From 7e3dbdc9f484332344cbbaa8dcd10c97f4808a40 Mon Sep 17 00:00:00 2001
From: Jonathan Berrisch <Jonathan@Berrisch.biz>
Date: Wed, 2 Oct 2024 14:01:29 +0200
Subject: [PATCH 01/16] Use Ubuntu 24.04 (WIP)

---
 Dockerfile                   | 17 ++++++++++-------
 install_scripts/install_r.sh |  6 ++----
 2 files changed, 12 insertions(+), 11 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 092061d..c2a6baa 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,4 +1,5 @@
-FROM ubuntu:jammy@sha256:58b87898e82351c6cf9cf5b9f3c20257bb9e2dcf33af051e12ce532d7f94e3fe
+FROM ubuntu:noble@sha256:b359f1067efa76f37863778f7b6d0e8d911e3ee8efa807ad01fbf5dc1ef9006b
+
 
 SHELL ["/bin/bash", "-c"]
 
@@ -10,10 +11,12 @@ ARG USER_UID=1000
 ARG USER_GID=$USER_UID
 ARG DEBIAN_FRONTEND=noninteractive
 
-# Add non root user
-RUN groupadd --gid $USER_GID $USERNAME \
-  && useradd -rm -d /home/$USERNAME -s /bin/bash -g root --uid $USER_UID --gid $USER_GID $USERNAME \
-  && addgroup $USERNAME staff
+# Rename ubuntu user to $USERNAME
+RUN usermod -l $USERNAME ubuntu \
+  # Add new group called $USERNAME
+  && groupadd $USERNAME \
+  # Add new user $USERNAME to the groups $USERNAME and staff
+  && usermod -a -G staff,$USERNAME $USERNAME
 
 # Create folders to mount extensions
 RUN mkdir -p /home/$USERNAME/.vscode-server/extensions \
@@ -116,7 +119,7 @@ RUN apt-get update &&\
   python3-dev \
   python3-venv && \
   # Python packages
-  pip3 install -U --no-cache-dir \
+  pip3 install -U --no-cache-dir --break-system-packages \
   $(grep -o '^[^#]*' package_lists/python_packages.txt | tr '\n' ' ')  \
   && apt-get autoclean -y \
   && rm -rf /var/lib/apt/lists/*
@@ -145,7 +148,7 @@ ENV PATH="/usr/local/texlive/bin/x86_64-linux:${PATH}"
 ENV R_VERSION=4.4.1
 
 # Set RSPM snapshot see:
-# https://packagemanager.posit.co/client/#/repos/cran/setup?r_environment=other&snapshot=2023-10-04&distribution=ubuntu-22.04
+# https://packagemanager.posit.co/client/#/repos/cran/setup?r_environment=other&snapshot=2024-10-01&distribution=ubuntu-22.04
 ENV R_REPOS=https://packagemanager.posit.co/cran/__linux__/jammy/2024-10-01
 
 COPY install_scripts/install_r.sh /tmp/install_r.sh
diff --git a/install_scripts/install_r.sh b/install_scripts/install_r.sh
index 6f018ed..cf0a167 100644
--- a/install_scripts/install_r.sh
+++ b/install_scripts/install_r.sh
@@ -1,9 +1,7 @@
 #!/bin/bash
 
-echo "deb http://cloud.r-project.org/bin/linux/ubuntu jammy-cran40/" >> /etc/apt/sources.list
-gpg --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
-gpg -a --export E298A3A825C0D65DFD57CBB651716619E084DAB9 | apt-key add -
-apt-get update
+echo "deb http://cloud.r-project.org/bin/linux/ubuntu noble-cran40/" >> /etc/apt/sources.list
+wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | sudo tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
 
 apt-get update
 

From cbb115b4fb663619540c5532c92c91d51f8fb4c1 Mon Sep 17 00:00:00 2001
From: Jonathan Berrisch <Jonathan@Berrisch.biz>
Date: Wed, 2 Oct 2024 14:11:12 +0200
Subject: [PATCH 02/16] Use "ubuntu" username instead of vscode

---
 Dockerfile | 10 +++-------
 1 file changed, 3 insertions(+), 7 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index c2a6baa..318aec6 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -6,17 +6,13 @@ SHELL ["/bin/bash", "-c"]
 ENV DISPLAY=:0 \
   TZ=Europe/Berlin
 
-ARG USERNAME=vscode
+ARG USERNAME=ubuntu
 ARG USER_UID=1000
 ARG USER_GID=$USER_UID
 ARG DEBIAN_FRONTEND=noninteractive
 
-# Rename ubuntu user to $USERNAME
-RUN usermod -l $USERNAME ubuntu \
-  # Add new group called $USERNAME
-  && groupadd $USERNAME \
-  # Add new user $USERNAME to the groups $USERNAME and staff
-  && usermod -a -G staff,$USERNAME $USERNAME
+# Add ubuntu user to ubuntu and staff groups
+RUN usermod -a -G staff,$USERNAME $USERNAME
 
