launches the plugin from *.jar, so it is required also for development
         dependsOn("buildWrappersBundle")
+        from("${project.buildDir}/bundledWrappers/smk-wrapper-storage-bundled.cbor")
+    }
+
+    instrumentedJar {
+        // modified (instrumented) JAR
         // :runIde, :test tasks launches the plugin from *.jar, so it is required also for development
+        dependsOn("buildWrappersBundle")
         from("${project.buildDir}/bundledWrappers/smk-wrapper-storage-bundled.cbor")
     }
 

gradle.properties

@@ -8,7 +8,7 @@ pluginName = snakecharm
 #   * {pluginVersion}{pluginPreReleaseSuffix}
 #   * plugin version is YEAR.MAJOR.MINOR, where YEAR.MAJOR is a minimal compatible platform version, MINOR is version digit.
 #   * {pluginPreReleaseSuffix}: Use empty string [..=] for release, for eap: [..=-eap] or [..=-eap.2]
-pluginVersion = 2023.3.1
+pluginVersion = 2024.1.1
 pluginPreReleaseSuffix=-eap
 #pluginPreReleaseSuffix=
 
@@ -20,13 +20,13 @@ pluginBuildCounter=SNAPSHOT
 #######################################################################################################################
 # See https://plugins.jetbrains.com/docs/intellij/build-number-ranges.html
 # for insight into build numbers and IntelliJ Platform versions.
-pluginSinceBuild = 233
-pluginUntilBuild = 233.*
+pluginSinceBuild = 241
+pluginUntilBuild = 241.*
 
 # Plugin Verifier integration -> https://github.com/JetBrains/gradle-intellij-plugin#plugin-verifier-dsl
 # See https://jb.gg/intellij-platform-builds-list for available build versions.
 # E.g. pluginVerifierIdeVersions = 2023.1, 2023.2, 232-EAP-SNAPSHOT, 233-EAP-SNAPSHOT
-pluginVerifierIdeVersions = 2023.3, 233-EAP-SNAPSHOT
+pluginVerifierIdeVersions = 2024.1, 241-EAP-SNAPSHOT
 
 # Versions: 2021.1.1, LATEST-EAP-SNAPSHOT, LATEST-TRUNK-SNAPSHOT, 201-EAP-SNAPSHOT, 201.7223.69
 # Platforms: PC, PY, IC
@@ -38,7 +38,7 @@ pluginVerifierIdeVersions = 2023.3, 233-EAP-SNAPSHOT
 # !!!! Uncomment one of the following settings: either pycharmPath or pythonPlugin !!!!
 # !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 
-platformPlugins = org.jetbrains.plugins.yaml
+platformPlugins = org.jetbrains.plugins.yaml, org.toml.lang
 
 # -- PyCharm: --
 # * Run Snakemake plugin inside PyCharm. The IDE will be downloaded automatically
@@ -49,8 +49,8 @@ platformType = PC
 # * latest release
 #platformVersion = 2023.1
 # * EAPs for next major release (or selected minor release)
-#platformVersion = 2023.2
-platformVersion = 233-EAP-SNAPSHOT
+platformVersion = 2024.1
+#platformVersion = 241-EAP-SNAPSHOT
 #platformVersion = LATEST-EAP-SNAPSHOT
 # * Night builds from master
 #platformVersion = LATEST-TRUNK-SNAPSHOT
@@ -106,6 +106,6 @@ gradleVersion = 8.0.2
 #    - build.script.snakemakeWrappersRepoVersion = v$TAG
 # (or findout how to configure via %vcsroot.BioLabs_SnakeCharmPlugin_SnakemakeWrappersLatestRelease.branch%)
 
-# * To checkout tag run: `git tag -l; git checkout tags/v$TAG -b tags/$TAG` (git checkout tags/v1.3.2 -b tags/v1.3.2)
-snakemakeWrappersRepoVersion=v2.9.1
+# * To checkout tag run: `git tag -l; TAG=3.8.0; git checkout tags/v$TAG -b tags/$TAG` (git checkout tags/v1.3.2 -b tags/v1.3.2)
+snakemakeWrappersRepoVersion=v3.8.0
 snakemakeWrappersRepoPath=/Users/romeo/work/git_repos/snakecharm_related/snakemake-wrappers

src/main/kotlin/com/jetbrains/snakecharm/codeInsight/ImplicitPySymbolsProvider.kt

@@ -76,7 +76,14 @@ class ImplicitPySymbolsProvider(
         val project = project
 
