Merge branch 'master' into features/#355-module-use-support

build.gradle.kts

@@ -17,7 +17,7 @@ plugins {
     // 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 "1.1.4"
+    id("org.jetbrains.intellij") version "1.1.3"
     // gradle-changelog-plugin - read more: https://github.com/JetBrains/gradle-changelog-plugin
     id("org.jetbrains.changelog") version "1.2.1"
     // detekt linter - read more: https://detekt.github.io/detekt/gradle.html

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

@@ -47,6 +47,9 @@ import com.jetbrains.snakecharm.lang.SnakemakeNames.SNAKEMAKE_IO_METHOD_REPORT
 import com.jetbrains.snakecharm.lang.SnakemakeNames.SNAKEMAKE_IO_METHOD_TEMP
 import com.jetbrains.snakecharm.lang.SnakemakeNames.SNAKEMAKE_IO_METHOD_TOUCH
 import com.jetbrains.snakecharm.lang.SnakemakeNames.SNAKEMAKE_IO_METHOD_UNPACK
+import com.jetbrains.snakecharm.lang.SnakemakeNames.WORKFLOW_CONTAINERIZED_KEYWORD
+import com.jetbrains.snakecharm.lang.SnakemakeNames.WORKFLOW_CONTAINER_KEYWORD
+import com.jetbrains.snakecharm.lang.SnakemakeNames.WORKFLOW_SINGULARITY_KEYWORD
 
 /**
  * Also see [ImplicitPySymbolsProvider] class
@@ -92,6 +95,9 @@ object SnakemakeAPI {
         SECTION_WRAPPER, SECTION_CWL, SECTION_NOTEBOOK
     )
 
+    /**
+     * Rule or checkpoint sections that allows only single argument
+     */
     val SINGLE_ARGUMENT_SECTIONS_KEYWORDS = setOf(
         SECTION_SHELL, SECTION_SCRIPT, SECTION_WRAPPER,
         SECTION_CWL, SECTION_BENCHMARK, SECTION_VERSION,
@@ -101,6 +107,14 @@ object SnakemakeAPI {
         SECTION_HANDOVER, SECTION_CONTAINERIZED
     )
 
+    /**
+     * Workflow top-level sections that allows only single argument
+     */
+    val SINGLE_ARGUMENT_WORKFLOWS_KEYWORDS = setOf(
+        WORKFLOW_CONTAINERIZED_KEYWORD, WORKFLOW_CONTAINER_KEYWORD,
+        WORKFLOW_SINGULARITY_KEYWORD
+    )
+
     /**
      * For rules parsing
      */
@@ -117,6 +131,7 @@ object SnakemakeAPI {
         SECTION_NAME,
         SECTION_HANDOVER
     )
+
     val RULE_OR_CHECKPOINT_SECTION_KEYWORDS = (RULE_OR_CHECKPOINT_ARGS_SECTION_KEYWORDS + setOf(SECTION_RUN))
 
     /**
@@ -245,7 +260,7 @@ object SnakemakeAPI {
         }
 
     /**
-     * Set of rule\checkpoint sections that does not expect keyword arguments
+     * Rule/checkpoint sections that does not allow keyword arguments
      */
     val SECTIONS_WHERE_KEYWORD_ARGS_PROHIBITED = setOf(
         SECTION_BENCHMARK, SECTION_VERSION, SECTION_MESSAGE, SECTION_SHELL, SECTION_THREADS, SECTION_SINGULARITY,
@@ -254,6 +269,15 @@ object SnakemakeAPI {
         SECTION_NAME, SECTION_HANDOVER
     )
 
+
+    /**
+     * Workflow top-level sections that does not allow keyword args
+     */
+    val WORKFLOWS_WHERE_KEYWORD_ARGS_PROHIBITED = setOf(
+        WORKFLOW_CONTAINERIZED_KEYWORD, WORKFLOW_CONTAINER_KEYWORD,
+        WORKFLOW_SINGULARITY_KEYWORD
+    )
+
     val IO_FLAG_2_SUPPORTED_SECTION: HashMap<String, List<String>> = hashMapOf(
         SNAKEMAKE_IO_METHOD_ANCIENT to listOf(SECTION_INPUT),
         SNAKEMAKE_IO_METHOD_PROTECTED to listOf(SECTION_OUTPUT, SECTION_LOG, SECTION_BENCHMARK),

