#12719 closed enhancement (fixed)
Upgrade to IPython 0.13
Reported by:  kini  Owned by:  tbd 

Priority:  critical  Milestone:  sage5.7 
Component:  packages: standard  Keywords:  sd40.5 
Cc:  iandrus, vbraun, jason, AlexanderDreyer, robertwb  Merged in:  sage5.7.beta1 
Authors:  Mike Hansen, Volker Braun, Jason Grout, Jeroen Demeyer  Reviewers:  Volker Braun, Mike Hansen, Jason Grout, Jeroen Demeyer 
Report Upstream:  N/A  Work issues:  
Branch:  Commit:  
Dependencies:  #13459, #9191, #13717, #13963  Stopgaps: 
Description (last modified by jdemeyer)
We need to upgrade IPython to the shiny new thing. Well, not really  the shiny new thing was 0.11, and 0.13 is now stable. It's been mostly rewritten and is now a lot more modular, as I understand it. Definitely worth using in Sage.
Note: To use the QT console (sage ipython qtconsole), you need qt/qtdevel in your base OS install, the optional zeromq/pyzmq spkgs from #12843, and the optional sip/PyQt spkgs from #13022.
Install the IPython 0.13.1 spkg at http://boxen.math.washington.edu/home/jdemeyer/spkg/ipython0.13.1.spkg
apply:
To the scripts repository:
 trac_12719scriptsvb.patch
 trac_12719_remove_sage_gdb_ipython.patch
 12719testdisplayhook.patch
 12719_run_cython.patch
 trac_12719hgignore.patch
 trac_12719_purge_ipy_profile_sage.patch
To the root repository:
To the sage library:
 trac_12719rebasedto13211vb.patch
 trac_12719move_to_preparser_rebased.patch
 trac_12719_ipython_fixes.patch
 trac_12719_dedent.patch
 trac_12719crash.patch
 trac_12719cellmagics013.patch
 12719newipythontake2.patch
 12719displayhook.patch
 12719fixtransformer.patch
 127195.4rc1.patch
 12719removeplugin.patch
 12719displayhooklibrary.patch
 trac_12719pager.patch
 trac_12719preparsedoctest.patch
 trac_12719gcdrepr.patch
 12719system.patch
 trac12719alwayspreparse.patch
 12719_ipython_test.patch
 12719_ipython_no_history.patch
So:
cd SAGE_ROOT ./sage hg qimport P http://trac.sagemath.org/sage_trac/rawattachment/ticket/12719/trac_12719_ROOT_configuration_files.patch ./sage hg qimport P http://trac.sagemath.org/sage_trac/rawattachment/ticket/12719/trac_12719rootspkginstall.patch ./sage hg R local/bin qimport P http://trac.sagemath.org/sage_trac/rawattachment/ticket/12719/trac_12719scriptsvb.patch ./sage hg R local/bin qimport P http://trac.sagemath.org/sage_trac/rawattachment/ticket/12719/trac_12719_remove_sage_gdb_ipython.patch ./sage hg R local/bin qimport P http://trac.sagemath.org/sage_trac/rawattachment/ticket/12719/12719testdisplayhook.patch ./sage hg R local/bin qimport P http://trac.sagemath.org/sage_trac/rawattachment/ticket/12719/12719_run_cython.patch ./sage hg R local/bin qimport P http://trac.sagemath.org/sage_trac/rawattachment/ticket/12719/trac_12719hgignore.patch ./sage hg R local/bin qimport P http://trac.sagemath.org/sage_trac/rawattachment/ticket/12719/trac_12719_purge_ipy_profile_sage.patch ./sage hg R devel/sage qimport P http://trac.sagemath.org/sage_trac/rawattachment/ticket/12719/trac_12719rebasedto13211vb.patch ./sage hg R devel/sage qimport P http://trac.sagemath.org/sage_trac/rawattachment/ticket/12719/trac_12719move_to_preparser_rebased.patch ./sage hg R devel/sage qimport P http://trac.sagemath.org/sage_trac/rawattachment/ticket/12719/trac_12719_ipython_fixes.patch ./sage hg R devel/sage qimport P http://trac.sagemath.org/sage_trac/rawattachment/ticket/12719/trac_12719_dedent.patch ./sage hg R devel/sage qimport P http://trac.sagemath.org/sage_trac/rawattachment/ticket/12719/trac_12719crash.patch ./sage hg R devel/sage qimport P http://trac.sagemath.org/sage_trac/rawattachment/ticket/12719/trac_12719cellmagics013.patch ./sage hg R devel/sage qimport P http://trac.sagemath.org/sage_trac/rawattachment/ticket/12719/12719newipythontake2.patch ./sage hg R devel/sage qimport P http://trac.sagemath.org/sage_trac/rawattachment/ticket/12719/12719displayhook.patch ./sage hg R devel/sage qimport P http://trac.sagemath.org/sage_trac/rawattachment/ticket/12719/12719fixtransformer.patch ./sage hg R devel/sage qimport P http://trac.sagemath.org/sage_trac/rawattachment/ticket/12719/127195.4rc1.patch ./sage hg R devel/sage qimport P http://trac.sagemath.org/sage_trac/rawattachment/ticket/12719/12719removeplugin.patch ./sage hg R devel/sage qimport P http://trac.sagemath.org/sage_trac/rawattachment/ticket/12719/12719displayhooklibrary.patch ./sage hg R devel/sage qimport P http://trac.sagemath.org/sage_trac/rawattachment/ticket/12719/trac_12719pager.patch ./sage hg R devel/sage qimport P http://trac.sagemath.org/sage_trac/rawattachment/ticket/12719/trac_12719preparsedoctest.patch ./sage hg R devel/sage qimport P http://trac.sagemath.org/sage_trac/rawattachment/ticket/12719/trac_12719gcdrepr.patch ./sage hg R devel/sage qimport P http://trac.sagemath.org/sage_trac/rawattachment/ticket/12719/12719system.patch ./sage hg R devel/sage qimport P http://trac.sagemath.org/sage_trac/rawattachment/ticket/12719/trac12719alwayspreparse.patch ./sage hg R devel/sage qimport P http://trac.sagemath.org/sage_trac/rawattachment/ticket/12719/12719_ipython_test.patch ./sage hg R devel/sage qimport P http://trac.sagemath.org/sage_trac/rawattachment/ticket/12719/12719_ipython_no_history.patch ./sage i http://sage.math.washington.edu/home/jason/ipython0.13.1.spkg ./sage br
Attachments (35)
Change History (318)
comment:1 Changed 4 years ago by jhpalmieri
comment:2 followup: ↓ 80 Changed 4 years ago by fbissey
Would be nice but we need some porting, here is what typically happen if you try to use ipython0.12 with sage (we had several reports in sageongentoo before I pinned down the version used by sage):
$ sage   Sage Version 4.7.2, Release Date: 20111029   Type notebook() for the GUI, and license() for information.   Traceback (most recent call last): File "/usr/bin/sageipython", line 19, in <module> from IPython.CrashHandler import CrashHandler ImportError: No module named CrashHandler
comment:3 Changed 4 years ago by kini
Yes, obviously :) I'm just making this ticket since it is absolutely must be an eventual goal for us and nobody else has made a ticket yet, even though IPython 0.12 has been out for about three months.
comment:4 Changed 4 years ago by fbissey
To be honest Fernando Perez and I talked about it on the mailing list at the time of ipython 0.11 and I said I would tell him what happens when we use ipython 0.11+ with sage because he is interested. For various reason I haven't been able to go back to it. But some sageongentoo users eventually got a taste of it when it finally landed in the portage tree.
So first hurdle: do something about the crash handling.
comment:5 Changed 4 years ago by iandrus
 Cc iandrus added
comment:6 Changed 4 years ago by mhansen
I'm working on this now, and have made quite a bit of progress. As an added bonus, making the Sage customizations to IPython is quite a bit cleaner. I should hopefully be able to clean out the mess in sage/misc/preparser_ipython.py and sage/misc/interpreter.py .
comment:7 Changed 4 years ago by mhansen
This will fix #4413.
comment:8 Changed 4 years ago by kini
Great, I'm glad you're on the case! :)
comment:9 Changed 4 years ago by vbraun
 Cc vbraun added
comment:10 Changed 4 years ago by vbraun
What about zmq/pyzmq? It would really add to the functionality and I'm interested in the parallel/cluster support. But, strictly speaking, its not necessary to run ipython. Its also used in the new notebook so maybe its time for it to become a standard package?
comment:11 Changed 4 years ago by kini
 Cc jason added
CCing Jason as he expressed interest on sagedevel.
comment:12 Changed 4 years ago by jason
mhansen: we'd love to see your workinprogress if it's available somewhere. I just spent some time reading the IPython docs again and thinking about how we could use it to implement the notebook hub and worker processes.
comment:13 Changed 4 years ago by mhansen
I've posted patches which let Sage work with IPython 0.12 as well as cleaning up some old messy code. These should be in a state where they're ready to review.
I haven't done anything with preparing an spkg yet.
comment:14 Changed 4 years ago by jason
 Description modified (diff)
I've updated the instructions in the description. Please correct if I messed something up.
comment:15 Changed 4 years ago by jason
 Status changed from new to needs_review
comment:16 Changed 4 years ago by jason
 Status changed from needs_review to needs_work
 Work issues set to spkg
comment:17 followup: ↓ 19 Changed 4 years ago by jason
Just curious: do your patches work with the current 0.12, or did you base them on the current git master (or does it not matter?). On the IPython mailing list, they mentioned that 0.12 had some big bugs, so they were thinking about cutting a quick 0.12.1. Also, they expect 0.13 in about a month.
comment:18 Changed 4 years ago by jason
I was thinking more about security today with the zmq messages. I think it may be more secure to have a default ipcontroller transport of IPC in a directory inside of $DOT_SAGE, rather than tcp over the loopback interface. That would be more secure in that random people on your computer wouldn't be able to try to register with the IPython hub. I emailed the IPython mailing list about it: http://thread.gmane.org/gmane.comp.python.ipython.devel/7789
What do you think?
comment:19 in reply to: ↑ 17 Changed 4 years ago by mhansen
Replying to jason:
Just curious: do your patches work with the current 0.12, or did you base them on the current git master (or does it not matter?). On the IPython mailing list, they mentioned that 0.12 had some big bugs, so they were thinking about cutting a quick 0.12.1. Also, they expect 0.13 in about a month.
I've looked at the current git master as I was making these changes, and I think these changes should work fine with what's on there. I'd be surprised if it made a difference.
comment:20 Changed 4 years ago by mhansen
I just tested things against git master and everything seems fine.
comment:21 Changed 4 years ago by jason
 Description modified (diff)
I'm trying to apply these to 5.0beta12. I think I probably got the order wrong in the description, so it would be great if you could check that. But regardless, none of the patches seem to apply to 5.0beta12 cleanly (each has rejects).
comment:22 Changed 4 years ago by jason
 Description modified (diff)
 Work issues changed from spkg to patches don't apply
I just tried applying to beta6 and the scripts patch still had problems.
