initial commit

Dockerfile

+FROM python:3.11.2-slim-bullseye AS base
+
+USER root
+
+# default values
+ARG PACK_ROOT="base"
+ARG USER=kufair
+ARG GNAME=kufair
+ARG PASSWD=kufair
+ARG UID=1853
+ARG GID=1853
+
+# environement variables
+ENV PACK_ROOT=${PACK_ROOT}
+ENV USER=${USER}
+ENV GNAME=${GNAME}
+ENV UID=${UID}
+ENV GID=${GID}
+ENV HOME=/home/${USER}
+
+# create user kufair (1853:1853)
+RUN if ! id -u "${USER}" > /dev/null 2>&1; then groupadd -g "${GID}" "${GNAME}" \
+ && useradd -m -s /bin/bash -g "${GNAME}" -u "${UID}" "${USER}" \
+ && chmod -R 777 /tmp \
+ && echo "${USER}:${PASSWD}" | chpasswd \
+ && chown -R "${USER}:${GID}" "${HOME}"; fi;
+
+# set shell
+SHELL ["/bin/bash", "-o", "pipefail", "-c"]
+
+# install deps as root
+RUN apt-get update -y && \
+    apt-get upgrade -y && \
+    apt-get install software-properties-common -y && \
+    add-apt-repository -y main && \
+    apt-get install  -y --no-install-recommends \
+            tini \
+            build-essential \
+            wget \
+            ca-certificates \
+            openssh-client \
+            curl \
+            bzip2 \
+            locales \
+            apt-utils \
+            cmake \
+            ftp \
+            g++ \
+            gcc-multilib \
+            gfortran \
+            git \
+            nano-tiny \
+            unzip \
+            jq \
+            vim-tiny \
+            astro-all
+    
+# clean packages
+RUN apt-get update -y && \
+    apt-get upgrade -y && \
+    apt-get purge --auto-remove -y
+
+# install python related deps
+#RUN apt-get update -y \
+# && apt-get install -y \
+#    python3 \
+#    python3-dev \
+#    python3-pip
+
+# Copying repo to base
+RUN mkdir ${HOME}/base
+COPY . ${HOME}/base/
+
+# make sure home is fully accessible
+RUN chown -R "${USER}:${GID}" "${HOME}"
+
+# set default workdir
+WORKDIR ${HOME}/base
+
+# set SHELL
+ENV SHELL=/bin/bash
+
+
+FROM base AS runner
+
+USER root
+
+# install global deps
+RUN ./install-deps.sh
+
+# install user virtual env
+USER ${USER}
+RUN ./install-venv.sh
+RUN ./setup-env.sh
+
+# entrypoint and cmd
+ENTRYPOINT ["bash", "-c"]
+ONBUILD CMD ["/home/kufair/base/run-wrapper.sh"]
+
+
+
+FROM base AS explorer
+
+USER root
+
+# install deps of jupyterlab
+RUN wget https://deb.nodesource.com/setup_20.x && \
+    chmod 550 setup_20.x && \
+    ./setup_20.x && \
+    apt-get install nodejs && \
+    apt-get clean && rm -rf /var/lib/apt/lists/* && rm -rf setup_20.x && \
+    update-alternatives --install /usr/bin/nano nano /bin/nano-tiny 10 && \
+    echo "en_US.UTF-8 UTF-8" > /etc/locale.gen && \
+    locale-gen
+
+# install micro (optional)
+RUN curl https://getmic.ro | bash && \
+    mv micro /usr/bin
+
+# install global deps
+RUN ./install-deps.sh
+
+# install user deps
+USER ${USER}
+RUN ./install-venv.sh
+RUN ./install-jupyterlab.sh
+RUN ./setup-env.sh
+
+# Exploration ENV
+ENV EXPLORE_WORKDIR=${HOME}
+ENV EXPLORE_USER=${USER}
+
+# entrypoint and cmd
+ENTRYPOINT ["bash", "-c"]
+CMD ["/home/kufair/base/explore-wrapper.sh"]

