Why does Mathematica use a different $PATH than terminal?

Question

I am trying to run bash commands from within Mathematica. Funnily enough, Mathematica seems to use a different $PATH environment than the system environment. If I try

Environment["PATH"]

or equivalently in Mathematica 10

RunProcess[$SystemShell, All, "echo $PATH"]

I get (in StandardOutput):

/usr/bin:/bin:/usr/sbin:/sbin

However, if I run echo $PATH on my (OS X) terminal, I get (both as user and root):

/opt/local/bin:/opt/local/sbin:/opt/local/bin:/opt/local/sbin:/usr/local/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Library/TeX/texbin:/Library/TeX/Distributions/.DefaultTeX/Contents/Programs/texbin/:/usr/texbin:/Users/frederik/bin

which is indeed the full path. Why doesn't use Mathematica the same environmental variable? Is this expected behaviour?

EDIT

I already mentioned in the comments why this question is different from this one, but to avoid getting this question marked as a duplicate I'll repeat it here.

That thread does not deal with system environment variables (it's an unfortunate wording in the topic title) but with Mathematica environment variables. The path variable for the latter is stored in $Path in Mathematica, while the former can be accessed by executing Environment["PATH"] (which gives the OS system environment path). I'm really asking about the system environment variable here, but thanks to ilian and m_goldberg I realise now that it is an OS X issue.

Answer 1

It is certainly an OS X issue. Assuming the default shell is configured, when Terminal starts up it runs the script file ~/.bash_profile, which usually modifies the PATH environment variable. You can do the same thing in Mathematica with

SetEnvironment["PATH" -> Import["!source ~/.bash_profile; echo $PATH", "Text"]]

After which

Environment["PATH"]

should match what you see in Terminal.

Answer 2

I think this is an OS X issue. Note that if you launch Mathematica from a terminal, you will get the value of Environment["PATH"] which you expected.

For GUI applications that are started through Finder/LaunchServices, the environment (and $PATH in particular) is different and determined by the OS (this is a related recent question that had to do with setting up umask).

This behavior may be changed, though the exact mechanism seems to evolve with each OS X release and I don't know off the top of my head what is the best approach to achieve this on Yosemite or El Capitan.

Answer 3

As noted by @ilian the easiest solution is to simply launch Mathematica from a Terminal window that has a PATH you like. On macOS:

/Applications/Mathematica.app/Contents/MacOS/Mathematica &

An even easier way is to launch Mathematica by opening a notebook using the open command from a Terminal window:

open whatever.nb

Then that instance of Mathematica will inherit the PATH of that Terminal session.

Or you can set the path directly in any notebook in which you care about this, as noted by @m_goldberg. I like this solution the best, since it is the least obtrusive and you can add only what you really need, e.g.:

SetEnvironment["PATH" -> "/usr/local/bin:" ~~ Environment["PATH"]~~":/Users/myname/bin"]

If you would like to set an application path permanently on macOS, you can:

sudo launchctl config user path $PATH

and then reboot and restart all applications (lest they hold the old path through the reboot). That will set the path for all applications and all users to the path you have in the terminal you ran that command from.

You could instead echo $PATH and then copy just the parts you want into the the launchctl command.

This can be undone on macOS with:

sudo defaults delete /private/var/db/com.apple.xpc.launchd/config/user.plist PathEnvironmentVariable

For any solution, you can verify the path the Mathematica kernel is currently using with:

Environment["PATH"]