Requirements fix (#9)

* Pinning requirements.txt

* Singleuser dockerfile update.

* Docker compose update (prod).

* Fix volume mounts for users (use fixed name (backwards compatibility).

* R kernel install updates.

* Requirements revert.

* Added workflow permissions.

Author: vladd-bit

.github/workflows/docker-build.yml

@@ -1,5 +1,8 @@
 name: docker-jupyter-hub-all
 
+permissions:
+  contents: read
+
 on:
   push:
     branches: ['**']

.github/workflows/submodule_sync.yml

@@ -1,5 +1,8 @@
 name: submodules-sync
 
+permissions:
+  contents: read
+
 on:
   push:
     branches: ['**']

Dockerfile_singleuser

@@ -216,7 +216,7 @@ COPY ./requirements.txt /srv/jupyterhub/
 RUN if [ "$GPU_BUILD" = "true" ] && [ "$CPU_ARCHITECTURE" = "amd64" ]; then \
       uv pip install --system --no-cache-dir -r /srv/jupyterhub/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/requirements.txt ; \
     fi
 
 #######################################################################################################

config/jupyterhub_config.py

@@ -106,7 +106,7 @@ class LocalNativeAuthenticator(NativeAuthenticator, LocalAuthenticator):
 class DockerSpawner(dockerspawner.DockerSpawner):
     def start(self):
         # username is self.user.name
-        #self.volumes = {"jupyterhub-user-{}".format(self.user.name): NOTEBOOK_DIR}
+        self.volumes = {"jupyterhub-user-{}".format(self.user.name): NOTEBOOK_DIR}
 
         # Mount the real users Docker volume on the host to the notebook user"s
         # # notebook directory in the container

docker/docker-compose.yml

@@ -18,8 +18,7 @@ services:
       - jupyter-hub-shared-scratch:/home/jovyan/scratch
       - jupyter-hub-vol:/srv/jupyterhub
       # Security configs
-      - ./${DEFAULT_SECURITY_DIR:-../security/}root-ca.key:/srv/jupyterhub/root-ca.key:ro
-      - ./${DEFAULT_SECURITY_DIR:-../security/}root-ca.pem:/srv/jupyterhub/root-ca.pem:ro
+      - ./${DEFAULT_SECURITY_DIR:-../security/}:/srv/jupyterhub/security:ro
       - ../config/jupyterhub_cookie_secret:/srv/jupyterhub/jupyterhub_cookie_secret:ro
       # User list and jupyter config
       - ../config/jupyterhub_config.py:/srv/jupyterhub/jupyterhub_config.py:ro

requirements.txt

@@ -1,9 +1,11 @@
 wheel==0.45.1
+
+
 virtualenv==20.31.2
 ipywidgets==8.1.7
 requests>=2.32.2
 jupyter==1.1.1
-jupyterlab>=4.2.7  
+jupyterlab>=4.2.0
 jupyterlab_widgets==3.0.15
 jupyter_contrib_core==0.4.2
 jupyter_contrib_nbextensions==0.7.0
@@ -42,12 +44,11 @@ PyYAML==6.0.2
 opencv-python==4.11.0.86
 plotly==6.1.1
 click==8.2.1
-torchvision>=0.20.1
 traitlets==5.14.3
 xnat>=0.5.2
 
 # ES stack
-opensearch-py>=2.0.0
+opensearch-py>=2.8.0
 
 # code utils
 ruff==0.12.12

scripts/r_kernel_install.sh

@@ -33,7 +33,6 @@ install.packages(
        )
 
 install.packages("lme4")
-install.packages("survminer")
 install.packages("nloptr")
 install.packages('IRkernel')