Changed 4 years ago by mhansen
comment:23 Changed 4 years ago by mhansen
The scripts patch should apply fine to the scripts repository. I've rebased the other ones to work on the newer 5.0 beta's.
comment:24 Changed 4 years ago by AlexanderDreyer
 Cc AlexanderDreyer added
After applying the patches to sage5.0 beta12 I still have ip = IPython.ipapi.get() at the end of sage/misc/edit_module.py, which crashes Sage on startup.
comment:25 Changed 4 years ago by jason
I get a crash when I apply these (with a latest git IPython). I've posted the crash report at http://sage.math.washington.edu/home/jason/Sage_crash_report.txt
comment:26 Changed 4 years ago by jason
Is the zmq communication in ipython going through tcp/localhost sockets, or through UDS sockets? I really think we should use UDS sockets with the files in $DOTSAGE so that it is more secure (i.e., random other people on the computer can't connect to the kernel).
comment:27 Changed 4 years ago by vbraun
By default we should not use zeromq. For example, if you want to fork you should do so before creating a zmq context. The zmq context creates threads and open file descriptors.
Apart from that, you should either use IPC or TCP+magic cookie, much like the X window system. Implementation wise its probably easiest to allow any socket and alway check the magic cookie.
comment:28 Changed 4 years ago by jason
I don't think we have a choice of whether or not to use zmq with the new ipython. ZMQ is an integral part of how it communicates results from the backend to the frontend. They do have a system for signing messages and ignoring unsigned messages (is that the magic cookie thing?). UDS sockets is IPC, so we're good there. My problem with TCP+magic cookie is that it still allows someone else to attempt to connect to the various sockets, whereas using IPC, with the socket files in $DOTSAGE, filesystem permissions prevent others from even attempting to connect.
comment:29 Changed 4 years ago by jason
It may be that I'm misunderstanding how ipython is using zmq when you just execute 'ipython'. It may be that it uses inprocess communication (using zmq) instead of opening ports on localhost. I've posted to the ipythondevel mailing list about this.
comment:30 Changed 4 years ago by vbraun
Given that you can build IPython without zeromq support it surely must be possible to run without?
I don't see the problem with tcp + magic cookie. Yes you can connect but your connection attempt will be ignored. And the difference in pyzmq to ipc + magic cookie is a single string. So why bother with ipc without magic cookie?
comment:31 Changed 4 years ago by jason
Thomas on the ipython mailing list confirmed that the plain ipython command doesn't use zmq, so that was a big misunderstanding I had about the new ipython. So never mind what I said about sockets.
Changed 4 years ago by mhansen
comment:32 Changed 4 years ago by mhansen
Okay, I fixed the problem with edit_module.
Sorry I wasn't clear about the default IPython not using zmq. There is a experimental console shell that uses two processes which can be accessed with "ipython console", but we aren't using that at all.
comment:33 Changed 4 years ago by jason
 Description modified (diff)
 Status changed from needs_work to needs_review
 Work issues patches don't apply deleted
comment:34 Changed 4 years ago by jason
For the record, the patches now apply to my 5.0beta12 and Sage starts up.
comment:35 Changed 4 years ago by jason
When doing %edit, I edit the sage library file, but the file isn't copied over to the library after editing, so the changes don't take effect. This doesn't hold back this issue, though, since it didn't work before either.
comment:36 Changed 4 years ago by vbraun
Although zeromq is not, strictly speaking, necessary for IPython it might be of interest that I made zeromq and pyzmq spkgs at #12843
comment:37 Changed 4 years ago by jason
 Description modified (diff)
comment:38 Changed 4 years ago by PierreCagne
Not working on sage5.0.rc0 (system Darwin 10.8.0).
I installed the spkg and applied the patches in the given order and places, but still have the following error lauching Sage :
Traceback (most recent call last): File "/Users/pece/sage5.0.rc0/local/bin/sageipython", line 19, in <module> from IPython.CrashHandler import CrashHandler ImportError: No module named CrashHandler
I even installed the patches from #12843 without any success.
comment:39 followup: ↓ 41 Changed 4 years ago by jason
I have OSX 10.6.8: Darwin Kernel Version 10.8.0. I'm running the IPython git master and the patches, and it seems to work well. Did you do sage b to compile the patches? Maybe the problem is in the IPython 0.12.1>0.13 changes.
comment:40 Changed 4 years ago by jason
Hmmm, it looks like the scripts/ patch wasn't applied (the problematic line is deleted in the patch). Can you check again that trac_12719scripts.patch is applied to the SAGE_ROOT/local/bin repository?
comment:41 in reply to: ↑ 39 ; followup: ↓ 125 Changed 4 years ago by slabbe
Replying to jason:
Maybe the problem is in the IPython 0.12.1>0.13 changes.
On sage5.0.rc0, I managed to apply the three patches and sage starts correctly. So I guess it's not a matter of IPython 0.13 changes. Although, the sage prompt is not in color anymore (my file .sage/ipython/ipythonrc is set to dark background color).
Is the ipython notebook suppose to work? How should I test it?
Also, doing sage ipython notebook creates this error :
$ sage ipython notebook Traceback (most recent call last): ... ImportError: The IPython Notebook requires tornado >= 2.1.0
comment:42 Changed 4 years ago by vbraun
The first patch (trac_12719.patch) applies only with fuzz 2 on sage5.0
comment:43 Changed 4 years ago by vbraun
 Keywords sd40.5 added
 Status changed from needs_review to needs_work
Lots of doctests fail because the display hook is not correctly set up. I'll have a look into this if nobody beats me to it...
comment:44 Changed 4 years ago by vbraun
 Description modified (diff)
The new ipython configuration files are once more incompatible with the previous ones. My patch versions the directory now (that is, it is named .sage/ipythonVERSION) and deletes the SAGE_ROOT/ipythonrc stuff. I think all sagespecific configuration should go into sage/misc/interface.py
comment:45 Changed 4 years ago by vbraun
Here is some reasonable documentation about Prefilter vs. InputSplitter: http://mail.scipy.org/pipermail/ipythondev/2011March/007334.html
comment:46 Changed 4 years ago by vbraun
 Description modified (diff)
 Reviewers set to Volker Braun
 Status changed from needs_work to needs_review
The trac_12719_ipython_fixes.patch switches form Prefilter to InputSplitter.
I'm giving a positive review to everything that Mike wrote.
comment:47 Changed 4 years ago by vbraun
With the new patch sage/misc/interpreter.py has 100% coverage.
comment:49 followup: ↓ 75 Changed 4 years ago by was
In Sage before this patch, the sage notebook, the Python command line, etc., we have:
for i in range(10): i
outputs the numbers up to 10.
With the new Ipython spkg, etc., we don't.
sage: for i in range(10): i sage: Exiting Sage (CPU time 0m0.07s, Wall time 2m3.22s). blastoff:sage wstein$ sage ipython Python 2.7.2 (default, May 17 2012, 13:12:30) In [1]: for i in range(10): i In [2]:
I'm disappointed, especially because I thought this through and in sagews I recently wrote code so this works correctly in a single cell, even if there are several instances of this. It's a matter of passing the 'single' option to exec, as is documented in the Python reference. I wonder why they screwed this up in Ipython 0.12...?
Anyway, I'm not saying this is a show stopper at all  I want the new ipython in sage. I'm just a little concerned that literally the first thing I tried shows that they made what I consider a bad design choice. Hopefully it was just bad luck.
comment:50 Changed 4 years ago by was
Cool  I tried out a bunch of other things including the new notebook (sage ipython notebook) and didn't run into any serious issues. So I'm happy with this from from a purely functional perspective. Also, deleting tons of ugly code (done in the patches), looks great.
comment:51 Changed 4 years ago by mhansen
It should be easy to get to get the correct functionality for for i in range(10): i. The shell.run_ast_nodes method just has to be called with interactivity="all" instead of interactivity="last_expr".
comment:52 Changed 4 years ago by mhansen
Here's a review of Volker's ipython_fixes patch:
 (minor) Remove \ on line 1071
 Do one of the following:
 Fix/deprecate/remove sagegdbipython since it depends on SAGE_CLEAN
 Just throw a deprecation warning with SAGE_CLEAN
 Turn autoindent back on.
 Why add debug=True and confirm_exit=False to default config.
 Load the startup file: line 1151
comment:53 Changed 4 years ago by vbraun
 Description modified (diff)
 Reviewers changed from Volker Braun to Volker Braun, Mike Hansen
1, 3, 5: done
4: I removed the debug, but I (and most others, I asked) definitely want to keep confirm_exit=False. Yes I really want to quit, geez!
2: I'm in favor of a) and removed it.
I've also renamed trac_13013_ROOT_configuration_files.patch (wrong ticket number) and added a patch to autodedent and eval in loops. Now the following works:
sage: for i in range(3): i 0 1 2
comment:54 Changed 4 years ago by mhansen
 Description modified (diff)
 Status changed from needs_review to positive_review
Volker's changes look good to me.
comment:55 Changed 4 years ago by mhansen
 Description modified (diff)
Changed 4 years ago by mhansen
comment:56 Changed 4 years ago by was
Mike's addition of trac_12719crash.patch looks *great* to me as an addition.
comment:57 Changed 4 years ago by jdemeyer
 Status changed from positive_review to needs_work
Unfortunately, this doesn't apply to sage5.1.beta1:
applying trac_12719.patch patching file doc/en/reference/misc.rst Hunk #1 succeeded at 30 with fuzz 2 (offset 2 lines). patching file sage/misc/interpreter.py Hunk #1 FAILED at 0 Hunk #3 FAILED at 271 Hunk #4 FAILED at 385 Hunk #5 FAILED at 449 4 out of 5 hunks FAILED  saving rejects to file sage/misc/interpreter.py.rej patch failed, unable to continue (try v) patch failed, rejects left in working dir errors during apply, please fix and refresh trac_12719.patch
comment:58 Changed 4 years ago by mhansen
 Description modified (diff)
 Status changed from needs_work to needs_review
I've rebased this on top of #11817.
comment:59 Changed 4 years ago by jhpalmieri
 Description modified (diff)
comment:60 Changed 4 years ago by jdemeyer
 Status changed from needs_review to needs_work
Now it applies but I get documentation errors:
dochtml.log:/padic/scratch/jdemeyer/merger/sage5.1.beta3/local/lib/python2.7/sitepackages/sage/misc/interpreter.py:docstring of sage.misc.interpreter:12: WARNING: Block quote ends without a blank line; unexpected unindent. dochtml.log:/padic/scratch/jdemeyer/merger/sage5.1.beta3/local/lib/python2.7/sitepackages/sage/misc/interpreter.py:docstring of sage.misc.interpreter:8: WARNING: Block quote ends without a blank line; unexpected unindent. dochtml.log:/padic/scratch/jdemeyer/merger/sage5.1.beta3/local/lib/python2.7/sitepackages/sage/misc/interpreter.py:docstring of sage.misc.interpreter:8: WARNING: Block quote ends without a blank line; unexpected unindent. dochtml.log:/padic/scratch/jdemeyer/merger/sage5.1.beta3/local/lib/python2.7/sitepackages/sage/misc/interpreter.py:docstring of sage.misc.interpreter:11: WARNING: Definition list ends without a blank line; unexpected unindent. dochtml.log:/padic/scratch/jdemeyer/merger/sage5.1.beta3/local/lib/python2.7/sitepackages/sage/misc/interpreter.py:docstring of sage.misc.interpreter:13: ERROR: Unexpected indentation.
comment:61 Changed 4 years ago by jdemeyer
Also, trac_12719scripts.patch needs a commit message.
comment:62 Changed 4 years ago by jason
It seems that double question mark, like trace??, doesn't bring up the source code anymore, but just brings up the docstring. It seems that trac_12719_ipython_fixes.patch broke this (double question marks work with just the first two patches, but not after that third patch).
comment:63 Changed 4 years ago by jason
 Description modified (diff)
comment:64 Changed 4 years ago by jason
 Description modified (diff)
Add two more patches to get the new IPython 0.13beta1 spkg above to work.
comment:65 Changed 4 years ago by jason
 Description modified (diff)
comment:66 Changed 4 years ago by jason
 Description modified (diff)
comment:67 Changed 4 years ago by jason
 Work issues set to ?? doesn't work
comment:68 Changed 4 years ago by jason
 Work issues changed from ?? doesn't work to ?? doesn't show code
comment:69 Changed 4 years ago by jason
 Description modified (diff)
comment:70 Changed 4 years ago by jason
 Description modified (diff)
comment:71 Changed 4 years ago by jason
I rebased trac_12719_ROOT_configuration_files.patch to sage 5.1beta6
comment:72 Changed 4 years ago by jason
 Description modified (diff)
 Reviewers changed from Volker Braun, Mike Hansen to Volker Braun, Mike Hansen, Jason Grout
 Summary changed from Upgrade to IPython 0.12 to Upgrade to IPython 0.13
comment:73 Changed 4 years ago by jason
I upgraded the spkg to 0.13, which was just released today.
comment:74 Changed 4 years ago by jason
 Description modified (diff)
comment:75 in reply to: ↑ 49 Changed 4 years ago by jason
Replying to was:
In Sage before this patch, the sage notebook, the Python command line, etc., we have:
for i in range(10): ioutputs the numbers up to 10.
