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test: Add comprehensive test suite for package management
Adds thorough testing coverage for the unified package system: - PackageSpecTest: Unit tests for package specifications - PackageManagerTest: Tests for package parsing and feature flags - package-test.nf: Basic usage examples and functionality tests - integration-test.nf: Tests backward compatibility and deprecation warnings with both old and new syntax Tests cover all major use cases including single packages, multiple packages, different providers, environment files, and configuration options. 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]> Signed-off-by: Edmund Miller <[email protected]>
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‎modules/nextflow/src/test/groovy/nextflow/packages/PackageManagerTest.groovy‎

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/*
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* Copyright 2013-2024, Seqera Labs
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*
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* Licensed under the Apache License, Version 2.0 (the "License");
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* you may not use this file except in compliance with the License.
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* You may obtain a copy of the License at
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*
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* http://www.apache.org/licenses/LICENSE-2.0
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*
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* Unless required by applicable law or agreed to in writing, software
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* distributed under the License is distributed on an "AS IS" BASIS,
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* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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* See the License for the specific language governing permissions and
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* limitations under the License.
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*/
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package nextflow.packages
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import nextflow.Session
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import spock.lang.Specification
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/**
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* Unit tests for PackageManager
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*
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* @author Edmund Miller <[email protected]>
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*/
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class PackageManagerTest extends Specification {
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def 'should parse string package definition'() {
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when:
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def spec = PackageManager.parseSpec('samtools=1.17', 'conda')
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then:
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spec.provider == 'conda'
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spec.entries == ['samtools=1.17']
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}
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def 'should parse list package definition'() {
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when:
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def spec = PackageManager.parseSpec(['samtools=1.17', 'bcftools=1.18'], 'conda')
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then:
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spec.provider == 'conda'
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spec.entries == ['samtools=1.17', 'bcftools=1.18']
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}
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def 'should parse map package definition'() {
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when:
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def spec = PackageManager.parseSpec([
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provider: 'pixi',
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packages: ['samtools=1.17', 'bcftools=1.18'],
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channels: ['conda-forge', 'bioconda']
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], 'conda')
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then:
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spec.provider == 'pixi'
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spec.entries == ['samtools=1.17', 'bcftools=1.18']
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spec.channels == ['conda-forge', 'bioconda']
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}
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def 'should parse map with environment file'() {
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when:
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def spec = PackageManager.parseSpec([
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provider: 'conda',
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environment: 'name: test\ndependencies:\n - samtools'
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], null)
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then:
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spec.provider == 'conda'
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spec.environment == 'name: test\ndependencies:\n - samtools'
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spec.hasEnvironmentFile()
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}
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def 'should use default provider when not specified'() {
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when:
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def spec = PackageManager.parseSpec([
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packages: ['samtools=1.17']
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], 'conda')
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then:
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spec.provider == 'conda'
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spec.entries == ['samtools=1.17']
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}
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def 'should handle single package in map'() {
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when:
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def spec = PackageManager.parseSpec([
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provider: 'pixi',
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packages: 'samtools=1.17'
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], null)
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then:
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spec.provider == 'pixi'
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spec.entries == ['samtools=1.17']
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}
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def 'should handle single channel in map'() {
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when:
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def spec = PackageManager.parseSpec([
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provider: 'conda',
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packages: ['samtools'],
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channels: 'bioconda'
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], null)
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then:
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spec.provider == 'conda'
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spec.entries == ['samtools']
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spec.channels == ['bioconda']
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}
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def 'should throw error for invalid package definition'() {
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when:
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PackageManager.parseSpec(123, 'conda')
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then:
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thrown(IllegalArgumentException)
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}
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def 'should check if feature is enabled'() {
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given:
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def session = Mock(Session) {
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getConfig() >> Mock() {
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navigate('nextflow.preview.package', false) >> enabled
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}
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}
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expect:
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PackageManager.isEnabled(session) == result
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where:
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enabled | result
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true | true
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false | false
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null | false
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}
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}

