Merge branch 'master' of https://github.com/JetBrains-Research/snakec…

…harm into features/#359-rules-unresolved

CHANGELOG.md

@@ -5,13 +5,32 @@
 
 ## [Unreleased]
 Released on ...
+
+### Changed
+- TODO  (see [#NNN](https://github.com/JetBrains-Research/snakecharm/issues/NNN)) 
+
+### Fixed
+- TODO  (see [#NNN](https://github.com/JetBrains-Research/snakecharm/issues/NNN)) 
+
+### Added
+- TODO  (see [#NNN](https://github.com/JetBrains-Research/snakecharm/issues/NNN)) 
+
+## [2021.3.661]
+Released on December 7th 2021
+
+### Changed
+- PyCharm 2021.3 compatibility (see [#444](https://github.com/JetBrains-Research/snakecharm/issues/444))
+  Released on December 7th 2021
+
+## [2021.2.657]
+Released on December 6th 2021
 
 ### Changed
 - Show argument preview for int indexes completion in `output[i]` (see [#378](https://github.com/JetBrains-Research/snakecharm/issues/378))
 - Allocation of all top-level sections into one token and support for unknown top-level sections (see [#373](https://github.com/JetBrains-Research/snakecharm/issues/373))
-- TODO  (see [#NNN](https://github.com/JetBrains-Research/snakecharm/issues/NNN)) 
 
 ### Fixed
+- Resolve and completion for 'script' section (see [#426](https://github.com/JetBrains-Research/snakecharm/issues/426))
 - Only snakemake file can't end with a comment (see [#365](https://github.com/JetBrains-Research/snakecharm/issues/365))
 - SmkSectionDuplicatedArgsInspection now checks workflow top-level sections (see [#407](https://github.com/JetBrains-Research/snakecharm/issues/407))
 - All inspections warnings now can be overridden (see [#423](https://github.com/JetBrains-Research/snakecharm/issues/423))
@@ -21,10 +40,11 @@ Released on ...
 - Inspection: Do not show warning that rule section is unused variable if rule is defined in method (see [#385](https://github.com/JetBrains-Research/snakecharm/issues/385))
 - SOE: From UnusedLocal inspection for SnakemakeSL expression  (see [#380](https://github.com/JetBrains-Research/snakecharm/issues/380))
 - Do not show syntax error for rule w/o body (see [#420](https://github.com/JetBrains-Research/snakecharm/issues/420))
-- TODO  (see [#NNN](https://github.com/JetBrains-Research/snakecharm/issues/NNN))
 
 ### Added
+- Color Settings Page (see [#431](https://github.com/JetBrains-Research/snakecharm/issues/431))
 - Inspection: highlights 'use rule' section which overrides several rules as one (see [#411](https://github.com/JetBrains-Research/snakecharm/issues/411))
+- Collecting wildcards from overridden rules in 'use' sections (see [#418](https://github.com/JetBrains-Research/snakecharm/issues/418))
 - Weak warnings for unused 'log' sections in 'use rule' (see [#414](https://github.com/JetBrains-Research/snakecharm/issues/414))
 - Weak warnings for unused 'log' sections (see [#300](https://github.com/JetBrains-Research/snakecharm/issues/300))
 - Support for 'module' and 'use' keywords (see [#355](https://github.com/JetBrains-Research/snakecharm/issues/355))
@@ -36,7 +56,6 @@ Released on ...
 - Completion features related to 'use' section (see [#413](https://github.com/JetBrains-Research/snakecharm/issues/413))
 - Add reference for 'snakefile:' in module declaration (see [#409](https://github.com/JetBrains-Research/snakecharm/issues/409))
 - Initial PEPs support (see [#360](https://github.com/JetBrains-Research/snakecharm/issues/360))
-- TODO  (see [#NNN](https://github.com/JetBrains-Research/snakecharm/issues/NNN))
 
