Merge pull request #85 from ucsd-ets/mamba-scipy-ml-fixup

Add more mamba statements to scipy-ml-fixup

images/datascience-notebook/Dockerfile

@@ -52,25 +52,30 @@ USER jovyan
 # Python/Mamba Deps
 ARG PY_VER_SHORT=3.11
 ## Package versions
-ARG JUPYTERSERVER_VERSION=2.12.5 JUPYTERHUB_VERSION=4.0.2 JUPYTERLAB_VERSION=4.1.2 NBCONVERT_VERSION=7.16.1 NOTEBOOK_VERSION=7.1.1 NBCLASSIC_VERSION=1.0.0
+ARG JUPYTERSERVER_VERSION=2.13.0 JUPYTERHUB_VERSION=4.1.1 JUPYTERLAB_VERSION=4.1.5 NBCONVERT_VERSION=7.16.3 NOTEBOOK_VERSION=7.1.2 NBCLASSIC_VERSION=1.0.0
 ARG PANDAS_VERSION=2.2.1 STATSMODELS_VERSION=0.14.1
 
 # Install essential+datascience pip packages 
 ## mistune added for nbgrader issues
-RUN pip install pillow typing-extensions tzlocal appdirs gputil mock pytest umap-learn \
-    nltk statsmodels==$STATSMODELS_VERSION pandas==$PANDAS_VERSION 'mistune>=2' --upgrade && \
-    pip install dpkt nose datascience && \
+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 && \
     python -c 'import matplotlib.pyplot' && \
     fix-permissions $CONDA_DIR && \
     fix-permissions /home/$NB_USER && \
-    pip cache purge
+    mamba clean --all
 
 # Install jupyterlab+extensions
-RUN pip install jupyterhub==$JUPYTERHUB_VERSION jupyter-server==$JUPYTERSERVER_VERSION jupyterlab==$JUPYTERLAB_VERSION notebook==$NOTEBOOK_VERSION nbclassic==$NBCLASSIC_VERSION jupyterlab_rise \
-    jupyter_server_terminals jupyter-collaboration jupyterlab-github jupyterlab-latex jupyterlab-git \
-    jupyterlab-fasta jupyterlab-pullrequests jupyterlab-geojson jupyterlab-link-share \
-    nbconvert==$NBCONVERT_VERSION && \
-    pip cache purge
+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=$NBCLASSIC_VERSION && \
+    mamba install -c conda-forge jupyterlab_rise jupyter_server_terminals jupyter-collaboration && \
+    mamba install -c conda-forge jupyterlab-github jupyterlab-latex jupyterlab-git jupyterlab-fasta jupyterlab-geojson && \
+    mamba install -c conda-forge nbconvert=$NBCONVERT_VERSION && \
+    fix-permissions $CONDA_DIR && \
+    fix-permissions /home/$NB_USER && \
+    mamba clean --all
+# TODO: Deprecated pkgs? Cause a massive downgrade
+### mamba install -c conda-forge jupyterlab-pullrequests jupyterlab-link-share
 
 # Install R packages
 RUN mamba install -c conda-forge r-markdown r-covr r-git2r r-crosstalk r-dt -y && \

images/scipy-ml-notebook/Dockerfile

@@ -66,15 +66,16 @@ RUN pip install --no-cache-dir protobuf==$PROTOBUF_VERSION
 ## 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 \
-    pyqt5 \
-    scapy \
-    pycocotools \
-    pillow && \
+    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.

images/spec.yml

@@ -6,7 +6,7 @@ images:
     build_args:
       PYTHON_VERSION: python-3.11.8
       PY_VER_SHORT: "3.11"
-      JUPYTERHUB_VERSION: 4.0.2
+      JUPYTERHUB_VERSION: 4.1.1
     info_cmds: [PY_VER, PIP_LIST, CONDA_INFO, CONDA_LIST, APT_PKG_LIST]
 
   rstudio-notebook:

images/tests_common/test_packages.py

@@ -48,14 +48,22 @@
     # Python
     "matplotlib-base": "matplotlib",
     "beautifulsoup4": "bs4",
+    "gputil": "GPUtil",
+    "jupyterlab-github": "jupyterlab_github",
+    "jupyterlab-latex": "jupyterlab_latex",
+    "jupyterlab-fasta": "jupyterlab_fasta",
+    "jupyterlab-geojson": "jupyterlab_geojson",
+    "jupyter-collaboration": "jupyter_collaboration",
     "scikit-learn": "sklearn",
     "scikit-image": "skimage",
     "spylon-kernel": "spylon_kernel",
+    "typing-extensions": "typing_extensions",
     "pytables": "tables",
     "pyqt": "PyQt5",
     "pillow": "PIL",
     "nltk_data": "nltk",
     "pytorch": "torch",
+    "umap-learn": "umap",
     # R
     "randomforest": "randomForest",
     "rsqlite": "DBI",