2025.4 (#96)

* Changed datascience image to install packages using uv

* isntalled typing extensions using conda

* fixed typo

* changed versioning from conda to pip

* fixed typo

* Redeclare JUPYTERHUB_VERSION after FROM call

* Small fix

* fixed typo

* fixed typo

* Migrated scipy-ml to uv

* Removed commented out notebooks

* Changed pyqt to PyQt5

* removed prepull from all notebooks

* Removed comments and migrated cuda to pip

* Added index-url

* Commented out cuda conda fix

* Removed comments

* datascience-notebook: add r-sf; ensure modern sqlite for JupyterLab; keep conda lib on loader path

* Update main.yml

* Update Dockerfile

* Update Dockerfile

* Update Dockerfile

* Update Dockerfile

* Update Dockerfile

* Update Dockerfile

* Update Dockerfile

* Update Dockerfile

* Update Dockerfile

* Update Dockerfile

* Update Dockerfile

---------

Co-authored-by: kevinsun0904 <kevinsun0904@gmail.com>
Co-authored-by: yifanzhu1121 <kiki.zhuyifan@gmail.com>
Co-authored-by: N2akiti <n2akiti@ucsd.edu>

Author: 4 people

images/datascience-notebook/Dockerfile

@@ -1,4 +1,4 @@
-# If you are building manually, pass PYTHON_VERSION/PY_VER_SHORT/JUPYTERHUB_VERSION with --build-arg
+# If you are building manually, pass PYTHON_VERSION/PY_VER_SHORT/JUPYTERHUB_VERSION with --build-arg    
 ARG PYTHON_VERSION=python-3.11.8
 ARG PY_VER_SHORT=3.11
 ARG JUPYTERHUB_VERSION=4.1.5
@@ -14,6 +14,12 @@ ENV DEBCONF_NOWARNINGS="yes"
 RUN apt-get update -y && \
     apt-get -qq install -y --no-install-recommends \
     git \
+    libgdal-dev \
+    libproj-dev \
+    libgeos-dev \
+    libudunits2-dev \
+    libgit2-dev \
+    pkg-config \
     curl \
     rsync \
     unzip \
@@ -64,35 +70,37 @@ 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 JUPYTERHUB_VERSION=4.1.5 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 PANDAS_VERSION=2.2.3 STATSMODELS_VERSION=0.14.4 BOTTLENECK_VERSION=1.4.2 NUMEXPR_VERSION=2.10.2
 
+# Install uv for faster package installations
+RUN pip3 install --no-cache-dir --upgrade uv
+
 # Install essential+datascience pip packages 
 ## mistune added for nbgrader issues
-RUN mamba install -c conda-forge pillow typing-extensions tzlocal appdirs gputil mock pytest umap-learn && \
-    mamba install -c conda-forge nltk statsmodels=$STATSMODELS_VERSION pandas=$PANDAS_VERSION mistune && \
-    mamba install -c conda-forge dpkt nose datascience pyarrow bottleneck=$BOTTLENECK_VERSION umap-learn numexpr=$NUMEXPR_VESION && \
+RUN uv pip install pillow typing-extensions tzlocal appdirs gputil mock pytest umap-learn --system && \
+    uv pip install nltk statsmodels==$STATSMODELS_VERSION pandas==$PANDAS_VERSION mistune --system && \
+    uv pip install dpkt nose datascience pyarrow bottleneck==$BOTTLENECK_VERSION umap-learn numexpr==$NUMEXPR_VERSION --system && \
     python -c 'import matplotlib.pyplot' && \
     fix-permissions $CONDA_DIR && \
     fix-permissions /home/$NB_USER && \
-    mamba clean --all
+    uv cache clean
 
