test julia + bump deps

images/datascience-notebook/Dockerfile

@@ -51,6 +51,11 @@ RUN cat /tmp/jupyter_notebook_config_extra.py >> /etc/jupyter/jupyter_notebook_c
     chmod -R uga+x /etc/jupyter/jupyter_server_config.py && \
     chmod -R uga+x /etc/jupyter/nbgrader_config.py
 
+# Copy our default configuration for jupyterlab extensions
+COPY /scripts/jupyter_settings_overrides.json /opt/conda/share/jupyter/lab/settings/overrides.json
+RUN chown -R jovyan:users /opt/conda/share/jupyter/lab/settings && \
+    chmod 644 /opt/conda/share/jupyter/lab/settings/overrides.json
+
 # Copy over R tests to /opt/manual_tests
 RUN mkdir /opt/manual_tests
 COPY /test/test_r_dump_packages.R /opt/manual_tests
@@ -64,7 +69,7 @@ USER jovyan
 
 # Python/Mamba Deps
 ## Package versions
-ARG JUPYTERSERVER_VERSION=2.14.2 NBGRADER_VERSION=0.9.3 JUPYTERLAB_VERSION=4.2.4 NBCONVERT_VERSION=7.16.4 NOTEBOOK_VERSION=7.2.1 NBCLASSIC_VERSION=1.1.0
+ARG JUPYTERSERVER_VERSION=2.14.2 NBGRADER_VERSION=0.9.3 JUPYTERLAB_VERSION=4.2.5 NBCONVERT_VERSION=7.16.4 NOTEBOOK_VERSION=7.2.1 NBCLASSIC_VERSION=1.1.0
 ARG PANDAS_VERSION=2.2.2 STATSMODELS_VERSION=0.14.2 BOTTLENECK_VERSION=1.3.6 NUMEXPR_VERSION=2.8.4
 
 # Install essential+datascience pip packages 
@@ -83,6 +88,7 @@ RUN mamba install -c conda-forge jupyterhub=$JUPYTERHUB_VERSION jupyter_server=$
     # (TODO: Re-enable collab once RTC is fixed) mamba install -c conda-forge jupyterlab_rise jupyter_server_terminals jupyter-collaboration && \
     mamba install -c conda-forge jupyterlab_rise jupyter_server_terminals && \
     mamba install -c conda-forge jupyterlab-latex jupyterlab-git jupyterlab-fasta jupyterlab-geojson && \
+    mamba install -c conda-forge jupyterlab_code_formatter isort black jupyter-archive jupyterlab-lsp python-lsp-server r-languageserver && \
     mamba install -c conda-forge nbconvert=$NBCONVERT_VERSION nbgrader=$NBGRADER_VERSION && \
     fix-permissions $CONDA_DIR && \
     fix-permissions /home/$NB_USER && \
@@ -102,6 +108,12 @@ RUN /usr/share/datahub/scripts/install-python-all.sh && \
 # Disable the jupyterlab extensions manager
 RUN jupyter labextension disable @jupyterlab/extensionmanager-extension
 
+## EXPERIMENTAL: "Enable" pluto NB/julia
+RUN chgrp -R users /opt/julia && \
+    chmod -R g+rw /opt/julia && \
+    chgrp -R users /opt/julia-1.10.2 && \
+    chmod -R g+rw /opt/julia-1.10.2
+
 # Cleanup
 ## nbgrader requires these variables set to just run the notebook server
 ENV NBGRADER_COURSEID="NA"

images/datascience-notebook/scripts/jupyter_settings_overrides.json

@@ -0,0 +1,24 @@
+{
+    "@jupyterlab/completer-extension:manager": {
+        "autoCompletion": true
+    },
+    "@jupyter-lsp/jupyterlab-lsp:plugin": {
+        "language_servers": {
+            "pylsp": {
+                "serverSettings": {
+                    "pylsp.plugins.pycodestyle.enabled": false
+                }
+            }
+        }
+    },
+    "@jupyter-lsp/jupyterlab-lsp:completion": {
+        "suppressTriggerCharacterIn": [
+            "Comment",
+            "BlockComment",
+            "LineComment",
+            "String",
+            ":",
+            ")"
+        ]
+    }
+}

images/scipy-ml-notebook/Dockerfile

@@ -1,5 +1,5 @@
 ARG BASE_TAG=latest
-FROM ghcr.io/ucsd-ets/datascience-notebook:${BASE_TAG}
+FROM ghcr.io/ucsd-ets/datascience-notebook:2024.4-stable
 
 USER root
 
@@ -11,8 +11,8 @@ USER root
 ## Package versions
 ## tf 2.13 does not work with torch 2.2.1. Both require conflicting versions of typing-extensions
 ## CUDA 11: ARG CUDA_VERSION=11.8 CUDNN_VERSION=8.7.0.84 \
-ARG CUDA_VERSION=12.0 CUDNN_VERSION=8.9.2.26 LIBNVINFER=7.2.2 LIBNVINFER_MAJOR_VERSION=7 \
-  TENSORFLOW_VERSION=2.15.0 KERAS_VERSION=2.15.0 TENSORRT_VERSION=8.6.1 TORCH_VERSION=2.2.1 \
+ARG CUDA_VERSION=12.1 CUDNN_VERSION=8.9.2.26 LIBNVINFER=7.2.2 LIBNVINFER_MAJOR_VERSION=7 \
+  TENSORFLOW_VERSION=2.16.2 KERAS_VERSION=3.5.0 TENSORRT_VERSION=8.6.1 TORCH_VERSION=2.3.1 \
   PROTOBUF_VERSION=3.20.3 
 
 # apt deps
@@ -51,9 +51,8 @@ USER jovyan
 # CUDA setup w/mamba
 ## TODO: Investigate this command, seems to duplicate cuda packages for nvidia (pypi + conda-forge). 
 # cuda-toolkit is a skeleton package on CUDA 12, unlike CUDA <= 11
-RUN mamba install -c "nvidia/label/cuda-12.0.0" cuda-nvcc \
+RUN mamba install -c "nvidia/label/cuda-12.1.1" cuda-nvcc \
     cuda-toolkit=$CUDA_VERSION \
-    # For CUDA 11: cudatoolkit=$CUDA_VERSION \
     cuda-version=$CUDA_VERSION \
     nccl \
     -y && \
@@ -81,6 +80,7 @@ RUN mamba install -c conda-forge pyqt pycocotools pillow scapy && \
     mamba clean --all
 
 # Install CUDA/Torch/Tensorflow/Keras w/pip
+# TF Compatibility Matrix: https://www.tensorflow.org/install/source?hl=en#gpu
 ## no purge required but no-cache-dir is used. pip purge will actually break the build here!
 ## Beware of potentially needing to update these if we update the drivers.
 ## Check tensorrt_env_vars.sh if you have to bump tensorrt!

images/tests_common/test_packages.py

@@ -64,6 +64,8 @@
     "nltk_data": "nltk",
     "pytorch": "torch",
     "umap-learn": "umap",
+    "jupyter-archive": "jupyter_archive",
+    "jupyterlab-lsp": "jupyterlab_lsp",
     # R
     "randomforest": "randomForest",
     "rsqlite": "DBI",
@@ -94,6 +96,7 @@
     "jupyterlab_rise[version='<0.40.0']",
     "jupyterlab-git",
     "jupyter-pluto-proxy",
+    "python-lsp-server",
 ]