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add docker layer caching and nb_conda_kernels #13

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merged 7 commits into from
Dec 16, 2022

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aryarm
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@aryarm aryarm commented Dec 16, 2022

This PR makes two changes:

  1. It adds docker layer caching to our Github action via these changes
    This allows us to cache portions of our build process, so that re-builds happen only for the portions of our Dockerfile that need to be rerun, potentially saving us substantial amounts of time.
    For example, let's say that we make a commit in which the only change is to one of our conda environment files. And let's say that the environment file in question gets COPY-ed into the container on line 10 of the Dockerfile.
    Docker layer caching means that when the container image gets rebuilt for this commit, Docker will automatically restart the build process on line 10 instead of starting from the beginning of the Dockerfile.
  2. It adds nb_conda_kernels in our Dockerfile and resolves use nb_conda_kernels instead of installing each kernel manually #10

@aryarm aryarm requested a review from wesuuu December 16, 2022 06:51
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aryarm commented Dec 16, 2022

Wesley, I'm marking you as a reviewer in case you have any comments. Besides a quick check on our work, we'd be curious to hear if you think any of these changes might have unintended side effects or if there are consequences we might not have considered. But also feel free to ignore this PR, especially if you're out for a (well deserved) holiday break now!

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aryarm commented Dec 16, 2022

Not sure why the build failed. The logs seem to indicate that it's some sort of permission issue. I'm guessing it's something to due with the fact that this PR originates from a fork.

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wesuuu commented Dec 16, 2022

@aryarm Your changes look good and I looked into this issue. I'm not sure if it's possible for a forked branch from another organization (e.g. biom262) is able to push to this ghcr.io repo (see docker/build-push-action#463 (comment)).

In any case, once you merge the pull request, the action should clear if the docker build is successful.

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aryarm commented Dec 16, 2022

ok, thanks for the quick response!

merging now

@aryarm aryarm merged commit 66b2834 into ucsd-ets:master Dec 16, 2022
aryarm added a commit that referenced this pull request Feb 9, 2023
remove rstudio from wi24 environment
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use nb_conda_kernels instead of installing each kernel manually
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