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Bump Nextflow 26.04.0
Signed-off-by: Ben Sherman <bentshermann@gmail.com>
1 parent d85d5f0 commit b7e1c77

6 files changed

Lines changed: 31 additions & 29 deletions

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‎build.gradle‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -34,7 +34,7 @@ configurations {
3434
}
3535

3636
dependencies {
37-
implementation 'io.nextflow:nf-lang:26.03.4-edge'
37+
implementation 'io.nextflow:nf-lang:26.04.0'
3838
implementation 'org.apache.groovy:groovy:4.0.31'
3939
implementation 'org.apache.groovy:groovy-json:4.0.31'
4040
implementation 'org.apache.groovy:groovy-yaml:4.0.31'
@@ -46,13 +46,13 @@ dependencies {
4646
runtimeOnly 'org.yaml:snakeyaml:2.2'
4747

4848
// include Nextflow runtime at build-time to extract language definitions
49-
nextflowRuntime 'io.nextflow:nextflow:26.03.4-edge'
49+
nextflowRuntime 'io.nextflow:nextflow:26.04.0'
5050
nextflowRuntime 'io.nextflow:nf-amazon:3.9.0'
5151
nextflowRuntime 'io.nextflow:nf-azure:1.22.2'
5252
nextflowRuntime 'io.nextflow:nf-google:1.27.2'
5353
nextflowRuntime 'io.nextflow:nf-k8s:1.5.2'
5454
nextflowRuntime 'io.nextflow:nf-seqera:0.19.0'
55-
nextflowRuntime 'io.nextflow:nf-tower:1.26.0'
55+
nextflowRuntime 'io.nextflow:nf-tower:1.27.0'
5656
nextflowRuntime 'io.nextflow:nf-wave:1.20.0'
5757

5858
testImplementation ('org.objenesis:objenesis:3.4')

‎src/main/java/nextflow/lsp/services/script/ScriptCodeLensProvider.java‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -152,7 +152,7 @@ public Map<String,Object> convertPipelineToTyped(FormattingOptions options) {
152152
var firstProcess = sn.getProcesses().get(0);
153153
var start = LanguageServerUtils.astNodeToRange(firstProcess).getStart();
154154
var range = new Range(start, start);
155-
var newText = "nextflow.preview.types = true\n\n";
155+
var newText = "nextflow.enable.types = true\n\n";
156156
addTextEdit(textEdits, uri, range, newText);
157157
}
158158
}
@@ -189,7 +189,7 @@ public Map<String,Object> convertScriptToTyped(String documentUri, FormattingOpt
189189
var firstProcess = sn.getProcesses().get(0);
190190
var start = LanguageServerUtils.astNodeToRange(firstProcess).getStart();
191191
var range = new Range(start, start);
192-
var newText = "nextflow.preview.types = true\n\n";
192+
var newText = "nextflow.enable.types = true\n\n";
193193
addTextEdit(textEdits, uri, range, newText);
194194
}
195195

‎src/test/groovy/nextflow/lsp/services/config/ConfigSpecTest.groovy‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -20,7 +20,7 @@ import nextflow.config.control.ConfigParser
2020
import nextflow.config.control.ConfigResolveVisitor
2121
import nextflow.lsp.services.LanguageServerConfiguration
2222
import nextflow.lsp.spec.PluginSpecCache
23-
import nextflow.script.types.Types
23+
import nextflow.script.dsl.Types
2424
import org.codehaus.groovy.control.SourceUnit
2525
import org.codehaus.groovy.control.messages.SyntaxErrorMessage
2626
import org.codehaus.groovy.control.messages.WarningMessage
@@ -241,7 +241,7 @@ class ConfigSpecTest extends Specification {
241241
warnings.size() == 1
242242
warnings[0].getContext().getStartLine() == 1
243243
warnings[0].getContext().getStartColumn() == 1
244-
warnings[0].getMessage() == "Config option 'trace.fields' cannot be assigned to value with type Boolean -- valid types are: List, String"
244+
warnings[0].getMessage() == "Config option 'trace.fields' cannot be assigned to value with type Boolean -- valid types are: List<String>, String"
245245
}
246246

