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Add Pixi-specific CLI options for container builds
Add support for Pixi build customization when building conda-based containers: - --pixi-build-image: Pixi builder image for package installation - --pixi-base-image: Base image for the final container - --pixi-base-packages: Base packages to include - --pixi-run-command: Custom Dockerfile RUN commands These options are passed via PixiOpts when building with conda packages or conda files, allowing users to customize Pixi-based container builds. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
1 parent 8c85b26 commit 9797b10

3 files changed

Lines changed: 234 additions & 2 deletions

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‎app/build.gradle‎

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@@ -19,8 +19,8 @@ repositories {
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}
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dependencies {
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implementation 'io.seqera:wave-api:1.31.0'
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implementation 'io.seqera:wave-utils:1.31.0'
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implementation 'io.seqera:wave-api:1.31.2'
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implementation 'io.seqera:wave-utils:1.31.2'
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implementation 'info.picocli:picocli:4.6.1'
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implementation 'com.squareup.moshi:moshi:1.15.2'
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implementation 'com.squareup.moshi:moshi-adapters:1.15.2'

‎app/src/main/java/io/seqera/wave/cli/App.java‎

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@@ -66,6 +66,7 @@
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import io.seqera.wave.cli.util.YamlHelper;
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import io.seqera.wave.config.CondaOpts;
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import io.seqera.wave.config.CranOpts;
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import io.seqera.wave.config.PixiOpts;
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import io.seqera.wave.util.DockerIgnoreFilter;
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import io.seqera.wave.util.Packer;
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import org.apache.commons.lang3.StringUtils;
@@ -176,6 +177,18 @@ public class App implements Runnable {
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@Option(names = {"--cran-run-command"}, paramLabel = "''", description = "Dockerfile RUN commands used to build the container.")
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private List<String> cranRunCommands;
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@Option(names = {"--pixi-build-image"}, paramLabel = "''", description = "Pixi builder image used to build the container (default: ${DEFAULT-VALUE}).")
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private String pixiBuildImage = PixiOpts.DEFAULT_PIXI_IMAGE;
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@Option(names = {"--pixi-base-image"}, paramLabel = "''", description = "Base image for the final Pixi container (default: ${DEFAULT-VALUE}).")
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private String pixiBaseImage = PixiOpts.DEFAULT_BASE_IMAGE;
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@Option(names = {"--pixi-base-packages"}, paramLabel = "''", description = "Base packages to be installed in the Pixi container (default: ${DEFAULT-VALUE}).")
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private String pixiBasePackages = PixiOpts.DEFAULT_PACKAGES;
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@Option(names = {"--pixi-run-command"}, paramLabel = "''", description = "Dockerfile RUN commands used to build the container.")
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private List<String> pixiRunCommands;
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@Option(names = {"--log-level"}, paramLabel = "''", description = "Set the application log level. One of: OFF, ERROR, WARN, INFO, DEBUG, TRACE and ALL")
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private String logLevel;
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@@ -631,6 +644,15 @@ private CranOpts cranOpts() {
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;
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}
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private PixiOpts pixiOpts() {
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return new PixiOpts()
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.withPixiImage(pixiBuildImage)
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.withBaseImage(pixiBaseImage)
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.withBasePackages(pixiBasePackages)
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.withCommands(pixiRunCommands)
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;
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}
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protected String containerFileBase64() {
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return !isEmpty(containerFile)
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? encodePathBase64(containerFile)
@@ -642,6 +664,7 @@ protected PackagesSpec packagesSpec() {
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return new PackagesSpec()
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.withType(PackagesSpec.Type.CONDA)
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.withCondaOpts(condaOpts())
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.withPixiOpts(pixiOpts())
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.withEnvironment(encodePathBase64(condaFile))
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.withChannels(condaChannels())
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;
@@ -651,6 +674,7 @@ protected PackagesSpec packagesSpec() {
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return new PackagesSpec()
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.withType(PackagesSpec.Type.CONDA)
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.withCondaOpts(condaOpts())
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.withPixiOpts(pixiOpts())
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.withEntries(condaPackages)
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.withChannels(condaChannels())
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;

