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add cuda fallback to pixi template #1071

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5c590d6
add cuda fallback to pixi template
mashehu Jul 3, 2026
e73736b
update tests
mashehu Jul 15, 2026
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13 changes: 6 additions & 7 deletions src/main/java/io/seqera/wave/util/TemplateUtils.java
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Original file line number Diff line number Diff line change
Expand Up @@ -158,7 +158,7 @@ static protected String condaFileTemplate1(String template, PixiOpts opts) {
final Map<String,String> binding = new HashMap<>();
binding.put("base_image", opts.baseImage);
binding.put("pixi_image", opts.pixiImage);
binding.put("base_packages", pixiAddBasePackage0(opts.basePackages,singularity));
binding.put("base_packages", pixiAddBasePackage0(opts.basePackages));

final String result = renderTemplate0(template, binding, List.of("wave_context_dir"));
return addCommands(result, opts.commands, singularity);
Expand Down Expand Up @@ -192,13 +192,12 @@ private static String mambaInstallBasePackage0(String basePackages, boolean sing
: "&& " + result + " \\";
}

private static String pixiAddBasePackage0(String basePackages, boolean singularity) {
String result = !StringUtils.isEmpty(basePackages)
? String.format("pixi add %s", basePackages)
private static String pixiAddBasePackage0(String basePackages) {
// rendered inline after `pixi add conda-forge::which` so that a single
// `pixi add` command solves the whole environment
return !StringUtils.isEmpty(basePackages)
? " " + basePackages
: null;
return result==null || singularity
? result
: "&& " + result + " \\";
}

static private String addCommands(String result, List<String> commands, boolean singularity) {
Expand Down
9 changes: 7 additions & 2 deletions src/main/resources/templates/conda-pixi-v1/dockerfile-conda-file.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,13 @@ COPY conda.yml /opt/wave/conda.yml
WORKDIR /opt/wave

RUN pixi init --import /opt/wave/conda.yml \
&& pixi add conda-forge::which \
{{base_packages}}
&& { pixi add conda-forge::which{{base_packages}} > /tmp/pixi.log 2>&1 \
&& cat /tmp/pixi.log \
|| { cat /tmp/pixi.log >&2 && grep -q __cuda /tmp/pixi.log \
&& pixi workspace system-requirements add cuda 99 \
&& export CONDA_OVERRIDE_CUDA="99" \
&& pixi add conda-forge::which{{base_packages}} ; } ; } \
&& pixi install \
&& pixi shell-hook > /shell-hook.sh \
&& echo 'exec "$@"' >> /shell-hook.sh \
&& echo ">> CONDA_LOCK_START" \
Expand Down
10 changes: 8 additions & 2 deletions src/main/resources/templates/conda-pixi-v1/singularityfile-conda-file.txt
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Expand Up @@ -5,8 +5,14 @@ From: {{pixi_image}}
%post
mkdir /opt/wave && cd /opt/wave
pixi init --import /scratch/conda.yml
pixi add conda-forge::which
{{base_packages}}
pixi add conda-forge::which{{base_packages}} > /tmp/pixi.log 2>&1 \
&& cat /tmp/pixi.log \
|| { cat /tmp/pixi.log >&2 && grep -q __cuda /tmp/pixi.log \
&& pixi workspace system-requirements add cuda 99 \
&& export CONDA_OVERRIDE_CUDA="99" \
&& pixi add conda-forge::which{{base_packages}} ; } \
|| exit 1
pixi install
pixi shell-hook > /shell-hook.sh
echo ">> CONDA_LOCK_START"
cat /opt/wave/pixi.lock
Expand Down
18 changes: 14 additions & 4 deletions src/test/groovy/io/seqera/wave/util/ContainerHelperTest.groovy
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Original file line number Diff line number Diff line change
Expand Up @@ -634,8 +634,13 @@ class ContainerHelperTest extends Specification {
WORKDIR /opt/wave

RUN pixi init --import /opt/wave/conda.yml \\
&& pixi add conda-forge::which \\
&& pixi add conda-forge::procps-ng \\
&& { pixi add conda-forge::which conda-forge::procps-ng > /tmp/pixi.log 2>&1 \\
&& cat /tmp/pixi.log \\
|| { cat /tmp/pixi.log >&2 && grep -q __cuda /tmp/pixi.log \\
&& pixi workspace system-requirements add cuda 99 \\
&& export CONDA_OVERRIDE_CUDA="99" \\
&& pixi add conda-forge::which conda-forge::procps-ng ; } ; } \\
&& pixi install \\
&& pixi shell-hook > /shell-hook.sh \\
&& echo 'exec "$@"' >> /shell-hook.sh \\
&& echo ">> CONDA_LOCK_START" \\
Expand Down Expand Up @@ -687,8 +692,13 @@ class ContainerHelperTest extends Specification {
WORKDIR /opt/wave