 ## [2021.2.424]
 Released on July 5th 2021

build.gradle.kts

@@ -1,5 +1,4 @@
 
-import io.gitlab.arturbosch.detekt.Detekt
 import org.jetbrains.changelog.date
 import org.jetbrains.changelog.markdownToHTML
 import org.jetbrains.kotlin.gradle.tasks.KotlinCompile
@@ -11,13 +10,13 @@ plugins {
     id("java")
 
     // Kotlin support
-    kotlin("jvm") version "1.5.31"
-    kotlin("plugin.serialization") version "1.5.31"
+    kotlin("jvm") version "1.6.0"
+    kotlin("plugin.serialization") version "1.6.0"
 
     // 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 "1.2.1"
+    id("org.jetbrains.intellij") version "1.3.0"
     // gradle-changelog-plugin - read more: https://github.com/JetBrains/gradle-changelog-plugin
     id("org.jetbrains.changelog") version "1.3.1"
     // detekt linter - read more: https://detekt.github.io/detekt/gradle.html
@@ -42,7 +41,7 @@ dependencies {
     testImplementation("org.jetbrains.kotlin:kotlin-test-junit")
     testImplementation("org.jetbrains.kotlin:kotlin-reflect")
     implementation("org.jetbrains.kotlin:kotlin-stdlib-jdk8")
-    implementation("org.jetbrains.kotlinx:kotlinx-serialization-cbor:1.3.0")
+    implementation("org.jetbrains.kotlinx:kotlinx-serialization-cbor:1.3.1")
 }
 
 // Configure gradle-intellij-plugin plugin.
@@ -97,18 +96,18 @@ detekt {
 }
 
 tasks {
-    // TODO [1.8] ?
-    // Set the compatibility versions to 11
-    withType<JavaCompile> {
-        sourceCompatibility = "11"
-        targetCompatibility = "11"
-    }
-    withType<KotlinCompile> {
-        kotlinOptions.jvmTarget = "11"
+    properties("javaVersion").let {
+        withType<JavaCompile> {
+            sourceCompatibility = it
+            targetCompatibility = it
+        }
+        withType<KotlinCompile> {
+            kotlinOptions.jvmTarget = it
+        }
     }
 
-    withType<Detekt> {
-        jvmTarget = "11"
+    wrapper {
+        gradleVersion = properties("gradleVersion")
     }
 
     patchPluginXml {
@@ -117,17 +116,17 @@ tasks {
         untilBuild.set(properties("pluginUntilBuild"))
 
         // Extract the <!-- Plugin description --> section from README.md and provide for the plugin's manifest
-        pluginDescription.set(
-            File(projectDir, "README.md").readText().lines().run {
-                val start = "<!-- Plugin description -->"
-                val end = "<!-- Plugin description end -->"
-
-                if (!containsAll(listOf(start, end))) {
-                    throw GradleException("Plugin description section not found in README.md:\n$start ... $end")
-                }
-                subList(indexOf(start) + 1, indexOf(end))
-            }.joinToString("\n").run { markdownToHTML(this) }
-        )
+       pluginDescription.set(
+           projectDir.resolve("README.md").readText().lines().run {
+               val start = "<!-- Plugin description -->"
+               val end = "<!-- Plugin description end -->"
+
+               if (!containsAll(listOf(start, end))) {
+                   throw GradleException("Plugin description section not found in README.md:\n$start ... $end")
+               }
+               subList(indexOf(start) + 1, indexOf(end))
+           }.joinToString("\n").run { markdownToHTML(this) }
+       )
 
