Forgot to port the docker changes

.github/workflows/dockerhub.yaml

@@ -11,6 +11,7 @@ on:
     paths:
       - 'Dockerfile'
       - 'Docker.Rprofile'
+      - 'Docker.bashrc'
       - 'renv/**'
       - 'renv.lock'
       - 'renv.cache/**'

Docker.bashrc

@@ -0,0 +1,118 @@
+# ~/.bashrc: executed by bash(1) for non-login shells.
+# see /usr/share/doc/bash/examples/startup-files (in the package bash-doc)
+# for examples
+
+# If not running interactively, don't do anything
+case $- in
+    *i*) ;;
+      *) return;;
+esac
+
+# don't put duplicate lines or lines starting with space in the history.
+# See bash(1) for more options
+HISTCONTROL=ignoreboth
+
+# append to the history file, don't overwrite it
+shopt -s histappend
+
+# for setting history length see HISTSIZE and HISTFILESIZE in bash(1)
+HISTSIZE=1000
+HISTFILESIZE=2000
+
+# check the window size after each command and, if necessary,
+# update the values of LINES and COLUMNS.
+shopt -s checkwinsize
+
+# If set, the pattern "**" used in a pathname expansion context will
+# match all files and zero or more directories and subdirectories.
+#shopt -s globstar
+
+# make less more friendly for non-text input files, see lesspipe(1)
+[ -x /usr/bin/lesspipe ] && eval "$(SHELL=/bin/sh lesspipe)"
+
+# set variable identifying the chroot you work in (used in the prompt below)
+if [ -z "${debian_chroot:-}" ] && [ -r /etc/debian_chroot ]; then
+    debian_chroot=$(cat /etc/debian_chroot)
+fi
+
+# set a fancy prompt (non-color, unless we know we "want" color)
+case "$TERM" in
+    xterm-color|*-256color) color_prompt=yes;;
+esac
+
+# uncomment for a colored prompt, if the terminal has the capability; turned
+# off by default to not distract the user: the focus in a terminal window
+# should be on the output of commands, not on the prompt
+#force_color_prompt=yes
+
+if [ -n "$force_color_prompt" ]; then
+    if [ -x /usr/bin/tput ] && tput setaf 1 >&/dev/null; then
+	# We have color support; assume it's compliant with Ecma-48
+	# (ISO/IEC-6429). (Lack of such support is extremely rare, and such
+	# a case would tend to support setf rather than setaf.)
+	color_prompt=yes
+    else
+	color_prompt=
+    fi
+fi
+
+if [ "$color_prompt" = yes ]; then
+    PS1='${debian_chroot:+($debian_chroot)}\[\033[01;32m\]\u@\h\[\033[00m\]:\[\033[01;34m\]\w\[\033[00m\]\$ '
+else
+    PS1='${debian_chroot:+($debian_chroot)}\u@\h:\w\$ '
+fi
+unset color_prompt force_color_prompt
+
+# If this is an xterm set the title to user@host:dir
+case "$TERM" in
+xterm*|rxvt*)
+    PS1="\[\e]0;${debian_chroot:+($debian_chroot)}\u@\h: \w\a\]$PS1"
+    ;;
+*)
+    ;;
+esac
+
+# enable color support of ls and also add handy aliases
+if [ -x /usr/bin/dircolors ]; then
+    test -r ~/.dircolors && eval "$(dircolors -b ~/.dircolors)" || eval "$(dircolors -b)"
+    alias ls='ls --color=auto'
+    #alias dir='dir --color=auto'
+    #alias vdir='vdir --color=auto'
+
+    alias grep='grep --color=auto'
+    alias fgrep='fgrep --color=auto'
+    alias egrep='egrep --color=auto'
+fi
+
+# colored GCC warnings and errors
+#export GCC_COLORS='error=01;31:warning=01;35:note=01;36:caret=01;32:locus=01:quote=01'
+
+# some more ls aliases
+alias ll='ls -alF'
+alias la='ls -A'
+alias l='ls -CF'
+
+# Add an "alert" alias for long running commands.  Use like so:
+#   sleep 10; alert
+alias alert='notify-send --urgency=low -i "$([ $? = 0 ] && echo terminal || echo error)" "$(history|tail -n1|sed -e '\''s/^\s*[0-9]\+\s*//;s/[;&|]\s*alert$//'\'')"'
+
+# Alias definitions.
+# You may want to put all your additions into a separate file like
+# ~/.bash_aliases, instead of adding them here directly.
+# See /usr/share/doc/bash-doc/examples in the bash-doc package.
+
+if [ -f ~/.bash_aliases ]; then
+    . ~/.bash_aliases
+fi
+
+# enable programmable completion features (you don't need to enable
+# this, if it's already enabled in /etc/bash.bashrc and /etc/profile
+# sources /etc/bash.bashrc).
+if ! shopt -oq posix; then
+  if [ -f /usr/share/bash-completion/bash_completion ]; then
+    . /usr/share/bash-completion/bash_completion
+  elif [ -f /etc/bash_completion ]; then
+    . /etc/bash_completion
+  fi
+fi
+source /var/python/3.10/virtualenv/bin/activate