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

@@ -5,9 +5,12 @@ import com.intellij.codeInspection.ProblemsHolder
 import com.jetbrains.python.psi.PyArgumentList
 import com.jetbrains.snakecharm.SnakemakeBundle
 import com.jetbrains.snakecharm.codeInsight.SnakemakeAPI.SINGLE_ARGUMENT_SECTIONS_KEYWORDS
+import com.jetbrains.snakecharm.codeInsight.SnakemakeAPI.SINGLE_ARGUMENT_WORKFLOWS_KEYWORDS
+import com.jetbrains.snakecharm.lang.psi.SmkArgsSection
 import com.jetbrains.snakecharm.lang.psi.SmkModuleArgsSection
 import com.jetbrains.snakecharm.lang.psi.SmkRuleOrCheckpointArgsSection
 import com.jetbrains.snakecharm.lang.psi.SmkSubworkflowArgsSection
+import com.jetbrains.snakecharm.lang.psi.SmkWorkflowArgsSection
 
 class SmkSectionMultipleArgsInspection : SnakemakeInspection() {
     override fun buildVisitor(
@@ -21,8 +24,17 @@ class SmkSectionMultipleArgsInspection : SnakemakeInspection() {
         }
 
         override fun visitSmkRuleOrCheckpointArgsSection(st: SmkRuleOrCheckpointArgsSection) {
-            if (st.name in SINGLE_ARGUMENT_SECTIONS_KEYWORDS) {
-                checkArgumentList(st.argumentList, st.name!!)
+            checkArgumentList(st, SINGLE_ARGUMENT_SECTIONS_KEYWORDS)
+        }
+
+        override fun visitSmkWorkflowArgsSection(st: SmkWorkflowArgsSection) {
+            checkArgumentList(st, SINGLE_ARGUMENT_WORKFLOWS_KEYWORDS)
+        }
+
+        private fun checkArgumentList(st: SmkArgsSection, sectionKeywords: Set<String>) {
+            val keyword = st.sectionKeyword
+            if (keyword != null && keyword in sectionKeywords) {
+                checkArgumentList(st.argumentList, keyword)
             }
         }
 

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

@@ -6,10 +6,12 @@ import com.jetbrains.python.psi.PyArgumentList
 import com.jetbrains.python.psi.PyKeywordArgument
 import com.jetbrains.snakecharm.SnakemakeBundle
 import com.jetbrains.snakecharm.codeInsight.SnakemakeAPI.SECTIONS_WHERE_KEYWORD_ARGS_PROHIBITED
+import com.jetbrains.snakecharm.codeInsight.SnakemakeAPI.WORKFLOWS_WHERE_KEYWORD_ARGS_PROHIBITED
 import com.jetbrains.snakecharm.lang.psi.SmkArgsSection
 import com.jetbrains.snakecharm.lang.psi.SmkModuleArgsSection
 import com.jetbrains.snakecharm.lang.psi.SmkRuleOrCheckpointArgsSection
 import com.jetbrains.snakecharm.lang.psi.SmkSubworkflowArgsSection
+import com.jetbrains.snakecharm.lang.psi.SmkWorkflowArgsSection
 
 class SmkSectionUnexpectedKeywordArgsInspection : SnakemakeInspection() {
     override fun buildVisitor(
@@ -23,7 +25,19 @@ class SmkSectionUnexpectedKeywordArgsInspection : SnakemakeInspection() {
         }
 
         override fun visitSmkRuleOrCheckpointArgsSection(st: SmkRuleOrCheckpointArgsSection) {
-            if (st.sectionKeyword in SECTIONS_WHERE_KEYWORD_ARGS_PROHIBITED) {
+            checkArgumentList(st, SECTIONS_WHERE_KEYWORD_ARGS_PROHIBITED)
+        }
+
+        override fun visitSmkWorkflowArgsSection(st: SmkWorkflowArgsSection) {
+            checkArgumentList(st, WORKFLOWS_WHERE_KEYWORD_ARGS_PROHIBITED)
+        }
+
+        private fun checkArgumentList(
+            st: SmkArgsSection,
+            sectionKeywords: Set<String>,
+        ) {
+            val keyword = st.sectionKeyword
+            if (keyword != null && keyword in sectionKeywords) {
                 checkArgumentList(st.argumentList, st)
             }
         }

src/main/kotlin/com/jetbrains/snakecharm/lang/SnakemakeNames.kt

@@ -8,24 +8,24 @@ object SnakemakeNames {
     const val RULE_KEYWORD = "rule"
     const val CHECKPOINT_KEYWORD = "checkpoint"
 