 # Create folders to mount extensions
 RUN mkdir -p /home/$USERNAME/.vscode-server/extensions \

From 698ad86807ec7567ecf6d0989c871261ae82d285 Mon Sep 17 00:00:00 2001
From: Jonathan Berrisch <Jonathan@Berrisch.biz>
Date: Wed, 2 Oct 2024 14:46:20 +0200
Subject: [PATCH 03/16] Remove sudo from install_r.sh

---
 install_scripts/install_r.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/install_scripts/install_r.sh b/install_scripts/install_r.sh
index cf0a167..699ff08 100644
--- a/install_scripts/install_r.sh
+++ b/install_scripts/install_r.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 
 echo "deb http://cloud.r-project.org/bin/linux/ubuntu noble-cran40/" >> /etc/apt/sources.list
-wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | sudo tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
+wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
 
 apt-get update
 

From aa0b130b478490a6aac84338022285e03805c757 Mon Sep 17 00:00:00 2001
From: Jonathan Berrisch <Jonathan@Berrisch.biz>
Date: Wed, 2 Oct 2024 15:17:46 +0200
Subject: [PATCH 04/16] Use apt-key again

---
 install_scripts/install_r.sh | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/install_scripts/install_r.sh b/install_scripts/install_r.sh
index 699ff08..2dc8fb5 100644
--- a/install_scripts/install_r.sh
+++ b/install_scripts/install_r.sh
@@ -1,7 +1,9 @@
 #!/bin/bash
 
 echo "deb http://cloud.r-project.org/bin/linux/ubuntu noble-cran40/" >> /etc/apt/sources.list
-wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
+gpg --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
+gpg -a --export E298A3A825C0D65DFD57CBB651716619E084DAB9 | apt-key add -
+apt-get update
 
 apt-get update
 

From dc7be38ee387f76686cea656aac2a09bf700d3fc Mon Sep 17 00:00:00 2001
From: Jonathan Berrisch <Jonathan@Berrisch.biz>
Date: Wed, 2 Oct 2024 18:00:35 +0200
Subject: [PATCH 05/16] Update install_r.sh + Add cargo to Dockerfile

---
 Dockerfile                   | 11 +++++++----
 install_scripts/install_r.sh | 19 +++++++++++--------
 2 files changed, 18 insertions(+), 12 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 318aec6..fa0f614 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -35,6 +35,7 @@ RUN echo "ttf-mscorefonts-installer msttcorefonts/accepted-mscorefonts-eula sele
   ccache \
   gfortran \
   netbase \
+  cargo \
   zip \
   unzip \
   xclip \
@@ -121,7 +122,7 @@ RUN apt-get update &&\
   && rm -rf /var/lib/apt/lists/*
 
 # Set PATH for user installed python packages
-ENV PATH="/home/vscode/.local/bin:${PATH}"
+ENV PATH="/home/${USERNAME}/.local/bin:${PATH}"
 
 # Install Latex
 COPY install_scripts/install_latex.sh /tmp/install_latex.sh
@@ -135,17 +136,19 @@ RUN chmod +x /tmp/install_latex.sh &&\
   && tlmgr option -- srcfiles 0 \
   && tlmgr install \
   $(grep -o '^[^#]*' /tmp/latex_packages.txt | tr '\n' ' ') \
-  && chown --recursive $USERNAME:$USERNAME /usr/local/texlive
+  && chown --recursive $USERNAME:$USERNAME /usr/local/texlive \
+  && cargo install tex-fmt
 
-# Set Latex Path
+# Set Latex Paths
 ENV PATH="/usr/local/texlive/bin/x86_64-linux:${PATH}"
+ENV PATH="/home/${USERNAME}/.cargo/bin:${PATH}"
 
 # Install R
 ENV R_VERSION=4.4.1
 
 # Set RSPM snapshot see:
 # https://packagemanager.posit.co/client/#/repos/cran/setup?r_environment=other&snapshot=2024-10-01&distribution=ubuntu-22.04
-ENV R_REPOS=https://packagemanager.posit.co/cran/__linux__/jammy/2024-10-01
+ENV R_REPOS=https://packagemanager.posit.co/cran/__linux__/noble/2024-10-01
 
 COPY install_scripts/install_r.sh /tmp/install_r.sh
 COPY package_lists/r_packages.txt /tmp/r_packages.txt
diff --git a/install_scripts/install_r.sh b/install_scripts/install_r.sh
index 2dc8fb5..b701c77 100644
--- a/install_scripts/install_r.sh
+++ b/install_scripts/install_r.sh
@@ -1,9 +1,14 @@
 #!/bin/bash
 