README.md

-# scitrace-jupyterlab-debian-astro-bullseye
+# scitrace-jupyterlab-python3-11
 
+The base package for Jupyterlab Exploration with python3.11
 
+## OS
 
-## Getting started
-
-To make it easy for you to get started with GitLab, here's a list of recommended next steps.
-
-Already a pro? Just edit this README.md and make it your own. Want to make it easy? [Use the template at the bottom](#editing-this-readme)!
-
-## Add your files
-
-- [ ] [Create](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#create-a-file) or [upload](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#upload-a-file) files
-- [ ] [Add files using the command line](https://docs.gitlab.com/ee/gitlab-basics/add-file.html#add-a-file-using-the-command-line) or push an existing Git repository with the following command:
-
-```
-cd existing_repo
-git remote add origin https://gitlab-p4n.aip.de/workflows/scitrace/base-packages/scitrace-jupyterlab-debian-astro-bullseye.git
-git branch -M main
-git push -uf origin main
-```
-
-## Integrate with your tools
-
-- [ ] [Set up project integrations](https://gitlab-p4n.aip.de/workflows/scitrace/base-packages/scitrace-jupyterlab-debian-astro-bullseye/-/settings/integrations)
-
-## Collaborate with your team
-
-- [ ] [Invite team members and collaborators](https://docs.gitlab.com/ee/user/project/members/)
-- [ ] [Create a new merge request](https://docs.gitlab.com/ee/user/project/merge_requests/creating_merge_requests.html)
-- [ ] [Automatically close issues from merge requests](https://docs.gitlab.com/ee/user/project/issues/managing_issues.html#closing-issues-automatically)
-- [ ] [Enable merge request approvals](https://docs.gitlab.com/ee/user/project/merge_requests/approvals/)
-- [ ] [Automatically merge when pipeline succeeds](https://docs.gitlab.com/ee/user/project/merge_requests/merge_when_pipeline_succeeds.html)
-
-## Test and Deploy
-
-Use the built-in continuous integration in GitLab.
-
-- [ ] [Get started with GitLab CI/CD](https://docs.gitlab.com/ee/ci/quick_start/index.html)
-- [ ] [Analyze your code for known vulnerabilities with Static Application Security Testing(SAST)](https://docs.gitlab.com/ee/user/application_security/sast/)
-- [ ] [Deploy to Kubernetes, Amazon EC2, or Amazon ECS using Auto Deploy](https://docs.gitlab.com/ee/topics/autodevops/requirements.html)
-- [ ] [Use pull-based deployments for improved Kubernetes management](https://docs.gitlab.com/ee/user/clusters/agent/)
-- [ ] [Set up protected environments](https://docs.gitlab.com/ee/ci/environments/protected_environments.html)
-
-***
-
-# Editing this README
-
-When you're ready to make this README your own, just edit this file and use the handy template below (or feel free to structure it however you want - this is just a starting point!). Thank you to [makeareadme.com](https://www.makeareadme.com/) for this template.
-
-## Suggestions for a good README
-Every project is different, so consider which of these sections apply to yours. The sections used in the template are suggestions for most open source projects. Also keep in mind that while a README can be too long and detailed, too long is better than too short. If you think your README is too long, consider utilizing another form of documentation rather than cutting out information.
-
-## Name
-Choose a self-explaining name for your project.
-
-## Description
-Let people know what your project can do specifically. Provide context and add a link to any reference visitors might be unfamiliar with. A list of Features or a Background subsection can also be added here. If there are alternatives to your project, this is a good place to list differentiating factors.
-
-## Badges
-On some READMEs, you may see small images that convey metadata, such as whether or not all the tests are passing for the project. You can use Shields to add some to your README. Many services also have instructions for adding a badge.
-
-## Visuals
-Depending on what you are making, it can be a good idea to include screenshots or even a video (you'll frequently see GIFs rather than actual videos). Tools like ttygif can help, but check out Asciinema for a more sophisticated method.
-
-## Installation
-Within a particular ecosystem, there may be a common way of installing things, such as using Yarn, NuGet, or Homebrew. However, consider the possibility that whoever is reading your README is a novice and would like more guidance. Listing specific steps helps remove ambiguity and gets people to using your project as quickly as possible. If it only runs in a specific context like a particular programming language version or operating system or has dependencies that have to be installed manually, also add a Requirements subsection.
-
-## Usage
-Use examples liberally, and show the expected output if you can. It's helpful to have inline the smallest example of usage that you can demonstrate, while providing links to more sophisticated examples if they are too long to reasonably include in the README.
-
-## Support
-Tell people where they can go to for help. It can be any combination of an issue tracker, a chat room, an email address, etc.
-
-## Roadmap
-If you have ideas for releases in the future, it is a good idea to list them in the README.
-
-## Contributing
-State if you are open to contributions and what your requirements are for accepting them.
-
-For people who want to make changes to your project, it's helpful to have some documentation on how to get started. Perhaps there is a script that they should run or some environment variables that they need to set. Make these steps explicit. These instructions could also be useful to your future self.
-
-You can also document commands to lint the code or run tests. These steps help to ensure high code quality and reduce the likelihood that the changes inadvertently break something. Having instructions for running tests is especially helpful if it requires external setup, such as starting a Selenium server for testing in a browser.
-
-## Authors and acknowledgment
-Show your appreciation to those who have contributed to the project.
-
-## License
-For open source projects, say how it is licensed.
-
-## Project status
-If you have run out of energy or time for your project, put a note at the top of the README saying that development has slowed down or stopped completely. Someone may choose to fork your project or volunteer to step in as a maintainer or owner, allowing your project to keep going. You can also make an explicit request for maintainers.
+Debian bullseye

