Merge branch 'master' into features/#407-duplicated-args-inspection-t…

…op-level
JetBrains-Research · Nov 20, 2021 · b3a6af1 · b3a6af1
2 parents d382440 + 2ea11e3
commit b3a6af1
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Showing 7 changed files with 33 additions and 27 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -13,6 +13,8 @@ Released on ...
 
 ### Fixed
 - 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))
+- Completion for .smk files in module 'snakefile' section (see [#428](https://github.com/JetBrains-Research/snakecharm/issues/428))
 - Default path "config/config.yaml" now supported (see [#363](https://github.com/JetBrains-Research/snakecharm/issues/363))
 - Access by index to input/output sections with 'multiext' function (see [#278](https://github.com/JetBrains-Research/snakecharm/issues/278))
 - 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))

diff --git a/src/main/kotlin/com/jetbrains/snakecharm/inspections/SmkRuleRedeclarationInspection.kt b/src/main/kotlin/com/jetbrains/snakecharm/inspections/SmkRuleRedeclarationInspection.kt
@@ -2,8 +2,7 @@ package com.jetbrains.snakecharm.inspections
 
 import com.intellij.codeInspection.LocalInspectionToolSession
 import com.intellij.codeInspection.ProblemHighlightType
-import com.intellij.codeInspection.ProblemHighlightType.GENERIC_ERROR
-import com.intellij.codeInspection.ProblemHighlightType.WEAK_WARNING
+import com.intellij.codeInspection.ProblemHighlightType.*
 import com.intellij.codeInspection.ProblemsHolder
 import com.intellij.psi.PsiElement
 import com.intellij.psi.util.PsiTreeUtil
@@ -102,7 +101,7 @@ class SmkRuleRedeclarationInspection : SnakemakeInspection() {
                         ) == null
 
                         val (msg, severity) = when {
-                            isTopLevelDeclaration -> SnakemakeBundle.message("INSP.NAME.rule.redeclaration") to GENERIC_ERROR
+                            isTopLevelDeclaration -> SnakemakeBundle.message("INSP.NAME.rule.redeclaration") to GENERIC_ERROR_OR_WARNING
                             else -> SnakemakeBundle.message("INSP.NAME.rule.redeclaration.possible") to WEAK_WARNING
                         }
                         registerProblem(ruleLike, msg, severity)

diff --git a/...ain/kotlin/com/jetbrains/snakecharm/inspections/SmkRuleSectionAfterExecutionInspection.kt b/...ain/kotlin/com/jetbrains/snakecharm/inspections/SmkRuleSectionAfterExecutionInspection.kt
@@ -45,7 +45,6 @@ class SmkRuleSectionAfterExecutionInspection : SnakemakeInspection() {
                                 "INSP.NAME.rule.section.after.execution.message",
                                 executionSection.name!!
                             ),
-                            ProblemHighlightType.GENERIC_ERROR,
                             null,
                             MoveExecutionSectionToEndOfRuleQuickFix(SmartPointerManager.createPointer(executionSection))
                         )

diff --git a/...tlin/com/jetbrains/snakecharm/inspections/smksl/SmkSLWildcardNameIsConfusingInspection.kt b/...tlin/com/jetbrains/snakecharm/inspections/smksl/SmkSLWildcardNameIsConfusingInspection.kt
@@ -12,10 +12,10 @@ import com.jetbrains.snakecharm.stringLanguage.lang.psi.references.SmkSLWildcard
 
 class SmkSLWildcardNameIsConfusingInspection : SnakemakeInspection() {
     override fun buildVisitor(
-                holder: ProblemsHolder,
-                isOnTheFly: Boolean,
-                session: LocalInspectionToolSession
-        ) = object : SmkSLInspectionVisitor(holder, session) {
+        holder: ProblemsHolder,
+        isOnTheFly: Boolean,
+        session: LocalInspectionToolSession
+    ) = object : SmkSLInspectionVisitor(holder, session) {
 
