Merge pull request #111 from nmfs-opensci/dev

ONBUILD task

appendix

@@ -39,20 +39,54 @@ RUN rm -rf ${REPO_DIR}/book ${REPO_DIR}/docs
 # Convert NB_USER to ENV (from ARG) so that it passes to the child dockerfile
 ENV NB_USER=${NB_USER}
 
-## ONBUILD section. These are run in child Dockerfiles. First thing that is run
+## ONBUILD section. These are run in child Dockerfiles. These are run right after the FROM image is loaded
 
 ONBUILD USER ${NB_USER}
 
 # ${REPO_DIR} is owned by ${NB_USER}
 ONBUILD COPY --chown=${NB_USER}:${NB_USER} . ${REPO_DIR}/childimage
 
+# repo2docker will load files from a .binder or binder directory if
+# present. We check if those directories exist.
+ONBUILD RUN echo "Checking for 'binder' or '.binder' subfolder" \
+        ; cd "${REPO_DIR}/childimage/" \
+        ; if [ -d binder ] ; then \
+        echo "Using 'binder/' build context" \
+        ; elif [ -d .binder ] ; then \
+        echo "Using '.binder/' build context" \
+        ; else \
+        echo "Using './' build context" \
+        ; fi
+
 # Copy Desktop files into ${REPO_DIR}/Desktop if they exist. start will copy to Application dir and Desktop
-ONBUILD RUN if [ -d ${REPO_DIR}/childimage/Desktop ]; then \
-        mkdir -p ${REPO_DIR}/Desktop && \
-        cp -r ${REPO_DIR}/childimage/Desktop/* ${REPO_DIR}/Desktop/; \
-    fi
+# Will not fail if Desktop dir exists but is empty
+ONBUILD RUN echo "Checking for 'Desktop directory'..." \
+        ; cd "${REPO_DIR}/childimage/" \
+        ; [ -d binder ] && cd binder \
+        ; [ -d .binder ] && cd .binder \
+        ; if test -d Desktop ; then \
+            mkdir -p "${REPO_DIR}/Desktop" && \
+            [ "$(ls -A Desktop 2>/dev/null)" ] && cp -r Desktop/* "${REPO_DIR}/Desktop/"; \
+        fi
+
+# Install apt packages specified in a apt.txt file if it exists.
+# blank lines and comments are supported in apt.txt
+ONBUILD USER root
+ONBUILD RUN echo "Checking for 'apt.txt'..." \
+        ; cd "${REPO_DIR}/childimage/" \
+        ; [ -d binder ] && cd binder \
+        ; [ -d .binder ] && cd .binder \
+        ; if test -f "apt.txt" ; then \
+        package_list=$(grep -v '^\s*#' apt.txt | grep -v '^\s*$' | sed 's/\r//g; s/#.*//; s/^[[:space:]]*//; s/[[:space:]]*$//' | awk '{$1=$1};1') \
+        && apt-get update --fix-missing > /dev/null \
+        && apt-get install --yes --no-install-recommends $package_list \
+        && apt-get autoremove --purge \
+        && apt-get clean \
+        && rm -rf /var/lib/apt/lists/* \
+        ; fi
+ONBUILD USER ${NB_USER}
 
-# Add the environment
+# Add the conda environment
 # sometimes package solving will get rid of pip installed packages. Make sure jupyter-remote-desktop-proxy does not disappear
 ONBUILD RUN echo "Checking for 'conda-lock.yml' or 'environment.yml'..." \
         ; cd "${REPO_DIR}/childimage/" \
@@ -72,6 +106,54 @@ ONBUILD RUN echo "Checking for 'conda-lock.yml' or 'environment.yml'..." \
         find ${NB_PYTHON_PREFIX}/lib/python*/site-packages/bokeh/server/static -follow -type f -name '*.js' ! -name '*.min.js' -delete \
         ; fi
 