bashrc

+cred="\033[1;31m"
+cgrn="\033[1;32m"
+cyel="\033[0;33m"
+cblu="\033[1;34m"
+cpur="\033[0;35m"
+ccya="\033[0;36m"
+cnon="\033[0m"
+
+HISTCONTROL=ignoreboth
+shopt -s histappend
+HISTSIZE=1000
+HISTFILESIZE=2000
+shopt -s checkwinsize
+
+function show_git_branch() {
+    git branch 2>/dev/null | sed -e '/^[^*]/d' -e 's/* \(.*\)/(\1)/'
+}
+
+function get_exit_status() {
+    es=${?}
+    if [ ${es} -ne 0 ]; then
+        echo -e "${cred}${es}${cnon} "
+    fi
+}
+
+ps1_prefix="\u@$(hostname) ${cpur}\w${cnon}"
+ps1_suffix="${cblu}\$ ${cnon}"
+if [[ $(id -u) -eq 0 ]]; then
+    ps1_suffix="${cred}# ${cnon} "
+fi
+export PS1="\$(get_exit_status)${ps1_prefix} ${ccya}\$(show_git_branch)${cnon} ${ps1_suffix}"
+
+alias ..="cd .."
+alias cl="clear"
+alias env="env | sort"
+alias gita="git add"
+alias gitd="git diff"
+alias gitc="git commit -m"
+alias gitl="git log"
+alias gitp="git pull"
+alias gits="git status"
+alias grep="grep --color"
+alias lsblk="lsblk -o name,maj:min,ro,rm,type,size,mountpoint,label,uuid,pttype,parttypename,type,vendor,model,serial"
+alias p="python"
+alias pkl="pkill -9"
+
+which micro >/dev/null 2>&1 && alias mic="micro"
+
+export LS_COLORS=${LS_COLORS}:"di=1;34":"*.txt=1;36":"*.md=0;35"
+alias l="ls --color=auto -CF"
+alias ll='ls --color=auto -lhF --group-directories-first --sort=extension'
+alias la="ls --color=auto -AlF"
+alias grep='grep --color=auto'
+alias fgrep='fgrep --color=auto'
+alias egrep='egrep --color=auto'
+
+# color gcc warning
+export GCC_COLORS='error=01;31:warning=01;35:note=01;36:caret=01;32:locus=01:quote=01'
+
+which mic >/dev/null 2>&1 && {
+    export EDITOR="mic"
+}
+
+if [[ -n "${HOME}" && -d "${HOME}" ]]; then
+    cd "${HOME}"
+fi
+
+# load virtual python env
+. ${HOME}/env/bin/activate