247247
def 'should check return type for dynamic config settings' () {

‎src/test/groovy/nextflow/script/types/TypeCheckingTest.groovy‎

Lines changed: 21 additions & 20 deletions
Original file line numberDiff line numberDiff line change
@@ -21,6 +21,7 @@ import nextflow.script.ast.FeatureFlagNode
2121
import nextflow.script.control.ScriptParser
2222
import nextflow.script.control.ScriptResolveVisitor
2323
import nextflow.script.control.TypeCheckingVisitorEx
24+
import nextflow.script.dsl.Types
2425
import org.codehaus.groovy.ast.ASTNode
2526
import org.codehaus.groovy.ast.ClassHelper
2627
import org.codehaus.groovy.ast.expr.ConstantExpression
@@ -53,7 +54,7 @@ class TypeCheckingTest extends Specification {
5354

5455
SourceUnit parse(String contents) {
5556
def source = scriptParser.parse('main.nf', contents.stripIndent())
56-
source.getAST()?.addFeatureFlag(new FeatureFlagNode("nextflow.preview.types", new ConstantExpression(true)))
57+
source.getAST()?.addFeatureFlag(new FeatureFlagNode("nextflow.enable.types", new ConstantExpression(true)))
5758
new ScriptResolveVisitor(source, scriptParser.compiler().compilationUnit(), Types.DEFAULT_SCRIPT_IMPORTS, Collections.emptyList()).visit()
5859
new TypeCheckingVisitorEx(source).visit()
5960
return source
@@ -145,7 +146,7 @@ class TypeCheckingTest extends Specification {
145146
when:
146147
def errors = getErrors(
147148
'''\
148-
nextflow.preview.types = true
149+
nextflow.enable.types = true
149150
150151
workflow hello {
151152
emit:
@@ -162,7 +163,7 @@ class TypeCheckingTest extends Specification {
162163
when:
163164
errors = getErrors(
164165
'''\
165-
nextflow.preview.types = true
166+
nextflow.enable.types = true
166167
167168
workflow hello {
168169
emit:
@@ -178,7 +179,7 @@ class TypeCheckingTest extends Specification {
178179
when:
179180
def errors = getErrors(
180181
'''\
181-
nextflow.preview.types = true
182+
nextflow.enable.types = true
182183
183184
workflow {
184185
main:
@@ -218,7 +219,7 @@ class TypeCheckingTest extends Specification {
218219
when:
219220
errors = getErrors(
220221
'''\
221-
nextflow.preview.types = true
222+
nextflow.enable.types = true
222223
223224
workflow {
224225
main:
@@ -651,7 +652,7 @@ class TypeCheckingTest extends Specification {
651652
expect:
652653
check(
653654
'''
654-
nextflow.preview.types = true
655+
nextflow.enable.types = true
655656
656657
workflow hello {
657658
take:
@@ -673,7 +674,7 @@ class TypeCheckingTest extends Specification {
673674
when:
674675
def exp = parseExpression(
675676
'''\
676-
nextflow.preview.types = true
677+
nextflow.enable.types = true
677678
678679
workflow hello {
679680
emit:
@@ -692,7 +693,7 @@ class TypeCheckingTest extends Specification {
692693
when:
693694
exp = parseExpression(
694695
'''\
695-
nextflow.preview.types = true
696+
nextflow.enable.types = true
696697
697698
workflow hello {
698699
emit:
@@ -711,7 +712,7 @@ class TypeCheckingTest extends Specification {
711712
when:
712713
exp = parseExpression(
713714
'''\
714-
nextflow.preview.types = true
715+
nextflow.enable.types = true
715716
716717
workflow hello {
717718
emit:
@@ -733,7 +734,7 @@ class TypeCheckingTest extends Specification {
733734
expect:
734735
check(
735736
'''
736-
nextflow.preview.types = true
737+
nextflow.enable.types = true
737738