-echo "deb http://cloud.r-project.org/bin/linux/ubuntu noble-cran40/" >> /etc/apt/sources.list
-gpg --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
-gpg -a --export E298A3A825C0D65DFD57CBB651716619E084DAB9 | apt-key add -
-apt-get update
+apt update -qq
+# install two helper packages we need
+apt install -y --no-install-recommends software-properties-common dirmngr
+# add the signing key (by Michael Rutter) for these repos
+# To verify key, run gpg --show-keys /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc 
+# Fingerprint: E298A3A825C0D65DFD57CBB651716619E084DAB9
+wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
+# add the R 4.X repo from CRAN
+add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu noble-cran40/"
 
 apt-get update
 
@@ -16,7 +21,6 @@ RUNDEPS="ca-certificates \
       libxml2-dev \
       vim-tiny \
       wget \
-      dirmngr \
       libmagick++-dev \
       libpoppler-cpp-dev \
       libudunits2-dev \
@@ -28,7 +32,6 @@ RUNDEPS="ca-certificates \
       libfribidi-dev \
       curl \
       libgit2-dev \
-      pandoc-citeproc \
       qpdf"
 
 # Install R amd dependencies
@@ -59,7 +62,7 @@ echo  'options(HTTPUserAgent = sprintf("R/%s R (%s)", getRversion(), paste(getRv
 Rscript -e "install.packages('docopt', repos= '$R_REPOS')"
 
 # Install alternative r console
-pip3 install -U --no-cache-dir radian
+pip3 install --user --no-cache-dir --break-system-packages radian
 
 # R packages on RSPM
 install2.r --error --skipinstalled --ncpus 32 \
@@ -70,7 +73,7 @@ installGithub.r \
     $(grep -o '^[^#]*' tmp/r_packages_github.txt | tr '\n' ' ')
 
 # Miniconda for Refinitiv and resp. python dependenies 
-R -e "Refinitiv::install_eikon()"
+# R -e "Refinitiv::install_eikon()"
 
 chown --recursive $USERNAME:$USERNAME /usr/local/lib/R/site-library
 

From 9492e9bd70209318384721b59e4333866196052d Mon Sep 17 00:00:00 2001
From: Jonathan Berrisch <Jonathan@Berrisch.biz>
Date: Wed, 2 Oct 2024 19:00:09 +0200
Subject: [PATCH 06/16] Fix cargo paths in Dockerfile

---
 Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index fa0f614..dac4adc 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -141,7 +141,7 @@ RUN chmod +x /tmp/install_latex.sh &&\
 
 # Set Latex Paths
 ENV PATH="/usr/local/texlive/bin/x86_64-linux:${PATH}"
-ENV PATH="/home/${USERNAME}/.cargo/bin:${PATH}"
+ENV PATH="/root/.cargo/bin:${PATH}"
 
 # Install R
 ENV R_VERSION=4.4.1

From 2e18bb10f4e4ca70d9e518211b8af95a06db3014 Mon Sep 17 00:00:00 2001
From: Jonathan Berrisch <Jonathan@Berrisch.biz>
Date: Wed, 2 Oct 2024 20:14:25 +0200
Subject: [PATCH 07/16] Fix cargo install / path

---
 Dockerfile | 57 +++++++++++++++++++++++++++---------------------------
 1 file changed, 29 insertions(+), 28 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index dac4adc..d952fc9 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -136,42 +136,43 @@ RUN chmod +x /tmp/install_latex.sh &&\
   && tlmgr option -- srcfiles 0 \
   && tlmgr install \
   $(grep -o '^[^#]*' /tmp/latex_packages.txt | tr '\n' ' ') \
-  && chown --recursive $USERNAME:$USERNAME /usr/local/texlive \
-  && cargo install tex-fmt
+  && chown --recursive $USERNAME:$USERNAME /usr/local/texlive
 
