FIX add default header and entrypoint to docker and singularity files #623

mvdoc · 2024-06-22T00:52:27Z

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 · 2024-06-22T01:42:50Z

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 88.06%. Comparing base (b7ddf6f) to head (41a3eef).
Report is 22 commits behind head on master.

❗ 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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yarikoptic · 2024-06-22T02:09:01Z

.codespellrc

@@ -0,0 +1,2 @@
+[codespell]
+ignore-words-list = softwares,didi


to not breed config files here we absorbed config to codespell within pyproject.toml, and it has already

❯ grep -A4 codespell pyproject.toml [tool.codespell] # didi -- some name Dear to someone ignore-words-list = "didi" skip = ".git,*.pdf,*.svg,versioneer.py,neurodocker/_version.py"

and probably not in effect for you because you also need tomli library -- otherwise codespell does not try to read from pyproject.toml :-/

as for softwares - let's better fix that changelog, I will send a quick PR

Ah that's the magic. OK removed the .codespellrc

mvdoc · 2024-07-04T20:30:04Z

@kaczmarj @yarikoptic should we merge?

yarikoptic · 2024-07-04T21:12:16Z

would it be too much to ask to add/extend some test to ensure we do not loose this again going forward?

mvdoc · 2024-07-05T17:25:57Z

@yarikoptic I added a test but now a different test is failing for unrelated reasons (#628)

yarikoptic · 2024-07-05T19:17:20Z

indeed unrelated, updated there, let's proceed here!

yarikoptic · 2024-07-05T19:17:49Z

we should release some time soon!

yarikoptic reviewed Jun 22, 2024

View reviewed changes

mvdoc added 5 commits June 21, 2024 20:05

FIX add default header and entrypoint to docker and singularity files

2b83d01

FIX check if the _default template is available

cfe24df

Move logic of default template to _base_generate

45e89bd

Make pre-commit happy

7695af4

Remove .codespellrc

8c60e28

mvdoc force-pushed the fix/addheader branch from ec0836e to 8c60e28 Compare June 22, 2024 03:06

FIX do not show _default template in CLI help

15c5300

mvdoc added 2 commits July 4, 2024 17:45

TST check we have the default header and entrypoint

3a75c2a

FIX changes by black

4e31268

yarikoptic merged commit 4f1fe0a into ReproNim:master Jul 5, 2024
7 of 12 checks passed

yarikoptic added the patch patch tag for release label Jul 5, 2024

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FIX add default header and entrypoint to docker and singularity files #623

FIX add default header and entrypoint to docker and singularity files #623

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yarikoptic commented Jul 5, 2024

		@@ -0,0 +1,2 @@
		[codespell]
		ignore-words-list = softwares,didi

FIX add default header and entrypoint to docker and singularity files #623

FIX add default header and entrypoint to docker and singularity files #623

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