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Use micromamba/v2 as default build template for conda packages #1024

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Use micromamba/v2 as default build template for conda packages #1024

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5209b67
Use micromamba/v2 as default build template for conda packages
pditommaso Apr 9, 2026
827895b
Fix BuildTemplateTest to expect CONDA_MICROMAMBA_V2 as default
pditommaso Apr 9, 2026
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8 changes: 4 additions & 4 deletions src/main/groovy/io/seqera/wave/util/ContainerHelper.groovy
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Original file line number Diff line number Diff line change
Expand Up @@ -61,12 +61,12 @@ class ContainerHelper {
final spec = req.packages

// Default templates based on package type (when no explicit template)
if( spec.type == PackagesSpec.Type.CONDA && (!req.buildTemplate || req.buildTemplate==CONDA_MICROMAMBA_V1) ) {
return CondaHelper.containerFile(spec, singularity)
}
if( req.buildTemplate == CONDA_MICROMAMBA_V2 ) {
if( spec.type == PackagesSpec.Type.CONDA && (!req.buildTemplate || req.buildTemplate==CONDA_MICROMAMBA_V2) ) {
return CondaHelper.containerFileV2(spec, req.containerImage, singularity)
}
if( req.buildTemplate == CONDA_MICROMAMBA_V1 ) {
return CondaHelper.containerFile(spec, singularity)
}
if( req.buildTemplate == CONDA_PIXI_V1 ) {
return PixiHelper.containerFile(spec, req.containerImage, singularity)
}
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8 changes: 4 additions & 4 deletions src/test/groovy/io/seqera/wave/util/ContainerHelperTest.groovy
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Expand Up @@ -52,7 +52,7 @@ class ContainerHelperTest extends Specification {
def CONDA_OPTS = new CondaOpts([basePackages: 'foo::one bar::two'])
def PACKAGES = ['https://foo.com/lock.yml']
def packages = new PackagesSpec(type: PackagesSpec.Type.CONDA, entries: PACKAGES, channels: CHANNELS, condaOpts: CONDA_OPTS)
def req = new SubmitContainerTokenRequest(packages: packages, format: 'sif')
def req = new SubmitContainerTokenRequest(packages: packages, format: 'sif', buildTemplate: BuildTemplate.CONDA_MICROMAMBA_V1)

when:
def result = ContainerHelper.containerFileFromRequest(req)
Expand Down Expand Up @@ -81,7 +81,7 @@ class ContainerHelperTest extends Specification {
def CONDA_OPTS = new CondaOpts([basePackages: 'foo::one bar::two'])
def PACKAGES = ['https://foo.com/lock.yml']
def packages = new PackagesSpec(type: PackagesSpec.Type.CONDA, entries: PACKAGES, channels: CHANNELS, condaOpts: CONDA_OPTS)
def req = new SubmitContainerTokenRequest(packages: packages)
def req = new SubmitContainerTokenRequest(packages: packages, buildTemplate: BuildTemplate.CONDA_MICROMAMBA_V1)

when:
def result = ContainerHelper.containerFileFromRequest(req)
Expand Down Expand Up @@ -109,7 +109,7 @@ class ContainerHelperTest extends Specification {
def CONDA_OPTS = new CondaOpts([basePackages: 'foo::one bar::two'])
def PACKAGES = ['bwa=0.7.15', 'salmon=1.1.1']
def packages = new PackagesSpec(type: PackagesSpec.Type.CONDA, entries: PACKAGES, channels: CHANNELS, condaOpts: CONDA_OPTS)
def req = new SubmitContainerTokenRequest(packages: packages, format: 'sif')
def req = new SubmitContainerTokenRequest(packages: packages, format: 'sif', buildTemplate: BuildTemplate.CONDA_MICROMAMBA_V1)

when:
def result = ContainerHelper.containerFileFromRequest(req)
Expand Down Expand Up @@ -139,7 +139,7 @@ class ContainerHelperTest extends Specification {
def CONDA_OPTS = new CondaOpts([basePackages: 'foo::one bar::two'])
def PACKAGES = ['bwa=0.7.15', 'salmon=1.1.1']
def packages = new PackagesSpec(type: PackagesSpec.Type.CONDA, entries: PACKAGES, channels: CHANNELS, condaOpts: CONDA_OPTS)
def req = new SubmitContainerTokenRequest(packages: packages)
def req = new SubmitContainerTokenRequest(packages: packages, buildTemplate: BuildTemplate.CONDA_MICROMAMBA_V1)

when:
def result = ContainerHelper.containerFileFromRequest(req)
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3 changes: 3 additions & 0 deletions wave-api/src/main/java/io/seqera/wave/api/BuildTemplate.java
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Expand Up @@ -58,6 +58,9 @@ public static String defaultTemplate(PackagesSpec packages) {
if (packages == null) {
return null;
}
if( packages.type == PackagesSpec.Type.CONDA ) {
return CONDA_MICROMAMBA_V2;
}
if( packages.type == PackagesSpec.Type.CRAN ) {
return CRAN_INSTALLR_V1;
}
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2 changes: 1 addition & 1 deletion wave-api/src/test/groovy/io/seqera/wave/api/BuildTemplateTest.groovy
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Expand Up @@ -30,7 +30,7 @@ class BuildTemplateTest extends Specification {
where:
PACKAGES | EXPECTED
new PackagesSpec(type: PackagesSpec.Type.CRAN) | BuildTemplate.CRAN_INSTALLR_V1
new PackagesSpec(type: PackagesSpec.Type.CONDA) | null
new PackagesSpec(type: PackagesSpec.Type.CONDA) | BuildTemplate.CONDA_MICROMAMBA_V2
null | null
new PackagesSpec() | null
}
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