RUN pixi init --import /opt/wave/conda.yml \\
&& pixi add conda-forge::which \\
&& pixi add foo::one bar::two \\
&& { pixi add conda-forge::which foo::one bar::two > /tmp/pixi.log 2>&1 \\
&& cat /tmp/pixi.log \\
|| { cat /tmp/pixi.log >&2 && grep -q __cuda /tmp/pixi.log \\
&& pixi workspace system-requirements add cuda 99 \\
&& export CONDA_OVERRIDE_CUDA="99" \\
&& pixi add conda-forge::which foo::one bar::two ; } ; } \\
&& pixi install \\
&& pixi shell-hook > /shell-hook.sh \\
&& echo 'exec "$@"' >> /shell-hook.sh \\
&& echo ">> CONDA_LOCK_START" \\
Expand Down
4 changes: 2 additions & 2 deletions src/test/groovy/io/seqera/wave/util/PixiHelperTest.groovy
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Original file line number Diff line number Diff line change
Expand Up @@ -44,7 +44,7 @@ class PixiHelperTest extends Specification {
result.contains('FROM public.cr.seqera.io/wave/pixi:0.61.0-noble AS build')
result.contains('COPY conda.yml /opt/wave/conda.yml')
result.contains('pixi init --import /opt/wave/conda.yml')
result.contains('pixi add conda-forge::procps-ng')
result.contains('pixi add conda-forge::which conda-forge::procps-ng')
result.contains('pixi shell-hook > /shell-hook.sh')
result.contains('FROM ubuntu:24.04 AS final')
result.contains('COPY --from=build /opt/wave/.pixi/envs/default /opt/wave/.pixi/envs/default')
Expand Down Expand Up @@ -104,7 +104,7 @@ class PixiHelperTest extends Specification {

then:
result.contains('FROM ghcr.io/prefix-dev/pixi:0.47.0-jammy-cuda-12.8.1 AS build')
result.contains('pixi add foo::one bar::two')
result.contains('pixi add conda-forge::which foo::one bar::two')
result.contains('FROM base/image AS final')
}

Expand Down
60 changes: 47 additions & 13 deletions src/test/groovy/io/seqera/wave/util/TemplateUtilsTest.groovy
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Original file line number Diff line number Diff line change
Expand Up @@ -358,8 +358,13 @@ class TemplateUtilsTest extends Specification {
WORKDIR /opt/wave

RUN pixi init --import /opt/wave/conda.yml \\
&& pixi add conda-forge::which \\
&& pixi add foo::bar \\
&& { pixi add conda-forge::which foo::bar > /tmp/pixi.log 2>&1 \\
&& cat /tmp/pixi.log \\
|| { cat /tmp/pixi.log >&2 && grep -q __cuda /tmp/pixi.log \\
&& pixi workspace system-requirements add cuda 99 \\
&& export CONDA_OVERRIDE_CUDA="99" \\
&& pixi add conda-forge::which foo::bar ; } ; } \\
&& pixi install \\
&& pixi shell-hook > /shell-hook.sh \\
&& echo 'exec "$@"' >> /shell-hook.sh \\
&& echo ">> CONDA_LOCK_START" \\
Expand Down Expand Up @@ -394,8 +399,13 @@ class TemplateUtilsTest extends Specification {
WORKDIR /opt/wave

RUN pixi init --import /opt/wave/conda.yml \\
&& pixi add conda-forge::which \\
&& pixi add conda-forge::procps-ng \\
&& { pixi add conda-forge::which conda-forge::procps-ng > /tmp/pixi.log 2>&1 \\
&& cat /tmp/pixi.log \\
|| { cat /tmp/pixi.log >&2 && grep -q __cuda /tmp/pixi.log \\
&& pixi workspace system-requirements add cuda 99 \\
&& export CONDA_OVERRIDE_CUDA="99" \\
&& pixi add conda-forge::which conda-forge::procps-ng ; } ; } \\
&& pixi install \\
&& pixi shell-hook > /shell-hook.sh \\
&& echo 'exec "$@"' >> /shell-hook.sh \\
&& echo ">> CONDA_LOCK_START" \\
Expand Down Expand Up @@ -433,8 +443,13 @@ class TemplateUtilsTest extends Specification {
WORKDIR /opt/wave