With the new Ipython spkg, etc., we don't.
sage: for i in range(10): i sage: Exiting Sage (CPU time 0m0.07s, Wall time 2m3.22s). blastoff:sage wstein$ sage ipython Python 2.7.2 (default, May 17 2012, 13:12:30) In [1]: for i in range(10): i In [2]:I'm disappointed, especially because I thought this through and in sagews I recently wrote code so this works correctly in a single cell, even if there are several instances of this. It's a matter of passing the 'single' option to exec, as is documented in the Python reference. I wonder why they screwed this up in Ipython 0.12...?
Anyway, I'm not saying this is a show stopper at all  I want the new ipython in sage. I'm just a little concerned that literally the first thing I tried shows that they made what I consider a bad design choice. Hopefully it was just bad luck.
Fernando Perez responded:
BTW, regarding William's comment, that was not a mistake or omission: it was a very deliberate choice we made after lots of thought. Given that we manage numbered prompts and history, and that matplotlib produces so many plots as side effects, after much experimentation we found it worked much better to only execute with 'interactive' mode the last block.
Sage doesn't distinguish stdout from python sys.displayhook, so the opposite behavior may be more desirable, but we actually consider that a 'bad design choice' of sage, because it loses an important distinction and the cache management of output history.
So in summary: our choice is actually sensible and consistent given IPython's internal design :)
comment:76 followup: ↓ 78 Changed 4 years ago by jason
Fernando: I looked in the IPython source, and it seems that IPython is a little more subtle than mentioned above. By default, it only executes the last block as interactive (compile in 'single' mode) if it is an expression. In Sage, we (by default) execute the last block always in 'single' mode. I think that is the difference here.
Given that (and if I understood correctly), could you explain again your reasoning for choosing to not compile in 'single' mode if it isn't an expression?
Note to self for future reference: for i in range(10): i invokes sys.displayhook 10 times to display i if compiled in 'single' mode.
comment:77 Changed 4 years ago by jason
Also, note to William: it is an easy option to set to have IPython *always* execute the last block in interactive mode. It's just not the default.
comment:78 in reply to: ↑ 76 Changed 4 years ago by jason
Replying to jason:
Fernando: I looked in the IPython source, and it seems that IPython is a little more subtle than mentioned above. By default, it only executes the last block as interactive (compile in 'single' mode) if it is an expression. In Sage, we (by default) execute the last block always in 'single' mode. I think that is the difference here.
Given that (and if I understood correctly), could you explain again your reasoning for choosing to not compile in 'single' mode if it isn't an expression?
And here is Fernando's response:
Precisely so that if the last block has a loop, it doesn't produce multiple Out [NN] cells. We want to keep a onetoone mapping between a cell and its output. For example it's quite common to write code like:
for i in x: plot(x[i], label='blah_i')
If we compile that as 'single', we'd get all the Matplotlib line collection results piling up at the bottom, one for each plot call.
We played a *lot* with various options, and settled on this behavior after much experimentation. After 2 years of using it, I remain convinced it's the right solution *for us*. Not to say that Sage can't make a different choice that works better for you guys, of course!
comment:79 Changed 4 years ago by jason
To change this, we just need to set ast_node_interactivity to "last" in the InteractiveShell.
comment:80 in reply to: ↑ 2 Changed 4 years ago by schilly
Replying to fbissey:
Would be nice but we need some porting, here is what typically happen if you try to use ipython0.12 with sage:
$ sage   Sage Version 4.7.2, Release Date: 20111029   Type notebook() for the GUI, and license() for information.   Traceback (most recent call last): File "/usr/bin/sageipython", line 19, in <module> from IPython.CrashHandler import CrashHandler ImportError: No module named CrashHandler
Hi fbissey, sorry for hijacking this a bit, but i had exactly the same problem over and over again. What I just found out (and I think it really helps) is to temporarily disable the paths containing ".local" in sys.path in the sageipython file. The reason is, that ipython seems to import the "site package" (disable it for pure python via "S"), because that's where my ipython 0.13 is.
So, by adding this to sageipython you I have both at the same time:
~~~ after import sys oldpath = sys.path sys.path = filter(lambda s : '.local' not in s, sys.path) import IPython sys.path = oldpath
comment:81 Changed 4 years ago by jason
 Description modified (diff)
comment:82 Changed 4 years ago by jason
I rebased the only rejected patch for 5.2beta1
comment:83 Changed 4 years ago by was
My 2 cents, after I forced myself to use this for the last few weeks on my laptop. I have found the new ipython to be pretty annoying. The cut and paste behavior and lack of autoindent at the command line is pretty painful. The thing that made me finally give up and revert to the old 0.10 ipython was when I hit controlc at the wrong moment when starting Sage, and somehow the ipython history sqlite database got in a weird locked state. Nothing I could think to do (including deleting $HOME/.sage/ipython) got this unstuck. Maybe rebooting would have worked; I don't know. I'm concerned about how stable and welltested in the wild the new ipython is. Proceed with caution.
comment:84 Changed 4 years ago by vbraun
Working cut&past and working autoindent are contradictory goals. The terminal just sees a stream of characters, you either inject indentation or not. AFAIR I turned off autoindent, we could turn that back on. Breaks pasting of indented text, of course.
The ipython dir is now versioned, you should have deleted $DOT_SAGE/ipython0.12 / $DOT_SAGE/ipython0.13
comment:85 Changed 4 years ago by vbraun
PS: Maybe you can upload your broken ipython dir somewhere, this would be a good testcase to catch the sqlite error...
comment:86 followup: ↓ 87 Changed 4 years ago by kini
IMO, leave autoindent on, and use %paste or %cpaste when you want to paste. %paste tries to automatically get the contents of your clipboard. If that's not working for whatever reason, %cpaste creates a prompt where you can paste text verbatim, which IPython doesn't read until you end input with Ctrl+D or a line containing only the text "".
comment:87 in reply to: ↑ 86 ; followup: ↓ 88 Changed 4 years ago by vbraun
Replying to kini:
IMO, leave autoindent on, and use %paste or %cpaste when you want to paste.
For the record, thats not how I use the commandline. I paste code all the time, but I almost never enter multiline statements manually. So I'd rather have autoindent off by default (and no need for %cpaste), and use %autoindent if I want it on. Though thats of course a matter of personal preferences, and I'm happy with whatever the majority prefers...
comment:88 in reply to: ↑ 87 Changed 4 years ago by was
Replying to vbraun:
Replying to kini:
IMO, leave autoindent on, and use %paste or %cpaste when you want to paste.
For the record, thats not how I use the commandline. I paste code all the time, but I almost never enter multiline statements manually. So I'd rather have autoindent off by default (and no need for %cpaste), and use %autoindent if I want it on. Though thats of course a matter of personal preferences, and I'm happy with whatever the majority prefers...
At least it is configurable, right? I think it is best not to change the default from what it is already in all previous versions of Sage, whether or not that is what the majority prefers (unless it is a huge majority). I'm not fan of changing UI's on people unless it is absolutely necessary.
comment:89 Changed 4 years ago by vbraun
Well IPythons defaults changed, we didn't just change stuff for the fun of it. For starters, vanilla IPython now disallows any superfluous indentation, i.e.
In [1]: 1 Out[1]: 1 In [2]: 1 IndentationError: unexpected indent (<ipythoninput20066badbf200>, line 1)
comment:90 Changed 4 years ago by jhpalmieri
Two more issues:
 when Sage starts, any lines in my init.sage file are echoed to the screen after the first "sage:" prompt. They aren't executed until I hit the return key:
  Sage Version 5.2, Release Date: 20120725   Type "notebook()" for the browserbased notebook interface.   Type "help()" for help.   sage: # Here is the beginning of init.sage. 2+2 # Here is another comment a = 5 # Here is the end of init.sage.
At this point, hitting <RETURN> inserts a 4, a newline, and the "sage:" prompt, and a is defined to be 5.
 when I evaluate or plot a graphics object, two plot windows are opened:
sage: P = plot(sin(x), (x, 0, 10)) sage: P # opens up two windows showing the same plot. Note also the blank line. sage: plot(P) # also opens up two windows. sage: show(P) # opens up only one window.
comment:91 Changed 4 years ago by iandrus
Regarding indentation, autoindent being on breaks sage inside Emacs (dumb terminal). So I think it should be off, at least in a dumb terminal, until/unless I can figure out how to fix this in Emacs. I haven't really looked into it at all, so it may be easy to fix inside Emacs by setting some environment variables or something. See #10504.
comment:92 Changed 4 years ago by jason
+1 for autoindent being on by default. That helps what is probably the vast majority of the casesinteractively typing into the command line.
comment:93 Changed 4 years ago by broken_symlink
I'm having a weird problem when I use IPython.parallel in sage. Here's what happens:
from IPython.parallel import Client rc = Client('/home/seshu/.sage/ipythonnew/profile_default/security/ipcontrollerclient.json') dview = rc[:] dview.map_sync(lambda x: x**10, range(32)) [0:apply]:  NameError Traceback (most recent call last)<string> in <module>() <ipythoninput4ad199b8d76dc> in <lambda>(x) NameError: global name 'Integer' is not defined
If I do anything that doesn't involve integers like dview.map_sync(lambda x: "hi", range(32)), it works fine. Sorry if this isn't the appropriate place to ask these questions. I wasn't sure where to ask since this is a bit bleeding edge. I would like to be able to use IPython.parallel from the sage notebook if possible.
comment:94 Changed 4 years ago by broken_symlink
The ipython engines need to import the sage modules. The fix is dview.execute("from sage.all import *"). Also I did sage sh ipcluster start.
comment:95 Changed 4 years ago by jason
Just FYI, for the *next* version (so not an issue on this ticket), https://github.com/ipython/ipython/pull/2299 broke Sage, I think by getting rid of PrefilterTransformer? tricks.
comment:96 Changed 4 years ago by jason
So I think that the only issue with this ticket is turning back on autoindentation and getting ?? to show the source code? Any other issues?