         DumbService.getInstance(project).runWhenSmart {
-            SlowOperations.allowSlowOperations<Throwable> { doRefreshCache(project, sdk, forceClear, null) }
+            SlowOperations.startSection(SlowOperations.KNOWN_ISSUE).use { ignore ->
+                // XXX: workaround because default code throws 100+ exceptions:  java.lang.Throwable: Slow operations are prohibited on EDT. See SlowOperations.assertSlowOperationsAreAllowed javadoc.
+                // SlowOperations.allowSlowOperations<Throwable> { .. }
+
+                // TODO: 1) should be in background 2) note that it requires some read actions to access PSI
+                // See: https://github.com/JetBrains-Research/snakecharm/issues/513
+                doRefreshCache(project, sdk, forceClear, null)
+            }
         }
     }
 

src/main/kotlin/com/jetbrains/snakecharm/codeInsight/completion/wrapper/SmkWrapperCompletionProvider.kt

@@ -14,7 +14,7 @@ import com.jetbrains.snakecharm.lang.SnakemakeNames
 import com.jetbrains.snakecharm.lang.psi.SmkRuleOrCheckpointArgsSection
 
 object SmkWrapperCompletionProvider : CompletionProvider<CompletionParameters>() {
-    private val WRAPPER_VERSION_REGEXP = Regex("(\\d+\\.\\d+\\.\\d+|master|latest).*")
+    private val WRAPPER_VERSION_REGEXP = Regex("(v?\\d+\\.\\d+\\.\\d+|master|latest).*")
 
     val CAPTURE = PlatformPatterns.psiElement()
             .inFile(SmkKeywordCompletionContributor.IN_SNAKEMAKE)

src/main/kotlin/com/jetbrains/snakecharm/codeInsight/completion/wrapper/SmkWrapperCrawler.kt

@@ -1,7 +1,6 @@
 package com.jetbrains.snakecharm.codeInsight.completion.wrapper
 
 import com.intellij.openapi.util.io.FileUtil
-import com.intellij.util.io.isDirectory
 import com.intellij.util.io.write
 import com.jetbrains.snakecharm.codeInsight.SnakemakeAPI
 import kotlinx.serialization.ExperimentalSerializationApi
@@ -11,6 +10,7 @@ import org.yaml.snakeyaml.Yaml
 import java.io.File
 import java.nio.file.Paths
 import kotlin.io.path.exists
+import kotlin.io.path.isDirectory
 
 object SmkWrapperCrawler {
     private val VERBOSE = false

src/main/kotlin/com/jetbrains/snakecharm/codeInsight/completion/wrapper/SmkWrapperStorage.kt

@@ -17,6 +17,7 @@ import kotlinx.serialization.Serializable
 import kotlinx.serialization.cbor.Cbor
 import kotlinx.serialization.decodeFromByteArray
 import java.net.URL
+import java.nio.file.Files
 import java.nio.file.Path
 import java.util.*
 import kotlin.io.path.exists
@@ -205,7 +206,7 @@ class SmkWrapperStorage(val project: Project) : Disposable {
         @ExperimentalSerializationApi
         private fun deserializeWrappers(storagePath: Path) =
             Cbor.decodeFromByteArray<Pair<String, List<SmkWrapperStorage.WrapperInfo>>>(
-                storagePath.readBytes()
+                Files.readAllBytes(storagePath)
             )
 
         @ExperimentalSerializationApi

src/main/kotlin/com/jetbrains/snakecharm/framework/SmkFrameworkConfigurableProvider.kt

@@ -4,11 +4,11 @@ import com.intellij.facet.ui.ValidationResult
 import com.intellij.openapi.options.Configurable
 import com.intellij.openapi.options.SearchableConfigurable
 import com.intellij.openapi.project.Project
-import com.intellij.util.io.isDirectory
 import com.jetbrains.snakecharm.SnakemakeBundle
 import java.nio.file.Paths
 import javax.swing.JComponent
 import kotlin.io.path.exists
+import kotlin.io.path.isDirectory
 
 /**
  * Registers project settings tab for snakemake settings ('supported framework')

src/main/kotlin/com/jetbrains/snakecharm/lang/psi/impl/SmkCheckPointImpl.kt

@@ -26,6 +26,6 @@ class SmkCheckPointImpl
 
     override fun acceptPyVisitor(pyVisitor: PyElementVisitor) = when (pyVisitor) {
         is SmkElementVisitor -> pyVisitor.visitSmkCheckPoint(this)
-        else -> super.acceptPyVisitor(pyVisitor)
+        else -> super<SmkRuleLikeImpl>.acceptPyVisitor(pyVisitor)
     }
 }

src/main/kotlin/com/jetbrains/snakecharm/lang/psi/impl/SmkModuleArgsSectionImpl.kt

