Update Dockerfile

Author: N2akiti

images/datascience-notebook/Dockerfile

@@ -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 \
@@ -67,29 +73,47 @@ USER jovyan
 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 PANDAS_VERSION=2.2.3 STATSMODELS_VERSION=0.14.4 BOTTLENECK_VERSION=1.4.2 NUMEXPR_VERSION=2.10.2
 
-# 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 && \
-    python -c 'import matplotlib.pyplot' && \
-    fix-permissions $CONDA_DIR && \
-    fix-permissions /home/$NB_USER && \
-    mamba clean --all
+RUN pip install uv
 
-# 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=$NBGRADER_VERSION && \
+RUN uv pip install --no-cache \ 
+    pillow \
+    typing-extensions \
+    tzlocal \
+    appdirs \
+    gputil \
+    mock \
+    pytest \
+    umap-learn \
+    nltk \
+    statsmodels=$STATSMODELS_VERSION \
+    pandas=$PANDAS_VERSION \
+    mistune \
+    dpkt \
+    nose \
+    datascience \
+    pyarrow \
+    bottleneck=$BOTTLENECK_VERSION \
+    numexpr=$NUMEXPR_VERSION \
+    jupyterhub=$JUPYTERHUB_VERSION \
+    jupyter_server=$JUPYTERSERVER_VERSION \
+    jupyterlab=$JUPYTERLAB_VERSION \
+    notebook=$NOTEBOOK_VERSION \
+    nbclassic=$NBCLASSIC_VERSION \
+    jupyterlab_rise \
+    jupyter_server_terminals \
+    jupyter-collaboration \
+    jupyterlab-latex \
+    jupyterlab-git \
+    jupyterlab-fasta \
+    jupyterlab-geojson \
+    nbconvert=$NBCONVERT_VERSION \
+    nbgrader=$NBGRADER_VERSION && \
+    python -c 'import matplotlib.pyplot' && \
     fix-permissions $CONDA_DIR && \
     fix-permissions /home/$NB_USER && \
-    mamba clean --all
 
 # 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
@@ -107,7 +131,6 @@ 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
+RUN uv cache clean
 
 WORKDIR /home/jovyan