Skip to content

Trim down the docker image size #55

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
pkonieczny wants to merge 1 commit into
base: master
Choose a base branch
from
Open

Trim down the docker image size #55

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
10 changes: 10 additions & 0 deletions .dockerignore
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,10 @@
.git
.github
test
Makefile
README.md
LICENSE
.dockerignore
**/__pycache__
**/*.pyc
.DS_Store
67 changes: 37 additions & 30 deletions Dockerfile
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,29 @@
# Extended from github.com/jupyter/docker-stacks
# See also http://blog.dscpl.com.au/2016/01/roundup-of-docker-issues-when-hosting.html

# Build the nss_wrapper separately
FROM python:3.13-slim-bullseye AS nss-builder

ENV DEBIAN_FRONTEND noninteractive
ENV NSS_WRAPPER_VERSION 1.1.2

RUN apt-get update && apt-get install -yq --no-install-recommends \
build-essential \
ca-certificates \
cmake \
wget \
&& rm -rf /var/lib/apt/lists/*

RUN wget -q https://ftp.samba.org/pub/cwrap/nss_wrapper-${NSS_WRAPPER_VERSION}.tar.gz && \
mkdir nss_wrapper && \
tar -xC nss_wrapper --strip-components=1 -f nss_wrapper-${NSS_WRAPPER_VERSION}.tar.gz && \
mkdir nss_wrapper/obj && \
(cd nss_wrapper/obj && \
cmake -DCMAKE_INSTALL_PREFIX=/usr/local -DLIB_SUFFIX=64 .. && \
make && \
make install)


FROM python:3.13-slim-bullseye

LABEL maintainer="Nick Greenfield <nick@onecodex.com>"
Expand All @@ -13,28 +36,20 @@ USER root
# features (e.g., download as all possible file formats)
ENV DEBIAN_FRONTEND noninteractive
RUN apt-get update && apt-get install -yq --no-install-recommends \
apt-transport-https \
build-essential \

@jairideout jairideout Aug 26, 2026

Copy link
Copy Markdown
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Can you confirm with @clausmith @lynchde on the wheel-only change?

bzip2 \
ca-certificates \
cmake \
curl \
fontconfig \
fonts-dejavu \
gcc \
gfortran \
git \
gnupg \
locales \
python-dev \
patch \
procps \
libffi7 \
libpango-1.0-0 \
libpangoft2-1.0-0 \
libcairo2 \
sudo \
unzip \
vim \
wget \
fonts-texgyre \
xz-utils \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/*

Expand All @@ -47,6 +62,8 @@ ADD https://github.com/krallin/tini/releases/download/${TINI_VERSION}/tini /usr/
RUN chmod +x /usr/local/bin/tini \
&& echo "12d20136605531b09a2c2dac02ccee85e1b874eb322ef6baf7561cd93f93c855 /usr/local/bin/tini" | sha256sum -c -

COPY --from=nss-builder /usr/local/lib64/libnss_wrapper.so /usr/local/lib64/

# Configure environment
ENV SHELL /bin/bash
ENV NB_USER jovyan
Expand All @@ -69,8 +86,12 @@ RUN mkdir /home/$NB_USER/work && \


ADD requirements.txt /root/
RUN pip install -U pip && \
pip install -q -r /root/requirements.txt
# Install Python packages, allow full access for the NB_USER
# 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 && \

@jairideout jairideout Aug 26, 2026

Copy link
Copy Markdown
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Are there other tests we could remove, e.g. scikit-bio's?

@pkonieczny pkonieczny Aug 26, 2026

Copy link
Copy Markdown
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Yes, but they're not that big - I figured simplicity wins over chipping away more tiny pieces 🤷

chown -R $NB_USER:root /usr/local/lib/python3.13

# Activate ipywidgets extension in the environment that runs the notebook server
RUN jupyter nbextension enable --py widgetsnbextension
Expand All @@ -79,18 +100,6 @@ RUN jupyter contrib nbextension install --user && \

WORKDIR /home/$NB_USER/work

# Install nss_wrapper
RUN wget https://ftp.samba.org/pub/cwrap/nss_wrapper-1.1.2.tar.gz && \
mkdir nss_wrapper && \
tar -xC nss_wrapper --strip-components=1 -f nss_wrapper-1.1.2.tar.gz && \
rm nss_wrapper-1.1.2.tar.gz && \
mkdir nss_wrapper/obj && \
(cd nss_wrapper/obj && \
cmake -DCMAKE_INSTALL_PREFIX=/usr/local -DLIB_SUFFIX=64 .. && \
make && \
make install) && \
rm -rf nss_wrapper

# Copy `onecodex` installed fonts to local directory
RUN cp /usr/local/lib/python3.13/site-packages/onecodex/assets/fonts/*.otf /usr/local/share/fonts && fc-cache

Expand Down Expand Up @@ -120,7 +129,8 @@ RUN chmod +x /usr/local/bin/token_notebook.py
# Add patch to jupyter notebook for export to One Codex document portal
COPY notebook/notebook.patch /usr/local/lib/python3.13/site-packages/notebook
RUN cd /usr/local/lib/python3.13/site-packages/notebook \
&& patch -p0 < notebook.patch
&& patch -p0 < notebook.patch \
&& chown -R $NB_USER:root /usr/local/lib/python3.13/site-packages/notebook

# Finally fix permissions on everything
# See https://github.com/jupyter/docker-stacks/issues/188
Expand All @@ -129,8 +139,5 @@ RUN chown -R $NB_USER:root /home/$NB_USER && find /home/$NB_USER -type d -exec c

ENV PYTHONPATH "/home/jovyan/.local/lib/python3.13"

# Provide full access to the Python directory to allow for pip installs
RUN chown -R $NB_USER:root /usr/local/lib/python3.13

# Switch to unprivileged user, jovyan
USER $NB_USER
1 change: 0 additions & 1 deletion requirements.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,7 +1,6 @@
# 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

@jairideout jairideout Aug 26, 2026

Copy link
Copy Markdown
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I wonder why we had this as a dependency

@pkonieczny pkonieczny Aug 26, 2026

Copy link
Copy Markdown
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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.

biopython
ipywidgets
jupyter_contrib_nbextensions
Expand Down
Loading