+    const val WORKFLOW_ONSUCCESS_KEYWORD = "onsuccess"
+    const val WORKFLOW_ONERROR_KEYWORD = "onerror"
+    const val WORKFLOW_ONSTART_KEYWORD = "onstart"
+    const val WORKFLOW_LOCALRULES_KEYWORD = "localrules"
+    const val WORKFLOW_RULEORDER_KEYWORD = "ruleorder"
     const val WORKFLOW_CONFIGFILE_KEYWORD = "configfile"
     const val WORKFLOW_REPORT_KEYWORD = "report"
     const val WORKFLOW_WILDCARD_CONSTRAINTS_KEYWORD = "wildcard_constraints"
     const val WORKFLOW_SINGULARITY_KEYWORD = "singularity"
     const val WORKFLOW_INCLUDE_KEYWORD = "include"
     const val WORKFLOW_WORKDIR_KEYWORD = "workdir"
-
-    const val WORKFLOW_LOCALRULES_KEYWORD = "localrules"
-
-    const val WORKFLOW_RULEORDER_KEYWORD = "ruleorder"
-
-    const val WORKFLOW_ONSUCCESS_KEYWORD = "onsuccess"
-    const val WORKFLOW_ONERROR_KEYWORD = "onerror"
-    const val WORKFLOW_ONSTART_KEYWORD = "onstart"
+    const val WORKFLOW_ENVVARS_KEYWORD = "envvars"
+    const val WORKFLOW_CONTAINER_KEYWORD = "container"
+    const val WORKFLOW_CONTAINERIZED_KEYWORD = "containerized"  // => 6.0.0
 
     const val SUBWORKFLOW_KEYWORD = "subworkflow"
-    const val SUBWORKFLOW_WORKDIR_KEYWORD  = WORKFLOW_WORKDIR_KEYWORD
-    const val SUBWORKFLOW_CONFIGFILE_KEYWORD  = WORKFLOW_CONFIGFILE_KEYWORD
+    const val SUBWORKFLOW_WORKDIR_KEYWORD = WORKFLOW_WORKDIR_KEYWORD
+    const val SUBWORKFLOW_CONFIGFILE_KEYWORD = WORKFLOW_CONFIGFILE_KEYWORD
     const val SUBWORKFLOW_SNAKEFILE_KEYWORD = "snakefile"
 
     const val MODULE_KEYWORD = "module"
@@ -51,9 +51,9 @@ object SnakemakeNames {
     const val SECTION_VERSION = "version"
     const val SECTION_MESSAGE = "message"
     const val SECTION_THREADS = "threads"
-    const val SECTION_SINGULARITY = "singularity"
+    const val SECTION_SINGULARITY = WORKFLOW_SINGULARITY_KEYWORD
     const val SECTION_PRIORITY = "priority"
-    const val SECTION_WILDCARD_CONSTRAINTS = "wildcard_constraints"
+    const val SECTION_WILDCARD_CONSTRAINTS = WORKFLOW_WILDCARD_CONSTRAINTS_KEYWORD
     const val SECTION_GROUP = "group"
     const val SECTION_CONDA = "conda" // >= 4.8
     const val SECTION_RESOURCES = "resources"
@@ -65,8 +65,8 @@ object SnakemakeNames {
     const val SECTION_SHADOW = "shadow"
     const val SECTION_RUN = "run"
     const val SECTION_CACHE = "cache" // >= 5.12.0
-    const val SECTION_CONTAINER = "container"
-    const val SECTION_CONTAINERIZED = "containerized" // => 6.0.0
+    const val SECTION_CONTAINER = WORKFLOW_CONTAINER_KEYWORD
+    const val SECTION_CONTAINERIZED = WORKFLOW_CONTAINERIZED_KEYWORD
     const val SECTION_NOTEBOOK = "notebook"
     const val SECTION_ENVMODULES = "envmodules" // >= 5.9
     const val SECTION_NAME = "name" // >= 5.31

src/main/kotlin/com/jetbrains/snakecharm/lang/validation/SmkSyntaxErrorAnnotator.kt

