Ivan Andrus's profile - activity

If you choose "Terminal Session > Sage (advanced)" from the menu, it will prompt you for command line arguments for sage. Type "-n jupyter", then enter and away you go. This is going to be easier once I finish http://trac.sagemath.org/ticket/19881

How did you install it? Did you use a different user? I'm not sure that's supported because Sagemath needs to write to it's install directory in some cases. You might try chown'ing the entire directory hierarchy, or perhaps chmod'ing everything.

I guess I've been out of the loop for a while with respect to Sage packaging. What's pacman, and how to I make sage_mode installable with sage -i?

You could try installing the latest spkg from bit bucket:

sage -i https://bitbucket.org/gvol/sage-mode/downloads/sage_mode-20150707.spkg

If you like the ap (which I hope you do), you can use the app from the downloaded version and just point it to your version of sagemath (in Preferences). You can also build the app yourself, but that's likely more work.

In GAP it is possible (at least in some circumstances) to display a matrix with . instead of 0 and without brackets. This makes the structure of the matrix much easier to see. Is there a way to do this in Sage?

e.g. to show

   1   3   3   .   9
   1   1   1   2   5
   1   1   3   2   3
   1   3   1   .   3
   1   1   1   .   5
   1   .   .   1   3
   1   1   3   .   3
   1   3   1   .   3
   1   1   1   .   3
   1   3   .   .   .
   1   .   1   .   2

instead of

[ [  1,  3,  3,  0,  9 ],
  [  1,  1,  1,  2,  5 ],
  [  1,  1,  3,  2,  3 ],
  [  1,  3,  1,  0,  3 ],
  [  1,  1,  1,  0,  5 ],
  [  1,  0,  0,  1,  3 ],
  [  1,  1,  3,  0,  3 ],
  [  1,  3,  1,  0,  3 ],
  [  1,  1,  1,  0,  3 ],
  [  1,  3,  0,  0,  0 ],
  [  1,  0,  1,  0,  2 ] ]

Feel free to open trac tickets and CC me for the Mac app pieces if they don't work.

Quitting the server from the menu _should_ stop the server. If not, it's a bug and I need to fix it. More details on your setup might be helpful in that case. That said, in the Preferences there is an option to not start the server when you open the app. I also think you use the default arguments in Preferences to change how the server starts. But that last might still be one of my local changes. (I'm away from my usual computer at the moment, so I can't check).

Does it open up Terminal.app and ask for a password? If it's the first time running it should, and it looks like that might be where it's failing. Try opening a terminal session and then typing `notebook()` to see if that gets around the problem.

Are you sure that's all that's in your .emacs? Please check to see if you are referencing sage-command before you (require 'sage "sage"). Does the problem go away if you comment out the require? Another thing you might trying is completely deleting /Applications/sage/local/share/emacs and reinstalling. You can also run emacs --debug-init to see where exactly the error is occurring.

Please let me know what the problem was so that I can fix it if I need to (e.g. deleting the directory first). Also, feel free to open a ticket on bitbucket for this or any other issue.

There is also a new version sage_mode-0.9. Unfortunately, I'm having a difficult time getting it reviewed to upgrade the spkg so that's it installed by default.

I don't know of any attempts to add an ob-sage.el. I maintain sage-mode and use org, but I use LaTeX to write papers so I haven't had a need (yet) for ob-sage. Coincidentally, there is a currently thread on the org list that talks about people having problems with persistent sessions with ob-python. There are three different python modes so it's not surprising that it doesn't work with all of them. You may wish to follow that thread and see if any fixes there resolve your problem.

I already have code in sage-mode to allow sage to work when exporting via latex, so I wouldn't mind adding ob-sage.el. I would suggest opening a ticket on bitbucket. Also, you can fork and open a pull request. If possible I would prefer to "hook into" ob-python rather than copy/paste/modify it, but such a thing may not be possible (or even desirable), I haven't looked. That way it will hopefully take advantage of improvements to ob-python. I think all that should need to change is the executable.

Or maybe a patch to ob-python to allow it to dynamically switch to Sage would be best. I don't know if such a change would be welcome in org, though I suspect it would. I have papers on file with the FSF so I can make such a change if desired.

Sage is python, so yes and no. :-) Basically Sage is a big python library so in a sage script you can import any python module you want. In other words, there is no reason not to use python. You won't incur any overhead etc.

I'm fairly certain this is fixed in sage-5.8.beta0 (and later). There was a bug where the Mac app sometimes didn't properly recognize the running server (and therefore wouldn't shut it down properly) which sounds like your problem here. If you want you can download the latest development version and compile it yourself. Or apply trac_11026-fix-parse-error.patch manually to your current version and rebuild the application. Neither is entirely trivial, but we can give you instructions if you would like. If not, you can just wait until the next release. Or I could probably send you a version of the app that I built on 10.8.2 (which I think should work on 10.6.8).

By "this" I mean this "answer", not the "question" on this page.

I think this is caused by a bug I just fixed in [bug #11026](http://trac.sagemath.org/sage_trac/ticket/11026). If anyone can help test this on Lion to get it positively reviewed I think it would be a huge help to everyone.

Jason Grout just pointed me to an [updated installation procedure](https://github.com/sagemath/sagecell/issues/344).

If you are using the GUI Sage.app, then you will have to set the environment variable in a way other than in a shell file. See this stackoverflow question for an overview of the ways to do that.

Also, you probably want to set SAGE_BROWSER to

SAGE_BROWSER='open -a Safari'

since it has to be something that you can run from the command line.

You have to install the Sage Cell server which is what powers Aleph. There are instructions on github, but I think they may be a little out of date since they didn't work for me using sage-5.4.beta2.

It works for me using Snow Leopard and ImageMagick installed via home brew. You can see if it's a permissions issue by checking permissions of `sage.misc.misc.tmp_dir()`. That should also help find the generated pngs (they will be in a sibling directory) and you can see if they are corrupted. I would also try running `convert` from within `sage -sh` since that should mimic the environment used by sage. You may need to use `sage-native-execute convert ...` to reset PATH, and LD_LIBRARY_PATH, etc.

My guess is that /opt/local/bin is not in your PATH for GUI applications. If you open a terminal and start the sage server there, I bet it will work (and I think you indicate that it does).

What happens is that GUI applications (including Sage.app) do not read .bash_profile etc. when they start up so they don't get any changes to PATH made there. You have to edit the file ~/.launchd.conf (10.7+) or ~/.MacOSX/environment.plist and add the correct PATH there. See this stackoverflow answer for details.

This is a very common problem on stackoverflow and similar sites. I wish I could figure out a way to make this easier for people to discover.

I've been aware of it, though I haven't tried it yet. I believe (but I'm not an expert) that once we get the new ipython in sage (trac #12719) we could actually run an IPython Notebook with Sage loaded so that the Emacs interaction would just work.

I have closed the issue and 0.8 will have the fix when it's released (hopefully soon).

What about errors after `run-sage`? The file `sage-mode` is not actually loaded at startup.

If sage-mode is properly installed then `sage-buffer` should definitely be defined! Are there any errors in the `*Messages*` buffer (accessible with C-h e)?

SAGE_ROOT and SAGE_DATA should not be defined as environment variables outside of a running Sage. They are meant to be placeholders for you to fill in. I just uploaded a new 0.8 spkg. After you install it, it will say expand them for you in the console giving what you already put in your .emacs i.e. "/home/maksim/Applications/...".

I've updated the wiki, and SPKG.txt.