Setting up your system

The following is a guide to help you prepare your system for developing with Invenio. A proper development environment setup can save a lot of time and frustrations. Note that the following guide, is not meant as a guide for setting up servers.

System setup

We support development on macOS and Linux-based systems (development on Windows is not supported).

macOS

We recommend that you install libraries and tools using the Homebrew package manager. Homebrew allows you to install two types of packages - cask and normal.

Cask packages

Cask packages are usually UI applications that end up in your Applications folder. You can install cask packages using the command:

$ brew cask install <packages>

Here are some recommended cask packages (only docker is required):

db-browser-for-sqlite # UI for SQLite
discord               # app that we use for chat among developers
docker                # docker setup for macOS
google-chrome         # needed for some end-to-end tests
iterm2                # a better terminal than Terminal.app
postico               # UI for PostgreSQL
spectacle             # organise windows with keyboard shortcuts
visual-studio-code    # a text editor used by many Invenio developers

Normal packages

Normal packages are usually command line tools/libraries that end up in /usr/local and that you use from the CLI. You can install normal packages using the command:

$ brew install <packages>

The following packages are libraries that are likely to be needed during Invenio development in order to install certain Python packages:

cairo
freetype
geoip
gettext
glib
imagemagick
jpeg
libffi
libmemcached
libpng
libtiff
libxml2
libxslt
readline
xz
zlib

Following are CLI tools that are useful during development:

cookiecutter # tool to bootstrap new modules from templates
chromedriver # selenium driver for chrome (used for end-to-end testing)
gh           # GitHub CLI client (useful e.g for checking out PRs)
gifify       # make short screen recordings for bug reports
git          # our version control system
hub          # extends git with github features

General CLI tools:

htop            # a better top
tree            # pretty print a directory structure
wget            # http client
zsh-completion  # if you use zsh as shell
base-completion # if you use bash as shell

CERN specific tools:

openshift-cli # if you deploy on openshift
xrootd        # library for accessing EOS storage cluster
sshuttle      # tunnel into CERN

Python

Invenio is developed using Python and JavaScript. We highly recommend that install pyenv and nvm - both tools manage version of python and node respectively. Install the following packages:

nvm
pyenv
pyenv-virtualenv
pyenv-virtualenvwrapper

Once you have installed above packages, you can proceed with installing Python versions. The following will install Python 3.6, 3.7 and 3.8 and set the default Python installation to Python 3.8 (node you can always install the latest patch-level release):

$ pyenv install 3.6.9
$ pyenv install 3.7.8
$ pyenv install 3.8.5
$ pyenv global 3.8.5

You should edit your .bashrc or .zshrc file to initialise pyenv:

# nvm setup
export NVM_DIR="$HOME/.nvm"
[ -s "/usr/local/opt/nvm/nvm.sh" ] && . "/usr/local/opt/nvm/nvm.sh"

# pyenv
eval "$(pyenv init -)"

# pyenv-virtualenv
eval "$(pyenv virtualenv-init -)"

# pyenv-virtualenvwrapper
pyenv virtualenvwrapper

Now, you can create e.g. Python virtual environments using the following commands:

$ mkvirtualenv <name>
$ mkvirtualenv -p python3.7 <name>
$ workon <name>

Fonts

In order to create e.g. DOI badges you need the DejaVu Sans font installed. Go to https://dejavu-fonts.github.io/ and follow the instructions.

Docker Desktop for Mac

You may need to increase the resources assigned to Docker Desktop for Mac See https://docs.docker.com/docker-for-mac/#resources.

A typical sign of needed more resources, is that services are not running or images are having problems building.

Ubuntu

System setup guide for Ubuntu.

General tools/packages useful during development:

$ apt install git-all                  # Distributed version control system
$ apt-get install sqlitebrowser        # UI for SQLite
$ snap install spectacle               # Organise windows with keyboard shortcuts
$ apt-get install libcairo2-dev        # Graphics library
$ apt-get install htop                 # A better top
$ apt-get install tree                 # Pretty print a directory structure
$ apt install wget                     # Http client
$ apt-get install hub                  # Extends git with github features
$ apt-get install bash-completion      # If bash is used as shell
$ apt install sshuttle iptables        # Needed for tunneling into CERN.

Docker

To install docker you can follow the instructions in docker for Ubuntu.

If you get the following error after installing Docker and running simple commands:

Got permission denied ... /var/run/docker.sock: connect: permission denied

see here for some tips on how to solve it.

docker-compose

For defining and running multi-container Docker applications.

$ sudo apt install docker-compose

Google chrome

Needed for some end-to-end tests.

$ sudo apt install gdebi-core wget
$ wget https://dl.google.com/linux/direct/google-chrome-stable_current_amd64.deb
$ sudo gdebi google-chrome-stable_current_amd64.deb

OC CLI

Needed if you deploy on openshift.

Download the latest OpenShift Origin files. As of this writing, that version number is 3.11.0.

