Re: [sage-devel] Whitespace patchbombs

[R. Andrew Ohana]

If I recall, when I originally setup the git-trac server, I included a hook
that would reject/warn any introduction of new trailing whitespace. I
believe this was a compromise made after a long discussion at a Sage days
-- there were a lot of concerns at the time about the effort required to
rebase mercurial patches with conflicts arising from a whitespace
patchbomb. I also believe that we included in the documentation and server
side hook a suggestion to use the trailing whitespace stripping commit hook
(and there was a sage-dev command that would automatically do that,
although sage-dev has now been removed in favor of vanilla git or Volker's
git trac).

On Tue, Feb 20, 2018 at 12:47 PM, Jeroen Demeyer  wrote:

> Interesting fact: the number of lines with trailing whitespace is
> generally *increasing* with every Sage release. So it seems to me that the
> biggest problem (if you find whitespace a problem) is preventing new
> whitespace.
>
>
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Re: [sage-devel] Re: how we develop sage

[R. Andrew Ohana]

On Tue, Apr 12, 2016 at 12:50 PM, kcrisman  wrote:

>  It doesn't mean that the normal visible
>> public API of Sage changes
>> at all.   Why do you think otherwise?
>>
>
> Well, reading this thread made me think that.  Because I don't see how we
> enforce all those "other pieces" working nicely together, so some would
> (perhaps quite quickly) drop by the wayside.  You are right, as I
> apparently didn't make clear, that it would be even better to have people
> more easily able to have separate packages that are quite narrow - and I
> think that a testing framework like R has would probably suffice for this
> (as long as breaking such packages was a blocker for release!).  (There's
> also the CRAN versus RForge etc. question...) But I don't see how this is
> possible with the *current* Sage.
>
> > Cars are built out of parts.
>
> Yes, parts that are, despite parts suppliers not being the same as the car
> companies, those parts have high tolerances and highly controlled supply
> chains.  (Or so my brief experience with a parts supplier long ago
> suggests.)  All your examples of "mature open source development" are not
> the same in their goal as Sage, which apparently aims to have all of
> mathematics at its fingertips (in the way that Maple and Mathematica,
> though presumably not Magma or Matlab, seem to).
>

This also seems to be the crux of why some Sage developers are not
interested in breaking things up (as opposed to why they actively do not
want to break things up) -- namely that Sage should be a monolithic
application just like the Maple and Mathematica, and that is all it should
be.

While in the early days a lot of Sage's functionality was simply wrapping
other open source libraries, now there is quite a bit that can only be
found in Sage's library -- it seems to me only like the right thing to do
to make it so that others in the open source community could easily benefit
from our work just like we have benefited from theirs.

This doesn't conflict with our mission statement, as it is still perfectly
possible to create a interactive shell with tons of functionality from a
collection of libraries (again, Sage started as this).

As for the technical concerns of having a modular library, it seems the
biggest worry is that it will be too hard to orchestrate all of the
inter-dependent components of Sage. At this point, I'm not too concerned on
this front -- many projects in the past have solved these sorts of issues
and I don't think Sage is special in this regard. I would want to see a
more formal technical proposal (something along the lines of a SEP) before
I would feel comfortable criticizing such a proposal.


> That's a lot harder to disentangle than the dozen or more R packages I've
> had occasion to use are, and presumably also the case in non-mathematical
> software.  Modularity in Sage and resolving our import fiasco isn't the
> same thing as saying that every folder in Sage has to be a separate
> project, which is what you seem to be implying; though since I
> misunderstood the very first point, maybe I'm wrong about that too.
>
> As an example, take game_theory.  This is exactly the kind of "narrow"
> thing one might think would survive better as a modular bit that could be
> imported.  Which one of the programs in question it relies on (gambit) is,
> in terms of Python, of course.  Yet there is a lot of opportunity with
> being inside of "real" Sage for them with interconnections with all kinds
> of other combinatorial and plotting and other stuff that they would be hard
> put to keep current without being in the Sage library.  Having access to
> all that other math makes the game_theory stuff more powerful.  I am
> skeptical that math can be pared down to just a few pieces that everything
> else fairly loosely holds fast to.
>
> But like I said, if you or ODK or someone else can make this vision
> happen, as long as the end user still gets the kitchen sink without having
> to do some wacky import yoga or use possibly-broken packages, I'm not
> complaining!  "I also don't have a problem with things like psage or any
> other such packages" - and if you're right that my view on that is
> selection bias, I would be very happy to be wrong.  (Well, not really that
> happy, because people have worked hard and Sage has had weird upgrades that
> broke their stuff.  But you know what I mean.)  Bring on the automated
> testing!  :-)
>
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Re: [sage-devel] https on the wiki

[R. Andrew Ohana]

On Wed, Jan 20, 2016 at 5:27 PM, William Stein  wrote:

> Hi,
>
> I thought about this some more today: I personally have zero interest
> or time for personally running wiki.sagemath.org anymore.  It's just
> been coasting for the last year or two.  The moment some spammer takes
> it over, the UW would just take it offline.   The only ways forward
> are either (1) somebody volunteers to take over running the site, or
> (2) we move to github's wiki pages.
>
> Right now I'm trying to find somebody who even remembers their
> password for sudo ssh on wiki.sagemath.org...
>
> Don't tell me (2) isn't possible.  If nothing else, we could just do a
> static dump of the site which would be hosted as part of
> www.sagemath.org, then start fresh with github (maybe copy over a few
> key things that get used a lot, e.g., upcoming sage days and maybe the
> interacts).
>

For (2), Chris Swenson and I did some experiments [1] a couple years ago
and it worked reasonably well. It is probably a decent place to start for
anyone interested in going in that direction.

[1] https://github.com/swenson/sagewiki


>
>  -- William
>
> On Wed, Jan 20, 2016 at 6:58 AM, William Stein  wrote:
> > On Wed, Jan 20, 2016 at 3:21 AM, mmarco  wrote:
> >> Since wiki.sagemath.org requires login for editing (that is, sending
> the
> >> password through the internet)... ¿shouldn't that be done through https?
> >
> > Yes.
> >
> >> On a related note, the certificate for trac.sagemath.org that I am
> getting
> >> is expired, and self-signed
> >
> > I think it always has been self-signed...
> >
> >> Could we get a certificate (for instance, from www.letsencrypt.org )
> that
> >> doesn't scare people away from using secure connections?
> >
> > That would be great.
> >
> > Are you volunteering to do everything?
> >
> > William
> >
> >>
> >> --
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> >
> >
> >
> > --
> > William (http://wstein.org)
>
>
>
> --
> William (http://wstein.org)
>
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Re: [sage-devel] Re: status on Python3

[R. Andrew Ohana]

At this point it all of sage's dependencies build with python 3, so if you
do the following

SAGE_PYTHON3=yes make

it will fail building some cython module in the sage library.

On Sat, Nov 14, 2015 at 7:45 PM, Nathan Dunfield 
wrote:

> can someone summarize the status on making SageMath Python3 compatible?
>> (...or more provocatively: When will SageMath start using Python3?)
>
>
> See
>
> http://trac.sagemath.org/ticket/15530
>
> and tickets 15980 and 16052 referenced therein.
>
> Best,
>
> Nathan
>
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Re: [sage-devel] Re: access denied on git

[R. Andrew Ohana]

You are using the read only git url, you need to use the ssh url to be able
to push. You can either add a new remote:

git remote add trac g...@trac.sagemath.org:sage.git

or modify your current remote:

git remote set-url origin g...@trac.sagemath.org:sage.git


On Mon, Sep 21, 2015 at 7:16 PM, Mike Zabrocki 
wrote:

> With some further experimenting I find that I can push from my old copy of
> sage (but I can't compile there).
>
> I can edit and compile on one copy of sage and push with another.  This is
> an awkward setup, but at least I can some edits to a ticket done.
> -Mike
>
>
> On Monday, 21 September 2015 21:57:10 UTC-4, Mike Zabrocki wrote:
>>
>> You are right that running Xcode did install the command line tools, but
>> that did not seem to fix the problem.
>> I continue to get the "fatal: remote error: access denied or repository
>> not exported: /sage.git" message.
>> -Mike
>>
>> On Monday, 21 September 2015 21:21:45 UTC-4, John H Palmieri wrote:
>>>
>>>
>>>
>>> On Monday, September 21, 2015 at 5:54:05 PM UTC-7, Mike Zabrocki wrote:

 I mistakenly installed XCode 7 and so to save myself I started working
 on a fresh copy of sage where I don't do too much compiling.

>>>
>>> Have you tried running Xcode once? It will install some command-line
>>> tools, and that may be what is necessary.
>>>
>>>   John
>>>
>>>
>>>
>>>

 In doing so I seem to have messed up my permissions to access git (or
 something).  I can checkout any branch I like, but I can't seem to push.

 $ git push

 fatal: remote error: access denied or repository not exported: /sage.git

 I thought it might be my ssh key, but I can authenticate:

 $ ssh g...@trac.sagemath.org info

 hello zabrocki, this is git@trac running gitolite3 (unknown) on git
 1.7.9.5


  R W sage

 Does anyone have an idea about what I am doing wrong?

 Thanks.
 -Mike

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Re: [sage-devel] Re: *.math.washington.edu hardware resources

[R. Andrew Ohana]

I just updated the project with some excel + csv files with a much more
indepth inventory.

Also, concerning ansible -- this is what I used when working on things this
summer (see https://github.com/ohanar/sagemath.org). I found that when you
use any well supported plugin, using ansible was very pleasant, but once
you stepped outside of the ecosystem -- it got to be a pain very quickly. A
lot of this can be solved by writing your own plugins, but I found that to
also have quite a learning curve (ansible does some python magic that
defines various global variables in your modules).

An alternative to look at is saltstack -- it is also written in python, and
also uses yaml as its primary configuration format. I've heard writing
plugins for it is simpler as well, but I haven't investigated it thoroughly.

On Wed, Sep 16, 2015 at 2:08 PM, kcrisman  wrote:

>
>
> Please try to understand, once again, that you are at CNRS in a very
>> fortunate and exceptional position, and many people are much less
>> lucky. Try to get a grant and manage it to see my point :-)
>>
>>
>>
> And (not speaking to Nathann or anyone else) try it when teaching a 3-3 or
> 4-4 load at a place where teaching by far is the main component to
> tenure... I am hoping that more and more of them will do like Greg Bard did
> and write a Sage teaching book, but that will take time (and maybe MBX!).
> But for developing it's a real challenge to find that reliable time.
>
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Re: [sage-devel] Re: *.math.washington.edu hardware resources

[R. Andrew Ohana]

As William mentioned, I don't really have the time to work on administering
the cluster, but I would be happy to part of the initial discussions (e.g
what I was planning on doing if I had the time, why I chose centos,
in-depth inventory of hardware, etc).

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Re: [sage-devel] Re: Please redirect the old homepage of my cohomology spkg

[R. Andrew Ohana]

Sage.math points to wstein.org (as per an earlier request by William). As
far as I'm aware, he is the only one with credentials to that system, I
certainly don't have access.

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Re: [sage-devel] Access to my cohomology spkgdocumentation is blocked

[R. Andrew Ohana]

Everybody was warned that things would go down back in April, so you should
have dealt with it awhile ago (but apparently didn't).

We can easily setup a redirect on the VM that hosts wstein.org (which is
where sage.math.washington.edu redirects to) if you find a place to host
your site. If your site is too big to host on github or the like, and we
can setup a vm for it (assuming your site falls within what is allowed by
the UW). If you need to get files, you can still access your home directory
from geom.math.washington.edu or comhinat.math.washington.edu.

