Trim down the docker image size - #55
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jairideout
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Aug 26, 2026
| # chown has to be run in the same command otherwise the files are copied in the next docker layer | ||
| RUN pip install --no-cache-dir -U pip && \ | ||
| pip install --no-cache-dir -q -r /root/requirements.txt && \ | ||
| rm -rf /usr/local/lib/python3.13/site-packages/biom/tests && \ |
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Are there other tests we could remove, e.g. scikit-bio's?
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Yes, but they're not that big - I figured simplicity wins over chipping away more tiny pieces 🤷
| ENV DEBIAN_FRONTEND noninteractive | ||
| RUN apt-get update && apt-get install -yq --no-install-recommends \ | ||
| apt-transport-https \ | ||
| build-essential \ |
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Can you confirm with @clausmith @lynchde on the wheel-only change?
| # jupyter_contrib_nbextensions imports pkg_resources, which setuptools removed | ||
| # in v81; the python:3.13-slim base image no longer ships setuptools at all. | ||
| setuptools<81 | ||
| awscli |
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I wonder why we had this as a dependency
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I vaguely remember at one point the main container uploading the ipynb file. It's now done in a sidecar that has a different image with awscli.
audy
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Aug 26, 2026
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This PR trims down the size of the docker image from ~3.8GB to ~1.2GB. Out of the remaining size, >1GB are the Python packages that we probably want to keep around.
The image could be further trimmed a bit but not without consequence (e.g. slower package loading on start). Let's only get to that if we deem it necessary.
Note: this PR removes the compilers and their tooling (~600MB) from the image so only Python packages with wheels can be installed, if a package requires compilation, it will fail the
pip install.