$ wget https://github.com/openshift/origin/releases/download/v3.11.0/openshift-origin-client-tools-v3.11.0-0cbc58b-linux-64bit.tar.gz

Once the file is downloaded, extract it with the command:

$ tar xvzf openshift*.tar.gz

Change into the newly-created directory with the command:

$ cd openshift-origin-client-tools*/

Move the kubectl and oc binaries with the command:

$ sudo mv  oc kubectl  /usr/local/bin/

Installation problems If during the installation you encounter broken packages, try the follwoing command:

$ sudo apt --fix-broken install

Python

Invenio is developed using Python and JavaScript.

If you want to check which version of Python you have, try the following:

# Check the system Python version
$ python --version

# Check the Python 2 version
$ python2 --version

# Check the Python 3 version
$ python3 --version

To install Python 3.8 type the following commands:

$ sudo apt-get update
$ sudo apt-get install python3.8 python3-pip

In the following list you can check if your system has the necessary requirements.

We highly recommend that install pyenv and nvm - both tools manage version of python and node respectively. Install the following packages:

nvm

$ curl -o- https://raw.githubusercontent.com/nvm-sh/nvm/v0.37.2/install.sh | bash

To check if you have the latest version of node installed type the following commands:

$ sudo npm cache clean -f
$ sudo npm install -g n
$ sudo n stable

Pyenv

Update and install the required dependencies.

$ sudo apt update -y
$ sudo apt install -y make build-essential libssl-dev zlib1g-dev libbz2-dev libreadline-dev libsqlite3-dev wget curl llvm libncurses5-dev libncursesw5-dev xz-utils tk-dev libffi-dev liblzma-dev python-openssl git

Clone the repository

$ git clone https://github.com/pyenv/pyenv.git ~/.pyenv

Configure the environment.

$ echo 'export PYENV_ROOT="$HOME/.pyenv"' >> ~/.bashrc
$ echo 'export PATH="$PYENV_ROOT/bin:$PATH"' >> ~/.bashrc
$ echo -e 'if command -v pyenv 1>/dev/null 2>&1; then\n eval "$(pyenv init -)"\nfi' >> ~/.bashrc

Restart shell.

$ exec "$SHELL"

Pipenv

Pipenv is a packaging tool for Python that solves some common problems associated with the typical workflow using pip and virtualenv. We suggest the following installation guide:

https://realpython.com/pipenv-guide/#pipenv-introduction

virtualenv

virtualenv is a CLI tool that needs a Python interpreter to run. We recommend the following installation guide:

https://virtualenv.pypa.io/en/latest/installation.html

virtualenvwrapper

Note that after the installation, virtualenvwrapper.sh can be found in ~/.local/bin

$ pip3 install --user virtualenvwrapper

Once you have installed above packages, you can proceed with installing Python versions. The following will install Python 3.6, 3.7 and 3.8 and set the default Python installation to Python 3.8 (node you can always install the latest patch-level release):

$ pyenv install 3.6.9
$ pyenv install 3.7.8
$ pyenv install 3.8.5
$ pyenv global 3.8.5

You should edit your .bashrc or .zshrc file to initialise pyenv:

# nvm setup
export NVM_DIR="$HOME/.nvm"
[ -s "/usr/local/opt/nvm/nvm.sh" ] && . "/usr/local/opt/nvm/nvm.sh"

# pyenv
eval "$(pyenv init -)"

# pyenv-virtualenv
eval "$(pyenv virtualenv-init -)"

# pyenv-virtualenvwrapper
pyenv virtualenvwrapper

Now, you can create e.g. Python virtual environments using the following commands:

$ mkvirtualenv <name>
$ mkvirtualenv -p python3.7 <name>
$ workon <name>

To deactivate the virtual environment simple type:

$ deactivate

cookiecutter

Tool to bootstrap new modules from templates.

pip install cookiecutter

Editor

You can use any code editor of your choice. Here we give a brief overview of some of the editors our existing developers are using. For all editors, the most important is support for EditorConfig

EditorConfig

All repositories have a .editorconfig file which defines indention style, text encoding, newlines etc. Many editors either come with built-in support or plugins that reads the .editorconfig file and configures your editor accordingly.

Visit EditorConfig to see the list of supported editors.

Editors

Following editors are used by our existing developers. Don’t hesitate to reach out on our Discord server, to ask for help for useful plugins:

Plugins for editors

The key plugins you should look for in your editor of choice are:

  • Python / JavaScript environment

  • PEP8 / PEP257 style checking

  • Isort plugin.

Working with Git and GitHub

There are a couple of utilities that allow you to work more efficiently with Git and GitHub.

CLI tools

  • GitHub CLI: command-line tool to interact with GitHub. Note that this tool is independent from the git CLI.

  • Hub: command-line wrapper around git that makes it easier to work with GitHub by adding new commands.

Git aliases

Use aliases to type frequent commands more efficiently. Note that your shell might offer more git aliases too, for example Oh My Zsh has the git plugin which among other things it will come with a few pre-configured aliases.

Debugging

There are several tools for debugging, we will list here the ones which are editor agnostic:

  • pytest: comes with builtin support for dropping into pdb.

  • ipdb: this is a terminal debugger with features tab completion, syntax highlighting among others. Note that the debugging session is opened as the output of the running program.

  • wdb: web debugger with a client server architecture. The debugging session is opened in a web browser. Suitable for remote debugging and programs which do not allow to open an interactive shell session (i.e. Celery).