(The same goes for anyone else who hosted things off of boxen.)

On Fri, Aug 28, 2015 at 02:15 Simon King simon.k...@uni-jena.de wrote:

 Hi!

 It was pointed out on sage-support that
 http://sage.math.washington.edu/home/SimonKing/Cohomology/
 is not available. That's bad, because the documentation of my
 optional group cohomology spkg is hosted there, the new
 to-be-reviewed version of the spkg is hosted there (I am afraid
 that the old versions would not work, because of backward incompatible
 changes in Sage), and as soon as I change the spkg to the new format,
 the upstream sources will be hosted there (at least I think it would
 be a logical place).

 How can that be solved? I don't think hosting it in Jena is a solution,
 since I am about to move to Cologne.

 Best regards,
 Simon


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Re: [sage-devel] Trac vs Wiki passwords

[R. Andrew Ohana]

On Sat, Aug 22, 2015 at 4:22 AM, Thierry sage-googlesu...@lma.metelu.net
wrote:

 Hi,

 trac and wiki accounts used to be linked (same username, same password). I
 changed my password on trac and it worked, but i can not use it on the
 wiki. Unfortunately, i am travelling and i do not have access to my
 previous password. How are the two system currently related ?


Not at all. You can't currently change your wiki password. Basically
through a series of hacks, we had hooked the wiki's authentication up to
trac, but I think that broke when the wiki was moved off of boxen last
summer.

On a slight tangent: I personally don't care for our current wiki,
MediaWiki -- it has caused us numerous issues over the years (e.g. memory
hog on boxen), and is a bit of a pain to administer. I'm not really aware
of any modern wiki platforms (other than gollum, which didn't handle large
wikis like ours when I checked it out 1.5 years ago), but if anyone has any
thoughts on the matter I would be happy to discuss it (maybe in a different
thread).



 Ciao,
 Thierry

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Re: [sage-devel] Trac vs Wiki passwords

[R. Andrew Ohana]

On Sat, Aug 22, 2015 at 10:07 PM, William Stein wst...@gmail.com wrote:

 On Sat, Aug 22, 2015 at 8:55 PM, R. Andrew Ohana andrew.oh...@gmail.com
 wrote:
 
 
  On Sat, Aug 22, 2015 at 4:22 AM, Thierry 
 sage-googlesu...@lma.metelu.net
  wrote:
 
  Hi,
 
  trac and wiki accounts used to be linked (same username, same
 password). I
  changed my password on trac and it worked, but i can not use it on the
  wiki. Unfortunately, i am travelling and i do not have access to my
  previous password. How are the two system currently related ?
 
 
  Not at all. You can't currently change your wiki password. Basically
 through
  a series of hacks, we had hooked the wiki's authentication up to trac,
 but I
  think that broke when the wiki was moved off of boxen last summer.
 
  On a slight tangent: I personally don't care for our current wiki,
 MediaWiki
  -- it has caused us numerous issues over the years (e.g. memory hog on
  boxen), and is a bit of a pain to administer. I'm not really aware of any
  modern wiki platforms (other than gollum, which didn't handle large wikis
  like ours when I checked it out 1.5 years ago), but if anyone has any
  thoughts on the matter I would be happy to discuss it (maybe in a
 different
  thread).

 What about

 https://github.com/sagemath/sage/wiki


Github's wiki is gollum.




 William

 
 
 
  Ciao,
  Thierry
 
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Re: [sage-devel] trac authentication failures

[R. Andrew Ohana]

Password reset on our trac instance doesn't work (and I have looked into it
a few times and haven't been able to figure out why it is broken).

I can create a temporary password for you manually and send it to you (at
which point you should be able to change your password from your user
preferences without issue).


On Fri, Aug 21, 2015 at 3:35 PM, AlexGhitza aghi...@gmail.com wrote:

 Hi,

 I tried logging into trac today after a long time away, and failed.
 Thinking that I had just forgotten my password, I asked for a password
 reset, and then retried with the automatically generated password that trac
 emailed me.  Still getting an authentication failure.

 Thoughts?


 Best,
 Alex

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Re: [sage-devel] trac chronic health problem

[R. Andrew Ohana]

There was a cron job setup for cleaning /tmp, but I just looked and it
seems like it was disabled... I re-enabled it and manually cleaned it at
the same time.

On Sun, Aug 16, 2015 at 6:48 AM, Vincent Delecroix 
20100.delecr...@gmail.com wrote:

 Hello,

 Again...

 
 Trac detected an internal error:

 OSError: [Errno 2] No such file or directory: '/tmp/tmpVRSiHH'
 

 Wouldn't be possible to set a cron job cleaning /tmp/?

 Vincent

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Re: [sage-devel] Re: Trac Server Issue

[R. Andrew Ohana]

This should now be resolved.

On Sun, Aug 16, 2015 at 6:10 PM, Kwankyu Lee ekwan...@gmail.com wrote:

 I looked into this thread because I have the same issue with the following
 ticket.

 http://trac.sagemath.org/ticket/18807

 Anyway, your ticket URL seems to have no problem :-)

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Re: [sage-devel] Trac notifications (was Re: Mutability of matrices with no entries)

[R. Andrew Ohana]

On Aug 1, 2015 13:21, Michael Orlitzky mich...@orlitzky.com wrote:

 On 07/31/2015 07:51 PM, Andrey Novoseltsev wrote:
  Hello,
 
  While working on http://trac.sagemath.org/ticket/18613 I ran into the
  following problem:

 Argh, the trac notifications still aren't fixed. Can someone please add
 a reverse DNS entry for 128.208.160.253 (the server that's sending the
 notifications)? The PTR should be trac.sagemath.org since that's the
 name the server is saying HELO with.

I've made a request to UW to add the DNS entry (since they are effectively
our ISP), but they like to take their time. I finally got a response on the
ticket I opened last night, so hopefully this will be resolved soon.


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Re: [sage-devel] Re: no trac mail notifications?

[R. Andrew Ohana]

Trac's ip address changed on Saturday, which that might have broken
something with the email signature. I'll take a look later today.
On Jul 20, 2015 10:27, Benjamin Hackl benjamin.ha...@aau.at wrote:

 Our mail system alters the subject (probably since today; wasn't like that
 last Thursday) like this:

 ***EVENTUELL*SPAM*** [4.979 / 4] Re: [sage-trac]

 Maybe this helps someone.

 All the best,
 Benjamin

 Am Montag, 20. Juli 2015 19:21:15 UTC+2 schrieb Daniel Krenn:

 Am 2015-07-20 um 19:08 schrieb Benjamin Hackl:
  ... might be just here at AAU. I found my notifications in the spam
 folder.

 I do not use the @aau.at address.

 Could there have been changes in trac's mails so that some servers do
 not accept the mails (or declare them as spam)?

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Re: [sage-devel] Re: Server Relocation

[R. Andrew Ohana]

Most of these sites should now be back up. The patchbot still needs a
little bit of setup (from Robert and Frederic), so it will be down until
they have a chance to look at it.

On Sat, Jul 18, 2015 at 9:26 AM, William Stein wst...@gmail.com wrote:



 On Friday, July 17, 2015, R. Andrew Ohana andrew.oh...@gmail.com wrote:

 Small update, we will be starting at around 8 AM PST tomorrow.

 On Sat, Jul 11, 2015 at 18:40 R. Andrew Ohana andrew.oh...@gmail.com
 wrote:

 Due to lack of funding (as previously mentioned by William), the servers
 that are currently hosting a number of the sagemath sites will need to be
 relocated. We are currently planning on doing this next Saturday (i.e.
 Saturday July 18), exactly when and for exactly how long is not quite
 clear, but you can probably expect things to be down for a few hours.

 List of sagemath sites that will be down:

 trac.sagemath.org
 git.sagemath.org
 wiki.sagemath.org
 files.sagemath.org
 files.old.sagemath.org
 patchbot.sagemath.org


 In addition, boxen.math.washington.edu will finally be going offline,
 and due to lack of space won't be coming back (at least for now). I am
 working on setting up a new cluster of machines for sage development (and
 for math research a little later down the road) using the old SMC cluster
 (which consists of around 20 machines).



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[sage-devel] Re: Server Relocation

[R. Andrew Ohana]

Small update, we will be starting at around 8 AM PST tomorrow.

On Sat, Jul 11, 2015 at 18:40 R. Andrew Ohana andrew.oh...@gmail.com
wrote:

 Due to lack of funding (as previously mentioned by William), the servers
 that are currently hosting a number of the sagemath sites will need to be
 relocated. We are currently planning on doing this next Saturday (i.e.
 Saturday July 18), exactly when and for exactly how long is not quite
 clear, but you can probably expect things to be down for a few hours.

 List of sagemath sites that will be down:

 trac.sagemath.org
 git.sagemath.org
 wiki.sagemath.org
 files.sagemath.org
 files.old.sagemath.org
 patchbot.sagemath.org


 In addition, boxen.math.washington.edu will finally be going offline, and
 due to lack of space won't be coming back (at least for now). I am working
 on setting up a new cluster of machines for sage development (and for math
 research a little later down the road) using the old SMC cluster (which
 consists of around 20 machines).



 --
 Andrew


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Re: [sage-devel] Server Relocation

[R. Andrew Ohana]

On Sun, Jul 12, 2015 at 6:02 AM, Jeroen Demeyer jdeme...@cage.ugent.be
wrote:

 On 2015-07-12 03:40, R. Andrew Ohana wrote:

 In addition, boxen.math.washington.edu
 http://boxen.math.washington.edu will finally be going offline, and
 due to lack of space won't be coming back (at least for now).


 Important question: what will happen with the data currently stored on
 boxen? Will you transfer it to the new machine?


It depends on what you mean by data currently on boxen. Do you mean things
under /home? If so then that will still be accessible on
geom.math.washington.edu and mod.math.washington.edu for the time being, as
it actually a network filesystem being exported from another machine.

My plan is to mount it as read only for a bit on the new machines, but
after a period of time (probably a couple of months) the storage machine of
the current/old sage cluster will be repurposed as a backup machine, at
which point I'll make a final snapshot of the /home directory on an
external usb drive.


Anything lying on the root and scratch filesystems on boxen will be wiped.


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[sage-devel] Server Relocation

[R. Andrew Ohana]

Due to lack of funding (as previously mentioned by William), the servers
that are currently hosting a number of the sagemath sites will need to be
relocated. We are currently planning on doing this next Saturday (i.e.
Saturday July 18), exactly when and for exactly how long is not quite
clear, but you can probably expect things to be down for a few hours.

List of sagemath sites that will be down:

trac.sagemath.org
git.sagemath.org
wiki.sagemath.org
files.sagemath.org
files.old.sagemath.org
patchbot.sagemath.org


In addition, boxen.math.washington.edu will finally be going offline, and
due to lack of space won't be coming back (at least for now). I am working
on setting up a new cluster of machines for sage development (and for math
research a little later down the road) using the old SMC cluster (which
consists of around 20 machines).