         // Get the latest available change notes from the changelog file
         changeNotes.set(provider { changelog.getLatest().toHTML() })
@@ -139,7 +138,6 @@ tasks {
     }
 
     publishPlugin {
-
         dependsOn("patchChangelog")
         token.set(properties("intellijPublishToken"))
         // plugin version is based on the SemVer (https://semver.org) and supports pre-release labels, like 2.1.7-alpha.3
@@ -173,8 +171,8 @@ tasks {
         dependsOn("compileKotlin", "compileJava")
         doLast {
             javaexec {
-                main = "com.jetbrains.snakecharm.codeInsight.completion.wrapper.SmkWrapperCrawler"
-                classpath =  project.sourceSets.main.get().runtimeClasspath + files(intellij.ideaDependency.get().jarFiles)
+                mainClass.set("com.jetbrains.snakecharm.codeInsight.completion.wrapper.SmkWrapperCrawler")
+                classpath =  project.sourceSets.main.get().runtimeClasspath + files(setupDependencies.get().idea.get().jarFiles)
                 enableAssertions = true
                 args = listOf(
                     properties("snakemakeWrappersRepoPath"),
@@ -202,7 +200,7 @@ tasks {
         doLast {
             javaexec {
                 mainClass.set("com.jetbrains.snakecharm.codeInsight.completion.wrapper.SmkWrapperCrawler")
-                classpath =  project.sourceSets.main.get().runtimeClasspath + files(intellij.ideaDependency.get().jarFiles)
+                classpath =  project.sourceSets.main.get().runtimeClasspath + files(setupDependencies.get().idea.get().jarFiles)
                 enableAssertions = true
                 args = listOf(
                         "${project.projectDir}/testData/wrappers_storage",

gradle.properties

@@ -7,7 +7,7 @@ pluginName = snakecharm
 # Version naming based on https://semver.org:
 #   * {pluginVersion}.{pluginBuildCounter}{pluginPreReleaseSuffix}
 #   * {pluginPreReleaseSuffix}: Use empty string [..=] for release, for eap: [..=-eap] or [..=-eap.2]
-pluginVersion = 2021.2
+pluginVersion = 2021.3
 pluginPreReleaseSuffix=-eap
 # Project build counter from CI. Can be overridden during build using `./gradlew -PbuildCounter=nnnn my_task_name`
 pluginBuildCounter=SNAPSHOT
@@ -17,12 +17,12 @@ pluginBuildCounter=SNAPSHOT
 #######################################################################################################################
 # See https://plugins.jetbrains.com/docs/intellij/build-number-ranges.html
 # for insight into build numbers and IntelliJ Platform versions.
-pluginSinceBuild = 211.6693.1
+pluginSinceBuild = 213
 pluginUntilBuild = 213.*
 
 # 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.
-pluginVerifierIdeVersions = 2021.2.2, 2021.2.3
+pluginVerifierIdeVersions = 2021.3
 
 # Versions: 2021.1.1, LATEST-EAP-SNAPSHOT, LATEST-TRUNK-SNAPSHOT, 201-EAP-SNAPSHOT, 201.7223.69
 # Platforms: PC, PY, IC
@@ -42,7 +42,8 @@ platformPlugins = org.jetbrains.plugins.yaml
 platformType = PC
 # 2021.1.1, 213-EAP-SNAPSHOT, LATEST-TRUNK-SNAPSHOT, LATEST-EAP-SNAPSHOT, 213.5281.17, 212.5457-EAP-CANDIDATE-SNAPSHOT
 # see: https://www.jetbrains.com/intellij-repository/snapshots/
-platformVersion = 2021.2
+platformVersion = 2021.3
+#platformVersion = LATEST-EAP-SNAPSHOT
 platformDownloadSources = true
 # Plugin Dependencies -> https://plugins.jetbrains.com/docs/intellij/plugin-dependencies.html
 # Example: platformPlugins = com.intellij.java, com.jetbrains.php:203.4449.22
@@ -70,12 +71,18 @@ pythonPlugin =
 # See https://plugins.jetbrains.com/docs/intellij/kotlin.html#kotlin-standard-library for details.
 kotlin.stdlib.default.dependency = false
 
