Singleuser updates (#10)

* Updated dockerfiles + requirements (handling cpu-only build packages).

* Updated medcat version, re-added m-cat scripts download.

Author: vladd-bit

.github/workflows/submodule_sync.yml

@@ -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

Dockerfile_hub

@@ -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+# https://download.pytorch.org/whl/cpu is out of date on packages, using alternative URL for CPU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

Dockerfile_singleuser

@@ -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
@@ -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