@@ -13,7 +13,7 @@ class SmkModuleArgsSectionImpl(node: ASTNode) : SmkArgsSectionImpl(node), SmkMod
     override fun acceptPyVisitor(pyVisitor: PyElementVisitor?) {
         when (pyVisitor) {
             is SmkElementVisitor -> pyVisitor.visitSmkModuleArgsSection(this)
-            else -> super.acceptPyVisitor(pyVisitor)
+            else -> super<SmkArgsSectionImpl>.acceptPyVisitor(pyVisitor)
         }
     }
 

src/main/kotlin/com/jetbrains/snakecharm/lang/psi/impl/SmkModuleImpl.kt

@@ -30,7 +30,7 @@ class SmkModuleImpl : SmkRuleLikeImpl<SmkModuleStub, SmkModule, SmkModuleArgsSec
     override fun acceptPyVisitor(pyVisitor: PyElementVisitor?) {
         when (pyVisitor) {
             is SmkElementVisitor -> pyVisitor.visitSmkModule(this)
-            else -> super.acceptPyVisitor(pyVisitor)
+            else -> super<SmkRuleLikeImpl>.acceptPyVisitor(pyVisitor)
         }
     }
 

src/main/kotlin/com/jetbrains/snakecharm/lang/psi/impl/SmkRuleImpl.kt

@@ -33,7 +33,7 @@ class SmkRuleImpl
 
     override fun acceptPyVisitor(pyVisitor: PyElementVisitor) = when (pyVisitor) {
         is SmkElementVisitor -> pyVisitor.visitSmkRule(this)
-        else -> super.acceptPyVisitor(pyVisitor)
+        else -> super<SmkRuleLikeImpl>.acceptPyVisitor(pyVisitor)
     }
 
     companion object {

src/main/kotlin/com/jetbrains/snakecharm/lang/psi/impl/SmkRuleOrCheckpointArgsSectionImpl.kt

@@ -20,7 +20,7 @@ open class SmkRuleOrCheckpointArgsSectionImpl(node: ASTNode) : SmkArgsSectionImp
 
     override fun acceptPyVisitor(pyVisitor: PyElementVisitor) = when (pyVisitor) {
         is SmkElementVisitor -> pyVisitor.visitSmkRuleOrCheckpointArgsSection(this)
-        else -> super.acceptPyVisitor(pyVisitor)
+        else -> super<SmkArgsSectionImpl>.acceptPyVisitor(pyVisitor)
     }
 
     override fun getReference(): PsiReference? =

src/main/kotlin/com/jetbrains/snakecharm/lang/psi/impl/SmkRunSectionImpl.kt

@@ -24,7 +24,7 @@ class SmkRunSectionImpl(node: ASTNode): PyElementImpl(node), SmkRunSection {
 
     override fun acceptPyVisitor(pyVisitor: PyElementVisitor) = when (pyVisitor) {
         is SmkElementVisitor -> pyVisitor.visitSmkRunSection(this)
-        else -> super.acceptPyVisitor(pyVisitor)
+        else -> super<PyElementImpl>.acceptPyVisitor(pyVisitor)
     }
 
     override fun getPresentation() = getPresentation(this)

src/main/kotlin/com/jetbrains/snakecharm/lang/psi/impl/SmkSubworkflowArgsSectionImpl.kt

@@ -9,7 +9,7 @@ class SmkSubworkflowArgsSectionImpl(node: ASTNode): SmkArgsSectionImpl(node), Sm
     override fun acceptPyVisitor(pyVisitor: PyElementVisitor) {
         when (pyVisitor) {
             is SmkElementVisitor -> pyVisitor.visitSmkSubworkflowArgsSection(this)
-            else -> super.acceptPyVisitor(pyVisitor)
+            else -> super<SmkArgsSectionImpl>.acceptPyVisitor(pyVisitor)
         }
     }
 }

