Fix common test failures for datasci

ucsd-ets · Mar 25, 2024 · 094edfb · 094edfb
1 parent dc9e975
commit 094edfb
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Showing 2 changed files with 8 additions and 8 deletions.
diff --git a/images/datascience-notebook/Dockerfile b/images/datascience-notebook/Dockerfile
@@ -57,15 +57,8 @@ 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 && \
-#    python -c 'import matplotlib.pyplot' && \
-#    fix-permissions $CONDA_DIR && \
-#    fix-permissions /home/$NB_USER && \
-#    pip cache purge
 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>=2' && \
+    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 && \

diff --git a/images/tests_common/test_packages.py b/images/tests_common/test_packages.py
@@ -48,14 +48,21 @@
     # Python
     "matplotlib-base": "matplotlib",
     "beautifulsoup4": "bs4",
+    "gputil": "GPUtil",
+    "jupyterlab-github": "jupyterlab_github",
+    "jupyterlab-latex": "jupyterlab_latex",
+    "jupyterlab-fasta": "jupyterlab_fasta",
+    "jupyterlab-geojson": "jupyterlab_geojson",
     "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",