 # Set Latex Paths
 ENV PATH="/usr/local/texlive/bin/x86_64-linux:${PATH}"
-ENV PATH="/root/.cargo/bin:${PATH}"
 
 # Install R
 ENV R_VERSION=4.4.1
 
 # Set RSPM snapshot see:
-# https://packagemanager.posit.co/client/#/repos/cran/setup?r_environment=other&snapshot=2024-10-01&distribution=ubuntu-22.04
-ENV R_REPOS=https://packagemanager.posit.co/cran/__linux__/noble/2024-10-01
-
-COPY install_scripts/install_r.sh /tmp/install_r.sh
-COPY package_lists/r_packages.txt /tmp/r_packages.txt
-COPY package_lists/r_packages_github.txt /tmp/r_packages_github.txt
-
-RUN chmod +x /tmp/install_r.sh &&\
+  # https://packagemanager.posit.co/client/#/repos/cran/setup?r_environment=other&snapshot=2024-10-01&distribution=ubuntu-22.04
+  ENV R_REPOS=https://packagemanager.posit.co/cran/__linux__/noble/2024-10-01
+  
+  COPY install_scripts/install_r.sh /tmp/install_r.sh
+  COPY package_lists/r_packages.txt /tmp/r_packages.txt
+  COPY package_lists/r_packages_github.txt /tmp/r_packages_github.txt
+  
+  RUN chmod +x /tmp/install_r.sh &&\
   /tmp/install_r.sh
-
-COPY --chown=$USERNAME .misc/.zshrc /home/$USERNAME/.
-
-COPY --chown=$USERNAME .misc/.Rprofile /home/$USERNAME/.
-
-RUN mkdir /home/$USERNAME/.R && chown -R $USERNAME /home/$USERNAME/.R
-COPY --chown=$USERNAME .misc/Makevars /home/$USERNAME/.R/.
-
-RUN mkdir /home/$USERNAME/.ccache && chown -R $USERNAME /home/$USERNAME/.ccache
-COPY --chown=$USERNAME .misc/ccache.conf /home/$USERNAME/.ccache/.
-
-RUN chown -R $USERNAME /usr/local/lib
-RUN chown -R $USERNAME /usr/local/include
-
-# Switch to non-root user
-USER $USERNAME
-
+  
+  COPY --chown=$USERNAME .misc/.zshrc /home/$USERNAME/.
+  
+  COPY --chown=$USERNAME .misc/.Rprofile /home/$USERNAME/.
+  
+  RUN mkdir /home/$USERNAME/.R && chown -R $USERNAME /home/$USERNAME/.R
+  COPY --chown=$USERNAME .misc/Makevars /home/$USERNAME/.R/.
+  
+  RUN mkdir /home/$USERNAME/.ccache && chown -R $USERNAME /home/$USERNAME/.ccache
+  COPY --chown=$USERNAME .misc/ccache.conf /home/$USERNAME/.ccache/.
+  
+  RUN chown -R $USERNAME /usr/local/lib
+  RUN chown -R $USERNAME /usr/local/include
+  
+  # Switch to non-root user
+  USER $USERNAME
+  
+  RUN cargo install tex-fmt
+  ENV PATH="/home/${USERNAME}/.cargo/bin:${PATH}"
+  
 # Start zsh
 CMD [ "zsh" ]
\ No newline at end of file

From 60a506801a64856097c5565c04492b232902e77f Mon Sep 17 00:00:00 2001
From: Jonathan Berrisch <Jonathan@Berrisch.biz>
Date: Wed, 2 Oct 2024 21:14:33 +0200
Subject: [PATCH 08/16] Adjust PATH

---
 Dockerfile | 56 +++++++++++++++++++++++++++---------------------------
 1 file changed, 28 insertions(+), 28 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index d952fc9..d96bb4a 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -145,34 +145,34 @@ ENV PATH="/usr/local/texlive/bin/x86_64-linux:${PATH}"
 ENV R_VERSION=4.4.1
 
 # Set RSPM snapshot see:
-  # https://packagemanager.posit.co/client/#/repos/cran/setup?r_environment=other&snapshot=2024-10-01&distribution=ubuntu-22.04
-  ENV R_REPOS=https://packagemanager.posit.co/cran/__linux__/noble/2024-10-01
-  
-  COPY install_scripts/install_r.sh /tmp/install_r.sh
-  COPY package_lists/r_packages.txt /tmp/r_packages.txt
-  COPY package_lists/r_packages_github.txt /tmp/r_packages_github.txt
-  
-  RUN chmod +x /tmp/install_r.sh &&\
-  /tmp/install_r.sh
-  
-  COPY --chown=$USERNAME .misc/.zshrc /home/$USERNAME/.
-  
-  COPY --chown=$USERNAME .misc/.Rprofile /home/$USERNAME/.
-  
-  RUN mkdir /home/$USERNAME/.R && chown -R $USERNAME /home/$USERNAME/.R
-  COPY --chown=$USERNAME .misc/Makevars /home/$USERNAME/.R/.
-  
-  RUN mkdir /home/$USERNAME/.ccache && chown -R $USERNAME /home/$USERNAME/.ccache
-  COPY --chown=$USERNAME .misc/ccache.conf /home/$USERNAME/.ccache/.
-  
-  RUN chown -R $USERNAME /usr/local/lib
-  RUN chown -R $USERNAME /usr/local/include
-  
-  # Switch to non-root user
-  USER $USERNAME
-  
-  RUN cargo install tex-fmt
-  ENV PATH="/home/${USERNAME}/.cargo/bin:${PATH}"
+# https://packagemanager.posit.co/client/#/repos/cran/setup?r_environment=other&snapshot=2024-10-01&distribution=ubuntu-22.04
+ENV R_REPOS=https://packagemanager.posit.co/cran/__linux__/noble/2024-10-01
+
+COPY install_scripts/install_r.sh /tmp/install_r.sh
+COPY package_lists/r_packages.txt /tmp/r_packages.txt
+COPY package_lists/r_packages_github.txt /tmp/r_packages_github.txt
+
+RUN chmod +x /tmp/install_r.sh &&\
+/tmp/install_r.sh
+
+COPY --chown=$USERNAME .misc/.zshrc /home/$USERNAME/.
+
+COPY --chown=$USERNAME .misc/.Rprofile /home/$USERNAME/.
+
+RUN mkdir /home/$USERNAME/.R && chown -R $USERNAME /home/$USERNAME/.R
+COPY --chown=$USERNAME .misc/Makevars /home/$USERNAME/.R/.
+
+RUN mkdir /home/$USERNAME/.ccache && chown -R $USERNAME /home/$USERNAME/.ccache
+COPY --chown=$USERNAME .misc/ccache.conf /home/$USERNAME/.ccache/.
+
+RUN chown -R $USERNAME /usr/local/lib
+RUN chown -R $USERNAME /usr/local/include
+
+# Switch to non-root user
+USER $USERNAME
+
+RUN cargo install tex-fmt
+ENV PATH="/home/ubuntu/.cargo/bin:${PATH}"
   