src/main/kotlin/com/jetbrains/snakecharm/lang/psi/impl/SmkSubworkflowImpl.kt

@@ -20,7 +20,7 @@ class SmkSubworkflowImpl:
     override fun acceptPyVisitor(pyVisitor: PyElementVisitor) {
         when (pyVisitor) {
             is SmkElementVisitor -> pyVisitor.visitSmkSubworkflow(this)
-            else -> super.acceptPyVisitor(pyVisitor)
+            else -> super<SmkRuleLikeImpl>.acceptPyVisitor(pyVisitor)
         }
     }
 }

src/main/kotlin/com/jetbrains/snakecharm/lang/psi/impl/SmkUseArgsSectionImpl.kt

@@ -12,7 +12,7 @@ class SmkUseArgsSectionImpl(node: ASTNode) : SmkArgsSectionImpl(node), SmkRuleOr
     override fun acceptPyVisitor(pyVisitor: PyElementVisitor?) {
         when (pyVisitor) {
             is SmkElementVisitor -> pyVisitor.visitSmkRuleOrCheckpointArgsSection(this)
-            else -> super.acceptPyVisitor(pyVisitor)
+            else -> super<SmkArgsSectionImpl>.acceptPyVisitor(pyVisitor)
         }
     }
 

src/main/kotlin/com/jetbrains/snakecharm/lang/psi/impl/SmkUseImpl.kt

@@ -30,7 +30,7 @@ class SmkUseImpl : SmkRuleLikeImpl<SmkUseStub, SmkUse, SmkRuleOrCheckpointArgsSe
     override fun acceptPyVisitor(pyVisitor: PyElementVisitor?) {
         when (pyVisitor) {
             is SmkElementVisitor -> pyVisitor.visitSmkUse(this)
-            else -> super.acceptPyVisitor(pyVisitor)
+            else -> super<SmkRuleLikeImpl>.acceptPyVisitor(pyVisitor)
         }
     }
 

src/main/kotlin/com/jetbrains/snakecharm/lang/psi/impl/SmkWorkflowArgsSectionImpl.kt

@@ -28,7 +28,7 @@ class SmkWorkflowArgsSectionImpl(node: ASTNode) : PyElementImpl(node), SmkWorkfl
 
     override fun acceptPyVisitor(pyVisitor: PyElementVisitor) = when (pyVisitor) {
         is SmkElementVisitor -> pyVisitor.visitSmkWorkflowArgsSection(this)
-        else -> super.acceptPyVisitor(pyVisitor)
+        else -> super<PyElementImpl>.acceptPyVisitor(pyVisitor)
     }
 
     override fun getSectionKeywordNode() = node

src/main/kotlin/com/jetbrains/snakecharm/lang/psi/impl/SmkWorkflowLocalrulesSectionImpl.kt

@@ -14,7 +14,7 @@ class SmkWorkflowLocalrulesSectionImpl(node: ASTNode): PyElementImpl(node), SmkW
 
     override fun acceptPyVisitor(pyVisitor: PyElementVisitor) = when (pyVisitor) {
         is SmkElementVisitor -> pyVisitor.visitSmkWorkflowLocalrulesSection(this)
-        else -> super.acceptPyVisitor(pyVisitor)
+        else -> super<PyElementImpl>.acceptPyVisitor(pyVisitor)
     }
 
     override fun getPresentation() = getPresentation(this)

src/main/kotlin/com/jetbrains/snakecharm/lang/psi/impl/SmkWorkflowPythonBlockSectionImpl.kt

@@ -21,7 +21,7 @@ class SmkWorkflowPythonBlockSectionImpl(node: ASTNode) : PyElementImpl(node), Sm
 
     override fun acceptPyVisitor(pyVisitor: PyElementVisitor) = when (pyVisitor) {
         is SmkElementVisitor -> pyVisitor.visitSmkWorkflowPythonBlockSection(this)
-        else -> super.acceptPyVisitor(pyVisitor)
+        else -> super<PyElementImpl>.acceptPyVisitor(pyVisitor)
     }
 
     override fun getPresentation() = getPresentation(this)

src/main/kotlin/com/jetbrains/snakecharm/lang/psi/impl/SmkWorkflowRuleorderSectionImpl.kt

@@ -14,7 +14,7 @@ class SmkWorkflowRuleorderSectionImpl(node: ASTNode): PyElementImpl(node), SmkWo
 
     override fun acceptPyVisitor(pyVisitor: PyElementVisitor) = when (pyVisitor) {
         is SmkElementVisitor -> pyVisitor.visitSmkWorkflowRuleorderSection(this)
-        else -> super.acceptPyVisitor(pyVisitor)
+        else -> super<PyElementImpl>.acceptPyVisitor(pyVisitor)
     }
 
     override fun getPresentation() = getPresentation(this)

src/main/kotlin/com/jetbrains/snakecharm/stringLanguage/lang/psi/SmkSLReferenceExpression.kt

