From e9dc7beb952a48a954761109984340b4a4bdebfd Mon Sep 17 00:00:00 2001
From: Eli Holmes - NOAA <eli.holmes@noaa.gov>
Date: Mon, 21 Oct 2024 22:17:04 -0700
Subject: [PATCH 01/12] Update environment.yml

---
 environment.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/environment.yml b/environment.yml
index daeebdb..195f8fd 100644
--- a/environment.yml
+++ b/environment.yml
@@ -62,4 +62,4 @@ dependencies:
   - pip
   - pip:
     # Access linux desktop from inside JupyterHub
-    - jupyter-desktop-server==0.1.3
+    - jupyter-remote-desktop-proxy

From 2a9874ded831bad882934a5ff16522a35e9e5f8a Mon Sep 17 00:00:00 2001
From: Eli Holmes - NOAA <eli.holmes@noaa.gov>
Date: Mon, 21 Oct 2024 22:20:44 -0700
Subject: [PATCH 02/12] Update apt-extras.txt

---
 apt-extras.txt | 16 ++++++++++------
 1 file changed, 10 insertions(+), 6 deletions(-)

diff --git a/apt-extras.txt b/apt-extras.txt
index 7cce795..754a95e 100644
--- a/apt-extras.txt
+++ b/apt-extras.txt
@@ -36,7 +36,8 @@ build-essential
 gfortran
 
 # Dependencies for nbconvert and myst
-# texlive is installed by R installation but not some of the common packages
+# texlive is installed by R installation
+# Add packages with tlmgr in rocker.sh
 
 # Other useful document-related tools
 # pandoc installed by R installation
@@ -58,14 +59,17 @@ tig  # console UI for git
 multitail
 tree
 
-## This section adds tools needed for desktop environment
+# This section adds tools needed for desktop environment
+# https://github.com/jupyterhub/jupyter-remote-desktop-proxy
 dbus-x11
+xfce4
+xfce4-panel
+xfce4-session
+xfce4-settings
 xorg
 xubuntu-icon-theme
-xfce4
-xfce4-goodies
-xclip
-xsel
+tigervnc-standalone-server
+tigervnc-xorg-extension
 
 # GUI text editors
 emacs

From c3f823c61d6b62283ffa3e1c9d7b1c4814dee19e Mon Sep 17 00:00:00 2001
From: Eli Holmes - NOAA <eli.holmes@noaa.gov>
Date: Tue, 22 Oct 2024 17:02:54 -0700
Subject: [PATCH 03/12] copy . to pyrocket-child in ONBUILD

---
 appendix | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/appendix b/appendix
index 39653af..773273c 100644
--- a/appendix
+++ b/appendix
@@ -26,9 +26,16 @@ RUN yes | unminimize
 ENV MANPATH="${NB_PYTHON_PREFIX}/share/man:${MANPATH}"
 RUN mandb
 
+# Clean up extra files in ${REPO_DIR}
+RUN rm -rf ${REPO_DIR}/book ${REPO_DIR}/docs
+
 # Copy Desktop files into ${REPO_DIR}/Desktop if they exist
-ONBUILD RUN mkdir -p ${REPO_DIR}/Desktop && \
-            if [ -d Desktop ]; then cp Desktop/* ${REPO_DIR}/Desktop/; fi
+ONBUILD COPY . /pyrocket-child/
+ONBUILD RUN if [ -d /pyrocket-child/Desktop ]; then \
+        mkdir -p ${REPO_DIR}/Desktop && \
+        cp -r /pyrocket-child/Desktop/* ${REPO_DIR}/Desktop/; \
+    fi && \
+    rm -rf /pyrocket-child
 
 # Revert to default user
 USER ${NB_USER}

From 6d7231d7f1cbe3281bacf95726e01ef600330867 Mon Sep 17 00:00:00 2001
From: Eli Holmes - NOAA <eli.holmes@noaa.gov>
Date: Tue, 22 Oct 2024 18:04:25 -0700
Subject: [PATCH 04/12] copy . to repo_dir

---
 appendix | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/appendix b/appendix
index 773273c..7fda650 100644
--- a/appendix
+++ b/appendix
@@ -29,13 +29,13 @@ RUN mandb
 # Clean up extra files in ${REPO_DIR}
 RUN rm -rf ${REPO_DIR}/book ${REPO_DIR}/docs
 
-# Copy Desktop files into ${REPO_DIR}/Desktop if they exist
-ONBUILD COPY . /pyrocket-child/
-ONBUILD RUN if [ -d /pyrocket-child/Desktop ]; then \
+# Copy Desktop files into ${REPO_DIR}/Desktop if they exist. First copy files to tmpbuild
+ONBUILD COPY . ${REPO_DIR}/tmpbuild/
+ONBUILD RUN if [ -d ${REPO_DIR}/tmpbuild/Desktop ]; then \
         mkdir -p ${REPO_DIR}/Desktop && \
-        cp -r /pyrocket-child/Desktop/* ${REPO_DIR}/Desktop/; \
+        cp -r ${REPO_DIR}/tmpbuild/Desktop/* ${REPO_DIR}/Desktop/; \
     fi && \
-    rm -rf /pyrocket-child
+    rm -rf ${REPO_DIR}/tmpbuild/
 