+# Java language level used to compile sources and to generate the files for - Java 11 is required since 2020.3
+javaVersion = 11
+
+# Gradle Releases -> https://github.com/gradle/gradle/releases
+gradleVersion = 7.3
+
 # Repo version for :buildWrappersBundle task. E.g. 'master', '0.68.0', 'xxx.yyy.zzz'.
 # Doesn't checkout directory, please ensure that wrappers repo content version matches the value used here
 # * Teamcity CI: SnakeCharm Plugin | VCS Roots | snakemake-wrappers root |
 #    - VCS root name: snakemake-wrappers (xxx.yyy.zzz release)
 #    - Branch default: refs/tags/xxx.yyy.zzz
 #    - Branch specification: +:refs/tags/xxx.yyy.zzz
 # * To checkout tag run: `git checkout tags/xxx.yyy.zzz -b tags/xxx.yyy.zzz`
-snakemakeWrappersRepoVersion=0.75.0
+snakemakeWrappersRepoVersion=0.80.2
 snakemakeWrappersRepoPath=/Users/romeo/work/git_repos/snakecharm_related/snakemake-wrappers

src/main/kotlin/com/jetbrains/snakecharm/SmkNotifier.kt

@@ -16,7 +16,8 @@ object SmkNotifier {
     fun notifySnakefileDetected(module: Module) {
         NotificationGroupManager.getInstance().getNotificationGroup(NOTIFICATION_GROUP_ID).createNotification(
             title = SnakemakeBundle.message("notifier.msg.framework.by.snakefile.title"),
-            content = SnakemakeBundle.message("notifier.msg.framework.by.snakefile", module.name)
+            content = SnakemakeBundle.message("notifier.msg.framework.by.snakefile", module.name),
+            type = NotificationType.INFORMATION
         ).addAction(object : NotificationAction(
             SnakemakeBundle.message("notifier.msg.framework.by.snakefile.action.configure")
         ) {

src/main/kotlin/com/jetbrains/snakecharm/actions/SmkGotoSymbolContributor.kt

@@ -2,7 +2,6 @@ package com.jetbrains.snakecharm.actions
 
 import com.intellij.navigation.ChooseByNameContributorEx
 import com.intellij.navigation.NavigationItem
-import com.intellij.openapi.project.Project
 import com.intellij.psi.search.GlobalSearchScope
 import com.intellij.psi.stubs.StubIndex
 import com.intellij.util.Processor

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

@@ -136,7 +136,7 @@ object SmkWrapperCrawler {
         wrapperFileExt: String,
         metaYamlContent: String
     ): SmkWrapperStorage.WrapperInfo {
-        val wrapperArgs: List<Pair<String, String>> = when (wrapperFileExt.toLowerCase()) {
+        val wrapperArgs: List<Pair<String, String>> = when (wrapperFileExt.lowercase()) {
             "py" -> parseArgsPython(wrapperFileContent)
             "r" -> parseArgsR(wrapperFileContent)
             else -> emptyList()

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

@@ -39,6 +39,7 @@ class SmkWrapperStorage(val project: Project) : Disposable {
 
     fun cleanVersion() = version.removePrefix("refs/tags/").removePrefix("refs/heads/")
 
+    @ExperimentalSerializationApi
     fun initOnStartup() {
         subscribeOnEvents()
 
@@ -62,6 +63,7 @@ class SmkWrapperStorage(val project: Project) : Disposable {
         }
     }
 
+    @ExperimentalSerializationApi
     private fun subscribeOnEvents() {
         val connection = project.messageBus.connect()
         connection.subscribe(SmkSupportProjectSettings.TOPIC, object : SmkSupportProjectSettingsListener {
@@ -121,6 +123,7 @@ class SmkWrapperStorage(val project: Project) : Disposable {
         Disposer.register(this, connection)
     }
 
+    @Suppress("PROVIDED_RUNTIME_TOO_LOW")
     @Serializable
     data class WrapperInfo(
         val path: String = "", // system independent separators