 # Start zsh
 CMD [ "zsh" ]
\ No newline at end of file

From 0e1cd2a103dbb903d4deeb18e47a35a8b3160c7d Mon Sep 17 00:00:00 2001
From: Jonathan Berrisch <Jonathan@Berrisch.biz>
Date: Wed, 2 Oct 2024 22:00:48 +0200
Subject: [PATCH 09/16] Update python packages path

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

diff --git a/Dockerfile b/Dockerfile
index d96bb4a..e2a891b 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -165,6 +165,8 @@ COPY --chown=$USERNAME .misc/Makevars /home/$USERNAME/.R/.
 RUN mkdir /home/$USERNAME/.ccache && chown -R $USERNAME /home/$USERNAME/.ccache
 COPY --chown=$USERNAME .misc/ccache.conf /home/$USERNAME/.ccache/.
 
+ENV PATH="/root/.local/bin:${PATH}"
+RUN chown -R $USERNAME /root/.local/bin
 RUN chown -R $USERNAME /usr/local/lib
 RUN chown -R $USERNAME /usr/local/include
 

From 45cf375e08c80eeee1938e401b380b2355f8ef9a Mon Sep 17 00:00:00 2001
From: Jonathan Berrisch <jonathan@berrisch.biz>
Date: Tue, 8 Oct 2024 11:02:09 +0200
Subject: [PATCH 10/16] Use python venv

---
 .devcontainer/devcontainer.json     |  5 +++--
 Dockerfile                          | 32 ++++++++++++++---------------
 install_scripts/install_r.sh        |  7 ++-----
 package_lists/python_packages.txt   |  1 +
 package_lists/r_packages.txt        |  1 +
 package_lists/r_packages_github.txt |  1 -
 6 files changed, 23 insertions(+), 24 deletions(-)

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index 7f0ad21..08d61ee 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -65,11 +65,12 @@
                 },
                 // Python
                 "jupyter.notebookFileRoot": "${workspaceFolder}",
-                "python.pythonPath": "/usr/bin/python3",
+        "python.pythonPath": "/opt/venv/python",
+        "python.defaultInterpreterPath": "/opt/venv/python",
                 "python.dataScience.interactiveWindowMode": "perFile",
                 "python.dataScience.sendSelectionToInteractiveWindow": true,
                 // R
-                "r.rterm.linux": "/usr/local/bin/radian",
+        "r.rterm.linux": "/opt/venv/radian",
                 "r.bracketedPaste": true,
                 "r.sessionWatcher": true,
                 "r.plot.useHttpgd": true,
diff --git a/Dockerfile b/Dockerfile
index e2a891b..3b79be8 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -6,6 +6,7 @@ SHELL ["/bin/bash", "-c"]
 ENV DISPLAY=:0 \
   TZ=Europe/Berlin
 
+ARG VIRTUAL_ENV=/opt/venv
 ARG USERNAME=ubuntu
 ARG USER_UID=1000
 ARG USER_GID=$USER_UID
@@ -47,6 +48,9 @@ RUN echo "ttf-mscorefonts-installer msttcorefonts/accepted-mscorefonts-eula sele
   ssh-client \
   fontconfig \
   pkg-config \
+  python3-pip  \
+  python3-dev \
+  python3-venv \
   default-libmysqlclient-dev \
   ttf-mscorefonts-installer \
   locales &&\
@@ -56,6 +60,11 @@ RUN echo "ttf-mscorefonts-installer msttcorefonts/accepted-mscorefonts-eula sele
   git clone --depth=1 https://github.com/sindresorhus/pure.git /home/$USERNAME/.zsh/pure \
   && rm -rf /home/$USERNAME/.zsh/pure/.git \
   && apt-get autoclean -y \
+  && apt-get clean \
+  && apt-get autoclean \
+  && rm -rf /var/cache/* \
+  && rm -rf /tmp/* \
+  && rm -rf /var/tmp/* \
   && rm -rf /var/lib/apt/lists/*
 