 # Install jupyterlab+extensions
-RUN mamba install -c conda-forge jupyterhub=$JUPYTERHUB_VERSION jupyter_server=$JUPYTERSERVER_VERSION && \
-    mamba install -c conda-forge jupyterlab=$JUPYTERLAB_VERSION notebook=$NOTEBOOK_VERSION nbclassic=$NBCLASSIC_VERSION && \
-    # (TODO: Re-enable collab once RTC is fixed) mamba install -c conda-forge jupyterlab_rise jupyter_server_terminals jupyter-collaboration && \
-    mamba install -c conda-forge jupyterlab_rise jupyter_server_terminals && \
-    mamba install -c conda-forge jupyterlab-latex jupyterlab-git jupyterlab-fasta jupyterlab-geojson && \
-    mamba install -c conda-forge nbconvert=$NBCONVERT_VERSION nbgrader=$NBGRADER_VERSION && \
+RUN uv pip install jupyterhub==$JUPYTERHUB_VERSION jupyter_server==$JUPYTERSERVER_VERSION --system && \
+    uv pip install jupyterlab==$JUPYTERLAB_VERSION notebook==$NOTEBOOK_VERSION nbclassic==$NBCLASSIC_VERSION --system && \
+    # (TODO: Re-enable collab once RTC is fixed) uv pip install jupyterlab_rise jupyter_server_terminals jupyter-collaboration --system && \
+    uv pip install jupyterlab_rise jupyter_server_terminals --system && \
+    uv pip install jupyterlab-latex jupyterlab-git jupyterlab-fasta jupyterlab-geojson --system && \
+    uv pip install nbconvert==$NBCONVERT_VERSION nbgrader==$NBGRADER_VERSION --system && \
     fix-permissions $CONDA_DIR && \
     fix-permissions /home/$NB_USER && \
-    mamba clean --all
+    uv cache clean
 
 # Install R packages
-RUN mamba install -c conda-forge r-markdown r-covr r-git2r r-crosstalk r-dt -y && \
+RUN R -e "install.packages(c('sf', 'markdown', 'covr', 'git2r', 'crosstalk', 'DT'), repos='https://cloud.r-project.org')" && \
     fix-permissions $CONDA_DIR && \
-    fix-permissions /home/$NB_USER && \
-    mamba clean -a -y
+    fix-permissions /home/$NB_USER
 
 # Run install-python + cleanup
 RUN /usr/share/datahub/scripts/install-python-all.sh && \
@@ -107,7 +115,4 @@ RUN jupyter labextension disable @jupyterlab/extensionmanager-extension
 ENV NBGRADER_COURSEID="NA"
 ENV JUPYTERHUB_USER=${NB_USER}
 