Dockerfile

@@ -22,7 +22,8 @@ RUN set -e \
         gnupg2 gnupg1 ca-certificates software-properties-common \
       && apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 \
       && add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/' \
-      && add-apt-repository ppa:git-core/ppa
+      && add-apt-repository ppa:git-core/ppa \
+      && add-apt-repository ppa:deadsnakes/ppa
 
 RUN apt-get update && \
     apt-get install -y --no-install-recommends \
@@ -70,10 +71,15 @@ RUN apt-get update && \
     supervisor \
     awscli \
     r-base-dev=$R_VERSION \
-    python3-venv \
+    python3.10 \
+    python3.10-dev \
+    python3.10-distutils \
+    python3.10-venv \
     # make sure we have up-to-date CA certs or curling some https endpoints (like python.org) may fail
     ca-certificates \
     # app user creation
+    && sudo ln -s /usr/bin/python3.10 /usr/local/bin/python \
+    && sudo ln -s /usr/bin/pip3 /usr/local/bin/pip \
     && useradd -m app \
     && mkdir -p /home/app \
     && chown -R app:app /home/app \
@@ -86,42 +92,31 @@ USER app
 ENV HOME /home/app
 
 #####
-# R
+# Python (managed via pyenv)
 #####
+# 
+ENV PYTHON_VERSION 3.10
+ENV VENV_ROOT /var/python/$PYTHON_VERSION/virtualenv
+COPY --chown=app:app gempyor_pkg $HOME/gempyor_pkg
 
-# Use packrat for R package management
-RUN sudo Rscript -e "install.packages('renv',repos='https://cloud.r-project.org/')" \
-    && cd /home/app
-    # && Rscript -e 'arrow::install_arrow()'
-COPY --chown=app:app renv.cache $HOME/.cache
-COPY --chown=app:app renv.lock $HOME/renv.lock
-COPY --chown=app:app renv $HOME/renv
-COPY --chown=app:app Docker.Rprofile $HOME/.Rprofile
+RUN sudo python -m venv $VENV_ROOT \
+  && sudo chown app:app -R $VENV_ROOT \
+  && $VENV_ROOT/bin/python3.10 -m pip install --upgrade setuptools pip \
+  && $VENV_ROOT/bin/python3.10 -m pip install $HOME/gempyor_pkg
 
+COPY --chown=app:app Docker.bashrc $HOME/.bashrc
+COPY --chown=root:root Docker.bashrc /root/.bashrc
 
 #####
-# Python (managed via pyenv)
+# R
 #####
 
-ENV PYENV_ROOT $HOME/.pyenv
-ENV PYTHON_VERSION 3.10.1
-ENV PYTHON_VENV_DIR $HOME/python_venv
-ENV PATH $PYENV_ROOT/shims:$PYENV_ROOT/bin:$PATH
-
-
-RUN git clone https://github.com/yyuu/pyenv.git $HOME/.pyenv \
-    && rm -rf $HOME/.pyenv/.git \
-    && env PYTHON_CONFIGURE_OPTS="--enable-shared" pyenv install -s $PYTHON_VERSION --verbose \
-    && pyenv rehash \
-    && echo 'eval "$(pyenv init -)"' >> ~/.bashrc \
-    && echo "pyenv shell $PYTHON_VERSION" >> ~/.bashrc \
-    && echo "PS1=\"\[\e]0;\u@\h: \w\a\] \h:\w\$ \"" >> ~/.bashrc
-
-# automatically activate the python venv when logging in
-COPY --chown=app:app gempyor_pkg $HOME/gempyor_pkg
-RUN eval "$(pyenv init -)" \
-    && pyenv shell $PYTHON_VERSION \
-    && pip install --upgrade pip setuptools \
-    && pip install --user $HOME/gempyor_pkg
+# Use renv for R package management
+RUN sudo Rscript -e "install.packages('renv',repos='https://cloud.r-project.org/')"
+COPY --chown=app:app renv.cache $HOME/.cache
+COPY --chown=app:app renv.lock $HOME/renv.lock
+COPY --chown=app:app renv $HOME/renv
+COPY --chown=app:app Docker.Rprofile $HOME/.Rprofile
+COPY --chown=app:app R/pkgs $HOME/pkgs
 
 CMD ["/bin/bash"]