 ENV LC_ALL=en_US.UTF-8 \
@@ -108,22 +117,16 @@ RUN git clone --depth=1 https://github.com/RUrlus/carma.git /usr/local/carma \
   && rm -rf /usr/local/carma
 
 # Install Python
+RUN python3 -m venv $VIRTUAL_ENV
+ENV PATH="$VIRTUAL_ENV/bin:$PATH"
 COPY package_lists/python_packages.txt /package_lists/python_packages.txt
 
-RUN apt-get update &&\
-  apt-get -y --no-install-recommends install \
-  python3-pip  \
-  python3-dev \
-  python3-venv && \
-  # Python packages
-  pip3 install -U --no-cache-dir --break-system-packages \
+RUN pip install --upgrade pip \
+  && pip3 install \
   $(grep -o '^[^#]*' package_lists/python_packages.txt | tr '\n' ' ')  \
   && apt-get autoclean -y \
   && rm -rf /var/lib/apt/lists/*
 
-# Set PATH for user installed python packages
-ENV PATH="/home/${USERNAME}/.local/bin:${PATH}"
-
 # Install Latex
 COPY install_scripts/install_latex.sh /tmp/install_latex.sh
 COPY package_lists/latex_packages.txt /tmp/latex_packages.txt
@@ -153,7 +156,7 @@ COPY package_lists/r_packages.txt /tmp/r_packages.txt
 COPY package_lists/r_packages_github.txt /tmp/r_packages_github.txt
 
 RUN chmod +x /tmp/install_r.sh &&\
-/tmp/install_r.sh
+  /tmp/install_r.sh
 
 COPY --chown=$USERNAME .misc/.zshrc /home/$USERNAME/.
 
@@ -165,16 +168,13 @@ COPY --chown=$USERNAME .misc/Makevars /home/$USERNAME/.R/.
 RUN mkdir /home/$USERNAME/.ccache && chown -R $USERNAME /home/$USERNAME/.ccache
 COPY --chown=$USERNAME .misc/ccache.conf /home/$USERNAME/.ccache/.
 
-ENV PATH="/root/.local/bin:${PATH}"
-RUN chown -R $USERNAME /root/.local/bin
-RUN chown -R $USERNAME /usr/local/lib
-RUN chown -R $USERNAME /usr/local/include
+RUN chown -R $USERNAME /usr/local
 
 # Switch to non-root user
 USER $USERNAME
 
 RUN cargo install tex-fmt
 ENV PATH="/home/ubuntu/.cargo/bin:${PATH}"
-  
+
 # Start zsh
 CMD [ "zsh" ]
\ No newline at end of file
diff --git a/install_scripts/install_r.sh b/install_scripts/install_r.sh
index b701c77..e2c62de 100644
--- a/install_scripts/install_r.sh
+++ b/install_scripts/install_r.sh
@@ -61,9 +61,6 @@ echo  'options(HTTPUserAgent = sprintf("R/%s R (%s)", getRversion(), paste(getRv
 # Install docopt which is used by littler to install packages
 Rscript -e "install.packages('docopt', repos= '$R_REPOS')"
 
-# Install alternative r console
-pip3 install --user --no-cache-dir --break-system-packages radian
-
 # R packages on RSPM
 install2.r --error --skipinstalled --ncpus 32 \
     $(grep -o '^[^#]*' tmp/r_packages.txt | tr '\n' ' ')
@@ -77,6 +74,6 @@ installGithub.r \
 
 chown --recursive $USERNAME:$USERNAME /usr/local/lib/R/site-library
 
-apt-get autoclean -y
-rm -rf /var/lib/apt/lists/*
+# apt-get autoclean -y
+# rm -rf /var/lib/apt/lists/*
 
diff --git a/package_lists/python_packages.txt b/package_lists/python_packages.txt
index 235bffe..5bdc970 100644
--- a/package_lists/python_packages.txt
+++ b/package_lists/python_packages.txt
@@ -31,6 +31,7 @@ Pyarrow
 pylint
 pyparsing==2.4.7
 pytest
+radian
 redis
 requests
 ruff
diff --git a/package_lists/r_packages.txt b/package_lists/r_packages.txt
index f517b6e..0999e18 100644
--- a/package_lists/r_packages.txt
+++ b/package_lists/r_packages.txt
@@ -51,6 +51,7 @@ gt
 Hmisc
 htmltools
 htmlwidgets
+httpgd
 igraph
 inline
 inspectdf
diff --git a/package_lists/r_packages_github.txt b/package_lists/r_packages_github.txt
index 33428a7..a93dfa8 100644
--- a/package_lists/r_packages_github.txt
+++ b/package_lists/r_packages_github.txt
@@ -2,6 +2,5 @@ BerriJ/strsplit.fix
 GreenGrassBlueOcean/RefinitivR
 jhelvy/renderthis
 ManuelHentschel/vscDebugger@*release
-nx10/httpgd
 sjp/grConvert
 stenevang/sftp

From e17da0e12b8dfb84cbd9aab765d7143f2ba79c88 Mon Sep 17 00:00:00 2001
From: Jonathan Berrisch <jonathan@berrisch.biz>
Date: Tue, 8 Oct 2024 11:58:59 +0200
Subject: [PATCH 11/16] Add cleanup of R

---
 Dockerfile                   | 1 -
 install_scripts/install_r.sh | 9 ++++++---
 2 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 3b79be8..4679d0c 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -61,7 +61,6 @@ RUN echo "ttf-mscorefonts-installer msttcorefonts/accepted-mscorefonts-eula sele
   && rm -rf /home/$USERNAME/.zsh/pure/.git \
   && apt-get autoclean -y \
   && apt-get clean \
-  && apt-get autoclean \
   && rm -rf /var/cache/* \
   && rm -rf /tmp/* \
   && rm -rf /var/tmp/* \
diff --git a/install_scripts/install_r.sh b/install_scripts/install_r.sh
index e2c62de..5657a8f 100644
--- a/install_scripts/install_r.sh
+++ b/install_scripts/install_r.sh
@@ -74,6 +74,9 @@ installGithub.r \
 
 chown --recursive $USERNAME:$USERNAME /usr/local/lib/R/site-library
 
-# apt-get autoclean -y
-# rm -rf /var/lib/apt/lists/*
-
+apt-get autoclean -y 
+apt-get clean 
+rm -rf /var/cache/* 
+rm -rf /tmp/* 
+rm -rf /var/tmp/* 
+rm -rf /var/lib/apt/lists/*
\ No newline at end of file

From 96ca106853ade75523fd3ad37e84e7b1029ca364 Mon Sep 17 00:00:00 2001
From: Jonathan Berrisch <jonathan@berrisch.biz>
Date: Tue, 8 Oct 2024 14:31:39 +0200
Subject: [PATCH 12/16] Minor refinements in Dockerfile

---
 Dockerfile | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 4679d0c..f573295 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -75,7 +75,6 @@ COPY .misc/lmroman10-regular-webfont.ttf /usr/share/fonts/truetype/.
 COPY .misc/lmroman10-italic-webfont.ttf /usr/share/fonts/truetype/.
 COPY .misc/lmroman10-bolditalic-webfont.ttf /usr/share/fonts/truetype/.
 COPY .misc/lmroman10-bold-webfont.ttf /usr/share/fonts/truetype/.
-
 RUN fc-cache -f -v
 
 # Install quarto
@@ -157,6 +156,8 @@ COPY package_lists/r_packages_github.txt /tmp/r_packages_github.txt
 RUN chmod +x /tmp/install_r.sh &&\
   /tmp/install_r.sh
 
+RUN chown -R $USERNAME /usr/local
+
 COPY --chown=$USERNAME .misc/.zshrc /home/$USERNAME/.
 
 COPY --chown=$USERNAME .misc/.Rprofile /home/$USERNAME/.
@@ -167,8 +168,6 @@ COPY --chown=$USERNAME .misc/Makevars /home/$USERNAME/.R/.
 RUN mkdir /home/$USERNAME/.ccache && chown -R $USERNAME /home/$USERNAME/.ccache
 COPY --chown=$USERNAME .misc/ccache.conf /home/$USERNAME/.ccache/.
 
-RUN chown -R $USERNAME /usr/local
-
 # Switch to non-root user
 USER $USERNAME
 

From ddf5d01c152137095e15bb8c9fad2aa338f5b3eb Mon Sep 17 00:00:00 2001
From: Jonathan Berrisch <Jonathan@Berrisch.biz>
Date: Wed, 9 Oct 2024 10:41:49 +0200
Subject: [PATCH 13/16] Install python packages as $USER

---
 Dockerfile | 20 +++++++++-----------
 1 file changed, 9 insertions(+), 11 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index f573295..49b70de 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -114,17 +114,6 @@ RUN git clone --depth=1 https://github.com/RUrlus/carma.git /usr/local/carma \
   && cmake --build . --config Release --target install \
   && rm -rf /usr/local/carma
 
-# Install Python
-RUN python3 -m venv $VIRTUAL_ENV
-ENV PATH="$VIRTUAL_ENV/bin:$PATH"
-COPY package_lists/python_packages.txt /package_lists/python_packages.txt
-
-RUN pip install --upgrade pip \
-  && pip3 install \
-  $(grep -o '^[^#]*' package_lists/python_packages.txt | tr '\n' ' ')  \
-  && apt-get autoclean -y \
-  && rm -rf /var/lib/apt/lists/*
-
 # Install Latex
 COPY install_scripts/install_latex.sh /tmp/install_latex.sh
 COPY package_lists/latex_packages.txt /tmp/latex_packages.txt
@@ -171,6 +160,15 @@ COPY --chown=$USERNAME .misc/ccache.conf /home/$USERNAME/.ccache/.
 # Switch to non-root user
 USER $USERNAME
 