-RUN pip cache purge
-RUN conda clean -t -p -i -y
-
 WORKDIR /home/jovyan

images/scipy-ml-notebook/Dockerfile

@@ -50,71 +50,42 @@ RUN chmod 777 /etc/datahub-profile.d/*.sh /tmp/activate.sh
 
 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-12.6.0" cuda-nvcc \
-    cuda-toolkit=$CUDA_VERSION \
-    # For CUDA 11: cudatoolkit=$CUDA_VERSION \
-    cuda-version=$CUDA_VERSION \
-    nccl \
-    -y && \
+RUN pip3 install --no-cache-dir --upgrade uv
+
+RUN uv pip install --system \
+        --extra-index-url https://pypi.nvidia.com \
+        --extra-index-url https://download.pytorch.org/whl/cu126 \
+        nvidia-cuda-nvcc-cu12 \
+        nvidia-nccl-cu12 \
+        cuda-python \
+        protobuf==$PROTOBUF_VERSION \
+        opencv-contrib-python-headless \
+        opencv-python \
+        PyQt5 \
+        pycocotools \
+        pillow \
+        scapy \
+        nvidia-cudnn-cu12==$CUDNN_VERSION \
+        torch==$TORCH_VERSION \
+        torchvision \
+        torchaudio \
+        tensorflow==$TENSORFLOW_VERSION \
+        tensorflow-datasets \
+        tensorrt==$TENSORRT_VERSION \
+        keras==$KERAS_VERSION \
+        tf-keras==$TF_KERAS_VERSION \
+        transformers \
+        datasets \
+        accelerate \
+        huggingface-hub \
+        timm \
+    && \
     fix-permissions $CONDA_DIR && \
     fix-permissions /home/$NB_USER && \
-    mamba clean -a -y
-
-# Install scipy pip packages
-## install protobuf to avoid weird base type error. seems like if we don't then it'll be installed twice.
-## https://github.com/spesmilo/electrum/issues/7825
-## pip cache purge didnt work here for some reason.
-RUN pip install --no-cache-dir protobuf==$PROTOBUF_VERSION
-## cuda-python installed to have parity with tensorflow and cudnn
-## Install pillow<7 due to dependency issue https://github.com/pytorch/vision/issues/1712
-## tensorrt installed to fix not having libnvinfer that has caused tensorflow issues.
-RUN pip install opencv-contrib-python-headless \
-    opencv-python && \
-    fix-permissions $CONDA_DIR && \ 
-    fix-permissions /home/$NB_USER && \
-    pip cache purge
-
-RUN mamba install -c conda-forge pyqt pycocotools pillow scapy && \
-    fix-permissions $CONDA_DIR && \
-    fix-permissions /home/$NB_USER && \
-    mamba clean --all
-
-# Install CUDA/Torch/Tensorflow/Keras w/pip
-## 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!
-
-## tf-keras is keras 2.x for higher versions of tensorflow that would normally require keras 3
-RUN pip install nvidia-cudnn-cu12==$CUDNN_VERSION torch==$TORCH_VERSION torchvision torchaudio --index-url https://download.pytorch.org/whl/cu126 && \
-  pip install tensorflow==$TENSORFLOW_VERSION tensorflow-datasets tensorrt==$TENSORRT_VERSION keras==$KERAS_VERSION tf-keras==$TF_KERAS_VERSION && \
-  fix-permissions $CONDA_DIR && \
-  fix-permissions /home/$NB_USER && \
-  mamba clean -a -y && \
-  pip cache purge
-
-RUN pip install transformers datasets accelerate huggingface-hub timm && \
-  fix-permissions $CONDA_DIR && \
-  fix-permissions /home/$NB_USER && \
-  mamba clean -a -y && \
-  pip cache purge
+    uv cache clean
 
 USER $NB_UID:$NB_GID
 ENV PATH=${PATH}:/usr/local/nvidia/bin:/opt/conda/bin
 
-# CUDA fixes for CONDA
-## Copy libdevice file to the required path
-RUN mkdir -p $CONDA_DIR/lib/nvvm/libdevice && \
-    cp $CONDA_DIR/nvvm/libdevice/libdevice.10.bc $CONDA_DIR/lib/nvvm/libdevice/
-    #CUDA 11: cp $CONDA_DIR/lib/libdevice.10.bc $CONDA_DIR/lib/nvvm/libdevice/
-
-# TensorRT fix for tensorflow
-## https://github.com/tensorflow/tensorflow/issues/61468 (could not find TensorRT)
-## This will most definitely have to be changed after 8.6.1...
-RUN ln -s /opt/conda/lib/python3.11/site-packages/tensorrt_libs/libnvinfer_plugin.so.8 /opt/conda/lib/python3.11/site-packages/tensorrt_libs/libnvinfer_plugin.so.$TENSORRT_VERSION && \
-    ln -s /opt/conda/lib/python3.11/site-packages/tensorrt_libs/libnvinfer.so.8 /opt/conda/lib/python3.11/site-packages/tensorrt_libs/libnvinfer.so.$TENSORRT_VERSION
-
 # Run datahub scripts
 RUN . /tmp/activate.sh

images/spec.yml

@@ -22,10 +22,10 @@ images:
     integration_tests: false
     info_cmds: [PY_VER, PIP_LIST, CUDA_VERSION, CONDA_INFO, CONDA_LIST, APT_PKG_LIST]
     prune: false # comment if scipy-ml stops being the last container
-    #prepull: false #-- uncomment to disable prepulling behavior for scipy-ml. gives you space on machine in exchange for build time.
+    # prepull: false #-- uncomment to disable prepulling behavior for scipy-ml. gives you space on machine in exchange for build time.
 
 tag:
-  prefix: "2025.2"
+  prefix: "2025.3"
 
 all_info_cmds:
   PY_VER: