Merge pull request #118 from nmfs-opensci/dev

remove apt-extras and postBuild

appendix

@@ -1,6 +1,6 @@
 USER root
 
-# repo2docker does not set this; name is vague. This is the default env in repo2docker type images
+# repo2docker does not set this. This is the default env in repo2docker type images
 ENV CONDA_ENV=notebook
 
 # Install R, RStudio via Rocker scripts
@@ -13,11 +13,9 @@ RUN PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin && \
   chmod +x ${REPO_DIR}/rocker.sh && \
   ${REPO_DIR}/rocker.sh
 
-# Install extra cmd line packages after R installation
-# The package_list part is reading the file and doing clean-up to just have the list of packages
-RUN package_list=$(grep -v '^\s*#' ${REPO_DIR}/apt-extras.txt | grep -v '^\s*$' | sed 's/\r//g; s/#.*//; s/^[[:space:]]*//; s/[[:space:]]*$//' | awk '{$1=$1};1') && \
-  apt-get update && \
-  apt-get install --yes --no-install-recommends $package_list && \
+# Install any missing build packages. Most are installed when R installed but get any missing packages
+RUN apt-get update && \
+  apt-get install --yes --no-install-recommends build-essential gfortran && \
   apt-get autoremove --purge && \
   apt-get clean && \
   rm -rf /var/lib/apt/lists/*
@@ -32,14 +30,19 @@ RUN yes | unminimize
 ENV MANPATH="${NB_PYTHON_PREFIX}/share/man:${MANPATH}"
 RUN mandb
 
+# Add custom jupyter config. You can also put config.py files in the same place
+RUN cp ${REPO_DIR}/custom_jupyter_server_config.json ${NB_PYTHON_PREFIX}/etc/jupyter/jupyter_server_config.d/
+RUN cp ${REPO_DIR}/custom_jupyter_server_config.json ${NB_PYTHON_PREFIX}/etc/jupyter/jupyter_notebook_config.d/
+
 # Clean up extra files in ${REPO_DIR}
 RUN rm -rf ${REPO_DIR}/book ${REPO_DIR}/docs
 
+###################
 # Set up behavior for child dockerfiles
 # Convert NB_USER to ENV (from ARG) so that it passes to the child dockerfile
 ENV NB_USER=${NB_USER}
 
-## ONBUILD section. These are run in child Dockerfiles. These are run right after the FROM image is loaded
+## ONBUILD section. These commands are run in child Dockerfiles. These are run right after the FROM image is loaded
 
 ONBUILD USER ${NB_USER}
 
@@ -154,6 +157,9 @@ ONBUILD RUN echo "Checking for 'postBuild'..." \
         && find ${CONDA_DIR} -follow -type f -name '*.js.map' -delete \
         ; fi
 
+## End ONBUILD section for child images
+################################
+
 # Revert to default user and home as pwd
 USER ${NB_USER}
 WORKDIR ${HOME}

apt-extras.txt → apt.txt

@@ -28,8 +28,7 @@ mc
 
 # Regular build tools for compiling common stuff
 # most installed with R installation
-build-essential
-gfortran
+# need to install after R so these added to appendix
 
 # Dependencies for nbconvert and myst
 # texlive is installed by R installation