I think the parallel issues above should be moved to another ticket.
comment:97 Changed 4 years ago by jason
Note: ?? shows the source code fine, it seems, in the notebook (at least there doesn't seem to be a regression; ?? shows source when doing tab completion, but not on evaluating, just like before the python upgrade). It is a regression on the command line, though.
comment:98 Changed 4 years ago by jhpalmieri
There are the issues I mentioned above. Can anyone else reproduce them?
comment:99 Changed 4 years ago by broken_symlink
The parallel issues only seem to effect the notebook. I've successfully gotten ipython.parallel and sage to run on a small 24 core amazon ec2 cluster, using ssh with the ipython 0.13.1 branch on github. According to the ipython guys, the ssh launcher in 0.13 is broken. I kinda have some idea of whats going with the parallel issues and the notebook as well, but i'm not sure how to fix it. I can write something for how to setup sage with ipython engines started over ssh if this package gets updated to 0.13.1.
comment:100 Changed 4 years ago by jason
Well, hopefully this gets merged before 0.13.1 comes out.
comment:101 Changed 4 years ago by jason
jhpalmieri, I can confirm both of the issues that you saw. I'm seeing them too.
comment:102 Changed 4 years ago by jason
 Work issues changed from ?? doesn't show code to ?? doesn't show code, init.sage displayed, double plot windows, autoindent disabled
comment:103 Changed 4 years ago by jason
 Work issues changed from ?? doesn't show code, init.sage displayed, double plot windows, autoindent disabled to ?? doesn't show code, init.sage displayed, double plot windows
actually, it looks like autoindent was turned back on: http://trac.sagemath.org/sage_trac/ticket/12719#comment:52
comment:104 Changed 4 years ago by jason
Does anyone know where in the code init.sage is run? I've searched the entire codebase for "init.sage" and I'm not finding anything that looks like it is responsible for running the file.
comment:105 Changed 4 years ago by jason
Ah, I found it. It's the last line in sage/misc/interpreter.py, the one that says self.shell.run_cell('%%load "%s"'%startup_file)
comment:106 Changed 4 years ago by jason
Okay, it looks like the problem is that we punt to the ipython load, which *pastes* the content so you can edit it first: http://ipython.org/ipythondoc/dev/interactive/qtconsole.html#load
comment:107 Changed 4 years ago by jason
So our conclusion on https://github.com/ipython/ipython/pull/2299 was that Sage should make %load an alias for IPython's %run, and beef up IPython's %run to be able to handle remote files. In fact, make IPython's %run use the same simple mechanism as IPython's %load would be great (though may not be possible%run uses filespecific features in python and execfile, etc.)
comment:108 Changed 4 years ago by jason
Is there a reason we didn't use a profile config file for all of our customizations?
I've started a different approach to the customizations we use here: https://github.com/jasongrout/sageipythonprofile
put these into the .sage/ipythonnew directory and then start with sage ipython profile=sage
comment:109 Changed 4 years ago by jason
 Description modified (diff)
Changed 4 years ago by jason
comment:110 Changed 4 years ago by jason
Okay, I think my "take2" patch significantly cleans things up and makes things more modular and more "IPythonic".
In particular, this seems to work nicely: do sage ipython notebook to launch the ipython notebook, then evaluate %load_ext sage.misc.sage_extension. All preparsing is turned on, etc. It's great!
There should probably be a bit more documentation in the sage_extension file, and full doctests should be run. But I think it's ready for other people to hammer on it too.
Here is one issue: something broke in sage startuptime. I'm not sure it's IPython's fault, though.
Oh, and I was working from IPython master, not IPython 0.13. I hope that doesn't put a wrench in the works...
comment:111 Changed 4 years ago by jason
Preliminary tests seem to indicate that these patches and the new take work just fine with IPython 0.13 (at least when I revert my IPython git repository). So it's still probably ready for more people to hammer on this.
comment:112 Changed 4 years ago by jason
 Work issues changed from ?? doesn't show code, init.sage displayed, double plot windows to ?? doesn't show code
My take2 patch seems to have solved the double plot window problem. It also solved the init.sage/load problems, as well as the ?? problem. So that was all of the issues listed...
comment:113 Changed 4 years ago by jason
 Work issues ?? doesn't show code deleted
Changed 4 years ago by jason
comment:114 Changed 4 years ago by jason
 Description modified (diff)
 Status changed from needs_work to needs_review
Since we now hook into the IPython display hook, we can delete our special display hook.
comment:115 Changed 4 years ago by jason
 Description modified (diff)
Fixed the startup issue with new patch to scripts repository
comment:116 Changed 4 years ago by jason
 Description modified (diff)
Changed 4 years ago by jason
comment:117 Changed 4 years ago by jason
 Description modified (diff)
Fix a transforming issue: see http://mail.scipy.org/pipermail/ipythondev/2012September/010329.html or the commit message.
comment:118 Changed 4 years ago by jdemeyer
 Dependencies set to #13459
 Status changed from needs_review to needs_work
This needs to be rebased to sage5.4.rc0, in particular #13459.
comment:119 Changed 4 years ago by jason
Also, #13361 includes the change in the startuptime.py patch, so we can delete it.
comment:120 Changed 4 years ago by jason
 Description modified (diff)
comment:121 Changed 4 years ago by jason
 Description modified (diff)
 Status changed from needs_work to needs_review
Add one more patch so we don't change directories anymore.
comment:122 followup: ↓ 127 Changed 4 years ago by jason
Something that seems to work fine now is starting up sage in the devel/sage directory. So it seems that the issue discussed in #13361 is fixed in this ipython upgrade.
Changed 4 years ago by jason
comment:123 Changed 4 years ago by jason
 Description modified (diff)
comment:124 Changed 4 years ago by jason
Okay, I think this may be ready for review again.
It's a big enough change that maybe it would be good to shoot for one of the first patches in the 5.5 release, so it gets plenty of testing???
comment:125 in reply to: ↑ 41 Changed 4 years ago by jhpalmieri
Replying to slabbe:
Also, doing sage ipython notebook creates this error :
$ sage ipython notebook Traceback (most recent call last): ... ImportError: The IPython Notebook requires tornado >= 2.1.0
I get this too. Should I just install tornado somehow, or should this be fixed as part of this ticket?
Edit: after installing tornado (with sage sh and easy_install tornado), it said I had to install pyzmq. So I did that, and now the notebook runs. It looks very nice, and feels pretty snappy, maybe snappier than the Sage notebook.
comment:126 Changed 4 years ago by jason
Yes, tornado and zmq (pyzmq) are required for the ipython notebook. That's not part of this ticket.
And yes, the ipython notebook is very nice. After loading it up, try doing
%load_ext sage.misc.sage_extension
to get some sage goodness, like the preparser, etc.!
comment:127 in reply to: ↑ 122 ; followup: ↓ 128 Changed 4 years ago by jdemeyer
comment:128 in reply to: ↑ 127 Changed 4 years ago by jason
Replying to jdemeyer:
Replying to jason:
Something that seems to work fine now is starting up sage in the devel/sage directory.
FYI: this was fixed by #13459.
But I reverted the "import sage" that #13459 does in trac_12719scripts.patch, and it still works fine for me (running sage in devel/sage and then import sage actually imports the sitepackages sage). Maybe IPython changed its handling of sys.path. What I'm saying is that we should test that my reverting of part of #13459 (the part where we imported sage in sageipython) actually does what I think it does.
comment:129 Changed 4 years ago by jhpalmieri
I'm getting doctest failures because of how lists of matrices are printed. For example, with matrix2.pyx:
File ".../sage5.4.rc1/devel/sage/sage/matrix/matrix2.pyx", line 11627: sage: (d, u, v) Expected: ( [ 1 0] [ 1 0] [ 1 w] [ 0 w + 9], [w 1], [ 0 1] ) Got: ([ 1 0] [ 0 w + 9], [ 1 0] [w 1], [ 1 w] [ 0 1])
That file has 7 failures altogether. Is this because you turned off Sage's displayhook?
comment:130 Changed 4 years ago by jason
Interesting. I thought I used Sage's displayhook (I know I was at one time anyway), but I've also noticed the same problems on my install with printing tuples of matrices and it's been frustrating to me. I'll take a look at it.
comment:131 Changed 4 years ago by jhpalmieri
12719displayhook.patch looks relevant, in particular removing the lines
import sage.misc.displayhook sage.misc.displayhook.install()
and removing the corresponding functions from sage/misc/displayhook.py. But I've never worked with this aspect of Sage before.
comment:132 Changed 4 years ago by jhpalmieri
When I use either time or %time, the rest of the line doesn't seem to be preparsed: try
sage: srange(1/10, 1/2, 1/10) [1/10, 1/5, 3/10, 2/5]
vs.
sage: %time srange(1/10, 1/2, 1/10)  ValueError Traceback (most recent call last) ... ValueError: srange() step argument must not be zero
Or even
sage: %time 1/10 CPU times: user 0.00 s, sys: 0.00 s, total: 0.00 s Wall time: 0.00 s 0 < note the answer!
comment:133 Changed 4 years ago by jason
The displayhook is activated when Sage is run (try running those matrix doctests from the command line). The problem is that the doctesting framework does *not* use the interactive version of Sage; it seems to use straight python. So the display hook is not set.
It seems that the display hook used to be set when just importing Sage as a library, maybe? If so, I think that's the wrong approach. Importing a library shouldn't obliterate the display hook.
So it sounds like we need to make the doctesting framework load the right Sage things, like the preparser, the display hook, etc.
comment:134 Changed 4 years ago by jason
I'll take a look at %time. That indeed seems to be a problem where the preparser isn't being run.
comment:135 Changed 4 years ago by jason
 Description modified (diff)
For some reason, the preparser explicitly turned itself off for magic lines. I'm not sure why but I'm posting a patch to fix that.
Changed 4 years ago by jason
comment:136 Changed 4 years ago by jason
 Description modified (diff)
comment:137 Changed 4 years ago by jason
John, you know the doctest framework a lot better than I do. If you start up sageipython and load the sage extension, it will install the display hook, import Sage, etc. John, do you know how to get the doctest runner to execute this as part of ipython: get_ipython().extension_manager.load_extension('sage.misc.sage_extension')
grout@tiny:~/sage% sage ipython ic "get_ipython().extension_manager.load_extension('sage.misc.sage_extension')" E:128 Python 2.7.3 (default, Oct 9 2012, 11:53:24) Type "copyright", "credits" or "license" for more information. IPython 0.13  An enhanced Interactive Python. ? > Introduction and overview of IPython's features. %quickref > Quick reference. help > Python's own help system. object? > Details about 'object', use 'object??' for extra details. In [1]: (identity_matrix(3), identity_matrix(5)) Out[1]: ( [1 0 0 0 0] [0 1 0 0 0] [1 0 0] [0 0 1 0 0] [0 1 0] [0 0 0 1 0] [0 0 1], [0 0 0 0 1] )
comment:138 Changed 4 years ago by jhpalmieri
I guess one reason to turn off the preparser for magic lines is so that in a line like
%ed file1.py
the "1" doesn't get preparsed. I don't know how the old "time" command was written; did it just call "%time"? If so, maybe that was to allow lines starting with "time" to be preparsed.
For doctesting, I don't know if IPython is used at all during doctesting. If it's possible to turn on this extension using pure Python, we can add it at the top of each file as it's doctested, with a patch like this to local/bin/sagedoctest:

sagedoctest
diff git a/sagedoctest b/sagedoctest
a b def extract_doc(file_name, library_code= 490 490 491 491 """ % os.path.join(os.getcwd(), file_name) 492 492 s += "from sage.all_cmdline import *; \n" 493 s += "ADD NEW CODE HERE\n" 493 494 s += "import sage.plot.plot; sage.plot.plot.DOCTEST_MODE=True\n" # turn off image popup 494 495 s += r""" 495 496 def warning_function(f):
Changed 4 years ago by jason
comment:139 Changed 4 years ago by jason
 Description modified (diff)
Updated instructions for new display hook patch that sets the display hook when doctesting.
comment:140 Changed 4 years ago by jason
For the %time command, I filed an issue with IPython a while ago: https://github.com/ipython/ipython/pull/2403
For now, it appears like we'll have to ship that patch ourselves.
comment:141 Changed 4 years ago by jason
 Work issues set to ship https://github.com/ipython/ipython/pull/2403
comment:142 Changed 4 years ago by jhpalmieri
The matrixprinting seems to work now, but I'm seeing a few other doctest failures:
sage t long force_lib devel/sage/sage/interfaces/sage0.py ********************************************************************** File "/scratch/palmieri/12719/sage5.4.rc1/devel/sagemain/sage/interfaces/sage0.py", line 489: sage: sage0(4).gcd Expected: <builtin method gcd of sage.rings.integer.Integer object at 0x...> Got: <function gcd> **********************************************************************
and several failures in sage_extension.py, which would take up too much room to include here.
comment:143 Changed 4 years ago by jhpalmieri
I think the errors in sage_extension.py are because file names in %runfile foo are being preparsed: for example, the first error message is pretty long, but it ends with
IOError: did not find file '/home/palmieri/.sage/temp/sage.math.washington.edu/Integer(21508)/dir_0/run_cell.py' to load or attach
Note that Integer(21508) in the file name; this should presumably just be 21508. This preparsing doesn't happen if the number is mixed in with letters, but for files or directories with purely numeric names, it seems to pop up. So from the command line:
sage: %runfile hello2.py # works sage: %runfile 123/hello2.py # fails sage: %runfile /home/palmieri/123/hello2.py # fails
The same thing happens with %attach, and I assume also with the other magic functions which take file names as arguments.
comment:144 Changed 4 years ago by jhpalmieri
I don't understand the sage0.py failure. Does the new IPython have a different default print representation for some objects? Before the patches here:
sage: a = 4 sage: a.gcd <builtin method gcd of sage.rings.integer.Integer object at 0x480e330> sage: a.gcd? Type: builtin_function_or_method Base Class: <type 'builtin_function_or_method'> String Form: <builtin method gcd of sage.rings.integer.Integer object at 0x480e330> Namespace: Interactive Definition: a.gcd(self, n) Docstring: ...
With the patches:
sage: a = 4 sage: a.gcd <function gcd> sage: a.gcd? Type: builtin_function_or_method String Form:<builtin method gcd of sage.rings.integer.Integer object at 0x5b7c5a0> Definition: a.gcd(self, n) Docstring: ...
With the old version, the print rep for a.gcd is the same as what's labeled the "String Form" when you do a.gcd?. With the new version, the print rep has changed but the "String Form" has not. I'm also confused by this behavior (with the patches):
sage: a = 4 sage: G = a.gcd sage: G.__repr__() '<builtin method gcd of sage.rings.integer.Integer object at 0x4b685a0>' sage: G <function gcd> sage: str(G) '<builtin method gcd of sage.rings.integer.Integer object at 0x4b685a0>'
Why isn't G printed using its __repr__ method?
I've tried out some other objects (e.g., matrices and elements of the Steenrod algebra) and my guess is that the print representations for methods defined in pyx files are getting changed to <function ...>, while those defined in py files haven't changed. Any ideas why? Looking at ipython0.10.2.p1/src/IPython/UserConfig/ipythonrc, I see the configuration option object_info_string_level 0, which looks relevant, but we're not using this style of configuration, right?
comment:145 Changed 4 years ago by broken_symlink
Just a heads up that iPython 0.13.1 is set to be released on Friday. It fixes all the bugs I was having with ipython.parallel.
Changed 4 years ago by jhpalmieri
comment:146 Changed 4 years ago by jhpalmieri
 Description modified (diff)
We need another patch, since the pager in IPython has moved. One instance of this was fixed in one of the patches, but we need to fix others.
Note the change to sagedoc.py; this needs to be tested.
comment:147 Changed 4 years ago by jason
It seems like you caught all of the instances of the IPython pager:
grout@tiny:~/sage/devel/sage/sage% ack genutils * interfaces/gap3.py 493: import IPython.genutils 494: IPython.genutils.page(helptext) misc/pager.py 27: import IPython.genutils 28: return IPython.genutils.page misc/sagedoc.py 833: from IPython.genutils import page
comment:148 Changed 4 years ago by jason
 Description modified (diff)
comment:149 Changed 4 years ago by jason
Positive review to the sagedoc.py changesearch_src didn't work before, but it does work after the change.
comment:150 Changed 4 years ago by jason
I uploaded an IPython 0.13.1 spkg, updating to the latest stable. (the old 0.13 spkg is still in my home directory too).
Changed 4 years ago by jhpalmieri
comment:151 Changed 4 years ago by jhpalmieri
 Description modified (diff)
trac_12719move_to_preparser.patch doesn't apply cleanly to 5.4.rc2. Here's a rebased version.
comment:152 followup: ↓ 157 Changed 4 years ago by jason
 Description modified (diff)
jhpalmieri: I uploaded a new IPython 0.13.1 spkg that applies https://github.com/ipython/ipython/pull/2403. This means we can delete the 12719preparsemagic.patch patch, which will solve the %runfile problems, but keep the preparsing for %time, %timeit, and %prun.
I've updated the instructions.
comment:153 Changed 4 years ago by jason
Whew, with all these patchesI can't wait until we move to using git (or even mercurial properly) and we have branches for this sort of thing.
comment:154 followup: ↓ 160 Changed 4 years ago by jason
The cython function printing issue appears to boil down to those functions being treated as builtin functions, so this line applies: https://github.com/ipython/ipython/blob/master/IPython/lib/pretty.py#L669, rather than this line: https://github.com/ipython/ipython/blob/master/IPython/lib/pretty.py#L671
Suggestions for how to fix this? How do we distinguish between builtin functions and Cython methods?
comment:155 Changed 4 years ago by jason
I've posted to the IPython list about the Cython method printing: http://mail.scipy.org/pipermail/ipythondev/2012October/010503.html
comment:156 Changed 4 years ago by jason
 Work issues changed from ship https://github.com/ipython/ipython/pull/2403 to Cython method printing
Are there any other outstanding issues other than the Cython method printing?
comment:157 in reply to: ↑ 152 Changed 4 years ago by jhpalmieri
Replying to jason:
jhpalmieri: I uploaded a new IPython 0.13.1 spkg that applies https://github.com/ipython/ipython/pull/2403. This means we can delete the 12719preparsemagic.patch patch, which will solve the %runfile problems, but keep the preparsing for %time, %timeit, and %prun.
Can you think of a way to doctest this? (I haven't tried anything at all, so it might be easy.)
comment:158 Changed 4 years ago by jason
If just putting in a magic %timeit ... doesn't work, then this should work *if* the doctesting framework is using IPython:
sage: get_ipython().run_line_magic('time', '594.factor()') CPU times: user 0.00 s, sys: 0.00 s, total: 0.00 s Wall time: 0.00 s 2 * 3^3 * 11
comment:159 Changed 4 years ago by jhpalmieri
 Description modified (diff)
Hey, let's add another patch to the pile!
Changed 4 years ago by jhpalmieri
comment:160 in reply to: ↑ 154 Changed 4 years ago by jhpalmieri
Replying to jason:
The cython function printing issue appears to boil down to those functions being treated as builtin functions, so this line applies: https://github.com/ipython/ipython/blob/master/IPython/lib/pretty.py#L669, rather than this line: https://github.com/ipython/ipython/blob/master/IPython/lib/pretty.py#L671
Suggestions for how to fix this? How do we distinguish between builtin functions and Cython methods?
I don't know. Even in previous versions of Sage:
sage: type(4.gcd) <type 'builtin_function_or_method'>
I wonder if changing this would require patching Cython. If we knew where the methods for Cython methods were defined, maybe we could just define a method _repr_pretty_, as described in https://github.com/ipython/ipython/blob/master/IPython/lib/pretty.py#L27. Line 37373740 of local/lib/python/sitepackages/Cython/Compiler/Nodes.py says
is_builtin_function_or_method = "PyCFunction_Check(%s)" % func_node_temp is_overridden = "(PyCFunction_GET_FUNCTION(%s) != (PyCFunction)%s)" % ( func_node_temp, self.py_func.entry.func_cname) code.putln("if (!%s  %s) {" % (is_builtin_function_or_method, is_overridden))
Is this relevant?
Alternatively, we could patch the file "pretty.py", modifying the definition of _type_pprinters somehow, although I'm not sure how.
Alternatively, we could temporarily accept the new print representation for Cythondefined methods, and create a new ticket for fixing this. It seems like a small issue to me, and maybe it shouldn't hold up the rest of this ticket.
comment:161 Changed 4 years ago by jason
 Cc robertwb added
Alternatively, we could post to the Cython list and ask them :).
Ccing robertwb (see the comment or two above about Cython function printing, as well as http://mail.scipy.org/pipermail/ipythondev/2012October/010503.html, which tries to lay out the issue more concisely).
comment:162 Changed 4 years ago by jhpalmieri
Asking the Cython developers is a great idea. Here's a real hack, but it seems to work: for builtin functions, if the print representation includes "sage.", we use that. (Now that I look at your post to the IPython list, it's just a version of the hack you described there.) This is a patch for IPython/lib/pretty.py:

pretty.py
old new 616 616 617 617 def _function_pprint(obj, p, cycle): 618 618 """Base pprint for all functions and builtin functions.""" 619 if obj.__ module__ in ('__builtin__', 'exceptions') or not obj.__module__:620 name = obj.__name__619 if obj.__repr__().find('sage.') != 1: 620 p.text(obj.__repr__()) 621 621 else: 622 name = obj.__module__ + '.' + obj.__name__ 623 p.text('<function %s>' % name) 622 if obj.__module__ in ('__builtin__', 'exceptions') or not obj.__module__: 623 name = obj.__name__ 624 else: 625 name = obj.__module__ + '.' + obj.__name__ 626 p.text('<function %s>' % name) 624 627 625 628 626 629 def _exception_pprint(obj, p, cycle):
comment:163 Changed 4 years ago by jhpalmieri
On the Cython users mailing list, in which I essentially quoted Jason's message to the IPython list, Bradley Froehle says
There's nothing to be done in Cython here. As you point out, a.seed is a builtin (i.e. compiled) method and type(a.seed) returns `builtin_function_or_method` correctly.
So I think our options are
 hack pretty.py
 wait for a real IPython fix
 change the doctests to match the current output for now, and open a new ticket to fix this later.
Preferences? Am I missing any good choices?
comment:164 Changed 4 years ago by jhpalmieri
Ping. Any opinions?
comment:165 Changed 4 years ago by jason
Is it hard to change the doctests (how many?). If that's easy, I'd say to change the doctests, especially given that any patch we make will take a long time to make it back into Sage through IPython. I'd veto "wait for a real IPython fix".
Is this the only thing holding us back now?
comment:166 Changed 4 years ago by jhpalmieri
 Description modified (diff)
I think there is only one failing doctest:
sage t long force_lib devel/sage/sage/interfaces/sage0.py ********************************************************************** File "/Users/palmieri/Desktop/Sage_stuff/sage_builds/12719/sage5.4.rc3/devel/sagemain/sage/interfaces/sage0.py", \ line 489: sage: sage0(4).gcd Expected: <builtin method gcd of sage.rings.integer.Integer object at 0x...> Got: <function gcd> **********************************************************************
and it should be trivial to fix. I also don't know how serious the issue is. I mean, it would be nice if 4.gcd printed more information, but it doesn't seem crucial in any way.
Changed 4 years ago by jhpalmieri
comment:167 Changed 4 years ago by jason
I'd say let's change our doctest, and then work with upstream to get a patch in. When the patch comes down (probably in a few months to a year?), we'll change our doctest again.
comment:168 Changed 4 years ago by jhpalmieri
I changed the doctest. All tests pass for me on sage.math. Since it was already positively reviewed once before, I think we can set it back to that. What do you think?
comment:169 Changed 4 years ago by jason
Yippee!!
comment:170 Changed 4 years ago by jhpalmieri
 Status changed from needs_review to positive_review
comment:171 Changed 4 years ago by jdemeyer
 Milestone changed from sage5.4 to sage5.5
 Work issues Cython method printing deleted
comment:172 Changed 4 years ago by jason
jdemeyer  it would be great if this were merged into one of the 5.5 betas.
comment:173 Changed 4 years ago by jdemeyer
Of course, don't worry.
comment:174 Changed 4 years ago by jdemeyer
 Description modified (diff)
comment:175 Changed 4 years ago by jdemeyer
 Dependencies changed from #13459 to #13459, #13211
 Milestone changed from sage5.5 to sagepending
With #13211, I get
applying /release/merger/patches/trac_127195.1beta1.patch patching file sage/interfaces/gap.py Hunk #2 FAILED at 1065 1 out of 2 hunks FAILED  saving rejects to file sage/interfaces/gap.py.rej
Note that #13211 isn't certain to be merged (there were some problems before and the fixes haven't been properly tested yet).
comment:176 Changed 4 years ago by jason
I don't think I've ever applied #13211, and I certainly don't have it applied now. I didn't realize it was a dependency (I've just been pasting in the instructions in the description). Can we just remove the dependency? I'm not sure why we even have it.
comment:177 Changed 4 years ago by jdemeyer
My point is that it should be made a dependency and be rebased to #13211.
comment:178 followup: ↓ 179 Changed 4 years ago by jason
But if #13211's future isn't sure yet, should we add that as a dependency? Granted that the rebase (for either ticket) is a simple 12 line fix, but it'd be a shame if this huge work didn't get in because #13211 for some reason didn't pass muster.
You're the release manager, so you make the calls. Do you still want me to rebase to depend on that ticket? Does that hurt our chances of getting into 5.5?
comment:179 in reply to: ↑ 178 Changed 4 years ago by jdemeyer
Replying to jason:
You're the release manager, so you make the calls. Do you still want me to rebase to depend on that ticket? Does that hurt our chances of getting into 5.5?
I will test #13211 and then I'll know better whether or not it will be merged. So let's wait for now.
The best chances for getting this merged is to respond quickly when I ask for it to be rebased.
Changed 4 years ago by jhpalmieri
comment:180 Changed 4 years ago by jhpalmieri
 Description modified (diff)
Here's a patch rebased to #13211. Let's keep the old patch, too, just in case.
comment:181 Changed 4 years ago by jdemeyer
 Dependencies changed from #13459, #13211 to #13459, #9191
 Description modified (diff)
 Status changed from positive_review to needs_work
Changed 4 years ago by jdemeyer
comment:182 Changed 4 years ago by jdemeyer
 Description modified (diff)
 Status changed from needs_work to needs_review
12719_run_cython.patch needs review.
comment:183 Changed 4 years ago by jhpalmieri
 Description modified (diff)
I think this looks okay. I'm building and running doctests one more time to make sure.
comment:184 Changed 4 years ago by jhpalmieri
 Status changed from needs_review to positive_review
Changed 4 years ago by jhpalmieri
comment:185 Changed 4 years ago by jhpalmieri
 Description modified (diff)
 Status changed from positive_review to needs_work
trac_12719hgignore.patch needs review.
comment:186 Changed 4 years ago by jhpalmieri
 Status changed from needs_work to needs_review
comment:187 Changed 4 years ago by jdemeyer
 Reviewers changed from Volker Braun, Mike Hansen, Jason Grout to Volker Braun, Mike Hansen, Jason Grout, Jeroen Demeyer
 Status changed from needs_review to positive_review
comment:188 Changed 4 years ago by jdemeyer
 Status changed from positive_review to needs_work
trac_12719scripts.patch is missing a commit message.
127195.4rc1.patch is missing a user name in the patch file.
trac_12719cellmagics013.patch has a commit message which is all on one line and too long. You should make sure that the lines in commit messages are not too long, but the first line should still be descriptive by itself, since that shows up in hg log.
positive review to trac_12719hgignore.patch
comment:189 Changed 4 years ago by jdemeyer
In SageInteractiveShell.system_raw, does libraries refer to a global or is that variable simply unused? Since false isn't guaranteed to return exit status 1 (on Solaris, it returns 255, POSIX specifies it must be nonzero), the doctest must be changed to something more portable. I also don't see this function discussed on #975.
So, I suggest the following patch:

sage/misc/interpreter.py
diff git a/sage/misc/interpreter.py b/sage/misc/interpreter.py
a b class SageInteractiveShell(TerminalInter 161 161 162 162 def system_raw(self, cmd): 163 163 """ 164 Adjust the libraries before calling system commands. See Trac 165 #975 for a discussion of this function. 164 Run a system command. 166 165 167 166 EXAMPLES:: 168 167 169 168 sage: from sage.misc.interpreter import get_test_shell 170 169 sage: shell = get_test_shell() 171 170 sage: shell.system_raw('false') 172 sage: shell.user_ns['_exit_code'] 173 256 171 sage: status = shell.user_ns['_exit_code'] 172 sage: os.WIFEXITED(status) and os.WEXITSTATUS(status) != 0 173 True 174 174 """ 175 sage_commands = os.listdir(os.environ['SAGE_ROOT']+"/local/bin/") 176 DARWIN_SYSTEM = os.uname()[0]=='Darwin' 177 if cmd in sage_commands: 178 return super(SageInteractiveShell, self).system_raw(cmd) 179 else: 180 libraries = 'LD_LIBRARY_PATH=$$SAGE_ORIG_LD_LIBRARY_PATH;' 181 if DARWIN_SYSTEM: 182 libraries += 'DYLD_LIBRARY_PATH=$$SAGE_ORIG_DYLD_LIBRARY_PATH;' 183 return super(SageInteractiveShell, self).system_raw(cmd) 175 return super(SageInteractiveShell, self).system_raw(cmd) 184 176 185 177 def ask_exit(self): 186 178 """
comment:190 Changed 4 years ago by jason
 Description modified (diff)
I've uploaded a patch to the system command. The point is that we need to reset the original system libraries if we run a nonsage command.
Changed 4 years ago by jason
comment:191 Changed 4 years ago by jason
 Status changed from needs_work to needs_review
Okay, I think I've taken care of the outstanding issues with the patches.
comment:192 Changed 4 years ago by jason
I updated the system patch to also include a doctest checking to see if a system command is running with the Sage LD_LIBRARY_PATH.
comment:193 Changed 4 years ago by jdemeyer
You should also doctest system_raw working succesfully.
I think you can replace
os.file.isfile(FILE)
by
os.access(FILE, os.X_OK):
since you want to check for an executable file.
Also, I assume that "cmd" uses shell syntax? Then you're doing it wrong. Correct shell syntax is
LD_LIBRARY_PATH="$SAGE_ORIG_LD_LIBRARY_PATH"; export LD_LIBRARY_PATH
comment:194 Changed 4 years ago by jdemeyer
 Status changed from needs_review to needs_work
comment:195 Changed 4 years ago by jhpalmieri
I'm not an expert on bash syntax (I assume this is using bash), but perhaps some (or all?) of these would work:
LD_LIBRARY_PATH="$SAGE_ORIG_LD_LIBRARY_PATH"; export LD_LIBRARY_PATH; ... export LD_LIBRARY_PATH="$SAGE_ORIG_LD_LIBRARY_PATH"; ... env LD_LIBRARY_PATH="$SAGE_ORIG_LD_LIBRARY_PATH" ... # note no semicolon LD_LIBRARY_PATH="$SAGE_ORIG_LD_LIBRARY_PATH" ... # ??
comment:196 Changed 4 years ago by jdemeyer
I don't know whether we can assume bash, I would go for Posix /bin/sh compatible.
For example
export LD_LIBRARY_PATH="$SAGE_ORIG_LD_LIBRARY_PATH";
is bashspecific and I'm not sure about
LD_LIBRARY_PATH="$SAGE_ORIG_LD_LIBRARY_PATH" ...
comment:197 Changed 4 years ago by jason
 Status changed from needs_work to needs_review
I hope this redo is good! Thanks for the tips.
comment:198 Changed 4 years ago by jdemeyer
 Status changed from needs_review to needs_work
You should replace $$ by $.
comment:199 Changed 4 years ago by jdemeyer
And please also doctest a nonSage command working successfully. For example
system_raw("true")
comment:200 Changed 4 years ago by jason
 Status changed from needs_work to needs_review
comment:201 Changed 4 years ago by jhpalmieri
All of the patches apply cleanly (on top of 5.5.beta0 + #9191), and the new 12719system.patch looks okay to me. Jeroen, what do you think?
I have one mild complaint: if I do
sage: note[TAB]
it doesn't complete to "notebook" anymore, saying that "%notebook" is also a valid completion. Would it be possible, here or on a followup ticket, to rename the "%notebook" magic command to "%ipython_notebook" or something similar?
comment:202 Changed 4 years ago by jdemeyer
 Status changed from needs_review to positive_review
Looks fine. As for the TABcompletion: a different ticket please.
comment:203 Changed 4 years ago by jdemeyer
 Milestone changed from sagepending to sage5.5
comment:204 Changed 4 years ago by jdemeyer
Upgrading from sage4.5 fails with a trial version of sage5.5.beta2 and this is the only ticket I can think of that could cause this problem. The error shows up in Twisted (part of sagenb now):
Installed /release/buildbot/sage/sage1/sage_upgrade_4.5/build/sage5.5.beta2/local/lib/python2.7/sitepackages/Twisted12.1.0py2.7linuxx86_64.egg Processing dependencies for Twisted==12.1.0 Searching for zope.interface Link to http://pypi.python.org/simple/zope.interface/ ***BLOCKED*** by allowhosts Couldn't find index page for 'zope.interface' (maybe misspelled?) Scanning index of all packages (this may take a while) Link to http://pypi.python.org/simple/ ***BLOCKED*** by allowhosts No local packages or download links found for zope.interface error: Could not find suitable distribution for Requirement.parse('zope.interface') Error installing Twisted12.1.0.tar.bz2 !
comment:205 Changed 4 years ago by jdemeyer
 Milestone changed from sage5.5 to sage5.6
Whether or not IPython causes the zope.interface problem, I won't have time anyway to test it...
comment:206 Changed 4 years ago by jason
This seems like it has to be a sagenb problem (that we aren't requiring zope.interface, and thus packaging zope.interface, in our sagenb prereqs).
Upgrading from sage 4.5? I'm almost sure that it's the sagenb upgrade at #13121, not this ticket.
comment:207 Changed 4 years ago by jason
Okay, here's what makes sense: the old IPython required zope.interface, so it was always installed when we installed the new notebook, so we never noticed that we needed it for the sage notebook. The new IPython no longer requires zope.interface, so when the notebook at #13121 checks for it, it isn't installed so sagenb tries to install it.
The correct fix is to make sagenb require and package zope.interface, like it should have before now, not to change this ticket.
comment:208 Changed 4 years ago by jason
 Dependencies changed from #13459, #9191 to #13459, #9191, #13717
I uploaded a new sagenb spkg at #13717
comment:209 Changed 4 years ago by jdemeyer
 Status changed from positive_review to needs_work
Another upgrade issue:
sage_root5.5.beta2 Machine: Darwin bsd.math.washington.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu1504.15.3~1/RELEASE_X86_64 x86_64 Deleting directories from past builds of previous/current versions of sage_root5.5.beta2 Extracting package /Users/buildbot/build/sage/bsd1/bsd_upgrade_4.6.2/build/sage5.5.beta2/spkg/standard/sage_root5.5.beta2.spkg ... rwrr 1 buildbot staff 323619 Nov 16 04:38 /Users/buildbot/build/sage/bsd1/bsd_upgrade_4.6.2/build/sage5.5.beta2/spkg/standard/sage_root5.5.beta2.spkg Finished extraction **************************************************** Host system uname a: Darwin bsd.math.washington.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu1504.15.3~1/RELEASE_X86_64 x86_64 **************************************************** **************************************************** CC Version gcc v Using builtin specs. COLLECT_GCC=gcc COLLECT_LTO_WRAPPER=/Users/buildbot/build/sage/bsd1/bsd_upgrade_4.6.2/build/sage5.5.beta2/local/libexec/gcc/x86_64appledarwin10.8.0/4.6.3/ltowrapper Target: x86_64appledarwin10.8.0 Configured with: ../src/configure prefix=/Users/buildbot/build/sage/bsd1/bsd_upgrade_4.6.2/build/sage5.5.beta2/local withlocalprefix=/Users/buildbot/build/sage/bsd1/bsd_upgrade_4.6.2/build/sage5.5.beta2/local withgmp=/Users/buildbot/build/sage/bsd1/bsd_upgrade_4.6.2/build/sage5.5.beta2/local withmpfr=/Users/buildbot/build/sage/bsd1/bsd_upgrade_4.6.2/build/sage5.5.beta2/local withmpc=/Users/buildbot/build/sage/bsd1/bsd_upgrade_4.6.2/build/sage5.5.beta2/local withsystemzlib disablemultilib Thread model: posix gcc version 4.6.3 (GCC) **************************************************** cp: ipython: No such file or directory Root repo: Error copying files from Sage root repo to /Users/buildbot/build/sage/bsd1/bsd_upgrade_4.6.2/build/sage5.5.beta2
The file spkg/rootspkginstall should be fixed.
comment:210 Changed 4 years ago by jdemeyer
Jason: that makes sense.
comment:211 Changed 4 years ago by jhpalmieri
 Description modified (diff)
 Status changed from needs_work to needs_review
I think this patch will fix the problem.
comment:212 Changed 4 years ago by jason
Here's another problem highlighted by https://github.com/sagemath/sagecell/issues/378:
"""string """; type(1)
does no preparsing on the second line because IPython doesn't do transformations for the second line (since it's inside quotes). IPython admits that this is a hackish and fragile strategy, and they are working on the issue. For example, they are implementing AST transformers and stateful line transformers. However, for now, we should run at least our preparser on every line of input, since we *do* keep track of state, so we need to be preparsing that second line.
I have a patch coming up shortly.
comment:213 Changed 4 years ago by jason
 Description modified (diff)
comment:214 Changed 4 years ago by jhpalmieri
Does this most recent patch need a doctest?
comment:215 Changed 4 years ago by jhpalmieri
By the way, this passes all doctests. I also upgraded Sage 5.2 successfully from a source distribution prepared using the patches here.
comment:216 Changed 3 years ago by jdemeyer
 Description modified (diff)
 Milestone changed from sage5.6 to sagepending
comment:217 Changed 3 years ago by vbraun
 Description modified (diff)
I've rediffed trac_12719scriptsvb.patch to account for pure whitespace changes in #13899 (merged in sage5.6.beta3)
comment:218 Changed 3 years ago by vbraun
 Description modified (diff)
comment:219 Changed 3 years ago by vbraun
 Description modified (diff)
 Status changed from needs_review to positive_review
Works for me and as far as I can tell all remaining issues have been addressed.
Does not fix #11223, %bg is not implemented in ipython0.13.1.
comment:220 Changed 3 years ago by jdemeyer
 Dependencies changed from #13459, #9191, #13717 to #13459, #9191, #13717, #13963
comment:221 Changed 3 years ago by jdemeyer
 Status changed from positive_review to needs_work
This seems to cause some problems on OpenSolaris.
First a doctest timeout:
Trying: sage0.eval('2+2')###line 320:_sage_ sage: sage0.eval('2+2') Expecting: '4' [...hangs...]
Interrupting this and restarting Sage gives:
buildbot@hawk:~/build/sage/hawk1/hawk_suncc/build/sage$ ./sage   Sage Version 5.7.beta0, Release Date: 20130120   Type "notebook()" for the browserbased notebook interface.   Type "help()" for help.   ********************************************************************** * * * Warning: this is a prerelease version, and it may be unstable. * * * ********************************************************************** ********************************************************************** Oops, Sage crashed. We do our best to make it stable, but... A crash report was automatically generated with the following information:  A verbatim copy of the crash traceback.  A copy of your input history during this session.  Data on your current Sage configuration. It was left in the file named: '/export/home/buildbot/.sage/ipythonnew/Sage_crash_report.txt' If you can email this file to the developers, the information in it will help them in understanding and correcting the problem. You can mail it to: sagesupport at sagesupport@googlegroups.com with the subject 'Sage Crash Report'. If you want to do it now, the following command will work (under Unix): mail s 'Sage Crash Report' sagesupport@googlegroups.com < /export/home/buildbot/.sage/ipythonnew/Sage_crash_report.txt To ensure accurate tracking of this issue, please file a report about it at: http://trac.sagemath.org/sage_trac Hit <Enter> to quit (your terminal may close)
Removing $HOME/.sage fixed that.
comment:222 followup: ↓ 223 Changed 3 years ago by vbraun
Can we have a beta0 with this ticket? Its a bit ridiculous to have to use a script to apply all these patches.
Also, .sage/ipythonnew? What are we going to do the next time the configuration file format changes, .sage/ipythonevennewer?
comment:223 in reply to: ↑ 222 Changed 3 years ago by jdemeyer
Replying to vbraun:
Can we have a beta0 with this ticket?
See http://sage.math.washington.edu/home/release/sage5.7.beta1
comment:224 Changed 3 years ago by jason
Volker, you're right that the config file directory is still a bit clunky. On the one hand, I didn't want to put the version number in there so that it changes every time we upgrade IPython. On the other hand, calling something 'new' doesn't scale.
What if we put the version number in there like this: ipython0.12orlater? That's weird too, but it also means that people don't have to keep moving their configuration files if IPython upgrades, but the config format stays the same.
comment:225 Changed 3 years ago by vbraun
I think we are smart enough to figure out that ipython0.12 is the directory for configuration files that were introduced with iPython 0.12 and that you might run a later (but still compatible) version.
comment:226 Changed 3 years ago by jason
But IIRC, Matplotlib uses a perversion config directory inside of .sage, so having two conventions could be confusing.
comment:227 Changed 3 years ago by jason
What about the name IPython0.12+?
comment:228 Changed 3 years ago by vbraun
I don't really care about the name as long as it has the version somewhere in there. Personally I find anything extra just confusing but feel free to pick what you like.
comment:229 Changed 3 years ago by vbraun
Jeroen: can you attach the /export/home/buildbot/.sage/ipythonnew/Sage_crash_report.txt
comment:230 Changed 3 years ago by vbraun
I tested this on OpenIndiana (OpenSolaris clone) and I don't see the timeout that Jeroen has. I get occasional nonreproducible timeouts on OI though, it might be something generally wonky with their PTYs. Remind me again why something that nobody is using or has access to is a primary platform?
comment:231 Changed 3 years ago by jhpalmieri
I see a crash on David Kirkby's machine hawk. Crash log posted here.
comment:232 Changed 3 years ago by vbraun
Sane catching of history database errors has been fixed upstream at https://github.com/ipython/ipython/commit/d347c347bab915df69d499521b4876d3c9b168b9, but not in a released version.
comment:233 Changed 3 years ago by vbraun
 Description modified (diff)
 Status changed from needs_work to needs_review
I've backported the changes to history.py, this should fix the startup failure.
comment:234 Changed 3 years ago by jason
Keeping track, I guess there's one more thing to do: change the config directory back to .sage/ipython0.12 in trac_12719ipythondir013.patch
comment:235 Changed 3 years ago by jason
Okay, I changed the ipythondir013.patch to use the config directory ipython0.12. So that needs review too.
comment:236 Changed 3 years ago by jason
 Work issues set to historyrelated crash, config directory name
Updating work issues with the things that need review.
comment:237 Changed 3 years ago by vbraun
 Status changed from needs_review to positive_review
 Work issues historyrelated crash, config directory name deleted
I'm fine with your patch for the directory name. Any expect interface on OpenIndiana occasionally crashes (maybe 1 in 20), but I've verified we are now not permanently stuck with a corrupted history file any more.
comment:238 followup: ↓ 239 Changed 3 years ago by jhpalmieri
On hawk, I see a doctest failure, but I'm not sure how it could be related to this ticket:
sage t long force_lib devel/sage/sage/tests/french_book/mpoly.py ********************************************************************** File "/export/home/palmieri/testing/clean/sage5.7.beta1/devel/sagemain/sage/tests/frenc\ h_book/mpoly.py", line 373: sage: J.variety(RDF) Expected: [{y: 396340.89..., x: 26.61226...}] Got: [{y: 396340.890167, x: 46.7888621592}] ********************************************************************** 1 items had failures: 1 of 151 in __main__.example_0 ***Test Failed*** 1 failures.