copy_secrets.sh

+#!/bin/bash
+
+if [ -d /secrets ]; then
+
+	# copy read-only secrets to HOME
+	cp -rpnv /secrets/. ${HOME}/
+
+	# define token_filepath if not yet
+	if [ -z "${token_filepath}" ]; then
+		token_filepath="${HOME}/.git-token.json"
+	fi
+
+	# if a git token access file is provided
+	if [ -f "${token_filepath}" ]; then
+
+		# the path to repo
+		if [ "${PACK_ROOT}" == "base" ]; then
+			# base packages
+			git_dir="${HOME}"/base/.git
+		else
+			# other packages
+			git_dir="/tmp/source/.git"
+		fi
+	
+		# extract url from repo
+		url=$(git --git-dir "${git_dir}" remote get-url origin)
+
+		# read git access token from secrets
+		git_access_token=$(jq -Mr ".access_token" "${token_filepath}")	
+		user_name=$(jq -Mr ".user.name" "${token_filepath}")
+		user_email=$(jq -Mr ".user.email" "${token_filepath}")
+		
+		# match url
+		re="(gitlab(-p4n)?.aip.de)(\/|:)(.*)"
+		if [[ $url =~ $re ]]; then    
+	    	repo=${BASH_REMATCH[4]}
+
+			# update url with access token
+			url="https://${user_name}:${git_access_token}@gitlab-p4n.aip.de/${repo}"
+
+			# reset git url
+			git --git-dir "${git_dir}" remote set-url origin "${url}"
+
+			# tell who you are
+			git --git-dir "${git_dir}" config --global user.name "${user_name}"
+			git --git-dir "${git_dir}" config --global user.email "${user_email}"
+		fi
+	fi
+
+else
+	echo "no secrets found"
+fi

explore-wrapper.sh

+#!/bin/bash
+
+# before script
+"${HOME}/base/copy_secrets.sh"
+
+# main explore script
+"${HOME}/base/explore.sh"
+
+# catch status of drun
+drun_status=$?
+
+exit ${drun_status}

explore.sh

+#!/bin/bash
+
+# missing config
+export PATH=$PATH:~/.local/bin/
+
+# activate the python env
+. ${HOME}/env/bin/activate
+
+# switch to home
+cd /
+
+# run the server on port 8080 (exposed)
+export NOTEBOOK_PASSWORD=`python3 -c "from notebook.auth import passwd; print(passwd('scitrace'))"`
+jupyter lab --no-browser --port=8080 --ip="0.0.0.0" --PasswordIdentityProvider.hashed_password=${NOTEBOOK_PASSWORD} 

install-deps.sh

+# install virtualenv globally
+pip3 install --upgrade pip
+pip3 install --upgrade virtualenv

install-jupyterlab.sh

+#!/bin/bash
+
+# create virtual env
+virtualenv --python=python3.11 ${HOME}/env
+
+# activate env
+. ${HOME}/env/bin/activate
+
+# update path
+PATH=$PATH:~/.local/bin:/${HOME}/.local/bin
+
+# install requirements
+pip install --upgrade \
+    jupyterlab==3.6.3 \
+    jupyterlab-git \
+    notebook \
+    jupyter_contrib_nbextensions \
+    bokeh
+
+JUPYTER_ENABLE_LAB=yes

install-venv.sh

+#!/bin/bash
+
+# create virtual env
+virtualenv --python=python3.11 ${HOME}/env
+

run-wrapper.sh

+#!/bin/bash
+
+# before script
+"${HOME}/base/copy_secrets.sh"
+
+# main script
+"${HOME}/${PACK_ROOT}/drun.sh"
+
+# catch status of drun
+drun_status=$?
+
+# make product fully accessible RWX for kufair (1853) group
+chmod -R 776 ${HOME}/${PACK_ROOT}/products
+
+exit ${drun_status}

setup-env.sh

+cp bashrc ${HOME}/.bashrc
+
+. ${HOME}/.bashrc