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

@@ -7,8 +7,8 @@ import com.jetbrains.snakecharm.codeInsight.ImplicitPySymbolsProvider
 import com.jetbrains.snakecharm.framework.SmkSupportProjectSettings
 import kotlinx.serialization.ExperimentalSerializationApi
 
+@ExperimentalSerializationApi
 class SnakemakeStartupActivity : StartupActivity.Background {
-    @ExperimentalSerializationApi
     override fun runActivity(project: Project) {
         val smkSettings = project.service<SmkSupportProjectSettings>()
         smkSettings.initOnStartup()

src/main/kotlin/com/jetbrains/snakecharm/codeInsight/refactoring/SmkAndSmkSLFindUsagesProvider.kt

@@ -8,10 +8,7 @@ import com.jetbrains.python.findUsages.PythonFindUsagesProvider
 import com.jetbrains.snakecharm.codeInsight.resolve.SmkFakePsiElement
 import com.jetbrains.snakecharm.lang.parser.SmkTokenTypes.WORKFLOW_TOPLEVEL_DECORATORS
 import com.jetbrains.snakecharm.lang.parser.SnakemakeLexer
-import com.jetbrains.snakecharm.lang.psi.SmkCheckPoint
-import com.jetbrains.snakecharm.lang.psi.SmkRule
-import com.jetbrains.snakecharm.lang.psi.SmkRuleOrCheckpointArgsSection
-import com.jetbrains.snakecharm.lang.psi.SmkSection
+import com.jetbrains.snakecharm.lang.psi.*
 import com.jetbrains.snakecharm.stringLanguage.lang.psi.SmkSLReferenceExpressionImpl
 
 /**
@@ -26,6 +23,7 @@ class SmkAndSmkSLFindUsagesProvider : PythonFindUsagesProvider() {
         is SmkRuleOrCheckpointArgsSection -> "rule section"
         is SmkRule -> "rule"
         is SmkCheckPoint -> "checkpoint"
+        is SmkUse -> "use rule"
         is SmkSection -> "section"
         is SmkFakePsiElement -> "element"
         is SmkSLReferenceExpressionImpl -> {

src/main/kotlin/com/jetbrains/snakecharm/inspections/SmkAvoidTabWhitespace.kt

@@ -10,11 +10,12 @@ class SmkAvoidTabWhitespace : SnakemakeInspection() {
     override fun buildVisitor(
         holder: ProblemsHolder,
         isOnTheFly: Boolean,
-        session: LocalInspectionToolSession
-    ) = object : SnakemakeInspectionVisitor(holder, session) {
+        session: LocalInspectionToolSession,
+    ) = object : SnakemakeInspectionVisitor(holder, getContext(session)) {
+
         override fun visitWhiteSpace(space: PsiWhiteSpace) {
             if (space.containingFile is SmkFile) {
-                val text =  space.text
+                val text = space.text
                 if (text.startsWith("\n") && '\t' in text) {
                     registerProblem(space, SnakemakeBundle.message("INSP.NAME.codestyle.avoid.whitespace.tab"))
                 }

src/main/kotlin/com/jetbrains/snakecharm/inspections/SmkCondaSectionNotAllowedWithRun.kt

@@ -11,7 +11,8 @@ class SmkCondaSectionNotAllowedWithRun : SnakemakeInspection() {
         holder: ProblemsHolder,
         isOnTheFly: Boolean,
         session: LocalInspectionToolSession
-    ) = object : SnakemakeInspectionVisitor(holder, session) {
+    ) = object : SnakemakeInspectionVisitor(holder, getContext(session)) {
+
         override fun visitSmkRuleOrCheckpointArgsSection(st: SmkRuleOrCheckpointArgsSection) {
             if (st.sectionKeyword == SnakemakeNames.SECTION_CONDA) {
                 val ruleOrCheckPoint = st.getParentRuleOrCheckPoint()

src/main/kotlin/com/jetbrains/snakecharm/inspections/SmkEnvmodulesNotAllowedSectionInspection.kt

