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Merged
merged 2 commits into from
Nov 20, 2025
Merged

Singleuser updates #10

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15957af
Updated dockerfiles + requirements (handling cpu-only build packages).
vladd-bit Nov 20, 2025
586b080
Updated medcat version, re-added m-cat scripts download.
vladd-bit Nov 20, 2025
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57 changes: 0 additions & 57 deletions .github/workflows/submodule_sync.yml
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2 changes: 1 addition & 1 deletion Dockerfile_hub
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Original file line number Diff line number Diff line change
Expand Up @@ -93,7 +93,7 @@ RUN apt-get clean autoclean && apt-get autoremove --purge -y
RUN pip3 install --no-cache-dir --upgrade pip

# utils for jupyterhub
RUN pip3 install --no-cache-dir setuptools wheel virtualenv cython netifaces
RUN pip3 install --no-cache-dir setuptools wheel

# jupyterhub stuff
RUN pip3 install --no-cache-dir ipywidgets importlib_metadata jupyterhub-firstuseauthenticator dockerspawner jupyterhub-nativeauthenticator
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10 changes: 8 additions & 2 deletions Dockerfile_singleuser
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Expand Up @@ -213,12 +213,18 @@ RUN uv pip install --upgrade --system pip setuptools wheel
# install the rest of the packages including medcat
COPY ./requirements.txt /srv/jupyterhub/

# https://download.pytorch.org/whl/cpu is out of date on packages, using alternative URL for CPU
RUN if [ "$GPU_BUILD" = "true" ] && [ "$CPU_ARCHITECTURE" = "amd64" ]; then \
uv pip install --system --no-cache-dir -r /srv/jupyterhub/requirements.txt ; \
uv pip install --system --no-cache-dir -r /srv/jupyterhub/requirements.txt && \
uv run python -m medcat download-scripts /srv/jupyterhub/medcat-scripts ; \
else \
uv pip install --system --no-cache-dir -r /srv/jupyterhub/requirements.txt ; \
uv pip install --system --no-cache-dir -r /srv/jupyterhub/requirements.txt --index-url https://pypi.org/simple && \
uv run python -m medcat download-scripts /srv/jupyterhub/medcat-scripts ; \
fi

# move notebooks
RUN mv /srv/jupyterhub/medcat-scripts/* /home/jovyan/work/.

#######################################################################################################

# install R and other dependencies
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4 changes: 3 additions & 1 deletion requirements.txt
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@@ -1,5 +1,7 @@
wheel==0.45.1

medcat==2.3.0
# TODO: cogstack-es 8/9 handling

virtualenv==20.31.2
ipywidgets==8.1.7
Expand Down Expand Up @@ -34,7 +36,7 @@ dataclasses==0.6
jsonpickle==4.1.0
jsonext==0.4.2
psycopg2==2.9.10
psycopg2-binary==2.9.10
psycopg2-binary>=2.9.10
pyodbc==5.2.0
openpyxl==3.1.5
dvc==3.59.2
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