RUN pixi init --import /opt/wave/conda.yml \\
&& pixi add conda-forge::which \\
&& pixi add conda-forge::procps-ng \\
&& { pixi add conda-forge::which conda-forge::procps-ng > /tmp/pixi.log 2>&1 \\
&& cat /tmp/pixi.log \\
|| { cat /tmp/pixi.log >&2 && grep -q __cuda /tmp/pixi.log \\
&& pixi workspace system-requirements add cuda 99 \\
&& export CONDA_OVERRIDE_CUDA="99" \\
&& pixi add conda-forge::which conda-forge::procps-ng ; } ; } \\
&& pixi install \\
&& pixi shell-hook > /shell-hook.sh \\
&& echo 'exec "$@"' >> /shell-hook.sh \\
&& echo ">> CONDA_LOCK_START" \\
Expand Down Expand Up @@ -684,8 +699,14 @@ class TemplateUtilsTest extends Specification {
%post
mkdir /opt/wave && cd /opt/wave
pixi init --import /scratch/conda.yml
pixi add conda-forge::which
pixi add conda-forge::procps-ng
pixi add conda-forge::which conda-forge::procps-ng > /tmp/pixi.log 2>&1 \\
&& cat /tmp/pixi.log \\
|| { cat /tmp/pixi.log >&2 && grep -q __cuda /tmp/pixi.log \\
&& pixi workspace system-requirements add cuda 99 \\
&& export CONDA_OVERRIDE_CUDA="99" \\
&& pixi add conda-forge::which conda-forge::procps-ng ; } \\
|| exit 1
pixi install
pixi shell-hook > /shell-hook.sh
echo ">> CONDA_LOCK_START"
cat /opt/wave/pixi.lock
Expand All @@ -705,8 +726,14 @@ class TemplateUtilsTest extends Specification {
%post
mkdir /opt/wave && cd /opt/wave
pixi init --import /scratch/conda.yml
pixi add conda-forge::which
pixi add conda-forge::procps-ng
pixi add conda-forge::which conda-forge::procps-ng > /tmp/pixi.log 2>&1 \\
&& cat /tmp/pixi.log \\
|| { cat /tmp/pixi.log >&2 && grep -q __cuda /tmp/pixi.log \\
&& pixi workspace system-requirements add cuda 99 \\
&& export CONDA_OVERRIDE_CUDA="99" \\
&& pixi add conda-forge::which conda-forge::procps-ng ; } \\
|| exit 1
pixi install
pixi shell-hook > /shell-hook.sh
echo ">> CONDA_LOCK_START"
cat /opt/wave/pixi.lock
Expand All @@ -733,7 +760,14 @@ class TemplateUtilsTest extends Specification {
%post
mkdir /opt/wave && cd /opt/wave
pixi init --import /scratch/conda.yml
pixi add conda-forge::which
pixi add conda-forge::which > /tmp/pixi.log 2>&1 \\
&& cat /tmp/pixi.log \\
|| { cat /tmp/pixi.log >&2 && grep -q __cuda /tmp/pixi.log \\
&& pixi workspace system-requirements add cuda 99 \\
&& export CONDA_OVERRIDE_CUDA="99" \\
&& pixi add conda-forge::which ; } \\
|| exit 1
pixi install
pixi shell-hook > /shell-hook.sh
echo ">> CONDA_LOCK_START"
cat /opt/wave/pixi.lock
Expand All @@ -754,7 +788,7 @@ class TemplateUtilsTest extends Specification {
def result = TemplateUtils.condaFileToDockerFileUsingPixi(PIXI_OPTS)

then:
result.contains('pixi add conda-forge::procps-ng')
result.contains('pixi add conda-forge::which conda-forge::procps-ng')
result.contains('RUN apt-get update')
result.contains('RUN apt-get install -y curl')
}
Expand All @@ -770,7 +804,7 @@ class TemplateUtilsTest extends Specification {
def result = TemplateUtils.condaFileToSingularityFileUsingPixi(PIXI_OPTS)

then:
result.contains('pixi add conda-forge::bash')
result.contains('pixi add conda-forge::which conda-forge::bash')
result.contains('%post')
result.contains('apt-get update')
result.contains('apt-get install -y nano')
Expand Down