-- 
Andrew

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Re: [sage-devel] The future of polybori

[R. Andrew Ohana]

On Sat, Jun 13, 2015 at 5:21 AM, 'Martin Albrecht' via sage-devel 
sage-devel@googlegroups.com wrote:

 Hi all,

 On Saturday 13 Jun 2015 10:41:15 Francois Bissey wrote:
  I think Andrew has already done quite a bit of the porting to autotools
 and
  some python 3 fixes. But neither he or I want to be a maintainer - at
 least
  for the long term.

 ah, sorry that I missed that. Great! How about this:

 1. We create an organisation on GitHub PolyBoRi3


 2. We move Andrew's current version over there


I can do this. I might also rebase a few of the commits while doing so (to
ease the review process), and probably rename it to BRiAl as per
Alexander's suggestion.


 3. I volunteer to be *a* maintainer, help would greatly be appreciated


I can add you to the github organization as an owner when I make it.


 I envision that it would be good to split PolyBoRi up roughly as follows to
 make maintenance simpler (please do tell me if this is silly). This way we
 keep dependencies of Sage as external dependencies and don't have to suck
 large parts into the Sage library proper:

 - polybori-core (libpolybori, Cudd, groebner (?))

 the C++ stuff that doesn't involve python at all. This would be a standard
 package in Sage (hopefully) and autotoolised.


The autotoolisation of this stuff is basically done. Mainly the testsuite
needs to be included.



 - polybori-python-binding-boost (PyPolyBoRi)

 the C++ boost stuff which does the Python bindings. This is not used by
 Sage -
 I believe - so we don't care much. Autotoolised, but not a priority,
 because
 Sage has its own Cython bindings reimplementing this stuff.


I think the main reason why Sage has its own Cython bindings is mainly
historical -- they existed before polybori added their own python bindings.
It would probably be a better idea to use polybori's own bindings in Sage
-- it makes no sense trying to maintain two sets of python bindings.


 - polybori-python

 The Python stuff which can be managed by distutils or whatever the kids are
 using now. This could in principle be an optional package, but I guess it
 might as well be standard given that's pure python and relatively small.

 Cheers,
 Martin

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Re: [sage-devel] The future of polybori

[R. Andrew Ohana]

On Thu, Jun 11, 2015 at 2:42 PM, Alexander Dreyer 
jan.alexander.dre...@gmail.com wrote:

 From my point of view a fork - or better call it sequel - would be the
 best.

 Unfortunately, all original developers like me went to industrial
 positions, which are completely unrelated to PolyBoRi or any kind of
 algebraic software.
 Meanwhile, family and the new jobs don't leave us time to work on pet
 projects. So, the real active branch is the ohanar github repository.

 At that repository, I already see great work in autotools support. I would
 adopt this for sure if I ever get the chance to get back to work on
 PolyBoRi. For the unlikely case of sudden freetime I would rather
 contribute to the new project than trying to resurrect the old one. ;-)

 However, to avoid confusion, you should rename your fork. Use TOSSFKAP or
 BRiAl or whatever you like to distinuish the projects.


Yes, I agree, I just didn't have a good name. Do you have a particular
favorite (and we could just use that).


 Also, I have to note, that in the autotools branch some headers from
 original Cudd were reintroduced.


Which ones exactly? I exported the mercurial repository into git and double
checked the files, but didn't notice any new headers.



 This might be a problem since some were intentionally left out due to
 unclear licenses. This had been suggested by the debian people some time
 ago.

 Best regards and good luck,
   Alexander

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Re: [sage-devel] The future of polybori

[R. Andrew Ohana]

On Fri, Jun 12, 2015 at 5:34 AM, 'Martin Albrecht' via sage-devel 
sage-devel@googlegroups.com wrote:

 Hi,

 so, the Singular team *wants* to keep PolyBoRi alive, but it's currently
 not
 clear if and when they *can* devote resources to it. This will be clarified
 over the next few months it seems.



What about this:

Now: We work on making polybori an optional package in sage.
  * At least going by this thread, the number of people who use polybori in
Sage is small enough for it to make sense to have polybori as an optional
package.
  * (I looked into this before I did the autotoolization) It shouldn't take
too much work to optionalize polybori -- the main effort will be its uses
in the crypto code.
  * Polybori is the sole dependency of Sage that doesn't at least build
against python 3 -- getting past this last major hurdle will make it much
easier to work on porting the actual sage library to python 3.

Future: The Singular team or whoever dedicates the time to maintain a
sequel to polybori.
  * This will be required once we stop supporting python 2 in the very
distant future (at least after 2020, which is the EOL for python 2).



 Cheers,
 Martin

 On Friday 12 Jun 2015 10:14:53 Martin Albrecht wrote:
  I started talking to some people from the symbolic computation community
 to
  discuss options (e.g. if someone wants to take over maintenance). Hence,
  don't rush to a conclusion please, I'd really like to keep PolyBoRi
 around
  somehow but don't want to be (sole) maintainer.
 
  Cheers,
  Martin
 
  On Thursday 11 Jun 2015 20:45:41 William Stein wrote:
   On Thursday, June 11, 2015, Ralf Stephan gtrw...@gmail.com wrote:
So folks, be careful when you fork---you might end up as maintainer.
  
   Good point.  I think we should either
  
   1. Remove polybori or
  
   2. Have a specific person (or persons) step up to be maintainer.
  
   I'm fine with either option.
  
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Re: [sage-devel] The future of polybori

[R. Andrew Ohana]

On Wed, Jun 10, 2015 at 6:40 PM, François Bissey 
francois.bis...@canterbury.ac.nz wrote:

 Hi all,

 over at http://trac.sagemath.org/ticket/18437 we have
 some heated debate about what to do about polybori.

 Let me summarize the situation.
 * at this moment polybori is dead upstream
 * polybori is the last package using scons
 * is one of the last packages, if not the last, not
 ready for python 3.x
 * polybori is actually python wrapper over another
 package called CUDD which is included in polybori
 and scons-ified.


This is a off, polybori is its own c++ library -- cudd is merely a
dependency (and polybori doesn't even use much of it). It is true that
polybori ships its own version of cudd (almost certainly because cudd's
build system is atrocious).


 There is a strong debate about what to do about
 the situation.

 * fork upstream and keep it as a separate package but
 no one really wants to be the maintainer.


I think Jeroen and I agree that we need to fork polybori -- the debate is
more in the details.



 * autotool CUDD (Andrew Ohanar prodded upstream to
 see if they would be willing to adopt any autotooling
 we provide without answer so far)


Upstream cudd has gotten back to me now, they are apparently planning a new
release sometime this summer which uses autotools for its build system.


 and move the
 python binding in sage itself making its maintenance
 a shared task amongst sage dev. CUDD would become
 a standard package to replace polybori. Note it is
 currently shipped inside polybori so it is not something
 new.

 * Hybrid in between those two.

 More details on the ticket. I would very much would
 go with autotooling CUDD and move the wrapper.
 The fork of polybori would also move to autotool
 as its build system at this stage.

 Because of strong opinions on the ticket and the burden
 of the various options, Jeroen pointed out that we
 should get some kind of consensus here before moving
 forward.

 So we would very much want to hear from other devs
 on what to do with polybori.

 Francois

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The main debate is around what we should do with the python bindings for
polybori. From the ticket:


As I see it there are three routes we could go with polybori:

   1. We adopt the route that we took with Pynac (as a fork of Ginac). Our
   fork might in the future become tightly coupled with Sage, but we maintain
   it as a separate package outside of Sage.
   2. We make a minimal fork, only include the minimal changes necessary to
   build polybori without scons. If more substantive changes are needed, we
   include those in the Sage library.
   3. A hybrid approach: maintain a minimal fork, and a maintain a set of
   patches for more substantive changes.


I would personally vote for 1 or 2, and very much against 3. Some pros and
cons of the various proposals I mentioned:

Pros of 1:

   - We already have pursed this model with Pynac.
   - It allows us to modify the c++ code in polybori if we need to.

Cons of 1:

   - Maintenance of Pynac has lapsed as people have gotten busy.
   - (From Jeroen) It isn't held to the same standard as our normal review
   process for Sage.


Pros of 2:

   - It distributes the burden of maintenance across the whole Sage
   community (in particular, it is easier for a Sage contributor to work on)
   - Polybori's bindings does things a bit differently if it is in a Sage
   environment (we included polybori before it had python bindings)


Con of 3:

   - Maintaining patches is more work than maintaining a forked version of
   the code (especially when upstream is dead).


If anybody has any better suggestions or thoughts on the matter, I would be
very open to hear them.

For what its worth, the hard part of making the autotools based build
system is done (at least for the components of polybori that Sage uses). At
this point it is mainly a matter of how we want to deal with the python
bindings, which will need to be updated to work with python 3.
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Re: [sage-devel] Re: How does trac's automerging work?

[R. Andrew Ohana]

If you want to know exactly how it is currently working, it is this one line

https://github.com/sagemath/sage_trac_plugin/blob/dddc41b60a7620ebe0e224973497d83c719d9cd9/sage_trac/git_merger.py#L92

(the rest of that function deals with trivial merges, and writing
unreferenced objects back to trac's git repository)

On Thu, May 28, 2015 at 12:39 AM, Volker Braun vbraun.n...@gmail.com
wrote:

 The commandline git client is better at merging, so sometimes it succeeds
 where pygit2/libgit2 fails.



 On Thursday, May 28, 2015 at 8:42:46 AM UTC+2, Jeroen Demeyer wrote:

 Hello,

 I frequently see red links on Trac git branches with the message
 trac's automerging failed. But when I try to merge with latest develop
 using the git command line, the merge succeeds without conflicts. Why is
 this? What does the Trac git plugin do to merge?

 And a different problem is that ticket dependencies aren't taken into
 account, but I know I lost that battle long ago.

 Jeroen.

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[sage-devel] Python 3 and the sage notebook

[R. Andrew Ohana]

In the interest of reducing the work required for supporting Python 3,
unless there is some champion out there who wants to do the hard work
making sagenb work with Python 3, the sage notebook will not be joining the
rest of sage with Python 3.

So, with that said, is there anyone interested in porting (and maintaining)
sagenb to python 3?

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Re: [sage-devel] Re: Python 3 and the sage notebook

[R. Andrew Ohana]

On Tue, May 26, 2015 at 11:53 AM, kcrisman kcris...@gmail.com wrote:




 In the interest of reducing the work required for supporting Python 3,
 unless there is some champion out there who wants to do the hard work
 making sagenb work with Python 3, the sage notebook will not be joining the
 rest of sage with Python 3.


 That would be really bad for backward incompatibility unless you mean
 Sage will support Python 2 and 3, but the notebook will only run under
 3.  Even the likely-appearing SMC personal edition is really not the
 same.


I mean that you will continue to be able to use sagenb under Python 2
(which Sage should support for a good long while), but unless someone ports
sagenb to also work under Python 3, then you will not be able to use sagenb
with sage on sagenb when you build sage with Python 3.



 So, with that said, is there anyone interested in porting (and
 maintaining) sagenb to python 3?


 https://github.com/sagemath/sagenb/issues/343

 I mean, how many Python 2-isms can there be in sagenb?   (Other than
 formatting, which we've already been trying to encourage people to switch
 over - I don't know that there are a lot of print statements.  Presumably
 there are other things.)

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Re: [sage-devel] Re: Is Sage living in a state of emergency ?

[R. Andrew Ohana]

On Mon, May 18, 2015 at 9:29 AM, William Stein wst...@gmail.com wrote:

 On Mon, May 18, 2015 at 8:37 AM, Thierry
 sage-googlesu...@lma.metelu.net wrote:
  Hi,
 
  On Mon, May 18, 2015 at 01:49:22AM -0700, Harald Schilly wrote:
   Is Sage living in a state of emergency ?
 
