python_installation.md

Python installation notes

• Install Anaconda

  • https://www.continuum.io/downloads

    • Consider miniconda if you don't need all the dev tools in the full anaconda distribution.

    • Recommended to download python v3.6 as your default distribution.

    • DO NOT INSTALL AS ROOT OR ADMIN!

• Modify path as necessary to point to Anaconda distribution (if not using pyenv)

• Installation of pyenv is recommended using homebrew:

  brew update
  brew install pyenv

• If you use miniconda, then install critical parts of python:

    conda install ipython
    conda install jupyter    

• Updates/installation of fundamental packages:

    conda install scipy
    conda install numpy
    conda install astropy

• pyND (this distribution; be sure to put it somewhere in your PYTHONPATH)

    git clone https://github.com/jchowk/pyND.git

You can download this directly from the site pointed to with that command. To update your PYTHONPATH variable to point to the directory, edit the file ~/.profile to include something like this:export PYTHONPATH="$PYTHONPATH:/Users/howk/python, where your pyND distribution is the directory containing the pyND distribution (which can be in a sub-directory).

• linetools

    git clone https://github.com/linetools/linetools.git
    cd linetools
    python setup.py develop

• pyigm

      git clone https://github.com/pyigm/pyigm.git
      cd pyigm
      python setup.py develop

• specdb

    git clone https://github.com/specdb/specdb.git
    cd specdb
    python setup.py develop

- grab the database (see installation notes in `igmspec`)

• astroquery [required for finder charts]

  pip install astroquery

• emcee and corner:

  pip install emcee  
  pip install corner```

- Install non-standard packages
    - aplpy  [recommended; not essential]

      `pip install aplpy`

    - pyregion [maybe?]

      `pip install pyregion`

    - pymc3 [only required for some f(N) analysis in pyigm]

    git clone https://github.com/pymc-devs/pymc3.git
    cd pymc3
    python setup.py install```

• For even more specific cases:

  • fitsio [only for DESI codes]

    • Grab from github (my fork)
    • git clone https://github.com/profxj/fitsio.git
    • cd fitsio
    • python setup.py install

  • matplotlib Basemap [For projection plots only]

    • conda install basemap

  • seaborn [Statistical plots; optional, but recommended]

    • conda install seaborn

  • bokeh [java figures; optional, but recommended]

    • conda install bokeh

  • ginga [Excellent imaging package; recommended]

    • git clone https://github.com/ejeschke/ginga.git
    • cd ginga
    • python setup.py install

  • PYPIT

    • See installation notes
    • https://github.com/PYPIT/PYPIT/blob/master/doc/installing.rst

  • pandoc — For notebook conversions to rst [optional]

    • https://github.com/jgm/pandoc/releases/tag/1.15.2

  • scikit

  • conda install scikit-learn

  • conda install scikit-image # For images

  • Progressbar (nice progress bars for long loops)

    • conda install progressbar

  • alis

    • git clone https://github.com/rcooke-ast/ALIS
    • ...

On rebuilds of astropy, git clean -fxd or sudo git clean -fxd is your friend.

WARNING: sudo python may give you a version of Python that you aren’t expecting!