Optimize Dockerfile

[radusuciu]

Hi, I'm submitting this as a draft PR because I think there's room for additional improvements here.

This initial and minimal change was motivated by a build server being down which impacted the ability to build the contrib Docker image since it was downloading sources for coinor and eigen from this build server. Apparently, those specific versions of those libraries aren't really needed and they can be pulled down from apt. Doing so reduces the container build-time significantly (700 -> 140 seconds on my machine).

As long as the team is interested, I would like to continue to optimize this image further, and then can look at these images as well: https://github.com/OpenMS/dockerfiles/, and eventually maybe we can move everything to the main OpenMS repo as suggested in this issue: OpenMS/dockerfiles#28

[radusuciu]

Next improvements:

• install all deps in one step
• revisit cmake install method
• make software.version LABEL dynamic (use build arg)
• move COPY . /contrib to last step
• add .dockerignore
• update action and make use of GHA cache

Also, I'd like to ask... is this even needed as a separate image?

[radusuciu]

One thing I haven't changed is the cmake install method. Here's the current:

RUN <<-EOF
    cmake_ubuntu_version=$(lsb_release -cs)
    if ! wget -q --method=HEAD "https://apt.kitware.com/ubuntu/dists/$cmake_ubuntu_version/Release"; then
      bash -c "$(wget -O - https://apt.kitware.com/kitware-archive.sh)"
    else
      wget -qO - https://apt.kitware.com/kitware-archive.sh | bash -s -- --release $cmake_ubuntu_version
    fi
    apt-get -y update
    apt-get install -y cmake
EOF

This requires a few packages including wget, whatever provides lsb_release, maybe ca-certificates and a few others.

Here's an alternative for your consideration:

ARG CMAKE_VERSION="3.28.1"

# installing cmake
WORKDIR /tmp
ADD https://github.com/Kitware/CMake/releases/download/v${CMAKE_VERSION}/cmake-${CMAKE_VERSION}-linux-x86_64.sh cmake.sh
RUN <<-EOF
    mkdir -p /opt/cmake
    sh cmake.sh --skip-license --prefix=/opt/cmake
    ln -s /opt/cmake/bin/cmake /usr/local/bin/cmake
    ln -s /opt/cmake/bin/ctest /usr/local/bin/ctest
    rm -rf /tmp/*
EOF

I like the alternative because the version is explicit and it requires fewer extra packages. However, I'm not really all that experience in this space, so please let me know if you'd like me to implement this change or just stick with what we've got.

[jpfeuffer]

No clear preference. Both should work. We can go with your solution.

[radusuciu]

Unless there are any other suggestions/comments, I think this is ready for merge.

I guess https://github.com/OpenMS/contrib/blob/master/dockerfiles/pyopenms/manylinux/Dockerfile could be the subject of a separate PR if you're interested in streamlining that too a bit?

[timosachsenberg]

@jpfeuffer looks good to me. What do you think?
I also think streamlining the manylinux one would be great!
Also feel free to add yourself to the AUTHORS file in the OpenMS repo. This work is highly appreciated!

[jpfeuffer]

Yes I think we are at a point that we can try merging and see. Thanks!!!

[radusuciu]

Thanks! Feel free to tag me in if there are any issues now or later

I'll take a look at the manylinux Dockerfile, seems it's pretty straightforward to reduce the number of layers at least