  Yes
 
  OK, so we should just breathe, give more details about the issue, call
 for
  help, and work all together. The Sage community is pretty wide, and
  hosting a VM is not a big deal for a university.

 Harald also submitted a $5K grant application to Google for Sage (not
 SageMath, Inc.) last week, which would pay all hosting easily for a
 while.  We haven't heard back yet from Google about that.We also
 may use the GSoC mentor stipends (about $2K) to cover hosting for a
 while.

 
  There were emails about this, for weeks. tl;dr: power button - off
 
  Could you please provide more details, in particular what is far from
  clear to me is which services are affected with this shut down. I do not
  want other services like git/trac/wiki/ask/... leave our hands just
  because we did not find time to turn over.

 I'm optimistic that this won't happen.  I don't necessarily have
 control though, and I strongly recommend that we get organized and
 move all services out of UW.

  Having the control of our
  infrastructure is pretty important (i do not want to think of what mess
  will happen when googlegroups will be shut up by lack of income (as
  googleID did recently)).

 googleID --  openid.  It was not shut down due to lack of income, but
 because there is a much better replacement that has been around for
 years.  Google didn't want to support an old and broken auth system,
 when they are also supporting a much better one.   They provided a lot
 of time for people to switch, and a message on every login.  The issue
 for sagenb at least was that -- despite repeated requests and emailing
 like 20,000 people (!) -- nobody actually had the time, resources, and
 expertise to take over sagenb and redo the auth system in time.   That
 did change though, and somebody has volunteered to do it, and I expect
 to see sagenb appear again sometime this summer (when they aren't busy
 teaching).

  I started a page on the wiki about our infrastructure so that we are less
  blind, as you will see, there are quite a few points that i could not
  discover myself.
 
  http://wiki.sagemath.org/Infrastructure
 
  Please do not hesitate to fill missing and incorrect entries if you know
  more. Also, please point which service will be affected by the shutdown,
  and the ressources required to maintain them.
 
  Representatives of universities are here? I didn't know that.
 
  There are a lot of permanent researchers/teachers from all over the world
  here, and as such, they can ask for some support to their institution.
 
  To give some recent sucessful examples:
  - Ohio State University is now hosting ask.sagemath.org
  - University of Frankfurt is now hosting sagecell.sagemath.org
 
  This is the right way. Decentralization of services among various
  universities is sustainable as they will not shut up simultaneously.
 
  Indded, we have lost ask.sagemath.org for quite a long time and public
  notebooks on sagenb.org forever because some spam on those could imply
  total shutdown on other services, this would not happend in a more
  distributed system.

 Having people volunteer to host things at random universities won't
 solve the problem above in the least.  You would need to also rewrite
 the relevant services, e.g., ask, sagecell, sagenb, etc., to be
 decentralized.  This is not easy in some cases...

 It's also worth keeping in mind that people may offer to host services
 at their university, unaware that what they are doing might
 potentially violate rules.  At least, I know from personal experience
 that this could be an issue..  It's interesting to compare:

 1. Univ of Washington's policy on use of equipment at [1] --

 with

 2. Google's cloud computing use policy at [2] -- basically, don't
 send spam or break the law.

 Regarding 1, UW's policy says University resources, including
 facilities, computers, and equipment, may not be used for [...]  for
 personal benefit or gain, or for the benefit or gain of any other
 individuals or outside organizations. [...] Supporting, promoting, or
 soliciting for an outside organization or group unless otherwise
 provided by law and University policy.[...] Assisting an election
 campaign, promoting or opposing a ballot proposition or initiative, or
 lobbying the state legislature.[...] Advertising and selling for
 commercial purposes. [...] online book sales or referral links to book
 publishers or sales houses.

 Wow, every time I look at [1] I realize there's another rule I didn't
 know about that is frequently violated.  For example the last rule
 mentioned above seems to say that if I publish something, I can't
 provide a link to the publisher.  That's frustrating given that
 publishers 

Re: [sage-devel] Re: trac errors out on some tickets

[R. Andrew Ohana]

There is some permissions issue with the git repository. Working on it...

On Wed, Apr 15, 2015 at 12:28 PM, Dima Pasechnik dimp...@gmail.com wrote:

 /tmp or some other filesystem ran out of space?


 On Wednesday, 15 April 2015 20:09:54 UTC+1, vdelecroix wrote:

 contamination...

 http://trac.sagemath.org/ticket/17818

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Re: [sage-devel] Re: trac errors out on some tickets

[R. Andrew Ohana]

Ok, hopefully it is fixed now. It looks like it is a bug in git (at least
the version that is on the trac server), see [1].

[1]
http://git.661346.n2.nabble.com/Problems-with-stale-keep-files-on-git-server-td6226633.html

On Wed, Apr 15, 2015 at 1:02 PM, R. Andrew Ohana andrew.oh...@gmail.com
wrote:

 There is some permissions issue with the git repository. Working on it...

 On Wed, Apr 15, 2015 at 12:28 PM, Dima Pasechnik dimp...@gmail.com
 wrote:

 /tmp or some other filesystem ran out of space?


 On Wednesday, 15 April 2015 20:09:54 UTC+1, vdelecroix wrote:

 contamination...

 http://trac.sagemath.org/ticket/17818

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Re: [sage-devel] Re: compatibility with fink, homebrew and macports under OS X

[R. Andrew Ohana]

Homebrew tries to avoid exposing headers and libraries for packages that
are already bundled with OS X or have alternatives on OS X (e.g. readline
vs libedit) by installing such packages into what they call Cellars. At
least in my personal experience, this has been successful, however I've
installed homebrew under my home directory (rather than the recommended
/usr/local) which is almost certainly helping the situation.

As far as Sage is concerned, I've only had one compatibility issue: In the
gcc SPKG we work around a bug in one of the headers in OS X 10.10 that
causes a few packages to fail to build correctly. Since Sage sees that I
have a usable gcc, it decides it doesn't need to install its own copy of
gcc, which means I don't get the fixed header. See
http://trac.sagemath.org/17169#comment:47 and comment 49.


On Fri, Apr 10, 2015 at 3:11 AM, Volker Braun vbraun.n...@gmail.com wrote:

 As far as I know it doesn't work, you'll get odd build failures. IMHO we
 should

 a) look for brew/port/... in the path and scrub the corresponding
 environment variables (including PATH) if found

 b) test it: right now we have one OSX build bot and I haven't installed
 any extra global cruft. Ideally we'd have independent buildbots for testing
 with extra crud littered in the file system.




 On Friday, April 10, 2015 at 11:15:01 AM UTC+2, Samuel Lelievre wrote:

 Under OS X, what is the state of compatibility of Sage
 with fink, homebrew and macports?

 Is there a trac ticket devoted to complete compatibility?

 Are there tricks to toggle off visibility of fink, homebrew
 and macports when building Sage, and toggle it back on
 when done building Sage?

 Could we have a Building Sage under OS X page
 in the wiki or in the developer guide, linked to from
 the main developer page at

 http://www.sagemath.org/doc/developer/

 and maybe from the readme at

 http://boxen.math.washington.edu/home/sagemath/sage-mirror/
 src/README.txt

 (if only to say that everything should work, if that is the case)?

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Re: [sage-devel] Re: Python 3 focused Sage Days

[R. Andrew Ohana]

On Thu, Jan 8, 2015 at 5:38 PM, kcrisman kcris...@gmail.com wrote:

 All our dependencies have proper support for Python 3,


 What about 17 and 18 at http://trac.sagemath.org/ticket/15530?


Yes, you are right. I had forgotten about those when I posted this. 17
(scons) only exists because of 18 (polybori) and csage, although there has
been some work to move off of scons for csage. I'm not really familiar with
the polybori situation, other than from the outside, the project appears to
be dead, so we would have to handle that somehow. Certainly, most of sage
*should* be usable without polybori, so we *should* be able to get
something up and running without it (considering how messed up the imports
are in sage though, it wouldn't surprise me if it would take a ton of work
to make sage usable without polybori).

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[sage-devel] Python 3 focused Sage Days

[R. Andrew Ohana]

As an alternative to the Bug Days William mentioned, we could hold a
workshop focused on porting Sage to Python 3 (this has apparently been a
frequent request for SMC).

All our dependencies have proper support for Python 3, so the main effort
at this point in time is porting the Sage library. A lot of effort has
already gone into fixing non-Python 3 compatible syntax and functionality
(see #15980 and #16052), although a decent amount of more effort is
required.

In particular, Sage currently relies a great deal on simple comparison (see
the recent discussion
https://groups.google.com/forum/#!topic/sage-devel/4Ho98yUmzco), which is
no longer supported in Python 3. Some decision will have to be made on how
we want to adapt the coercion framework to only rely on rich comparison,
and how we want to handle classes that (currently) only support simple
comparison.

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Re: [sage-devel] where are the bots ?

[R. Andrew Ohana]

The buildbot was having some issues and was reporting everything as a
failure. I disabled it until I get a moment to fix it.

On Tue, Oct 21, 2014 at 1:18 PM, Frédéric Chapoton fchapot...@gmail.com
wrote:

 Hello,

 it seems that the bots have disappeared. Both the buildbot (was top left)
 and the patchbot (top right).

 The patchbot links are broken (used to be colored little round things).

 And http://patchbot.sagemath.org points to William's homepage.

 Can we we hope that the bots will be back soon ?

 Frédéric

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Re: [sage-devel] Buildbot link on needs work tickets.

[R. Andrew Ohana]

On Sat, Oct 4, 2014 at 2:49 AM, Jonas Jermann jjerma...@gmail.com wrote:

 Hi

 On 04.10.2014 11:18, Ralf Stephan wrote:

 On Saturday, October 4, 2014 12:09:19 AM UTC+2, Jonas Jermann wrote:

 
 --
 sage -t src/sage/crypto/mq/sr.py  # 5 doctests failed
 sage -t src/sage/modular/modform/numerical.py  # 2 doctests failed
 sage -t src/sage/rings/polynomial/multi_polynomial_sequence.py  # 9
 doctests failed
 sage -t src/sage/rings/polynomial/pbori.pyx  # Killed due to
 segmentation fault
 sage -t src/sage/rings/polynomial/polynomial_element.pyx  # 2
 doctests
 failed
 sage -t src/sage/rings/real_double.pyx  # 2 doctests failed
 
 --


 Same with http://trac.sagemath.org/ticket/12455 so this
 appears buildbot related. Many of recent buildbot failures
 show these tests failing, although the pattern seems unclear:
 http://build.sagedev.org/trac/one_line_per_build


 It seems to be related to the (now closed) ticket #17071 resp. #17072:
 http://trac.sagemath.org/ticket/17071


Yes, unfortunately the sage build system is still flaky (especially with
upgrades), which makes automatic testing a bit hard. I can clear the build
cache once the next beta is released.




 Best
 Jonas


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Re: [sage-devel] Trac searching is broken

[R. Andrew Ohana]

Ok, it should be fixed now. I disabled version control since we shouldn't
be using it anymore (finger's crossed that doesn't break something else
that I missed).

On Mon, Sep 15, 2014 at 12:26 AM, Jeroen Demeyer jdeme...@cage.ugent.be
wrote:

 The Search box on the Trac webpage is broken: any kind of search (for
 example http://trac.sagemath.org/search?q=foo gives

  Trac detected an internal error:

 ProgrammingError: relation revision does not exist
 LINE 3: FROM revision WHERE (rev ILIKE '%foo%' E...
  ^

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Re: [sage-devel] Re: Trac update

[R. Andrew Ohana]

On Sun, Sep 7, 2014 at 1:05 AM, Maarten Derickx m.derickx.stud...@gmail.com
 wrote:

 Hi Andrew,

 Thanks for upgrading.

 Recently we received a request on the sage-trac-account to reset a
 forgotten password, and it seems that it is no longer possible to use the
 webpage: http://trac.sagemath.org/admin/accounts/users to change user
 account (there used to be an update button next to the add button which
 now disapeared.


This should now be fixed (I just downgraded things from the latest
development version since we don't need anything from them anymore).


 Another thing that is broken is the reset password button for users:
 http://trac.sagemath.org/reset_password (this is why we need the admin
 page to reset passwords quite often in the first place) but this was
 already broken before the upgrade (see
 https://groups.google.com/forum/#!searchin/sage-trac-account/volker%7Csort:date/sage-trac-account/15Wk1fL2XBI/4eM2GZrMQZgJ
 ).



Yup, I'm aware. This may or may not have been fixed. If it is still broken,
I don't know how to fix it (seems to be a bug with the plugin).





 Le samedi 30 août 2014 04:38:35 UTC+2, R. Andrew Ohana a écrit :

 I'm about to update the trac server with some bug fixes + the initial
 buildbot support I mentioned in https://groups.google.com/
 forum/#!topic/sage-devel/zYpEM7W-7cQ, so trac will not be reliable for
 the next little bit. I'll post back here when I'm done.

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[sage-devel] Re: trac push error

[R. Andrew Ohana]

Hi Aly,

So it looks like you cloned the git-trac-command repository under your sage
directory and tried to add it (probably accidentally) in this commit:
http://git.sagemath.org/sage.git/commit/?h=u/aly.deines/ticket/13568id=87d42644c5909a3c3d02881cbe15f8581a39097a
.

Git won't add other git repositories when you tell it to, instead it just
adds a reference to another project. The trac plugin code assumes that you
never do this, that all references are to files/directories within the
project, so it should be easy enough to fix in the trac plugin code,
although you should make sure to do the following with that branch (from
the root directory):

$ git rm git-trac-command
$ echo git-trac-command  .git/info/exclude

The first command will remove it from whatever you are currently working
on, and the second command will make it so git ignores that directory in
the future.

I should get out a fix for the trac module sometime this afternoon, but in
the meantime doing the above and pushing should make the ticket viewable
again.



On Fri, Aug 29, 2014 at 8:18 AM, Volker Braun vbraun.n...@gmail.com wrote:

 Andrew, I think this is your code.. do you understand what is going on?


 File
 /usr/local/lib/python2.7/dist-packages/Trac-1.1.2dev-py2.7.egg/trac/web/main.py,
 line 497, in _dispatch_request
   dispatcher.dispatch(req)
 File
 /usr/local/lib/python2.7/dist-packages/Trac-1.1.2dev-py2.7.egg/trac/web/main.py,
 line 233, in dispatch
   content_type)
 File
 /usr/local/lib/python2.7/dist-packages/Trac-1.1.2dev-py2.7.egg/trac/web/chrome.py,
 line 995, in render_template
   stream |= self._filter_stream(req, method, filename, stream, data)
 File /usr/local/lib/python2.7/dist-packages/genshi/core.py, line 133, in
 __or__
   return Stream(_ensure(function(self)), serializer=self.serializer)
 File
 /usr/local/lib/python2.7/dist-packages/Trac-1.1.2dev-py2.7.egg/trac/web/chrome.py,
 line 1175, in inner
   data)
 File
 /usr/local/lib/python2.7/dist-packages/sage_trac-0.1-py2.7.egg/sage_trac/ticket_branch.py,
 line 73, in filter_stream
   ret = self.get_merge(branch)
 File
 /usr/local/lib/python2.7/dist-packages/sage_trac-0.1-py2.7.egg/sage_trac/git_merger.py,
 line 20, in get_merge
   ret = self._merge(commit)
 File
 /usr/local/lib/python2.7/dist-packages/sage_trac-0.1-py2.7.egg/sage_trac/git_merger.py,
 line 110, in _merge
   merge_tree = recursive_write(repo.get(merge_tree))
 File
 /usr/local/lib/python2.7/dist-packages/sage_trac-0.1-py2.7.egg/sage_trac/git_merger.py,
 line 108, in recursive_write
   self._git.write(pygit2.GIT_OBJ_BLOB, obj.read_raw())



 On Friday, August 29, 2014 1:28:54 PM UTC+1, aly.d...@gmail.com wrote:

 I tried to push a patch to sage trac this morning and got the following
 error:

 Trac detected an internal error:
 AttributeError: 'NoneType' object has no attribute 'read_raw'

 You can see this error when you look at the ticket:
 http://trac.sagemath.org/ticket/13568

 What do I need to do to fix this?




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[sage-devel] Trac update

[R. Andrew Ohana]

I'm about to update the trac server with some bug fixes + the initial
buildbot support I mentioned in
https://groups.google.com/forum/#!topic/sage-devel/zYpEM7W-7cQ, so trac
will not be reliable for the next little bit. I'll post back here when I'm
done.

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[sage-devel] Re: Trac update

[R. Andrew Ohana]

Ok, I'm done updating. Let me know if I broke anything.


On Fri, Aug 29, 2014 at 7:38 PM, R. Andrew Ohana andrew.oh...@gmail.com
wrote:

 I'm about to update the trac server with some bug fixes + the initial
 buildbot support I mentioned in
 https://groups.google.com/forum/#!topic/sage-devel/zYpEM7W-7cQ, so trac
 will not be reliable for the next little bit. I'll post back here when I'm
 done.

 --
 Andrew




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[sage-devel] Re: (eventual) patchbot replacement

[R. Andrew Ohana]

bump.

In case anyone has actual feedback. I will try to roll out these changes
sometime next week.


On Sat, Jun 28, 2014 at 7:03 PM, R. Andrew Ohana andrew.oh...@gmail.com
wrote:

 Hi all,

 I've been working on setting up an instance of buildbot for the eventual
 replacement of patchbot. It doesn't have all the features of patchbot yet,
 so for the moment being it is an addition, not a replace.

 If you would like to try it out, I have setup a sandbox trac server at
 http://trac-sandbox.sagedev.org to play with.

 How to use:

 1. Push and pull to g...@trac-sandbox.sagedev.org like you would the
 normal trac server
 2. Put your branch on some ticket, and mark it as needs review or positive
 review. This will trigger the buildbot to test your branch.
 3. You should see on the ticket (right below the ticket number) the status
 of the buildbot. Once the build has started, this should provide a link to
 the build.

 Things to know (caveats):

 1. The sandbox is based on a snapshot of the trac server from a few weeks
 ago, nothing that has happened in the meantime will be seen on the snapshot.
 2. The branch links will likely be broken -- this is a side affect of not
 setting up a second cgit instance (and will not be broken once this stuff
 migrates back to the real trac instance).
 3. Anything you put on the sandbox should be considered lost -- it will
 not be migrated back over to the real trac server.
 4. Right now there is a single buildslave, so only one ticket will be
 tested at a time. You can see the overall status of the buildbot at
 http://build.sagedev.org/waterfall.
 5. Changes that require new upstream tarballs won't currently work (unless
 your tarball is already in a standard place) -- adding this is on the TODO
 list.

 -

 I have also done a bit of refactoring with some of the other trac plugin
 code, so please make sure that I haven't broken your favorite feature.

 -

 Finally, for those of you who use the xmlrpc interface (all 3 of you),
 I've added the following new functions:

  - str merger.getMerge(int) -- takes a ticket number and returns the merge
 that trac uses both for the diff display, and for the buildbot
  - list buildbot.get_build(int) -- takes a ticket number and returns a
 3-tuple [builder_name, build_number, status], where status is -1 for in
 progress, and is the buildbot result code for completed builds (0 for
 success, 1 for warnings, 2 for failures, etc...)



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 Andrew




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[sage-devel] Re: [sage-cloud] network access from projects

[R. Andrew Ohana]

Some observations from this change:

1) The From Internet button in the +New tab is right now a complete lie,
and gives un-user friendly error messages. Either you should remove this
button (for now), or somehow make it bypass the whitelist.
2) You cannot ssh out (nor use any services that rely on ssh tunnels, e.g.
sshfs).
3) It seems like only some of *.sagemath.org is whitelisted: you can
download packages, but you cannot interact with the repository at
git.sagemath.org.
3b) Because of 2, you cannot contribute to sage development.
4) It makes working on the distribution part of sage (whether reviewing, or
upgrading packages) pretty much impossible at the moment.

At the very least 1 and 3 should be fixed ASAP (and not wait for this vague
quota thing).



On Thu, Jun 19, 2014 at 10:56 AM, William Stein wst...@gmail.com wrote:

 Hi,

 Unfortunately, due to malicious abuse of resources, most access *to*
 the outside internet *from* a SageMathCloud projects will soon be
 removed.  This will restrict what is possible using SMC (e.g., wget
 from a terminal, downloading files from the web, etc.).  We will
 have a very small whitelist, which may be the following:

- github
- bitbucket
- dropbox

 If there is anything else you desperately need on such a whitelist,
 let me know and we'll consider it.

 Note: this is not at all a should-we or should-we-not discussion --
 this is the way it will be.

 Similar remarks apply to sagenb.org, the sage cell server, etc.

 At some point later this summer, there will be another setting under
 quota, which will allow for more general network access for specific
 projects (which I'll have to initially manually enable on a
 per-project basis).

   -- William


 --
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 University of Washington
 http://wstein.org

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Re: [sage-devel] Re: Recommendations for a new Parent/Element pair

[R. Andrew Ohana]

Yeah, I also found some morphisms in the polynomial ring code, but like the
QQ - ZZ code, it seemed dated (and hence might not follow recommended
practices).

As for sage.algebras.*, I didn't really see anything other than Boolean
return values.


On Fri, Jun 6, 2014 at 9:21 AM, Vincent Delecroix 20100.delecr...@gmail.com
 wrote:

 2014-06-06 17:12 UTC+02:00, Travis Scrimshaw tsc...@ucdavis.edu:
  I don't think there's much documentation beyond what's in
  _coerce_map_from_() in Parent.
 
  If it returns re, then it uses _element_constructor_ to construct the
  morphism. Otherwise you return a morphism. I think there's some examples
 in
 
  src/algebras which returns morphisms (I'm pretty sure I've seen it,
  definitely wrote some code on it, but I don't remember off-hand for
 what).

 Two other examples are ZZ - QQ and QQ-ZZ which are respectively a
 Morphism and a Map (see sage/rings/rational.pyx at the very end of the
 file).

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Re: [sage-devel] Re: Recommendations for a new Parent/Element pair

[R. Andrew Ohana]

Ok, follow up question. Is there much documentation on morphisms, or am I
just blind and missing it?

At least as far as I can tell, the documentation on the coercion seems to
recommend implementing morphisms for _coerce_map_from_, but in the toy
examples, only boolean return values are used (which is great for getting
started, but doesn't seem like a wise long term plan).



On Mon, Jun 2, 2014 at 3:05 PM, Nicolas M. Thiery nicolas.thi...@u-psud.fr
wrote:

 On Thu, May 29, 2014 at 11:30:36PM +0200, Nicolas M. Thiery wrote:
  Funny, I had exactly the same discussion yesterday. I am apparently
  not lazy enough, and getting bitten by it: I should have written
  something about this in the documentation a long time ago. I started
  doing this today, and will post a ticket probably tomorrow.