 # Revert to default user
 USER ${NB_USER}

From 1ccf23dd8f5f06d10c566443bbe713e57ae920b6 Mon Sep 17 00:00:00 2001
From: Eli Holmes - NOAA <eli.holmes@noaa.gov>
Date: Tue, 22 Oct 2024 18:39:12 -0700
Subject: [PATCH 05/12] try copying files again

---
 appendix | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/appendix b/appendix
index 7fda650..469e2ee 100644
--- a/appendix
+++ b/appendix
@@ -30,12 +30,12 @@ RUN mandb
 RUN rm -rf ${REPO_DIR}/book ${REPO_DIR}/docs
 
 # Copy Desktop files into ${REPO_DIR}/Desktop if they exist. First copy files to tmpbuild
-ONBUILD COPY . ${REPO_DIR}/tmpbuild/
-ONBUILD RUN if [ -d ${REPO_DIR}/tmpbuild/Desktop ]; then \
+ONBUILD COPY . /tmpbuild/
+ONBUILD RUN if [ -d /tmpbuild/Desktop ]; then \
         mkdir -p ${REPO_DIR}/Desktop && \
-        cp -r ${REPO_DIR}/tmpbuild/Desktop/* ${REPO_DIR}/Desktop/; \
-    fi && \
-    rm -rf ${REPO_DIR}/tmpbuild/
+        cp -r /tmpbuild/Desktop/* ${REPO_DIR}/Desktop/; \
+    fi
+ONBUILD RUN whoami && rm -rf /tmpbuild
 
 # Revert to default user
 USER ${NB_USER}

From eca6c66b338c524317b37fb7365548dd6f92f475 Mon Sep 17 00:00:00 2001
From: Eli Holmes - NOAA <eli.holmes@noaa.gov>
Date: Tue, 22 Oct 2024 19:27:18 -0700
Subject: [PATCH 06/12] ONBUILD USER root

---
 appendix | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/appendix b/appendix
index 469e2ee..7458eca 100644
--- a/appendix
+++ b/appendix
@@ -30,12 +30,14 @@ RUN mandb
 RUN rm -rf ${REPO_DIR}/book ${REPO_DIR}/docs
 
 # Copy Desktop files into ${REPO_DIR}/Desktop if they exist. First copy files to tmpbuild
+ONBUILD USER root
 ONBUILD COPY . /tmpbuild/
 ONBUILD RUN if [ -d /tmpbuild/Desktop ]; then \
         mkdir -p ${REPO_DIR}/Desktop && \
         cp -r /tmpbuild/Desktop/* ${REPO_DIR}/Desktop/; \
     fi
 ONBUILD RUN whoami && rm -rf /tmpbuild
+ONBUILD USER ${NB_USER}
 
 # Revert to default user
 USER ${NB_USER}

From 0e3227cdcfef6c311924d3ec730970eade50bd38 Mon Sep 17 00:00:00 2001
From: Eli Holmes - NOAA <eli.holmes@noaa.gov>
Date: Wed, 23 Oct 2024 09:22:30 -0700
Subject: [PATCH 07/12] Update start

---
 start | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/start b/start
index e145224..c26d494 100644
--- a/start
+++ b/start
@@ -28,8 +28,10 @@ mkdir -p "${DESKTOP_DIR}"
 for desktop_file_path in ${REPO_DIR}/Desktop/*.desktop; do
     cp "${desktop_file_path}" "${APPLICATIONS_DIR}/."
 
-    # Symlink application to desktop
+    # Symlink application to desktop and set execute permission so xfce (desktop) doesn't complain
     desktop_file_name="$(basename ${desktop_file_path})"
+    # Set execute permissions on the copied .desktop file
+    chmod +x "${APPLICATIONS_DIR}/${desktop_file_name}"
     ln -sf "${APPLICATIONS_DIR}/${desktop_file_name}" "${DESKTOP_DIR}/${desktop_file_name}"
 done
 update-desktop-database "${APPLICATIONS_DIR}"

From eb13078e9129d27b0e394afb15422654ffcdd35a Mon Sep 17 00:00:00 2001
From: Eli Holmes - NOAA <eli.holmes@noaa.gov>
Date: Wed, 23 Oct 2024 10:12:35 -0700
Subject: [PATCH 08/12] Update appendix

---
 appendix | 1 +
 1 file changed, 1 insertion(+)

diff --git a/appendix b/appendix
index 7458eca..8140ff1 100644
--- a/appendix
+++ b/appendix
@@ -38,6 +38,7 @@ ONBUILD RUN if [ -d /tmpbuild/Desktop ]; then \
     fi
 ONBUILD RUN whoami && rm -rf /tmpbuild
 ONBUILD USER ${NB_USER}
+ONBUILD RUN whoami
 
