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ReproNim
FIX add default header and entrypoint to docker and singularity files
Thanks to the archeological work by @yarikoptic in #620 it was relatively easy to fix. The _header.yaml template was not added anywhere. BTW, I had to rename the template from _header to _default because _header is in conflict with SingularityRenderer._header. Some examples before/after below:
Closes #620
BEFORE $ neurodocker generate docker --base-image ubuntu:20.04 --pkg-manager apt
# Generated by Neurodocker and Reproenv.
FROM ubuntu:20.04
# Save specification to JSON.
RUN printf '{ \
"pkg_manager": "apt", \
"existing_users": [ \
"root" \
], \
"instructions": [ \
{ \
"name": "from_", \
"kwds": { \
"base_image": "ubuntu:20.04" \
} \
} \
] \
}' > /.reproenv.json
# End saving to specification to JSON.
AFTER $ neurodocker generate docker --base-image ubuntu:20.04 --pkg-manager apt
# Generated by Neurodocker and Reproenv.
FROM ubuntu:20.04
ENV LANG="en_US.UTF-8" \
LC_ALL="en_US.UTF-8" \
ND_ENTRYPOINT="/neurodocker/startup.sh"
RUN export ND_ENTRYPOINT="/neurodocker/startup.sh" \
&& apt-get update -qq \
&& apt-get install -y -q --no-install-recommends \
apt-utils \
bzip2 \
ca-certificates \
curl \
locales \
unzip \
&& rm -rf /var/lib/apt/lists/* \
&& sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen \
&& dpkg-reconfigure --frontend=noninteractive locales \
&& update-locale LANG="en_US.UTF-8" \
&& chmod 777 /opt && chmod a+s /opt \
&& mkdir -p /neurodocker \
&& if [ ! -f "$ND_ENTRYPOINT" ]; then \
echo '#!/usr/bin/env bash' >> "$ND_ENTRYPOINT" \
&& echo 'set -e' >> "$ND_ENTRYPOINT" \
&& echo 'export USER="${USER:=`whoami`}"' >> "$ND_ENTRYPOINT" \
&& echo 'if [ -n "$1" ]; then "$@"; else /usr/bin/env bash; fi' >> "$ND_ENTRYPOINT"; \
fi \
&& chmod -R 777 /neurodocker && chmod a+s /neurodocker
ENTRYPOINT ["/neurodocker/startup.sh"]
# Save specification to JSON.
RUN printf '{ \
"pkg_manager": "apt", \
"existing_users": [ \
"root" \
], \
"instructions": [ \
{ \
"name": "from_", \
"kwds": { \
"base_image": "ubuntu:20.04" \
} \
}, \
{ \
"name": "env", \
"kwds": { \
"LANG": "en_US.UTF-8", \
"LC_ALL": "en_US.UTF-8", \
"ND_ENTRYPOINT": "/neurodocker/startup.sh" \
} \
}, \
{ \
"name": "run", \
"kwds": { \
"command": "export ND_ENTRYPOINT=\\"/neurodocker/startup.sh\\"\\napt-get update -qq\\napt-get install -y -q --no-install-recommends \\\\\\n apt-utils \\\\\\n bzip2 \\\\\\n ca-certificates \\\\\\n curl \\\\\\n locales \\\\\\n unzip\\nrm -rf /var/lib/apt/lists/*\\nsed -i -e '"'"'s/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/'"'"' /etc/locale.gen\\ndpkg-reconfigure --frontend=noninteractive locales\\nupdate-locale LANG=\\"en_US.UTF-8\\"\\nchmod 777 /opt && chmod a+s /opt\\nmkdir -p /neurodocker\\nif [ ! -f \\"$ND_ENTRYPOINT\\" ]; then\\n echo '"'"'#!/usr/bin/env bash'"'"' >> \\"$ND_ENTRYPOINT\\"\\n echo '"'"'set -e'"'"' >> \\"$ND_ENTRYPOINT\\"\\n echo '"'"'export USER=\\"${USER:=`whoami`}\\"'"'"' >> \\"$ND_ENTRYPOINT\\"\\n echo '"'"'if [ -n \\"$1\\" ]; then \\"$@\\"; else /usr/bin/env bash; fi'"'"' >> \\"$ND_ENTRYPOINT\\";\\nfi\\nchmod -R 777 /neurodocker && chmod a+s /neurodocker" \
} \
}, \
{ \
"name": "entrypoint", \
"kwds": { \
"args": [ \
"/neurodocker/startup.sh" \
] \
} \
} \
] \
}' > /.reproenv.json
# End saving to specification to JSON.
BEFORE $ neurodocker generate singularity --base-image ubuntu:20.04 --pkg-manager apt