 A first draft is on #16427. The final recommendations shall depend
 on serious benchmarks. We are working on this with Florent.

 Comments/suggestions/reviews are welcome even now though!

 Cheers,
 Nicolas
 --
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 http://Nicolas.Thiery.name/

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[sage-devel] Recommendations for a new Parent/Element pair

[R. Andrew Ohana]

Hi,

Reading through the documentation (from the latest beta) on the coercion
framework and category framework, it isn't exactly clear to me what the
recommended way to implement a new Parent/Element pair as part of the Sage
ecosystem.

For instance, what is the recommended class I should inherit from for my
parent class? I see at the top of sage.rings.rings, that it is not
recommended that I inherit from the Ring class anymore (maybe?), but should
use the category framework. In which case, what should I inherit from?
Parent directly? If I was looking to add a group, there is no such warning
in sage.groups.groups, so should I inherit from Group in that case?

Same goes for my elements, what is the correct base class to use?

Moreover, the two frameworks documentation don't really mention anything
about each other, or how they interact. From my understanding, they were
built up independently, so it would make some sense if they don't interact.
However, the two frameworks do try to solve similar issues, so it seems
like there would be at least some interactions between them. Anything in
particular I should look out for? And should I prefer one framework over
the other if they both solve some issue that I'm encountering?

I don't really have much in the way of specifics at the moment as I'm just
starting out, but I would like to go down the recommended path from the
start, rather than going off my old knowledge which is certainly dated by a
few years in this area.

(P.S. For those interested, I'm looking to flesh out the algebraic function
field functionality over the summer)

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Fwd: [sage-devel] Re: Notification if a branch gets merge conflicts (changes form green to red)

[R. Andrew Ohana]

On Sat, May 17, 2014 at 2:27 PM, leif not.rea...@online.de wrote:

 R. Andrew Ohana wrote:

 Well it is a bit different than other changes, since nothing actually
 changes in the ticket itself (which would prompt a notification). Rather
 the plugin is just a special render for the branch field, so the merge
 is not actually checked until someone actually loads the page for the
 first time (results of the merge are cached in the trac database until
 invalidated).

 If something along these lines were added, it would have to be in the
 release management scripts (potentially coupled with a xmlrpc interface
 to the trac plugin).


 Yep.  But any bot able to comment on tickets (or to send mail) could
 presumably trigger a recheck when the default milestone changes (i.e., upon
 a release), and hence indirectly (or directly) notify the involved people
 if a branch no longer applies.

 [How exactly does the cache entry get invalidated?  Does is just expire?]


When the head of the develop branch moves, or the plugin can't find the
relevant commit (most likely due to git garbage collecting unreferenced
commits). If you're really curious, the relevant code:
https://github.com/sagemath/sage_trac_plugin/blob/master/sage_trac/git_merger.py
.




 -leif

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Re: [sage-devel] Notification if a branch gets merge conflicts (changes form green to red)

[R. Andrew Ohana]

Well it is a bit different than other changes, since nothing actually
changes in the ticket itself (which would prompt a notification). Rather
the plugin is just a special render for the branch field, so the merge is
not actually checked until someone actually loads the page for the first
time (results of the merge are cached in the trac database until
invalidated).

If something along these lines were added, it would have to be in the
release management scripts (potentially coupled with a xmlrpc interface to
the trac plugin).

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Re: [sage-devel] Re: git diff branch1..develop

[R. Andrew Ohana]

On Thu, May 1, 2014 at 9:30 AM, leif not.rea...@online.de wrote:

 Travis Scrimshaw wrote:

 That happens when you've started making a comment (or any other change
 to the ticket) as part of the preview.


 Hardly related, but is it intentional that trac meanwhile also colors (and
 even strikes!) trac user names in replies / quotes (depending on or
 according to the /state of the ticket/)?


No, this came about from upgrading our version of trac -- it seemed so
minor that I didn't spend the time investigating it.


 Just asking...


 -leif

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Re: [sage-devel] Re: ipython notebook in sage?

[R. Andrew Ohana]

On Mon, Apr 28, 2014 at 2:03 PM, Jean-Baptiste Priez elix...@gmail.comwrote:

 Hello,

 I would like to know what is the new line which is equivalent to

 %load_ext sage.misc.sage_extension


 with sage 6.2?


%load_ext sage

should now work.



 The ticket #16050 (I think...) moved some code so...

 Cheers,

 Jean-Baptiste Priez

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Re: [sage-devel] Re: new layout breaks sagenb development?

[R. Andrew Ohana]

The symbolic link exists for the sole reason that previously you could not
install sagenb as a standard python package (it cared deeply about its
location in the SAGE_ROOT); this was necessary for getting sagenb to
initially work on the git version of Sage. The symbolic link was made (as a
hack) because I didn't know what (and didn't want to deal with) other
things might be affected if I actually moved that directory. However, it
should probably be physically moved, and not just linked.


On Tue, Apr 8, 2014 at 8:30 AM, P Purkayastha ppu...@gmail.com wrote:

 Hello Jonathan,

  In my experience, making a symbolic link to the root of the sagenb
 directory does not work. Making a symbolic link to the sagenb directory
 *inside the sagenb root* also does not work.

  My suggestion would be to change the layout of the sagenb root directory
 and move flask_version to inside the sagenb/sagenb, instead of having it as
 a symbolic link.

 - basu.



 On Tue, Apr 8, 2014 at 11:21 PM, Jonathan gu...@uwosh.edu wrote:

 Another solution that works is to work with a separate sagenb git
 repository and then rename the directory sagenb inside the egg to something
 like sagenb_old.  Then create a symlink to your development git repository
 named sagenb.  This is almost the same solution as Basu's.

 On Tuesday, April 8, 2014 10:07:30 AM UTC-5, kcrisman wrote:

 Hey Basu,  thanks!  That sounds great.

 Can you open a ticket to fix the developer guide with this information
 (the last section on sagenb development)?  (Suitably generic, of course.)

 - kcrisman

 On Tuesday, April 8, 2014 10:45:24 AM UTC-4, P Purkayastha wrote:

 There is an easy fix. The main reason why it has broken sagenb
 development is because sagenb/sagenb/flask_version is a symbolic link to
 sagenb/flask_version - I do not know why it is set up like this. So,
 doing the following will allow you to work on sagenb dev - I will assume
 that your sage is in ~/sage and sagenb is in ~/sagenb:

 $ cd ~/sagenb/sagenb
 $ rm flask_version
 $ mv ../flask_version .
 $ cd ~/sage/local/lib/python/site-packages/sagenb-0.10.8.2-py2.7.egg
 $ mv sagenb{,-0.10.8.2}
 $ ln -s ~/sagenb/sagenb .


 And now, you can continue to work on sagenb dev in ~/sagenb.

 - basu.

 On Tuesday, April 8, 2014 10:33:03 AM UTC+8, kcrisman wrote:

 With the new directory layout, http://www.sagemath.org/doc/
 developer/sagenb/index.html no longer makes any sense, and I don't
 see any easy way to do any sagenb development without making new (s)pkgs.
  Is that correct?  Any ideas for making this simpler?

 Thanks,
 - kcrisman

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Re: [sage-devel] Re: Sage as a Python Library

[R. Andrew Ohana]

On Fri, Apr 4, 2014 at 3:27 AM, Volker Braun vbraun.n...@gmail.com wrote:

 On Friday, April 4, 2014 1:55:40 AM UTC+1, R. Andrew Ohana wrote:

 I'm a bit confused at what you are saying. I agree that the act of
 cleaning up the imports is essentially impossible right now due to the
 combinatorial explosion, but unless I'm missing something, we could track
 the modules that can be imported (without causing circular import issues)
 and have a regression requirements to insure that this list doesn't shrink.


 What I'm trying to say is: You can trivially make every module importable
 by first importing everything else (well everything before that module in
 sage.all). That is presumably not what you want ;)  So there should also be
 a mechanism to restrict the available modules, e.g. via a custom importer
 while said module is loading.


Ah ok, I understand now. I'm not necessarily convinced this is the right
way to go -- I think the cost of making a developer jump through hoops to
get some functionality from a module foo from bar, just because bar is not
allowed to import foo, outweighs the benefit.

I think that a lot of our circular import issues stem from the (unofficial)
convention of using the `from foo import bar` syntax over the `import foo`
syntax (for anyone not really familiar with this, see [1] for a good
explanation). I often wish the reverse convention was chosen for namespace
reasons (and readability reasons). Just looking at the absolute imports
within the sage library we have [2]

- thereof lines of the form from sage.foo import bar 19,581 - thereof
lines of the form import sage.foo (as baz) 1,650

[1]
http://stackoverflow.com/questions/3955790/python-circular-imports-once-again-aka-whats-wrong-with-this-design
[2] http://trac.sagemath.org/15985

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Re: [sage-devel] Re: sagemath wiki migrated

[R. Andrew Ohana]

On Fri, Apr 4, 2014 at 3:19 AM, Volker Braun vbraun.n...@gmail.com wrote:

 What happened to the plan of migrating to another wiki (was it gollum?).
 Just curious ...


Got busy with school...

Some work still needed to be done since gollum doesn't scale well with
large repositories (both in number of commits and in actual storage size).
The plan was to flatten the history (currently around 25k commits), and
modify gollum to use static images (that were not stored in the actual
repository), but the later was never completed (plus my limited ruby
knowledge meant it was going to take a bit of learning, most likely).


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Re: [sage-devel] Skynet build cluster

[R. Andrew Ohana]

Sorry, bit late to this (mainly got reminded by the 10.4 support thread).

For Solaris support, what about setting up an x86_64 Solaris VM as a
buildbot? This doesn't deal with the issue of SPARC support, but at least
it would make sure that we continued to test against Solaris.


On Wed, Mar 19, 2014 at 12:43 PM, William Stein wst...@gmail.com wrote:

 Hi,

 Unfortunately, the skynet build cluster will shutdown on May 31, 2014.
Please move any data you have off there before then.

 This might mean we have to discontinue support for Solaris for Sage;
 I'm not sure.

  -- William

 --
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 http://wstein.org

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[sage-devel] Sage as a Python Library

[R. Andrew Ohana]

Personally I would find it incredibly useful to be able to use Sage as a
Python Library. While this is technically possible at the moment (by doing
import sage.all and when done making sure to run sage.all.quit_sage),
it isn't very useful, since you still have to import everything in Sage
when you might need only a few things (the second it takes to import
everything gets very tiresome during the debugging process).

As I see it, there are 2 major issues, and one lesser issue that prevents
Sage from usable python library.

1. setting up and cleaning up C level libraries/structures (e.g. the
integer pool)

2. Sage's import hell

3. (lesser) Non-standard all.py modules


For 1, I'm not really familiar with these components of Sage, but at least
naively it seems to me that this stuff could be dealt with in Cython
classes (e.g. making the integer pool an actual Cython class, and using
__cinit__ and __dealloc__ to handle the setup and cleanup).

2 is a mess, I don't really have any idea how to resolve this, although it
looks to me like it might be a blocker for adding Python 3 support (see
#15985), unless I'm misdiagnosing the problem (which could be the case).

For 3: The all.py's are really just our way of constructing the global sage
namespace. They also a common cause of branch collision (which is certainly
much less painful to deal with now, but still is an issue). My proposal is
very rough, and fuzzy, so bear with me, I'll try to describe how you might
transition a module or a package over to my proposed scheme.