‎app/src/test/groovy/io/seqera/wave/cli/AppPixiOptsTest.groovy‎

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@@ -0,0 +1,208 @@
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/*
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* Copyright 2023-2025, 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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*/
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package io.seqera.wave.cli
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import java.nio.file.Files
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import io.seqera.wave.api.PackagesSpec
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import io.seqera.wave.config.PixiOpts
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import picocli.CommandLine
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import spock.lang.Specification
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/**
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* Test App Pixi prefixed options
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*
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* @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
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*/
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class AppPixiOptsTest extends Specification {
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def 'should include pixi opts with conda package' () {
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given:
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def app = new App()
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String[] args = ["--conda-package", "foo"]
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when:
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new CommandLine(app).parseArgs(args)
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and:
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def req = app.createRequest()
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then:
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req.packages.type == PackagesSpec.Type.CONDA
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req.packages.entries == ['foo']
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and:
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req.packages.pixiOpts == new PixiOpts(
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pixiImage: PixiOpts.DEFAULT_PIXI_IMAGE,
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baseImage: PixiOpts.DEFAULT_BASE_IMAGE,
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basePackages: PixiOpts.DEFAULT_PACKAGES
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)
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}
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def 'should include pixi opts with conda file' () {
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given:
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def CONDA_RECIPE = '''
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name: my-recipe
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dependencies:
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- one=1.0
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- two:2.0
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'''.stripIndent(true)
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and:
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def folder = Files.createTempDirectory('test')
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def condaFile = folder.resolve('conda.yml');
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condaFile.text = CONDA_RECIPE
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and:
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def app = new App()
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String[] args = ["--conda-file", condaFile.toString()]
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when:
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new CommandLine(app).parseArgs(args)
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and:
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def req = app.createRequest()
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then:
74+
req.packages.type == PackagesSpec.Type.CONDA
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and:
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req.packages.pixiOpts == new PixiOpts(
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pixiImage: PixiOpts.DEFAULT_PIXI_IMAGE,
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baseImage: PixiOpts.DEFAULT_BASE_IMAGE,
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basePackages: PixiOpts.DEFAULT_PACKAGES
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)
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cleanup:
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folder?.deleteDir()
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}
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def 'should include custom pixi build image with conda package' () {
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given:
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def app = new App()
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String[] args = [
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"--conda-package", "foo",
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"--pixi-build-image", "my/pixi:latest"
92+
]
93+
94+
when:
95+
new CommandLine(app).parseArgs(args)
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and:
97+
def req = app.createRequest()
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then:
99+
req.packages.type == PackagesSpec.Type.CONDA
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req.packages.entries == ['foo']
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and:
102+
req.packages.pixiOpts == new PixiOpts(
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pixiImage: 'my/pixi:latest',
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baseImage: PixiOpts.DEFAULT_BASE_IMAGE,
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basePackages: PixiOpts.DEFAULT_PACKAGES
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)
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}
108+
109+
def 'should include custom pixi base image with conda package' () {
110+
given:
111+
def app = new App()
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String[] args = [
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"--conda-package", "foo",
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"--pixi-base-image", "ubuntu:22.04"
115+
]
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117+
when:
118+
new CommandLine(app).parseArgs(args)
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and:
120+
def req = app.createRequest()
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then:
122+
req.packages.type == PackagesSpec.Type.CONDA
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req.packages.entries == ['foo']
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and:
125+
req.packages.pixiOpts == new PixiOpts(
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pixiImage: PixiOpts.DEFAULT_PIXI_IMAGE,
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baseImage: 'ubuntu:22.04',
128+
basePackages: PixiOpts.DEFAULT_PACKAGES
129+
)
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}
131+
132+
def 'should include custom pixi base packages with conda package' () {
133+
given:
134+
def app = new App()
135+
String[] args = [
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"--conda-package", "foo",
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"--pixi-base-packages", "conda-forge::curl"
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]
139+
140+
when:
141+
new CommandLine(app).parseArgs(args)
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and:
143+
def req = app.createRequest()
144+
then:
145+
req.packages.type == PackagesSpec.Type.CONDA
146+
req.packages.entries == ['foo']
147+
and:
148+
req.packages.pixiOpts == new PixiOpts(
149+
pixiImage: PixiOpts.DEFAULT_PIXI_IMAGE,
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baseImage: PixiOpts.DEFAULT_BASE_IMAGE,
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basePackages: 'conda-forge::curl'
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)
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}
154+
155+
def 'should include pixi run commands with conda package' () {
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given:
157+
def app = new App()
158+
String[] args = [
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"--conda-package", "foo",
160+
"--pixi-run-command", "RUN apt-get update",
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"--pixi-run-command", "RUN apt-get install -y curl"
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]
163+
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when:
165+
new CommandLine(app).parseArgs(args)
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and:
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def req = app.createRequest()
168+
then:
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req.packages.type == PackagesSpec.Type.CONDA
170+
req.packages.entries == ['foo']
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and:
172+
req.packages.pixiOpts == new PixiOpts(
173+
pixiImage: PixiOpts.DEFAULT_PIXI_IMAGE,
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baseImage: PixiOpts.DEFAULT_BASE_IMAGE,
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basePackages: PixiOpts.DEFAULT_PACKAGES,
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commands: ['RUN apt-get update', 'RUN apt-get install -y curl']
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)
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}
179+
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def 'should include all pixi options' () {
181+
given:
182+
def app = new App()
183+
String[] args = [
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"--conda-package", "foo",
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"--conda-package", "bar",
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"--pixi-build-image", "custom/pixi:v1",
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"--pixi-base-image", "debian:12",
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"--pixi-base-packages", "conda-forge::wget",
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"--pixi-run-command", "RUN one",
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"--pixi-run-command", "RUN two"
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]
192+
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when:
194+
new CommandLine(app).parseArgs(args)
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and:
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def req = app.createRequest()
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then:
198+
req.packages.type == PackagesSpec.Type.CONDA
199+
req.packages.entries == ['foo', 'bar']
200+
and:
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req.packages.pixiOpts == new PixiOpts(
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pixiImage: 'custom/pixi:v1',
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baseImage: 'debian:12',
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basePackages: 'conda-forge::wget',
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commands: ['RUN one', 'RUN two']
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)
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}
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}

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