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Merged
jairideout merged 1 commit into from
Dec 15, 2025
Merged

Upgrade to Python 3.13 #51

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16 changes: 8 additions & 8 deletions Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
# Extended from github.com/jupyter/docker-stacks
# See also http://blog.dscpl.com.au/2016/01/roundup-of-docker-issues-when-hosting.html

FROM python:3.9-slim-bullseye
FROM python:3.13-slim-bullseye

LABEL maintainer="Nick Greenfield <nick@onecodex.com>"

Expand Down Expand Up @@ -92,7 +92,7 @@ RUN wget https://ftp.samba.org/pub/cwrap/nss_wrapper-1.1.2.tar.gz && \
rm -rf nss_wrapper

# Copy `onecodex` installed fonts to local directory
RUN cp /usr/local/lib/python3.9/site-packages/onecodex/assets/fonts/*.otf /usr/local/share/fonts && fc-cache
RUN cp /usr/local/lib/python3.13/site-packages/onecodex/assets/fonts/*.otf /usr/local/share/fonts && fc-cache

# Configure container startup
EXPOSE 8888
Expand All @@ -103,8 +103,8 @@ CMD ["jupyter", "notebook"]

# Add assets
RUN mkdir /opt/onecodex/
COPY notebook/notebook.html /usr/local/lib/python3.9/site-packages/notebook/templates
COPY notebook/override.css /usr/local/lib/python3.9/site-packages/notebook/static/notebook/css
COPY notebook/notebook.html /usr/local/lib/python3.13/site-packages/notebook/templates
COPY notebook/override.css /usr/local/lib/python3.13/site-packages/notebook/static/notebook/css
COPY notebook/onecodex.js /home/$NB_USER/.jupyter/custom/
COPY notebook/one-codex-spinner.svg /home/$NB_USER/.jupyter/custom/
COPY notebook/override.css /home/$NB_USER/.jupyter/custom/custom.css
Expand All @@ -118,19 +118,19 @@ RUN jupyter nbextension install /usr/local/share/jupyter/customextensions/ \
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/python3.9/site-packages/notebook
RUN cd /usr/local/lib/python3.9/site-packages/notebook \
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

# Finally fix permissions on everything
# See https://github.com/jupyter/docker-stacks/issues/188
# RUN chown -R $NB_USER:root /home/$NB_USER && chmod -R u+rw,g+rw /home/$NB_USER
RUN chown -R $NB_USER:root /home/$NB_USER && find /home/$NB_USER -type d -exec chmod 775 {} \;

ENV PYTHONPATH "/home/jovyan/.local/lib/python3.9"
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/python3.9
RUN chown -R $NB_USER:root /usr/local/lib/python3.13

# Switch to unprivileged user, jovyan
USER $NB_USER
2 changes: 1 addition & 1 deletion requirements.txt
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Expand Up @@ -7,5 +7,5 @@ openpyxl
xlrd
statsmodels
onecodex[all,reports]==0.19.1
taxonomy==0.10.0
taxonomy
widgetsnbextension