- To transition a module foo over, add an __all__ to foo with the names
that should be part of the global namespace. (it would probably be nice if
we settled on a convention -- either have __all__ be the last thing or the
first thing in the module). Updated the corresponding package's all.py with
'from foo import *'

- To transition a package over, first make sure that all modules in that
package have made the transition. Then add an __all_modules__ that lists
the modules and subpackages in that package that have names that need to be
exported to the global namespace. Remove the package's all.py. Remove that
package from its parent's all.py. Finally, add the package to the global
list of transitioned packages.

As an example of these, see
http://git.sagemath.org/sage.git/commit/?h=u/ohanar/all_removal_exampleid=6f92ece7642c4dd94f9e7e64ebf88431afbe9ab2(this
branch doesn't actually pass doctests, since the doctesting framework
would probably have to be updated as well, and I only made changes to the
actual starting up of Sage).

The idea is that each individual module individually declares what are the
important (for the user) names, and each package declares what are the
important modules and subpackages. I think doing something along these
lines will organically help with 2 (although probably not completely fix
it), as well as 1.

Things that I've not really considered:

- Lazy imports?

- Refactoring of namespace (e.g. graphs.Tab)


I'm curious what other people think -- not just about my very fuzzy
proposal, but about how we might address the issues of Sage as a Python
library.

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Re: [sage-devel] Re: Sage as a Python Library

[R. Andrew Ohana]

On Thu, Apr 3, 2014 at 3:49 PM, Volker Braun vbraun.n...@gmail.com wrote:


 Simplifying the import process would definitely be nice. We should have
 some mechanism enforce a somewhat linear order, e.g. by introducing
 barriers where you are only allowed to (module-level) import stuff that
 finished importing before the previous barrier. Perhaps ideally a linear
 order where you can only import from the previously imported modules, one
 can always dream

 One general problem with the Python library goal are cyclic imports.
 There are a lot of places where you have to import modules in the right
 order. Once you do away with a single sage.all entry point then it'll be
 tricky to get Sage running at all. And the combinatorial explosion prevents
 us from any meaningful test coverage.

 I'm a bit confused at what you are saying. I agree that the act of
cleaning up the imports is essentially impossible right now due to the
combinatorial explosion, but unless I'm missing something, we could track
the modules that can be imported (without causing circular import issues)
and have a regression requirements to insure that this list doesn't shrink.

I also vaguely recall Robert creating a graph of the module dependencies
some years ago -- if that code is still around (with potentially a little
updating), it would at least give us a good idea of what components of sage
are currently approachable in regards to this issue.

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Re: [sage-devel] %load

[R. Andrew Ohana]

On Sun, Mar 23, 2014 at 3:36 PM, William Stein wst...@gmail.com wrote:

 Hi,

 In Sage 0.0 - 5.12, I could create a file foo.sage and type

   sage: load foo.sage   # or %load foo.sage

 and evaluate its contents.  In sage-6.2(beta) I get some interactive
 script loaded, that makes me evaluate the contents interactively, and
 sort of edit it.  Umh, yuck.  How do I get %load behavior back?


So the current %load matches the %load behavior of ipython, I think this
was changed when we upgraded to 0.13 (maybe?). In ipython %run matches the
behavior of our old load command, but it doesn't handle preparsing, which
was why the mostly redundant %runfile was introduced to replace the load
behavior. The best fix for this would be in upstream ipython to have %run
to use the transformers that the interpreter already uses.

I've been of-and-on working on cleaning up and refactoring code surrounding
this (haven't posted anything yet, since it is still a mess), but I've
noticed a number of other broken things (like actually editing the lines
that you get with %iload).


 There's also %run on a sage file, but it doesn't preparse.

 William

 --
 William Stein
 Professor of Mathematics
 University of Washington
 http://wstein.org

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Re: [sage-devel] %load

[R. Andrew Ohana]

On Sun, Mar 23, 2014 at 4:50 PM, William Stein wst...@gmail.com wrote:

 On Sun, Mar 23, 2014 at 4:31 PM, R. Andrew Ohana andrew.oh...@gmail.com
 wrote:
 
  On Sun, Mar 23, 2014 at 3:36 PM, William Stein wst...@gmail.com wrote:
 
  Hi,
 
  In Sage 0.0 - 5.12, I could create a file foo.sage and type
 
sage: load foo.sage   # or %load foo.sage
 
  and evaluate its contents.  In sage-6.2(beta) I get some interactive
  script loaded, that makes me evaluate the contents interactively, and
  sort of edit it.  Umh, yuck.  How do I get %load behavior back?
 
 
  So the current %load matches the %load behavior of ipython, I think this
 was
  changed when we upgraded to 0.13 (maybe?).

 -1.  But I guess we've had this discussion before...


We did, but it seemed to die off with no clear vote one way or another.


In ipython %run matches the
  behavior of our old load command, but it doesn't handle preparsing, which
  was why the mostly redundant %runfile was introduced to replace the load
  behavior. The best fix for this would be in upstream ipython to have
 %run to
  use the transformers that the interpreter already uses.
 
  I've been of-and-on working on cleaning up and refactoring code
 surrounding
  this (haven't posted anything yet, since it is still a mess), but I've
  noticed a number of other broken things (like actually editing the lines
  that you get with %iload).
 
 
  There's also %run on a sage file, but it doesn't preparse.
 
  William
 
  --
  William Stein
  Professor of Mathematics
  University of Washington
  http://wstein.org
 
  --
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 Groups
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 University of Washington
 http://wstein.org

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[sage-devel] Re: sage-6.x git-motivated re-organization seriously breaks system-wide sage

[R. Andrew Ohana]

This doesn't at least look to be a regression, so much as a long term bug.
The offending path has always been a subpath of SAGE_ROOT since sage was
initially checked into a repository (it was SAGE_ROOT/data/extcode/octave
before). My guess is that if you are only experiencing issues with recent
versions of sage, is that there was some other change that is trying to
write to a file under that path.


On Sun, Mar 9, 2014 at 1:09 PM, William Stein wst...@gmail.com wrote:

 Hi,


 I install sage-6.x systemwide for https://cloud.sagemath.com.   Now it
 seems impossible for a normal user to use the octave interface (and
 probably many others), which is a _major_ regression:


 sage: octave.eval('rand(2)')
 Traceback (most recent call last):
   File
 /usr/local/sage/sage-6.2/local/lib/python2.7/site-packages/sage/interfaces/expect.py,
 line 1208, in eval
 for L in code.split('\n') if L != ''])
   File
 /usr/local/sage/sage-6.2/local/lib/python2.7/site-packages/sage/interfaces/expect.py,
 line 813, in _eval_line
 self._start()
   File
 /usr/local/sage/sage-6.2/local/lib/python2.7/site-packages/sage/interfaces/octave.py,
 line 285, in _start
 Expect._start(self)
   File
 /usr/local/sage/sage-6.2/local/lib/python2.7/site-packages/sage/interfaces/expect.py,
 line 389, in _start
 sage_makedirs(dir)
   File
 /usr/local/sage/sage-6.2/local/lib/python2.7/site-packages/sage/misc/misc.py,
 line 73, in sage_makedirs
 os.makedirs(dir)
   File /usr/local/sage/sage-6.2/local/lib/python/os.py, line 150, in
 makedirs
 makedirs(head, mode)
   File /usr/local/sage/sage-6.2/local/lib/python/os.py, line 157, in
 makedirs
 mkdir(name, mode)
 OSError: [Errno 13] Permission denied:
 '/usr/local/sage/sage-6.2/local/share/sage/ext/octave'


 I was able to get things to work by doing

mkdir -p /usr/local/sage/sage-6.2/local/share/sage/ext/octave/user
chown a+rwx /usr/local/sage/sage-6.2/local/share/sage/ext/octave/user

 I particularly *HATE* the second chown -- yes, you must give write to
 everybody.
 This of means any user could just fill up that directory and bring down the
 system.

 Anyway, what happened?


  -- William




-- 
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[sage-devel] Re: sage-6.x git-motivated re-organization seriously breaks system-wide sage

[R. Andrew Ohana]

On Sun, Mar 9, 2014 at 9:39 PM, William Stein wst...@gmail.com wrote:

 On Sun, Mar 9, 2014 at 8:53 PM, R. Andrew Ohana andrew.oh...@gmail.com
 wrote:
  This doesn't at least look to be a regression, so much as a long term
 bug.

 Do you mean it isn't a regression *resulting from the git
 reorganization*?


I mean it doesn't look like it should be a regression. If it is, it is some
magic foo going on. In particular between 5.13 and 6.0, the source code for
sage.interfaces was only touched by trac #15440 (some maxima funkiness),
and SAGE_EXTCODE wasn't touched (it hasn't been changed for over a year by
this point).

Or do you mean that you think this has always been
 broken?


Looking at the code, it should have been.


 Install Sage as one user, then run it as another.  In sage-5.10,11,12,
 I think the following worked, but in sage-6.2.beta it doesn't:

 octave.eval('rand(4)')

 Anyway, I guess I'll try to fix this someday...


A work-around (not a proper fix) is to mimic the standard interfaces
initialization, i.e.

-octave = Octave(script_subdirectory='user')
+octave = Octave(script_subdirectory=None)

and similarly for the other optional interfaces that seem to get very
little attention.


  -- William


 
 
  On Sun, Mar 9, 2014 at 1:09 PM, William Stein wst...@gmail.com wrote:
 
  Hi,
 
 
  I install sage-6.x systemwide for https://cloud.sagemath.com.   Now it
  seems impossible for a normal user to use the octave interface (and
  probably many others), which is a _major_ regression:
 
 
  sage: octave.eval('rand(2)')
  Traceback (most recent call last):
File
 
 /usr/local/sage/sage-6.2/local/lib/python2.7/site-packages/sage/interfaces/expect.py,
  line 1208, in eval
  for L in code.split('\n') if L != ''])
File
 
 /usr/local/sage/sage-6.2/local/lib/python2.7/site-packages/sage/interfaces/expect.py,
  line 813, in _eval_line
  self._start()
File
 
 /usr/local/sage/sage-6.2/local/lib/python2.7/site-packages/sage/interfaces/octave.py,
  line 285, in _start
  Expect._start(self)
File
 
 /usr/local/sage/sage-6.2/local/lib/python2.7/site-packages/sage/interfaces/expect.py,
  line 389, in _start
  sage_makedirs(dir)
File
 
 /usr/local/sage/sage-6.2/local/lib/python2.7/site-packages/sage/misc/misc.py,
  line 73, in sage_makedirs
  os.makedirs(dir)
File /usr/local/sage/sage-6.2/local/lib/python/os.py, line 150, in
  makedirs
  makedirs(head, mode)
File /usr/local/sage/sage-6.2/local/lib/python/os.py, line 157, in
  makedirs
  mkdir(name, mode)
  OSError: [Errno 13] Permission denied:
  '/usr/local/sage/sage-6.2/local/share/sage/ext/octave'
 
 
  I was able to get things to work by doing
 
 mkdir -p /usr/local/sage/sage-6.2/local/share/sage/ext/octave/user
 chown a+rwx /usr/local/sage/sage-6.2/local/share/sage/ext/octave/user
 
  I particularly *HATE* the second chown -- yes, you must give write to
  everybody.
  This of means any user could just fill up that directory and bring down
  the
  system.
 
  Anyway, what happened?
 
