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

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Merged
pditommaso merged 5 commits into from
Jun 14, 2026
Merged

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
4a510ad
Merge branch 'master' into default-micromamba-v2-template
pditommaso Jun 4, 2026
eeecf09
Merge branch 'master' into default-micromamba-v2-template
pditommaso Jun 14, 2026
745e323
test: cover default conda template routing to micromamba v2
pditommaso Jun 14, 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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46 changes: 42 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)
Expand Down Expand Up @@ -751,6 +751,44 @@ class ContainerHelperTest extends Specification {
'''.stripIndent()
}

def 'should create conda docker file with packages using micromamba v2 by default'() {
given:
def CHANNELS = ['conda-forge', 'bioconda']
def PACKAGES = ['bwa=0.7.15', 'salmon=1.1.1']
def packages = new PackagesSpec(
type: PackagesSpec.Type.CONDA,
entries: PACKAGES,
channels: CHANNELS)
and:
// no explicit build template: should default to micromamba v2
def req = new SubmitContainerTokenRequest(packages:packages)
when:
def result = ContainerHelper.containerFileFromRequest(req)

then:
result =='''\
FROM mambaorg/micromamba:2-amazon2023 AS build
COPY --chown=$MAMBA_USER:$MAMBA_USER conda.yml /tmp/conda.yml
RUN (micromamba install -y -n base -f /tmp/conda.yml > /tmp/mamba.log 2>&1 \\
&& cat /tmp/mamba.log \\
|| (cat /tmp/mamba.log >&2 && grep -q __cuda /tmp/mamba.log \\
&& CONDA_OVERRIDE_CUDA="99" micromamba install -y -n base -f /tmp/conda.yml)) \\
&& micromamba install -y -n base conda-forge::procps-ng \\
&& micromamba clean -a -y \\
&& micromamba env export --name base --explicit > environment.lock \\
&& echo ">> CONDA_LOCK_START" \\
&& cat environment.lock \\
&& echo "<< CONDA_LOCK_END"

FROM ubuntu:24.04 AS prod
ARG MAMBA_ROOT_PREFIX="/opt/conda"
ENV MAMBA_ROOT_PREFIX=$MAMBA_ROOT_PREFIX
COPY --from=build "$MAMBA_ROOT_PREFIX" "$MAMBA_ROOT_PREFIX"
USER root
ENV PATH="$MAMBA_ROOT_PREFIX/bin:$PATH"
'''.stripIndent()
}

def 'should create conda docker file with packages and micromamba v2 custom image'() {
given:
def CHANNELS = ['conda-forge', 'bioconda']
Expand Down
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;
}
Expand Down
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
}
Expand Down
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