@@ -9,6 +9,8 @@ import com.jetbrains.snakecharm.lang.psi.SmkSection
 import com.jetbrains.snakecharm.stringLanguage.lang.psi.references.SmkSLWildcardReference
 
 interface SmkSLReferenceExpression : PyReferenceExpression, SmkSLExpression, PsiNameIdentifierOwner {
+    override fun getName(): String?
+
     fun containingRuleOrCheckpointSection(): SmkRuleOrCheckpointArgsSection? =
         PsiTreeUtil.getParentOfType(injectionHost(), SmkRuleOrCheckpointArgsSection::class.java)
 

src/main/kotlin/com/jetbrains/snakecharm/stringLanguage/lang/psi/SmkSLReferenceExpressionImpl.kt

@@ -36,7 +36,7 @@ class SmkSLReferenceExpressionImpl(node: ASTNode) : PyReferenceExpressionImpl(no
 
     override fun acceptPyVisitor(pyVisitor: PyElementVisitor) = when (pyVisitor) {
         is SmkSLElementVisitor -> pyVisitor.visitSmkSLReferenceExpression(this)
-        else -> super.acceptPyVisitor(pyVisitor)
+        else -> super<PyReferenceExpressionImpl>.acceptPyVisitor(pyVisitor)
     }
 
     override fun getReference(context: PyResolveContext): PsiPolyVariantReference {

src/main/kotlin/com/jetbrains/snakecharm/stringLanguage/lang/psi/SmkSLSubscriptionExpression.kt

@@ -1,6 +1,28 @@
 package com.jetbrains.snakecharm.stringLanguage.lang.psi
 
+import com.intellij.lang.ASTNode
+import com.jetbrains.python.ast.PyAstElementVisitor
+import com.jetbrains.python.psi.PyExpression
 import com.jetbrains.python.psi.PySubscriptionExpression
 
 interface SmkSLSubscriptionExpression : SmkSLReferenceExpression, PySubscriptionExpression {
+    override fun acceptPyVisitor(pyVisitor: PyAstElementVisitor?) {
+        super<SmkSLReferenceExpression>.acceptPyVisitor(pyVisitor)
+    }
+
+    override fun getQualifier(): PyExpression? {
+        return super<SmkSLReferenceExpression>.getQualifier()
+    }
+
+    override fun isQualified(): Boolean {
+        return super<SmkSLReferenceExpression>.isQualified()
+    }
+
+    override fun getReferencedName(): String? {
+        return super<SmkSLReferenceExpression>.getReferencedName()
+    }
+
+    override fun getNameElement(): ASTNode? {
+        return super<SmkSLReferenceExpression>.getNameElement()
+    }
 }

src/main/kotlin/com/jetbrains/snakecharm/stringLanguage/lang/psi/SmkSLSubscriptionExpressionImpl.kt

@@ -101,7 +101,7 @@ class SmkSLSubscriptionExpressionImpl(node: ASTNode) : SmkSLElementImpl(node), S
 
     override fun acceptPyVisitor(pyVisitor: PyElementVisitor) = when (pyVisitor) {
         is SmkSLElementVisitor -> pyVisitor.visitSmkSLSubscriptionExpression(this)
-        else -> super.acceptPyVisitor(pyVisitor)
+        else -> super<SmkSLElementImpl>.acceptPyVisitor(pyVisitor)
     }
 
     override fun getIndexExpression() = this.childToPsi<SmkSLSubscriptionIndexKeyExpressionImpl>(KEY_EXPRESSION)

src/main/kotlin/com/jetbrains/snakecharm/stringLanguage/lang/psi/SmkSLSubscriptionIndexKeyExpressionImpl.kt

@@ -36,7 +36,7 @@ class SmkSLSubscriptionIndexKeyExpressionImpl(node: ASTNode) : PyReferenceExpres
 
     override fun acceptPyVisitor(pyVisitor: PyElementVisitor) = when (pyVisitor) {
         is SmkSLElementVisitor -> pyVisitor.visitSmkSLSubscriptionExpressionKey(this)
-        else -> super.acceptPyVisitor(pyVisitor)
+        else -> super<PyReferenceExpressionImpl>.acceptPyVisitor(pyVisitor)
     }