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CU-869az43jq: MedCAT v2: Distribute cogstack-es and medcat-scripts #6

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Merged
merged 7 commits into from
Oct 29, 2025
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CU-869az43jq: MedCAT v2: Distribute cogstack-es and medcat-scripts #6

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4860d4b
CU-869az43jq: Remvoe gitmodules
mart-r Oct 27, 2025
3c3a394
CU-869az43jq: Add explicit medcat requirement
mart-r Oct 27, 2025
0c20f0b
CU-869az43jq: Initial changes for new cogstack-es and medcat-scripts
mart-r Oct 27, 2025
cfc10fa
CU-869az43jq: Remove whitespace
mart-r Oct 29, 2025
43e4582
CU-869az43jq: Update download script usage for scripts download
mart-r Oct 29, 2025
1b266e8
CU-869az43jq: Add cogstack-es installation
mart-r Oct 29, 2025
133fb7b
CU-869az43jq: Remove submodule sync workflow
mart-r Oct 29, 2025
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54 changes: 0 additions & 54 deletions .github/workflows/submodule_sync.yml
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6 changes: 0 additions & 6 deletions .gitmodules
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17 changes: 12 additions & 5 deletions Dockerfile_singleuser
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,9 @@ ARG http_proxy
ARG https_proxy
ARG no_proxy

# NOTE: set to ES8 or Elasticsearch 8 or OS for Opensearch
ARG COGSTACK_BACKEND=ES9

# set to "true" for the GPU build
ARG GPU_BUILD=false

Expand Down Expand Up @@ -212,16 +215,20 @@ RUN uv pip install --upgrade --system pip setuptools wheel

# install the rest of the packages including medcat
COPY ./requirements.txt /srv/jupyterhub/
# install requirements for working with cogstack scripts
COPY notebooks/demo_working_with_cogstack/requirements.txt /srv/jupyterhub/working_with_cogstack_requirements.txt

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/working_with_cogstack_requirements.txt ; \
# NOTE: it'll create the medcat-scripts folder within
uv run python -m medcat download-scripts /srv/jupyterhub/ && \
uv pip install --system --no-cache-dir -r /srv/jupyterhub/medcat-scripts/requirements.txt ; \
else \
uv pip install --system --no-cache-dir -r /srv/jupyterhub/requirements.txt --extra-index-url https://download.pytorch.org/whl/cpu/ && \
uv pip install --system --no-cache-dir -r /srv/jupyterhub/working_with_cogstack_requirements.txt --extra-index-url https://download.pytorch.org/whl/cpu/ ; \
fi
uv run python -m medcat download-scripts /srv/jupyterhub/ && \
uv pip install --system --no-cache-dir -r /srv/jupyterhub/medcat-scripts/requirements.txt --extra-index-url https://download.pytorch.org/whl/cpu/ ; \
fi && \
# install cogstack-es (Cogstack class)
uv pip install "cogstack-es[$COGSTACK_BACKEND]" && \
mv /srv/jupyterhub/medcat-scripts/notebooks/* /home/jovyan/work/. # move notebooks

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

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2 changes: 2 additions & 0 deletions requirements.txt
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Original file line number Diff line number Diff line change
@@ -1,4 +1,6 @@
wheel==0.45.1
medcat==2.2.0
# TODO: cogstack-es
virtualenv==20.31.2
ipywidgets==8.1.7
jupyter==1.1.1
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