# Generated by Neurodocker and Reproenv.
Bootstrap: docker
From: ubuntu:20.04
%post
# Save specification to JSON.
printf '{ \
"pkg_manager": "apt", \
"existing_users": [ \
"root" \
], \
"instructions": [ \
{ \
"name": "from_", \
"kwds": { \
"base_image": "ubuntu:20.04" \
} \
} \
] \
}' > /.reproenv.json
# End saving to specification to JSON.
AFTER $ neurodocker generate singularity --base-image ubuntu:20.04 --pkg-manager apt
$ neurodocker generate singularity --base-image ubuntu:20.04 --pkg-manager apt
# Generated by Neurodocker and Reproenv.
Bootstrap: docker
From: ubuntu:20.04
%environment
export LANG="en_US.UTF-8"
export LC_ALL="en_US.UTF-8"
export ND_ENTRYPOINT="/neurodocker/startup.sh"
%post
export ND_ENTRYPOINT="/neurodocker/startup.sh"
apt-get update -qq
apt-get install -y -q --no-install-recommends \
apt-utils \
bzip2 \
ca-certificates \
curl \
locales \
unzip
rm -rf /var/lib/apt/lists/*
sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen
dpkg-reconfigure --frontend=noninteractive locales
update-locale LANG="en_US.UTF-8"
chmod 777 /opt && chmod a+s /opt
mkdir -p /neurodocker
if [ ! -f "$ND_ENTRYPOINT" ]; then
echo '#!/usr/bin/env bash' >> "$ND_ENTRYPOINT"
echo 'set -e' >> "$ND_ENTRYPOINT"
echo 'export USER="${USER:=`whoami`}"' >> "$ND_ENTRYPOINT"
echo 'if [ -n "$1" ]; then "$@"; else /usr/bin/env bash; fi' >> "$ND_ENTRYPOINT";
fi
chmod -R 777 /neurodocker && chmod a+s /neurodocker
# Save specification to JSON.
printf '{ \
"pkg_manager": "apt", \
"existing_users": [ \
"root" \
], \
"instructions": [ \
{ \
"name": "from_", \
"kwds": { \
"base_image": "ubuntu:20.04" \
} \
}, \
{ \
"name": "env", \
"kwds": { \
"LANG": "en_US.UTF-8", \
"LC_ALL": "en_US.UTF-8", \
"ND_ENTRYPOINT": "/neurodocker/startup.sh" \
} \
}, \
{ \
"name": "run", \
"kwds": { \
"command": "export ND_ENTRYPOINT=\\"/neurodocker/startup.sh\\"\\napt-get update -qq\\napt-get install -y -q --no-install-recommends \\\\\\n apt-utils \\\\\\n bzip2 \\\\\\n ca-certificates \\\\\\n curl \\\\\\n locales \\\\\\n unzip\\nrm -rf /var/lib/apt/lists/*\\nsed -i -e '"'"'s/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/'"'"' /etc/locale.gen\\ndpkg-reconfigure --frontend=noninteractive locales\\nupdate-locale LANG=\\"en_US.UTF-8\\"\\nchmod 777 /opt && chmod a+s /opt\\nmkdir -p /neurodocker\\nif [ ! -f \\"$ND_ENTRYPOINT\\" ]; then\\n echo '"'"'#!/usr/bin/env bash'"'"' >> \\"$ND_ENTRYPOINT\\"\\n echo '"'"'set -e'"'"' >> \\"$ND_ENTRYPOINT\\"\\n echo '"'"'export USER=\\"${USER:=`whoami`}\\"'"'"' >> \\"$ND_ENTRYPOINT\\"\\n echo '"'"'if [ -n \\"$1\\" ]; then \\"$@\\"; else /usr/bin/env bash; fi'"'"' >> \\"$ND_ENTRYPOINT\\";\\nfi\\nchmod -R 777 /neurodocker && chmod a+s /neurodocker" \
} \
}, \
{ \
"name": "entrypoint", \
"kwds": { \
"args": [ \
"/neurodocker/startup.sh" \
] \
} \
} \
] \
}' > /.reproenv.json
# End saving to specification to JSON.
%runscript
/neurodocker/startup.sh
Codecov Report
All modified and coverable lines are covered by tests :white_check_mark:
Project coverage is 88.06%. Comparing base (
b7ddf6f) to head (41a3eef). Report is 22 commits behind head on master.
:exclamation: Current head 41a3eef differs from pull request most recent head 15c5300
Please upload reports for the commit 15c5300 to get more accurate results.
Additional details and impacted files
@@ Coverage Diff @@
## master #623 +/- ##
==========================================
+ Coverage 88.00% 88.06% +0.05%
==========================================
Files 11 11
Lines 1034 1039 +5
==========================================
+ Hits 910 915 +5
Misses 124 124
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would it be too much to ask to add/extend some test to ensure we do not loose this again going forward?
@yarikoptic I added a test but now a different test is failing for unrelated reasons (#628)