+# Install Python Packages
+RUN python3 -m venv $VIRTUAL_ENV
+ENV PATH="$VIRTUAL_ENV/bin:$PATH"
+COPY package_lists/python_packages.txt /package_lists/python_packages.txt
+
+RUN pip install --upgrade pip \
+  && pip3 install \
+  $(grep -o '^[^#]*' package_lists/python_packages.txt | tr '\n' ' ')
+
 RUN cargo install tex-fmt
 ENV PATH="/home/ubuntu/.cargo/bin:${PATH}"
 

From 4e9da65bd475d7a2c23fb33b882761e4ac546ad7 Mon Sep 17 00:00:00 2001
From: Jonathan Berrisch <Jonathan@Berrisch.biz>
Date: Wed, 9 Oct 2024 11:15:08 +0200
Subject: [PATCH 14/16] Update python venv location

---
 Dockerfile                   | 2 +-
 package_lists/r_packages.txt | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index 49b70de..c9baa6a 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -6,8 +6,8 @@ SHELL ["/bin/bash", "-c"]
 ENV DISPLAY=:0 \
   TZ=Europe/Berlin
 
-ARG VIRTUAL_ENV=/opt/venv
 ARG USERNAME=ubuntu
+ARG VIRTUAL_ENV=/home/$USERNAME/python/venv
 ARG USER_UID=1000
 ARG USER_GID=$USER_UID
 ARG DEBIAN_FRONTEND=noninteractive
diff --git a/package_lists/r_packages.txt b/package_lists/r_packages.txt
index 0999e18..24aac25 100644
--- a/package_lists/r_packages.txt
+++ b/package_lists/r_packages.txt
@@ -30,6 +30,7 @@ fontawesome
 foreach
 forecast
 gamlss.dist
+MixGHD
 gamlss.lasso
 GAS
 gdata

From 71feb93e9abbdabac51f2f87ee16595a422f951b Mon Sep 17 00:00:00 2001
From: Jonathan Berrisch <Jonathan@Berrisch.biz>
Date: Wed, 9 Oct 2024 12:08:53 +0200
Subject: [PATCH 15/16] Install R packages to /home/$USERNAME/R/library

---
 Dockerfile | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index c9baa6a..e2f7bc6 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -7,6 +7,7 @@ ENV DISPLAY=:0 \
   TZ=Europe/Berlin
 
 ARG USERNAME=ubuntu
+ENV R_LIBS_USER=/home/$USERNAME/R/library
 ARG VIRTUAL_ENV=/home/$USERNAME/python/venv
 ARG USER_UID=1000
 ARG USER_GID=$USER_UID
@@ -18,6 +19,7 @@ RUN usermod -a -G staff,$USERNAME $USERNAME
 # Create folders to mount extensions
 RUN mkdir -p /home/$USERNAME/.vscode-server/extensions \
   /home/$USERNAME/.vscode-server-insiders/extensions \
+  /home/$USERNAME/R/library \
   workspaces \
   && chown -R $USERNAME \
   /home/$USERNAME/.vscode-server \
@@ -145,7 +147,8 @@ COPY package_lists/r_packages_github.txt /tmp/r_packages_github.txt
 RUN chmod +x /tmp/install_r.sh &&\
   /tmp/install_r.sh
 
-RUN chown -R $USERNAME /usr/local
+RUN chown -R $USERNAME /usr/local/lib
+RUN chown -R $USERNAME /usr/local/include
 
 COPY --chown=$USERNAME .misc/.zshrc /home/$USERNAME/.
 
@@ -166,7 +169,7 @@ ENV PATH="$VIRTUAL_ENV/bin:$PATH"
 COPY package_lists/python_packages.txt /package_lists/python_packages.txt
 
 RUN pip install --upgrade pip \
-  && pip3 install \
+  && pip --no-cache-dir install \
   $(grep -o '^[^#]*' package_lists/python_packages.txt | tr '\n' ' ')
 
 RUN cargo install tex-fmt

From a77185d287a20ebf1329da1b4000f28975c5b945 Mon Sep 17 00:00:00 2001
From: Jonathan Berrisch <Jonathan@Berrisch.biz>
Date: Wed, 9 Oct 2024 12:49:36 +0200
Subject: [PATCH 16/16] Fix R permissions

---
 install_scripts/install_r.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/install_scripts/install_r.sh b/install_scripts/install_r.sh
index 5657a8f..c819d02 100644
--- a/install_scripts/install_r.sh
+++ b/install_scripts/install_r.sh
@@ -72,7 +72,7 @@ installGithub.r \
 # Miniconda for Refinitiv and resp. python dependenies 
 # R -e "Refinitiv::install_eikon()"
 
-chown --recursive $USERNAME:$USERNAME /usr/local/lib/R/site-library
+chown --recursive $USERNAME:$USERNAME /home/$USERNAME/R/library
 
 apt-get autoclean -y 
 apt-get clean