@@ -11,14 +11,22 @@ import com.jetbrains.snakecharm.lang.psi.*
 
 object SmkSyntaxErrorAnnotator : SmkAnnotator() {
     override fun visitSmkRuleOrCheckpointArgsSection(st: SmkRuleOrCheckpointArgsSection) {
-        if (!SnakemakeLanguageDialect.isInsideSmkFile(st)) {
+        findAndHighlightIncorrectArguments(st)
+    }
+
+    override fun visitSmkWorkflowArgsSection(st: SmkWorkflowArgsSection) {
+        findAndHighlightIncorrectArguments(st)
+    }
+
+    private fun findAndHighlightIncorrectArguments(argsSection: SmkArgsSection) {
+        if (!SnakemakeLanguageDialect.isInsideSmkFile(argsSection)) {
             return
         }
 
         val seenKeywords2Value = HashMap<String, String>()
         var encounteredKeywordArgument = false
 
-        st.argumentList?.arguments?.forEach { arg ->
+        argsSection.argumentList?.arguments?.forEach { arg ->
             when (arg) {
                 is PyKeywordArgument -> {
                     arg.keyword?.let { keyword ->
@@ -30,7 +38,7 @@ object SmkSyntaxErrorAnnotator : SmkAnnotator() {
                             holder.newAnnotation(
                                 ERROR,
                                 SnakemakeBundle.message("ANN.keyword.argument.already.provided", keywordValue)
-                            ).range(arg.keywordNode!!).create()
+                            ).range(arg.keywordNode ?: return@let).create()
                         }
                     }
                     encounteredKeywordArgument = true

src/test/resources/features/highlighting/inspections/multiple_args_inspection.feature

@@ -62,4 +62,26 @@ Feature: Inspection for multiple arguments in various sections
       | notebook      |
       | container     |
       | containerized |
-      | handover      |
+      | handover      |
+
+  Scenario Outline: Multiple arguments in workflow section
+    Given a snakemake project
+    Given I open a file "foo.smk" with text
+    """
+    <section_name>: "a", "b", "c"
+    """
+    And SmkSectionMultipleArgsInspection inspection is enabled
+    Then I expect inspection error on <"b"> with message
+    """
+    Only one argument is allowed for '<section_name>' section.
+    """
+    And I expect inspection error on <"c"> with message
+    """
+    Only one argument is allowed for '<section_name>' section.
+    """
+      When I check highlighting errors
+    Examples:
+      | section_name  |
+      | containerized |
+      | singularity   |
+      | container     |

src/test/resources/features/highlighting/inspections/unexpected_keyword_args_inspection.feature

@@ -79,3 +79,21 @@ Feature: Inspection for unexpected keyword arguments in section
       | checkpoint | log                  |
       | checkpoint | resources            |
       | checkpoint | wildcard_constraints |
+
+  Scenario Outline: Unexpected keyword arguments in workflow
+    Given a snakemake project
+    Given I open a file "foo.smk" with text
+    """
+    <section_name>: a="foo.bar"
+    """
+    And SmkSectionUnexpectedKeywordArgsInspection inspection is enabled
+    Then I expect inspection error on <a="foo.bar"> with message
+    """
+    Section '<section_name>' does not support keyword arguments
+    """
+    When I check highlighting errors
+    Examples:
+      | section_name  |
+      | containerized |
+      | singularity   |
+      | container     |

src/test/resources/features/highlighting/smk_syntax_error_annotator.feature

@@ -20,6 +20,20 @@ Feature: Annotate syntax errors
       """
       When I check highlighting errors
 
+  Scenario: Annotate keyword argument duplication in workflow
+    Given a snakemake project
+    Given I open a file "foo.smk" with text
+      """
+      wildcard_constraints:
+          foo = ".*",
+          foo = "other.*"
+      """
+    Then I expect inspection error on <foo> in <foo = "other.*"> with message
+      """
+      Keyword argument already provided: foo = \".*\".
+      """
+    When I check highlighting errors
+
   Scenario Outline: Annotate positional argument after keyword argument
     Given a snakemake project
     Given I open a file "foo.smk" with text