How to setup a fresh install of Ubuntu 18.04 for Python for sciences

This is just an example (2018-07-10), but it is useful for me (Pierre Augier) to have this page, so it may be useful to others.

• Install some useful compilers, libraries and utilities:

  sudo apt install \
    clang-6.0 gfortran cmake \
    libpng-dev libfftw3-dev libfftw3-mpi-dev \
    libhdf5-dev libopenmpi-dev \
    qt5-default \
    curl ack meld pandoc \
    fish \
    python2.7 python-pip \
    git emacs \
    libopenblas-dev
  

  • python 2.7 and pip are used to install Mercurial !

    python2 -m pip install mercurial hg-git hg-evolve --user
    # in Ubuntu 18.04 ~/.local/bin is not in $PATH !
    echo -e "\nexport PATH=\$HOME/.local/bin/:\$PATH\n" >> ~/.bashrc
    hg config --edit
    

    Be prepared to use Vi! Good luck :-)

    See http://fluiddyn.readthedocs.io/en/latest/mercurial_bitbucket.html

  • Setup emacs, for example with https://foss.heptapod.net/fluiddyn/fluid_emacs.d

• Setup Bash (.bashrc and .bash_aliases)

• Setup https://fishshell.com/ (if you want Fish!):

  chsh -s $(which fish)
  fish
  echo 'set -gx PATH $PATH $HOME/.cask/bin $HOME/.local/bin/' >> ~/.config/fish/config.fish
  

• Install miniconda:

  wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
  bash ./Miniconda3-latest-Linux-x86_64.sh
  

• To build CPython, we first have to modify a file (see http://cpython-devguide.readthedocs.io/setup/#build-dependencies):

  sudo apt edit-sources
  

  Then:

  sudo apt update
  sudo apt build-dep python3.6
  

• Install pyenv (see https://github.com/pyenv/pyenv):

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

  Then, for Bash:

  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
  exec "$SHELL"
  

  And for Fish, see https://github.com/fisherman/pyenv (It’s a bit tricky so read carefully. The file ~/.config/fish/conf.d/000-env.fish is needed).

• Build nice Python versions and use Python 3.6 or 3.7:

  pyenv install 3.6.6
  pyenv install 3.7.2
  pyenv install pypy3.5-6.0.0
  pyenv global 3.7.2  # or 3.6.6
  

  Then install several packages (as wheels) using pip:

  pip install --upgrade pip
  pip install pipenv
  pip install pytest coverage
  pip install ipython jupyterlab
  pip install numpy scipy matplotlib pandas ipympl
  pip install h5py h5netcdf
  pip install imageio pims
  pip install cython mako colorlog pythran
  pip install mpi4py
  pip install future
  pip install pyfftw
  pip install pylint flake8 mypy black yapf
  pip install trio
  pip install sphinx numpydoc sphinx-rtd-theme
  pip install pyqt5
  pip install spyder
  pip install pyqtgraph
  
  pip install opencv-python
  
  pip install scikit-image scikit-learn
  

  Note that pip install numpy installs a numpy wheel containing openblas.

• More Jupyter:

  sudo apt install nodejs npm
  
  jupyter labextension install @jupyter-widgets/jupyterlab-manager
  jupyter labextension install jupyter-matplotlib
  jupyter labextension install @ijmbarr/jupyterlab_spellchecker
  
  sudo apt install chromium-browser
  jupyter-lab --generate-config
  echo 'c.NotebookApp.browser = "/usr/bin/chromium-browser"' >> ~/.jupyter/jupyter_notebook_config.py
  

• Install https://code.visualstudio.com

• Setup ~/.pythranrc:

  wget https://foss.heptapod.net/fluiddyn/fluiddyn/raw/branch/default/doc/simple.pythranrc -O ~/.pythranrc
  

  Note that with this setup, Pythran needs clang and openblas (which have been install previously).

• Fix Gnome:

  sudo apt install chrome-gnome-shell gnome-tweak-tool
  

  • Install

    • https://extensions.gnome.org/extension/484/workspace-grid/

    • https://extensions.gnome.org/extension/15/alternatetab/

    • https://extensions.gnome.org/extension/826/suspend-button/

  • Using gnome-tweaks, set static workspaces

  • Dock: hidden and smaller (in Settings)

• Install Latex:

  sudo apt install dvipng texlive-latex-extra texlive-fonts-recommended texlive-fonts-extra
  

If needed

• Install GMT 6 and gmt-python:

  sudo apt install gmt-gshhg libgdal-dev libpcre2-dev libnetcdf-dev ghostscript
  
  git clone https://github.com/GenericMappingTools/gmt
  cd gmt/
  cp cmake/ConfigUserTemplate.cmake cmake/ConfigUser.cmake
  mkdir build
  cd build/
  
  cmake -DCMAKE_INSTALL_PREFIX=/usr/share/gmt-6 -DCMAKE_BUILD_TYPE=RelWithDebInfo ..
  make -j4
  sudo make -j4 install
  
  pip install https://github.com/GenericMappingTools/gmt-python/archive/master.zip
  

  Then, set the environment variables PATH and LD_LIBRARY_PATH as needed by modifying your ~/.bashrc.