I also see a time out:
sage t long force_lib devel/sage/sage/interfaces/sage0.py *** *** Error: TIMED OUT! PROCESS KILLED! *** *** [1800.2 s]
which perhaps is related to this ticket.
comment:239 in reply to: ↑ 238 Changed 3 years ago by jdemeyer
Replying to jhpalmieri:
sage t long force_lib devel/sage/sage/tests/french_book/mpoly.py
Not related to this ticket.
sage t long force_lib devel/sage/sage/interfaces/sage0.py *** *** Error: TIMED OUT! PROCESS KILLED! *** *** [1800.2 s]
This is indeed related to this ticket, see 221. But I haven't tried with the latest version of the spkg.
comment:240 Changed 3 years ago by jdemeyer
 Status changed from positive_review to needs_work
Patches trac_12719_ROOT_configuration_files.patch and trac_12719ipythondir013.patch combined and rebased. And moved the setting of IPYTHONDIR to sageenv where it belongs.
comment:241 Changed 3 years ago by jdemeyer
 Description modified (diff)
 Status changed from needs_work to needs_review
comment:242 Changed 3 years ago by vbraun
 Status changed from needs_review to positive_review
Sounds good to me.
comment:243 Changed 3 years ago by jdemeyer
 Milestone changed from sagepending to sage5.7
comment:244 Changed 3 years ago by jason
Volker and Jeroen: thanks for both of you working quickly on the last remaining issues!
comment:245 Changed 3 years ago by jhpalmieri
 Description modified (diff)
comment:246 followup: ↓ 247 Changed 3 years ago by jhpalmieri
One patch doesn't apply cleanly to 5.6.rc1:
adding trac_12719rebasedto13211vb.patch to series file applying trac_12719rebasedto13211vb.patch patching file sage/interfaces/gap.py Hunk #1 FAILED at 177 1 out of 2 hunks FAILED  saving rejects to file sage/interfaces/gap.py.rej
I think that the hang on hawk is gone with the latest versions, but I'm testing again to make sure.
comment:247 in reply to: ↑ 246 Changed 3 years ago by vbraun
Replying to jhpalmieri:
One patch doesn't apply cleanly to 5.6.rc1:
You might be missing a dependency since the patch is in sage5.7.beta1...
comment:248 Changed 3 years ago by jhpalmieri
 Status changed from positive_review to needs_work
I didn't think that 5.7.beta0 had been released. Am I supposed to use the unofficial version of it?
By the way, since the file ipy_profile_sage.py has been deleted, any mention of it should also be removed from sagemake_devel_packages and sagespkginstall.
comment:249 Changed 3 years ago by jason
Can someone test something really quick with the official version of the ticket, if it's convenient?
Do:
1; 2
Does it print out both 1 and 2 in both the command line and the notebook? Right now, aleph only prints out 2, and I've narrowed it down to how IPython handles the 'print out the last expression' (IPython prints out the last expression, while Sage prints out the last physical line).
comment:250 Changed 3 years ago by vbraun
John, see comment:223. Since Jeroen linked to it I'd say its official ;)
Jason, works for me (this is with the sagenb update but it shouldn't matter):
[vbraun@volkerdesktop sage5.7.beta1]$ ./sage   Sage Version 5.7.beta1, Release Date: 20130121   Type "notebook()" for the browserbased notebook interface.   Type "help()" for help.   ********************************************************************** * * * Warning: this is a prerelease version, and it may be unstable. * * * ********************************************************************** sage: 1; 2 1 2
comment:251 Changed 3 years ago by vbraun
 Description modified (diff)
 Status changed from needs_work to positive_review
I've removed the last occurrences from ipy_profile_sage.py.
comment:252 followup: ↓ 253 Changed 3 years ago by jason
Volker: and in the sage notebook, it does the same thing? I think it should, but I just want to make sure.
comment:253 in reply to: ↑ 252 Changed 3 years ago by vbraun
Replying to jason:
Volker: and in the sage notebook, it does the same thing?
Yes, same (correct) output in the notebook (with the sagenb0.10.4 spkg).
comment:254 Changed 3 years ago by jdemeyer
comment:255 Changed 3 years ago by jason
I think both of those can be closed. The new config system is set up with IPYTHONDIR, which is in DOTSAGE. sage ipython should use that now.
comment:256 Changed 3 years ago by novoselt
Hello,
I just want to confirm that this is expected with this ticket:
  Sage Version 5.6, Release Date: 20130121   Type "notebook()" for the browserbased notebook interface.   Type "help()" for help.   sage: exit 'Use CtrlD (i.e. EOF), %Exit, or %Quit to exit without confirmation.' sage:
Was "just exit for exit" a feature of old IPython or Sage?
Changed 3 years ago by jdemeyer
comment:257 Changed 3 years ago by jdemeyer
 Description modified (diff)
 Status changed from positive_review to needs_work
comment:258 Changed 3 years ago by jdemeyer
 Status changed from needs_work to needs_review
12719_ipython_test.patch needs review
comment:259 Changed 3 years ago by vbraun
I don't know whats up with the overly attached Python interpreter but at least CtrlD works. Imho exit should just do that but that can be done (and doctested) on another ticket.
Jeroen's patch looks good to me.
comment:260 Changed 3 years ago by vbraun
 Status changed from needs_review to positive_review
comment:261 Changed 3 years ago by vbraun
 Description modified (diff)
comment:262 Changed 3 years ago by jdemeyer
The timeout on hawk of 221 still exists, I'll have a look.
comment:263 Changed 3 years ago by jdemeyer
This is the cause of the crash on hawk, it still has to do with the history database: http://boxen.math.washington.edu/home/buildbot/crashlogs/hawk_ipython_crash.log
comment:264 Changed 3 years ago by jdemeyer
 Status changed from positive_review to needs_work
We should probably disable the command history for the sage0() interface, but I don't know how one can do that.
comment:265 Changed 3 years ago by vbraun
Can be done in IPython with
ipython HistoryManager.hist_file=:memory:
comment:266 followup: ↓ 267 Changed 3 years ago by vbraun
How about we run sage0 with nodotsage?
comment:267 in reply to: ↑ 266 Changed 3 years ago by jdemeyer
Replying to vbraun:
How about we run sage0 with nodotsage?
No, having access to the IPython crash log would be good.
I'm preparing a patch, hang on...
Changed 3 years ago by jdemeyer
comment:268 Changed 3 years ago by jdemeyer
 Description modified (diff)
 Status changed from needs_work to needs_review
comment:269 Changed 3 years ago by jdemeyer
comment:270 Changed 3 years ago by vbraun
I've reported the issue upstream: https://github.com/ipython/ipython/issues/2845
comment:271 Changed 3 years ago by vbraun
 Status changed from needs_review to positive_review
Sounds good to me. I've verified that this disables caching. I don't have a harddisk that is slow enough to trigger the locking issue ;)
comment:272 Changed 3 years ago by jdemeyer
On sage.math, over NFS it's fairly easy to reproduce.
comment:273 Changed 3 years ago by jdemeyer
 Merged in set to sage5.7.beta1
 Resolution set to fixed
 Status changed from positive_review to closed
comment:274 Changed 3 years ago by jdemeyer
John Cremona reports on sagerelease:
jec@fermat%./sage   Sage Version 5.7.beta1, Release Date: 20130126   Type "notebook()" for the browserbased notebook interface.   Type "help()" for help.   ********************************************************************** * * * Warning: this is a prerelease version, and it may be unstable. * * * **********************************************************************  NameError Traceback (most recent call last) /home/jec/sage5.7.beta1/local/lib/python2.7/sitepackages/IPython/utils/py3compat.pyc in execfile(fname, *where) 176 else: 177 filename = fname > 178 __builtin__.execfile(filename, *where) /home/jec/.sage/init.sage in <module>() > 1 load /home/jec/sage/ecdb.py NameError: name 'load' is not defined
comment:275 Changed 3 years ago by jdemeyer
Volker Braun reports:
/mnt/storage2TB/patchbot/Sage/sage5.7.beta1/local/lib/python2.7/sitepackages/sage/misc/sage_extension.pyc in print_branch(self=<sage.misc.sage_extension.SageCustomizations object>) 423 def set_quit_hook(self): 424 """ 425 Set the exit hook to cleanly exit Sage. This does not work in all cases right now. 426 """ 427 def quit(shell): 428 import sage 429 sage.all.quit_sage() 430 self.shell.set_hook('shutdown_hook', quit) 431 432 def print_branch(self): 433 """ 434 Print the branch we are on currently 435 """ 436 from sage.misc.misc import branch_current_hg_notice, branch_current_hg 437 branch = branch_current_hg_notice(branch_current_hg()) > 438 if branch and not self.shell.test_shell: branch = 'Loading Sage library. Current Mercurial branch is: 0' self.shell.test_shell = undefined 439 print branch 440 441 def init_environment(self): 442 """ 443 Set up Sage commandline environment 444 """ 445 try: 446 self.shell.run_cell('from sage.all import Integer, RealNumber') 447 except Exception: 448 import traceback 449 print "Error importing the Sage library" 450 traceback.print_exc() 451 print 452 print "To debug this, you can run:" 453 print 'sage ipython i c "import sage.all"' AttributeError: 'SageInteractiveShell' object has no attribute 'test_shell'
comment:276 Changed 3 years ago by vbraun
I've created #14024 to collect any patches that we need on top of Sage5.7.beta1
comment:277 Changed 3 years ago by jdemeyer
 Description modified (diff)
comment:278 Changed 3 years ago by jdemeyer
Please have a look at #14042, another followup.
comment:279 Changed 3 years ago by jdemeyer
There is still this problem:
jec@fermat%./sage   Sage Version 5.7.beta1, Release Date: 20130126   Type "notebook()" for the browserbased notebook interface.   Type "help()" for help.   ********************************************************************** * * * Warning: this is a prerelease version, and it may be unstable. * * * **********************************************************************  NameError Traceback (most recent call last) /home/jec/sage5.7.beta1/local/lib/python2.7/sitepackages/IPython/utils/py3compat.pyc in execfile(fname, *where) 176 else: 177 filename = fname > 178 __builtin__.execfile(filename, *where) /home/jec/.sage/init.sage in <module>() > 1 load /home/jec/sage/ecdb.py NameError: name 'load' is not defined
comment:280 Changed 3 years ago by jason
#14066 was opened to deal with all remaining issues.
comment:281 Changed 3 years ago by jhpalmieri
How are users supposed to configure Sage's IPython now? See sagesupport. Right now, it looks like IPython's config files (either .sage/ipython0.12/profile_default/ipython_config.py or .sage/ipython0.12/profile_sage/ipython_config.py) are not loaded when Sage initializes its terminal. A possible solution:

sage/misc/interpreter.py
diff git a/sage/misc/interpreter.py b/sage/misc/interpreter.py
a b 672 672 673 673 def __init__(self, **kwargs): 674 674 # Overwrite the default Sage configuration with the user's. 675 from IPython.frontend.terminal.ipapp import load_default_config 675 676 new_config = Config() 676 677 new_config._merge(DEFAULT_SAGE_CONFIG) 677 678 new_config._merge(kwargs.get('config', Config())) 679 new_config._merge(load_default_config()) 678 680 kwargs['config']=new_config 679 681 super(SageTerminalApp, self).__init__(**kwargs) 680 682
Then .sage/ipython0.12/profile_default/ipython_config.py will be read and merged with Sage's configuration. Is this the right solution? Should I open a ticket? Or am I missing something?
comment:282 Changed 3 years ago by vbraun
Looks good to me
comment:283 Changed 3 years ago by jhpalmieri
See #14188.
See #12167 for a related ticket: how we deal with IPython configuration files.