mitiaging Docker issues with conda, rise, and pip

Dockerfile

@@ -1,33 +1,40 @@
-FROM jupyter/minimal-notebook:python-3.9.7
+FROM jupyter/minimal-notebook:python-3.10.11
 
 # keep env var name in sync with config_local.yml
 ARG PARTICIPANT_BUCKET_READ_SECRET
 ENV PARTICIPANT_BUCKET_READ_SECRET=${PARTICIPANT_BUCKET_READ_SECRET}
 
 RUN if [ -z "$PARTICIPANT_BUCKET_READ_SECRET" ]; \
       then echo "The build arg PARTICIPANT_BUCKET_READ_SECRET must be set to non-zero, e.g. \
-by passing the flag --build-arg PARTICIPANT_BUCKET_READ_SECRET=$PARTICIPANT_BUCKET_READ_SECRET. " &&\
+      by passing the flag --build-arg PARTICIPANT_BUCKET_READ_SECRET=$PARTICIPANT_BUCKET_READ_SECRET. " &&\
       echo "If running in CI, this variable should have been included as GH secret in the repository settings." &&\
       echo "If you are building locally and the env var is not set,  \
-you might find the corresponding value inside config.yml under the 'secret' key." &&\
+      you might find the corresponding value inside config.yml under the 'secret' key." &&\
       exit 1; \
-    fi
+      fi
 
 USER root
 RUN apt-get update && apt-get upgrade -y
 
 # pandoc needed for docs, see https://nbsphinx.readthedocs.io/en/0.7.1/installation.html?highlight=pandoc#pandoc
 # gh-pages action uses rsync
-RUN apt-get -y install pandoc git-lfs rsync
+RUN apt-get -y install \
+      build-essential \
+      libblas-dev \
+      liblapack-dev \
+      gfortran \
+      pandoc \
+      git-lfs \
+      rsync
 
 USER ${NB_UID}
 
 WORKDIR /tmp
 COPY build_scripts build_scripts
 RUN bash build_scripts/install_presentation_requirements.sh
 
-COPY requirements-test.txt .
-RUN pip install -r requirements-test.txt
+# COPY requirements-test.txt .
+# RUN pip install -r requirements-test.txt
 
 
 # NOTE: this breaks down when requirements contain pytorch (file system too large to fit in RAM, even with 16GB)

build_scripts/install_presentation_requirements.sh

@@ -37,7 +37,8 @@ BUILD_DIR=$(dirname "$0")
 
 (
   cd "${BUILD_DIR}/.." || (echo "Unknown error, could not find directory ${BUILD_DIR}" && exit 255)
-  conda install -y -c conda-forge notebook==6.5.6 jupyter rise==5.7.1 sphinx sphinx_rtd_theme jupyter-book jupyter_contrib_nbextensions jupyter_nbextensions_configurator
+  conda install -y -c conda-forge notebook==6.5.6 jupyter sphinx sphinx_rtd_theme jupyter-book jupyter_contrib_nbextensions jupyter_nbextensions_configurator
+  pip install rise==5.7.1
   python build_scripts/configure_spellcheck_dict.py
   jupyter contrib nbextension install --user
   jupyter nbextensions_configurator enable --user

requirements.txt

@@ -130,7 +130,7 @@ tensorboard-data-server==0.7.2
 tensorflow==2.15.0
 tensorflow-estimator==2.15.0
 tensorflow-io-gcs-filesystem==0.34.0
-tensorflow-macos==2.15.0
+# tensorflow-macos==2.15.0
 tensorflow-probability==0.23.0
 termcolor==2.4.0
 terminado==0.18.0