# 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`.