@@ -11,7 +11,8 @@ class SmkEnvmodulesNotAllowedSectionInspection : SnakemakeInspection() {
         holder: ProblemsHolder,
         isOnTheFly: Boolean,
         session: LocalInspectionToolSession
-    ) = object : SnakemakeInspectionVisitor(holder, session) {
+    ) = object : SnakemakeInspectionVisitor(holder, getContext(session)) {
+
         override fun visitSmkRuleOrCheckpointArgsSection(st: SmkRuleOrCheckpointArgsSection) {
             if (st.sectionKeyword == SnakemakeNames.SECTION_ENVMODULES) {
                 val ruleOrCheckPoint = st.getParentRuleOrCheckPoint()

src/main/kotlin/com/jetbrains/snakecharm/inspections/SmkExecutionSubsectionInUseSectionInspection.kt

@@ -5,14 +5,15 @@ import com.intellij.codeInspection.ProblemsHolder
 import com.jetbrains.snakecharm.SnakemakeBundle
 import com.jetbrains.snakecharm.codeInsight.SnakemakeAPI
 import com.jetbrains.snakecharm.lang.SnakemakeNames
-import com.jetbrains.snakecharm.lang.psi.*
+import com.jetbrains.snakecharm.lang.psi.SmkRuleOrCheckpointArgsSection
+import com.jetbrains.snakecharm.lang.psi.SmkUse
 
 class SmkExecutionSubsectionInUseSectionInspection : SnakemakeInspection() {
     override fun buildVisitor(
         holder: ProblemsHolder,
         isOnTheFly: Boolean,
         session: LocalInspectionToolSession
-    ) = object : SnakemakeInspectionVisitor(holder, session) {
+    ) = object : SnakemakeInspectionVisitor(holder, getContext(session)) {
 
         override fun visitSmkRuleOrCheckpointArgsSection(st: SmkRuleOrCheckpointArgsSection) {
             val sectionNamePsi = st.nameIdentifier

src/main/kotlin/com/jetbrains/snakecharm/inspections/SmkFileEndsWithCommentInspection.kt

@@ -13,12 +13,13 @@ import com.jetbrains.snakecharm.SnakemakeBundle
 import com.jetbrains.snakecharm.lang.psi.SmkFile
 import com.jetbrains.snakecharm.stringLanguage.lang.psi.SmkSLExpression
 
-class SmkFileEndsWithCommentInspection  : SnakemakeInspection() {
+class SmkFileEndsWithCommentInspection : SnakemakeInspection() {
     override fun buildVisitor(
         holder: ProblemsHolder,
         isOnTheFly: Boolean,
-        session: LocalInspectionToolSession
-    ) = object : SnakemakeInspectionVisitor(holder, session) {
+        session: LocalInspectionToolSession,
+    ) = object : SnakemakeInspectionVisitor(holder, getContext(session)) {
+
         override fun visitComment(comment: PsiComment) {
             if(comment.containingFile !is SmkFile) {
                 return

src/main/kotlin/com/jetbrains/snakecharm/inspections/SmkIgnorePyInspectionExtension.kt

@@ -45,7 +45,7 @@ class SmkIgnorePyInspectionExtension : PyInspectionExtension() {
             // Ignore references imported by 'module' from remote file
             //
             // First check that reference is in `use` imported rules list
-            if (use.getImportedRuleNames()?.any { it == refElement } == true) {
+            if (use.getDefinedReferencesOfImportedRuleNames()?.any { it == refElement } == true) {
                 val module = use.getModuleName()?.reference?.resolve()
                 val file = (module as? SmkModule)?.getPsiFile()?.virtualFile
                 return module != null && (file == null || file is HttpVirtualFile)