         override fun visitSmkSLReferenceExpression(expr: SmkSLReferenceExpressionImpl) {
             // expr.isQualified: 'wildcards' in 'wildcards.input'
@@ -28,16 +28,20 @@ class SmkSLWildcardNameIsConfusingInspection : SnakemakeInspection() {
                     expr.containingSection()?.getParentRuleOrCheckPoint() ?: return
 
                     registerProblem(
-                            expr,
-                            SnakemakeBundle.message("INSP.NAME.wildcards.confusing.name.like.section.message", wildcardName),
-                            PyRenameElementQuickFix(expr)
+                        expr,
+                        SnakemakeBundle.message(
+                            "INSP.NAME.wildcards.confusing.name.like.section.message",
+                            wildcardName
+                        ),
+                        ProblemHighlightType.WARNING,
+                        null,
+                        PyRenameElementQuickFix(expr),
                     )
                 } else if ('.' in wildcardName) {
                     // E.g. 'wildcards.name' or 'foo.boo.doo'
                     registerProblem(
-                            ref.getWildcardTrueExpression(),
-                            SnakemakeBundle.message("INSP.NAME.wildcards.confusing.name.with.dot.message", wildcardName),
-                            ProblemHighlightType.GENERIC_ERROR
+                        ref.getWildcardTrueExpression(),
+                        SnakemakeBundle.message("INSP.NAME.wildcards.confusing.name.with.dot.message", wildcardName)
                     )
                 }
             }

diff --git a/src/main/kotlin/com/jetbrains/snakecharm/lang/psi/SmkFileReference.kt b/src/main/kotlin/com/jetbrains/snakecharm/lang/psi/SmkFileReference.kt
@@ -171,7 +171,7 @@ class SmkIncludeReference(
     path: String
 ) : SmkFileReference(element, textRange, stringLiteralExpression, path) {
     override fun getVariants() = collectFileSystemItemLike {
-        it is SmkFile && it.name != element.containingFile.name
+        it is SmkFile && it.originalFile != element.containingFile.originalFile
     }
 }
 

diff --git a/src/main/resources/META-INF/plugin.xml b/src/main/resources/META-INF/plugin.xml
@@ -474,7 +474,7 @@
     <localInspection
             language="SnakemakeSL" shortName="SmkSLWildcardNameIsConfusingInspection"
             enabledByDefault="true"
-            level="WARNING"
+            level="ERROR"
             suppressId="SmkSLWildcardNameIsConfusing"
             bundle="SnakemakeBundle"
             groupKey="INSP.GROUP.snakemake"

diff --git a/src/test/resources/features/completion/path_in_section_completion.feature b/src/test/resources/features/completion/path_in_section_completion.feature
@@ -2,28 +2,30 @@ Feature: Complete file name in conda section
 
   Scenario Outline: Completion list in path dependent section
     Given a snakemake project
-    Given a file "xoo.<ext>" with text
+    Given a file "<file>" with text
     """
     """
     Given I open a file "foo.smk" with text
     """
     <rule_like> NAME:
-      <section>: "x"
+      <section>: ""
     """
-    When I put the caret after x
+    When I put the caret after : "
     And I invoke autocompletion popup and see a text:
     """
     <rule_like> NAME:
-      <section>: "xoo.<ext>"
+      <section>: "<file>"
     """
     Examples:
-      | rule_like  | section   | ext      |
-      | rule       | conda     | yaml     |
-      | checkpoint | conda     | yaml     |
-      | rule       | conda     | yml      |
-      | rule       | notebook  | py.ipynb |
-      | rule       | notebook  | r.ipynb  |
-      | module     | snakefile | smk      |
+      | rule_like  | section   | file                  |
+      | rule       | conda     | xoo.yaml              |
+      | checkpoint | conda     | xoo.yaml              |
+      | rule       | conda     | xoo.yml               |
+      | rule       | notebook  | xoo.py.ipynb          |
+      | rule       | notebook  | xoo.r.ipynb           |
+      | module     | snakefile | xoo.smk               |
+      | module     | snakefile | other/files/foo.smk   |
+      | module     | snakefile | other/files/Snakefile |
 
   Scenario Outline: Completion list when there are no appropriate files
     Given a snakemake project