 # Revert to default user
 USER ${NB_USER}

From 0c360c02e68b839a1a7f59decb9de9ffd7740410 Mon Sep 17 00:00:00 2001
From: Eli Holmes - NOAA <eli.holmes@noaa.gov>
Date: Wed, 23 Oct 2024 12:18:37 -0700
Subject: [PATCH 09/12] Update start

---
 start | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/start b/start
index c26d494..2b0b289 100644
--- a/start
+++ b/start
@@ -1,14 +1,15 @@
 #!/bin/bash
 set -euo pipefail
 
-# Set any environment variables here
+# Start - Set any environment variables here
 # These are inherited by all processes, *except* RStudio
-
-# Tell applications where to open desktop apps - this allows notebooks to
-# pop open GUIs
+# USE export <parname>=value
+# Tell applications where to open desktop apps - this allows notebooks to pop open GUIs
 export DISPLAY=":1.0"
 # source this file to get the variables defined in the rocker Dockerfile
 source ${REPO_DIR}/env.txt
+# End - Set any environment variables here
+
 
 # The for loops will fail if they return null (no files). Set shell option nullglob
 shopt -s nullglob

From ba5417f53cb01341081887c06ae9f7865d1909da Mon Sep 17 00:00:00 2001
From: Eli Holmes - NOAA <eli.holmes@noaa.gov>
Date: Wed, 23 Oct 2024 12:36:52 -0700
Subject: [PATCH 10/12] Update appendix

---
 appendix | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/appendix b/appendix
index 8140ff1..e72e86f 100644
--- a/appendix
+++ b/appendix
@@ -29,9 +29,15 @@ RUN mandb
 # Clean up extra files in ${REPO_DIR}
 RUN rm -rf ${REPO_DIR}/book ${REPO_DIR}/docs
 
-# Copy Desktop files into ${REPO_DIR}/Desktop if they exist. First copy files to tmpbuild
+# Set up behavior for child dockerfiles
+# Define NB_USER since that is not exported by the parent dockerfile (py-rocket-base)
+# This works because py-rocket-base sets user to NB_USER
+ONBUILD RUN export NB_USER=$(whoami)
+ONBUILD ENV NB_USER=${NB_USER}
+
 ONBUILD USER root
 ONBUILD COPY . /tmpbuild/
+# Copy Desktop files into ${REPO_DIR}/Desktop if they exist. First copy files to tmpbuild
 ONBUILD RUN if [ -d /tmpbuild/Desktop ]; then \
         mkdir -p ${REPO_DIR}/Desktop && \
         cp -r /tmpbuild/Desktop/* ${REPO_DIR}/Desktop/; \

From 27cc0a5a065c5504e2676eeb35802575b65c4f47 Mon Sep 17 00:00:00 2001
From: Eli Holmes - NOAA <eli.holmes@noaa.gov>
Date: Wed, 23 Oct 2024 13:45:11 -0700
Subject: [PATCH 11/12] Update appendix

---
 appendix | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/appendix b/appendix
index e72e86f..8479822 100644
--- a/appendix
+++ b/appendix
@@ -30,10 +30,8 @@ RUN mandb
 RUN rm -rf ${REPO_DIR}/book ${REPO_DIR}/docs
 
 # Set up behavior for child dockerfiles
-# Define NB_USER since that is not exported by the parent dockerfile (py-rocket-base)
-# This works because py-rocket-base sets user to NB_USER
-ONBUILD RUN export NB_USER=$(whoami)
-ONBUILD ENV NB_USER=${NB_USER}
+# Convert NB_USER to ENV (from ARG) so that it passes to the child dockerfile
+ENV NB_USER=${NB_USER}
 
 ONBUILD USER root
 ONBUILD COPY . /tmpbuild/

From c2fb15dede4854d8f6c5886d8ce688073588b2ba Mon Sep 17 00:00:00 2001
From: Eli Holmes - NOAA <eli.holmes@noaa.gov>
Date: Wed, 23 Oct 2024 15:47:17 -0700
Subject: [PATCH 12/12] fix permissions when copy child files in

---
 appendix | 16 +++++++---------
 1 file changed, 7 insertions(+), 9 deletions(-)

diff --git a/appendix b/appendix
index 8479822..a4cbac9 100644
--- a/appendix
+++ b/appendix
@@ -33,16 +33,14 @@ 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 USER root
-ONBUILD COPY . /tmpbuild/
-# Copy Desktop files into ${REPO_DIR}/Desktop if they exist. First copy files to tmpbuild
-ONBUILD RUN if [ -d /tmpbuild/Desktop ]; then \
+# ${REPO_DIR} is owned by ${NB_USER}
+ONBUILD COPY --chown=${NB_USER}:${NB_USER} . ${REPO_DIR}/childimage
+# 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 /tmpbuild/Desktop/* ${REPO_DIR}/Desktop/; \
+        cp -r ${REPO_DIR}/childimage/Desktop/* ${REPO_DIR}/Desktop/; \
     fi
-ONBUILD RUN whoami && rm -rf /tmpbuild
-ONBUILD USER ${NB_USER}
-ONBUILD RUN whoami
 
-# Revert to default user
+# Revert to default user and home as pwd
 USER ${NB_USER}
+WORKDIR ${HOME}