Installation with Macports

Macports is a popular package manager on Mac. Gammapy is available via Macports.

To install Gammapy and it’s core dependencies:

sudo port install py36-gammapy

The commands to update Gammapy and it’s dependencies to the latest stable versions are:

sudo port selfupdate
sudo port upgrade outdated

The rest of this section is a quick crash course about Macports, to explain the most common commands and how to set up and check things. There’s not really anything Gammapy-specific here, but we thought it might be useful to summarise this information for Macports users here.

To check that Gammapy is installed, and which version you have:

port installed '*gammapy'
/opt/local/bin/python3.5 -c 'import gammapy; print(gammapy.__version__)'

Macports supports several versions of Python, so you can choose the one you want. Parallel installation of multiple Python versions works well, but is only really useful for developers. So if you want Python 2.7 or Python 3.6, you would have to adapt the commands given in this section to use that version number instead. If you’re not sure which version to use, at this time (January 2017) we recommend you choose Python 3.5 (because Python 3 is the future, and 3.6 was just released and there are still a few minor issues being ironed out).

Usually if you’re using Macports, you will add this line to your ~/.profile file:

export PATH="/opt/local/bin:/opt/local/sbin:$PATH"

This means that you can just execute Python via python3.5 and will get the Macports Python (and not some other Python, like e.g. the system Python in /usr/bin or an Anaconda Python in $HOME).

Macports also has a convenience command port select built in to select a given Python version:

sudo port select python python36

This will create a symbolic link /opt/local/bin/python -> /opt/local/bin/python3.5 and means that now if you execute python, you will get the Macports Python 3.5. If you’re not sure what your configuration is, you can use these commands to find out:

port select --summary # show selection and list other things where one can select a default version
which python
ls -l `which python`
python --version

From here on out, we assume that you’ve done this setup and python is the correct Python you want to use.

Many other software, including several optional dependencies of Gammapy, is available via Macports. Here’s some examples for some scientific computing and astronomy packages:

sudo port install \
    py36-pip py36-pytest \
    py36-scipy py36-matplotlib \
    py36-emcee py36-ipython py36-uncertainties \
    py36-healpy py36-cython

To search which software is available in Macports (searches package name and description):

port search <name>

There are about 100,000 Python packages on PyPI. Many of those aren’t re-packaged and available in Macports, and some are outdated (although usually Macports packages are updated within days or weeks of the release of new package versions).

Using the Macports Python as the basis, you can use the Macports pip to install more Python packages. The default should be to use Macports and to only pip install what’s not available there, because then updates usually just work (see commands above), whereas with pip it’s usually a more manual process.

python -m pip install --no-deps --user \
    naima reproject astroplan iminuit

There’s a few things worth pointing out about how we execute pip to install packages:

  • Instead of using the command line tool pip, we’re executing via python -m pip. This is because users frequently accidentally execute the wrong pip (e.g. from system Python or Anaconda) that happens to be on their $PATH and then either the install fails, or it succeeds but then trying to import the package fails because it’s in a site-packages folder that’s unrelated to the python they are using.
  • The --no-deps option instructs pip to not recursively fetch and install all dependencies. Of course, auto-installing all dependencies can be convenient, but it also often happens that this leads to the installation of many packages (e.g. Numpy, Scipy, ….) and is not what you want. So being explicit about which packages to install is the safer thing to do here.
  • We’re not using sudo here and we are using the --user option. Using sudo python -m pip install would result in the installation of packages in opt/local/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages, the site-packages folder where Macports installs packages. This will usually work, but can then cause problems later on when you try to upgrade or add packages via sudo port install. Macports updates work so well because it is very well organised and e.g. keeps manifests of all files installed (you can list them with port contents py36-gammapy). So basically, to not mess with this, you should never touch files in /opt/local except through port commands. The --user option of pip means “install in my user site-packages folder”, which at this time on macOS is /Users/<username>/Library/Python/3.5/lib/python/site-packages and is by default on the list of folders searched by Python to find packages to import.

To uninstall Python packages:

sudo port uninstall <packagename>
python -m pip uninstall <packagename>

To check where a given package you’re using is installed:

python -c 'import numpy; print(numpy.__file__)'
python -c 'import gammapy; print(gammapy.__file__)'