+# If a requirements.txt file exists, use pip to install packages
+# listed there. We don't want to save cached wheels in the image
+# to avoid wasting space.
+ONBUILD RUN echo "Checking for pip 'requirements.txt'..." \
+        ; cd "${REPO_DIR}/childimage/" \
+        ; [ -d binder ] && cd binder \
+        ; [ -d .binder ] && cd .binder \
+        ; if test -f "requirements.txt" ; then \
+        ${NB_PYTHON_PREFIX}/bin/pip install --no-cache -r requirements.txt \
+        ; fi
+
+# Add the r packages
+ONBUILD RUN echo "Checking for 'install.R" \
+        ; cd "${REPO_DIR}/childimage/" \
+        ; [ -d binder ] && cd binder \
+        ; [ -d .binder ] && cd .binder \
+        ; if test -f "install.R" ; then echo "Using install.R" & \
+        Rscript install.R \
+        ; fi
+
+# If a start file exists, put that under ${REPO_DIR}/childimage/start. 
+# This is sourced in ${REPO_DIR}/start
+ONBUILD RUN echo "Checking for 'start'..." \
+        ; cd "${REPO_DIR}/childimage/" \
+        ; [ -d binder ] && cd binder && cp start ${REPO_DIR}/childimage/start \
+        ; [ -d .binder ] && cd .binder && cp start ${REPO_DIR}/childimage/start \
+        ; if test -f "start" ; then \
+        chmod +x start \
+        ; fi
+
+# If a postBuild file exists, run it!
+# After it's done, we try to remove any possible cruft commands there
+# left behind under $HOME - particularly stuff that jupyterlab extensions
+# leave behind.
+ONBUILD RUN echo "Checking for 'postBuild'..." \
+        ; cd "${REPO_DIR}/childimage/" \
+        ; [ -d binder ] && cd binder \
+        ; [ -d .binder ] && cd .binder \
+        ; if test -f "postBuild" ; then \
+        chmod +x postBuild \
+        && ./postBuild \
+        && rm -rf /tmp/* \
+        && rm -rf ${HOME}/.cache ${HOME}/.npm ${HOME}/.yarn \
+        && rm -rf ${NB_PYTHON_PREFIX}/share/jupyter/lab/staging \
+        && find ${CONDA_DIR} -follow -type f -name '*.a' -delete \
+        && find ${CONDA_DIR} -follow -type f -name '*.js.map' -delete \
+        ; fi
+
 # Revert to default user and home as pwd
 USER ${NB_USER}
 WORKDIR ${HOME}

apt-extras.txt

@@ -12,26 +12,22 @@ manpages-posix-dev
 curl
 wget
 
-# Core text editors on a *nix box: vim and emacs
+# command line text editors
 vim
 emacs-nox
 emacs-goodies-el
-
-# A couple of CLI editors that are easier than vim
-# micro  # currently not working on 18.04
 nano
-jed
-jed-extra
+
+# GUI text editors
+emacs
+vim-gtk3
+gedit
 
 # powerful terminal-based file manager, better than the one in JLab
 mc
 
-# for easily managing multiple repositories with one command (perl-doc
-# is needed for its help pages to work)
-mr
-perl-doc
-
 # Regular build tools for compiling common stuff
+# most installed with R installation
 build-essential
 gfortran
 
@@ -71,11 +67,6 @@ xubuntu-icon-theme
 tigervnc-standalone-server
 tigervnc-xorg-extension
 
-# GUI text editors
-emacs
-vim-gtk3
-gedit
-
 # Git clients and tools
 git-gui
 gitg

book/_quarto.yml

@@ -19,6 +19,7 @@ book:
     - index.qmd
     - customizing.qmd
     - configuration_files.qmd
+    - r-packages.qmd
     - desktop.qmd
     - tex.qmd
     - jupyter-config.qmd

start

@@ -46,4 +46,7 @@ for mime_file_path in ${REPO_DIR}/Desktop/*.xml; do
 done
 update-mime-database "${MIME_DIR}"
 
+# Run child start in a subshell to contain its environment
+[ -f ${REPO_DIR}/childimage/start ] && ( source ${REPO_DIR}/childimage/start )
+
 exec "$@"