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Fix no-user-in-docker-container-when-using---build-template-condapixiv1 #974

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Fix no-user-in-docker-container-when-using---build-template-condapixiv1 #974

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4 changes: 4 additions & 0 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 @@ -17,6 +17,10 @@ FROM {{base_image}} AS final
COPY --from=build /opt/wave/.pixi/envs/default /opt/wave/.pixi/envs/default
COPY --from=build /shell-hook.sh /shell-hook.sh

# set user and environment variables for Python compatibility
USER root
ENV USER=root

# set the entrypoint to the shell-hook script (activate the environment and run the command)
# no more pixi needed in the final container
ENTRYPOINT ["/bin/bash", "/shell-hook.sh"]
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20 changes: 14 additions & 6 deletions src/test/groovy/io/seqera/wave/util/ContainerHelperTest.groovy
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Expand Up @@ -646,6 +646,10 @@ class ContainerHelperTest extends Specification {
COPY --from=build /opt/wave/.pixi/envs/default /opt/wave/.pixi/envs/default
COPY --from=build /shell-hook.sh /shell-hook.sh

# set user and environment variables for Python compatibility
USER root
ENV USER=root

# set the entrypoint to the shell-hook script (activate the environment and run the command)
# no more pixi needed in the final container
ENTRYPOINT ["/bin/bash", "/shell-hook.sh"]
Expand Down Expand Up @@ -676,28 +680,32 @@ class ContainerHelperTest extends Specification {
then:
result =='''\
FROM ghcr.io/prefix-dev/pixi:0.47.0-jammy-cuda-12.8.1 AS build

COPY conda.yml /opt/wave/conda.yml
WORKDIR /opt/wave

RUN pixi init --import /opt/wave/conda.yml \\
&& pixi add foo::one bar::two \\
&& pixi shell-hook > /shell-hook.sh \\
&& echo 'exec "$@"' >> /shell-hook.sh \\
&& echo ">> CONDA_LOCK_START" \\
&& cat /opt/wave/pixi.lock \\
&& echo "<< CONDA_LOCK_END"

FROM base/image AS final

# copy the pixi environment in the final container
COPY --from=build /opt/wave/.pixi/envs/default /opt/wave/.pixi/envs/default
COPY --from=build /shell-hook.sh /shell-hook.sh


# set user and environment variables for Python compatibility
USER root
ENV USER=root

# set the entrypoint to the shell-hook script (activate the environment and run the command)
# no more pixi needed in the final container
ENTRYPOINT ["/bin/bash", "/shell-hook.sh"]

# Default command for "docker run"
CMD ["/bin/bash"]
'''.stripIndent()
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12 changes: 12 additions & 0 deletions src/test/groovy/io/seqera/wave/util/TemplateUtilsTest.groovy
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Expand Up @@ -371,6 +371,10 @@ class TemplateUtilsTest extends Specification {
COPY --from=build /opt/wave/.pixi/envs/default /opt/wave/.pixi/envs/default
COPY --from=build /shell-hook.sh /shell-hook.sh

# set user and environment variables for Python compatibility
USER root
ENV USER=root

# set the entrypoint to the shell-hook script (activate the environment and run the command)
# no more pixi needed in the final container
ENTRYPOINT ["/bin/bash", "/shell-hook.sh"]
Expand Down Expand Up @@ -402,6 +406,10 @@ class TemplateUtilsTest extends Specification {
COPY --from=build /opt/wave/.pixi/envs/default /opt/wave/.pixi/envs/default
COPY --from=build /shell-hook.sh /shell-hook.sh

# set user and environment variables for Python compatibility
USER root
ENV USER=root

# set the entrypoint to the shell-hook script (activate the environment and run the command)
# no more pixi needed in the final container
ENTRYPOINT ["/bin/bash", "/shell-hook.sh"]
Expand Down Expand Up @@ -436,6 +444,10 @@ class TemplateUtilsTest extends Specification {
COPY --from=build /opt/wave/.pixi/envs/default /opt/wave/.pixi/envs/default
COPY --from=build /shell-hook.sh /shell-hook.sh

# set user and environment variables for Python compatibility
USER root
ENV USER=root

# set the entrypoint to the shell-hook script (activate the environment and run the command)
# no more pixi needed in the final container
ENTRYPOINT ["/bin/bash", "/shell-hook.sh"]
Expand Down