738739
process hello {
739740
input:
@@ -756,7 +757,7 @@ class TypeCheckingTest extends Specification {
756757
and:
757758
check(
758759
'''
759-
nextflow.preview.types = true
760+
nextflow.enable.types = true
760761
761762
process hello {
762763
input:
@@ -775,7 +776,7 @@ class TypeCheckingTest extends Specification {
775776
and:
776777
check(
777778
'''
778-
nextflow.preview.types = true
779+
nextflow.enable.types = true
779780
780781
process hello {
781782
input:
@@ -798,7 +799,7 @@ class TypeCheckingTest extends Specification {
798799
and:
799800
check(
800801
'''
801-
nextflow.preview.types = true
802+
nextflow.enable.types = true
802803
803804
process hello {
804805
input:
@@ -826,7 +827,7 @@ class TypeCheckingTest extends Specification {
826827
expect:
827828
check(
828829
'''\
829-
nextflow.preview.types = true
830+
nextflow.enable.types = true
830831
831832
process hello {
832833
input:
@@ -845,7 +846,7 @@ class TypeCheckingTest extends Specification {
845846
and:
846847
check(
847848
'''\
848-
nextflow.preview.types = true
849+
nextflow.enable.types = true
849850
850851
process hello {
851852
input:
@@ -867,7 +868,7 @@ class TypeCheckingTest extends Specification {
867868
when:
868869
def exp = parseExpression(
869870
'''\
870-
nextflow.preview.types = true
871+
nextflow.enable.types = true
871872
872873
process hello {
873874
input:
@@ -892,7 +893,7 @@ class TypeCheckingTest extends Specification {
892893
when:
893894
exp = parseExpression(
894895
'''\
895-
nextflow.preview.types = true
896+
nextflow.enable.types = true
896897
897898
process hello {
898899
input:
@@ -917,7 +918,7 @@ class TypeCheckingTest extends Specification {
917918
when:
918919
exp = parseExpression(
919920
'''\
920-
nextflow.preview.types = true
921+
nextflow.enable.types = true
921922
922923
process hello {
923924
input:
@@ -942,7 +943,7 @@ class TypeCheckingTest extends Specification {
942943
when:
943944
exp = parseExpression(
944945
'''\
945-
nextflow.preview.types = true
946+
nextflow.enable.types = true
946947
947948
process hello {
948949
input:
@@ -969,7 +970,7 @@ class TypeCheckingTest extends Specification {
969970
expect:
970971
check(
971972
'''
972-
nextflow.preview.types = true
973+
nextflow.enable.types = true
973974
974975
process hello {
975976
output:

‎src/test/groovy/nextflow/script/types/TypeCheckingUtilsTest.groovy‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -124,7 +124,7 @@ class TypeCheckingUtilsTest extends Specification {
124124
when:
125125
def exp = parseExpression(
126126
'''
127-
nextflow.preview.types = true
127+
nextflow.enable.types = true
128128
129129
process hello {
130130
input:
@@ -154,7 +154,7 @@ class TypeCheckingUtilsTest extends Specification {
154154
when:
155155
def exp = parseExpression(
156156
'''
157-
nextflow.preview.types = true
157+
nextflow.enable.types = true
158158
159159
workflow hello {
160160
take:

‎src/test/groovy/nextflow/script/types/TypesTest.groovy‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -16,6 +16,7 @@
1616

1717
package nextflow.script.types
1818

19+
import nextflow.script.dsl.Types
1920
import org.codehaus.groovy.ast.ClassHelper
2021
import org.codehaus.groovy.ast.ClassNode
2122
import org.codehaus.groovy.ast.GenericsType

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