‎modules/nextflow/src/test/groovy/nextflow/packages/PackageSpecTest.groovy‎

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/*
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* Copyright 2013-2024, Seqera Labs
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*
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* Licensed under the Apache License, Version 2.0 (the "License");
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* you may not use this file except in compliance with the License.
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* You may obtain a copy of the License at
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*
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* http://www.apache.org/licenses/LICENSE-2.0
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*
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* Unless required by applicable law or agreed to in writing, software
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* distributed under the License is distributed on an "AS IS" BASIS,
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* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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* See the License for the specific language governing permissions and
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* limitations under the License.
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*/
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package nextflow.packages
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import spock.lang.Specification
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/**
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* Unit tests for PackageSpec
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*
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* @author Edmund Miller <[email protected]>
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*/
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class PackageSpecTest extends Specification {
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def 'should create package spec with builder pattern'() {
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when:
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def spec = new PackageSpec()
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.withProvider('conda')
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.withEntries(['samtools=1.17', 'bcftools=1.18'])
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.withChannels(['conda-forge', 'bioconda'])
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then:
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spec.provider == 'conda'
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spec.entries == ['samtools=1.17', 'bcftools=1.18']
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spec.channels == ['conda-forge', 'bioconda']
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spec.isValid()
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spec.hasEntries()
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!spec.hasEnvironmentFile()
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}
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def 'should create package spec with environment file'() {
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when:
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def spec = new PackageSpec()
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.withProvider('conda')
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.withEnvironment('name: myenv\ndependencies:\n - samtools=1.17')
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then:
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spec.provider == 'conda'
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spec.environment == 'name: myenv\ndependencies:\n - samtools=1.17'
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spec.isValid()
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!spec.hasEntries()
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spec.hasEnvironmentFile()
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}
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def 'should validate spec correctly'() {
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expect:
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new PackageSpec().withProvider('conda').withEntries(['samtools']).isValid()
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new PackageSpec().withProvider('conda').withEnvironment('deps').isValid()
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!new PackageSpec().withProvider('conda').isValid() // no entries or environment
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!new PackageSpec().withEntries(['samtools']).isValid() // no provider
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}
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def 'should handle constructor with parameters'() {
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when:
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def spec = new PackageSpec('pixi', ['samtools=1.17'], [channels: ['conda-forge']])
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then:
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spec.provider == 'pixi'
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spec.entries == ['samtools=1.17']
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spec.options == [channels: ['conda-forge']]
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}
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def 'should handle empty or null values'() {
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when:
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def spec = new PackageSpec('conda', null, null)
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then:
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spec.provider == 'conda'
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spec.entries == []
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spec.options == [:]
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}
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}

‎tests/integration-test.config‎

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/*
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* Configuration for integration test
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* Tests both old and new package management systems
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*/
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// Enable the new package management system
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nextflow.preview.package = true
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// Configure package providers
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packages {
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provider = 'conda' // default provider
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}
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// Keep existing conda/pixi configs for backward compatibility
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conda {
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enabled = true
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channels = ['conda-forge', 'bioconda']
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}
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pixi {
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enabled = true
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}

‎tests/integration-test.nf‎

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#!/usr/bin/env nextflow
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/*
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* Integration test for the unified package management system
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* This test demonstrates the new package directive with backward compatibility
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*/
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nextflow.enable.dsl=2
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// Old style conda directive - should show deprecation warning when preview.package is enabled
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process oldStyleConda {
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conda 'samtools=1.17'
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output:
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stdout
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script:
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"""
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echo "Old style conda: \$(samtools --version 2>/dev/null | head -1 || echo 'not available')"
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"""
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}
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// Old style pixi directive - should show deprecation warning when preview.package is enabled
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process oldStylePixi {
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pixi 'samtools'
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output:
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stdout
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script:
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"""
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echo "Old style pixi: \$(samtools --version 2>/dev/null | head -1 || echo 'not available')"
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"""
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}
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// New style package directive with explicit provider
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process newStyleExplicit {
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package "samtools=1.17", provider: "conda"
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output:
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stdout
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script:
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"""
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echo "New style explicit: \$(samtools --version 2>/dev/null | head -1 || echo 'not available')"
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"""
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}
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// New style package directive with default provider (from config)
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process newStyleDefault {
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package "samtools=1.17"
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output:
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stdout
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script:
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"""
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echo "New style default: \$(samtools --version 2>/dev/null | head -1 || echo 'not available')"
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"""
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}
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// New style package directive with multiple packages
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process newStyleMultiple {
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package ["samtools=1.17", "bcftools=1.18"], provider: "conda"
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output:
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stdout
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script:
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"""
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echo "New style multiple: samtools \$(samtools --version 2>/dev/null | head -1 | cut -d' ' -f2 || echo 'n/a'), bcftools \$(bcftools --version 2>/dev/null | head -1 | cut -d' ' -f2 || echo 'n/a')"
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"""
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}
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workflow {
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oldStyleConda() | view
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oldStylePixi() | view
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newStyleExplicit() | view
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newStyleDefault() | view
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newStyleMultiple() | view
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}

‎tests/package-test.config‎

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/*
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* Configuration file for package management test
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*/
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// Enable the preview feature
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nextflow.preview.package = true
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// Configure the default package provider
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packages {
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provider = 'conda'
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conda {
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channels = ['conda-forge', 'bioconda']
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}
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}

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