 
   -- William
 
 
 
 
  --
  Andrew



 --
 William Stein
 Professor of Mathematics
 University of Washington
 http://wstein.org




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Re: [sage-devel] Re: Patchbot gets priority and status of a ticket totally wrong

[R. Andrew Ohana]

On Mon, Mar 3, 2014 at 3:04 AM, Volker Braun vbraun.n...@gmail.com wrote:

 There was some attempt to replace it with Jenkins at SD56, but I don't
 know how how far that progressed. Since the changeset information is now
 easily accessible through git it would make sense to replace it with a more
 run-of-the-mill continuous integration tool.


Yes, I was looking into that, but it didn't seem quite like the tool for
the job. I was going to take a look at how one by configure buildbot to
perform patchbot-like duties, but school started and my studies took over
all my time.

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Re: [sage-devel] Re: trac update

[R. Andrew Ohana]

On Fri, Feb 14, 2014 at 4:25 PM, Travis Scrimshaw tsc...@ucdavis.eduwrote:

 Hey Andrew,
Thanks for fixing that. However I'm afraid I have another problem. On
 http://trac.sagemath.org/ticket/15822, it's already showing the branch as
 being merged when it clearly has not.


Both branches that you put there seem to just be pointers to the latest
beta, which is why it is reporting that they are already merged (and also
why there are no commits or links or anything, because there is nothing new
in those branches).

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Re: [sage-devel] Re: trac update

[R. Andrew Ohana]

On Tue, Feb 11, 2014 at 4:28 PM, Travis Scrimshaw tsc...@ucdavis.eduwrote:

 Hey Andrew,
I inputed the wrong branch on http://trac.sagemath.org/ticket/15668and 
 then trac would not load the page. I worked around this by uploading a
 branch with the typo, but the issue with trac is still there.


Ok, this should now be fixed:
https://github.com/sagemath/sage_trac_plugin/commit/63512d425dc75734e1e171c53a8e6dab66a48859
.

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[sage-devel] trac update

[R. Andrew Ohana]

Hi Everyone,

I just pushed out an update to our trac plugin. The main change is that
merged branches now have links for the merge into develop (i.e. the merge
commit), as well as the list of commits that were merged. There were some
other minor changes + bug fixes, and a significant bit of code refactoring.
For anyone who is interested, the code is at
http://github.com/sagemath/sage_trac_plugin

Volker: If you could have your closer script replace the branch field with
the merged sha1, that would make it so that users are able to delete their
branches (the plugin can deal with sha1 hashes just fine).

-- 
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Re: [sage-devel] Re: What do we do with patches that touch all files ?

[R. Andrew Ohana]

On Feb 7, 2014 3:27 AM, Volker Braun vbraun.n...@gmail.com wrote:

 Its better to do smaller chunks. And I highly doubt that 2to3 will be
able to deal with the whole Sage library, Cython and all.

Cython should be less of an issue since it produces c code that can be
compiled against python 2 and 3. Obviously certain things will have to be
updated (truediv vs div, required richcmp, no built-in cmp or reduce, etc),
but most python 2 syntax in cython should be fine.

I would be against running 2to3 on the sage library, rather we should get
it to a state where 2to3 can be called by distutils and produce a working
python 3 library.

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Re: [sage-devel] Re: What do we do with patches that touch all files ?

[R. Andrew Ohana]

On Fri, Feb 7, 2014 at 3:25 PM, Francois Bissey 
francois.bis...@canterbury.ac.nz wrote:

 Truth to be told I would feel better if someone was fixing all (or at
 least some of) the cython warnings we currently
 have before trying anything new.


Almost certainly not possible unless you rewrite everything using gmp/mpir
to use the c++ class wrappers since you never assign mpz_t variables (even
then, you would probably have some of these warnings). It would be nice if
there was an option to Cython to suppress such warnings.

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[sage-devel] Re: Broken optional packages...

[R. Andrew Ohana]

On Sat, Feb 1, 2014 at 10:36 PM, William Stein wst...@gmail.com wrote:

 Hi,

 I just wanted to raise awareness (and apologize) that the
 re-organization of the layout of Sage broke so many optional spkg's.
 In case people run into similar problems, here's what I'm doing to
 workaround this mess for sage-6.2 in SageMathCloud.

 1. These databases are broken:

 cunningham_tables
 database_jones_numfield
 database_kohel
 database_odlyzko_zeta
 database_sloane_oeis
 database_stein_watkins_mini.p0


As per Volker's post (
https://groups.google.com/forum/#!topic/sage-devel/onWFAVz-LDA) these
packages need updated copyright information. The copyright for the sloane
database is provided in that thread, as is permission to use Andrew
Odlyzko's database, but for the others copyright information is still
needed.

One workaround is to do this:

  # in SAGE_ROOT
  ln -s local/share data

 but the SAGE_DATA variable is gone as well... so you have to add this
 *BACK* to src/bin/sage-env (after SAGE_SHARE):

 # this is to be compatible with optional packages that haven't
 # been updated to not use SAGE_DATA
 export SAGE_DATA=$SAGE_SHARE

 (Hopefully, this can be added back or the packages fixed for sage-6.3.)

 2. Another broken package is

   p_group_cohomology

 which doesn't build:

  pGroupCohomology/resolution.pxd:21:0: 'interrupt.pxi' not found

 I don't know a fix.

 3. There's an optional package called pybtex which doesn't work.

 The package TOPCOM-0.17.4 fails to build:

 ./spkg-install: line 11: cd:
 /usr/local/sage/sage-6.1/spkg/standard/: No such file or directory


Using this

sage -i topcom

works just fine for me. If you are doing

sage -i TOPCOM

you are probably getting the old spkg that doesn't work with the new layout
(this should really be fixed so that the packages are case-insensitive).

I don't know a fix.

 This is all on Ubuntu 12.04 with pretty much anything imaginable installed.

 Trac http://trac.sagemath.org/ticket/14962 is supposed to be about
 packages broken by the git reorganization, but it's closed.

   -- William

 --
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 Professor of Mathematics
 University of Washington
 http://wstein.org




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Re: [sage-devel] Re: Git reviewing help needed

[R. Andrew Ohana]

On Thu, Jan 23, 2014 at 5:22 PM, kcrisman kcris...@gmail.com wrote:


 By including another parameter id2=... or perhaps h=... or
 b=... it should be possible to specify the state relative to which you
 want to see the diff. It should in principle be possible to paste in the
 hash of the #15107 commit somewhere and get the diff relative to that. I
 think we had that option before, but I cannot see it now


 Agreed, this would be useful.

 Here is the log of my first attempt at reviewing with git.  I don't know
 but that it might help with documenting what to do.

 $ cd Downloads/
 $ git clone git://github.com/sagemath/sage.git
 Cloning into 'sage'...
 remote: Reusing existing pack: 200480, done.
 remote: Total 200480 (delta 0), reused 0 (delta 0)
 Receiving objects: 100% (200480/200480), 58.29 MiB | 91 KiB/s, done.
 Resolving deltas: 100% (133590/133590), done.
 Checking out files: 100% (3926/3926), done.
 $ cd sage
 $ export MAKE=make -j3
 $ make
 lots of new messages early on, including downloads of mpir - I was not
 expecting to need to be on the internet to build Sage, just to download the
 source


The Sage repository should not contain binary files nor non-sage specific
source code, so
naturally cloning the sage repository would not include compressed tarballs
of upstream
code. There are two ways to get a copy of sage with these files (so you can
do an offline
build): either use the source distribution that you find on sagemath
website, or run the
`make download` after cloning the source. These should both be documented
(they might
already be, but I don't know).

Elapsed time: 240.4 seconds.
 Done building the documentation!
 $ ./sage
 ┌┐
 │ Sage Version 6.0, Release Date: 2013-12-17 │
 │ Type notebook() for the browser-based notebook interface.│
 │ Type help() for help.│
 └┘
 sage: dev.checkout?
 sage: 2+2
 4
 sage: exit
 Exiting Sage (CPU time 0m0.46s, Wall time 1m38.05s).
 $ ./sage -dev checkout --ticket 15693
 Trac username: kcrisman
 #  Your trac username has been written to a configuration file for future
 #  sessions. To reset your username, use dev.trac.reset_username().
 On ticket #15693 with associated local branch ticket/15693.

 #  Use sage --dev merge to include another ticket/branch.
 #  Use sage --dev commit to save changes into a new commit.
 $ ./sage -dev diff
 $ ./sage -dev log
 usage: sage-dev [-h] subcommand ...

 Note that, other than implied by
 http://sagemath.org/doc/developer/walk_through.html#reviewing there is no
 diff of the branch I just checked out, and further there is no apparent
 equivalent to hg/git log.  I know it worked, though, because

 $ git log
 commit 39a19781a1c59a99afde43171117eea804541cac
 Author: Punarbasu Purkayastha ppu...@gmail.com
 Date:   Thu Jan 23 23:41:20 2014 +0800

 Remove simplify_radical from documentation of simplify_full

 Resuming my attempt:

 $ ./sage -b
 many minutes of Cythonizing

   Didn't I JUST BUILD SAGE?  Note that the ticket in question touches
 one .pyx file and doesn't even change any code - it's a nearly trivial
 documentation fix.


You just built Sage 6.0, although for the ticket in question, it was based
off 6.1.beta5, so you will have
to compile any changes between 6.0 and 6.1.beta5 in addition to the nearly
trivial documentation
fix. I agree that this can be a pain when jumping around between a lot of
tickets, however using ccache
and cycache can alleviate a lot of the pain (it will not really fix this
particular rebuild, since you hadn't
ever built 6.1.beta5 before -- it would help you once you jump back to
running 6.0).

One thing to note is that for most people who want to develop, you will
almost certainly want to download
the latest beta, but the default action when you clone the sage repository
is to get the latest stable
release (this could be trivially changed, but it is certainly worth some
discussion [but not on this thread]).

I really just followed the guide (well, I followed Volker's instructions
 somewhere, because there is no mention of git in the installation guide)
 and this is not encouraging.  And obviously the huge work by Andrew, David,
 et al. has been very good overall, because a lot of people are very
 successful with it.  But perhaps at the very least this thread can be a
 place to collate suggestions for improving the developer and install manual
 so that it is, to paraphrase David Joyner, ridiculously easy to develop.

 Oh, and it's not clear to me from
 http://sagemath.org/doc/developer/walk_through.html#reviewing what to do
 when I'm *done* reviewing!  I guess one checks out master but that is
 just something I sort of got through osmosis and I don't know if it's
 right, nor the sage -dev syntax for this.

 $ ./sage -dev checkout master
 usage: sage-dev [-h] subcommand ...
 

Re: [sage-devel] Re: Python as build-time dependency

[R. Andrew Ohana]

I'm a fan of gentoo's package manager specification (PMS) [1], however the
only package manager that is fully compliant is portage, which I don't
think is appropriate for sage. In particular:

1. It requires a noticeably bigger bootstrapping of the world. Lmonade
reduces this to only ~20 more packages than we already have (if I recall),
but imo this is still too many.
2. Portage itself has many dependencies, often with very explicit version
requirements. This makes non-Linux platforms a pain, since you need things
like gnu coreutils and findutils.
3. It does not support tree relocation.
4. (Lesser) The Portage source is atrocious, and it performs terribly.

Imo, the most promising implementation of the PMS is paludis, however it is
not fully compliant (in particular prefix support is incomplete, and
binaries are assumed to be in the ELF format).

[1] http://wiki.gentoo.org/wiki/Project:PMS

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Re: [sage-devel] Re: Broken ticket update on trac?

[R. Andrew Ohana]

Well, I did fix it, but the trac server was still pulling up the old one
sometimes. I've noticed it does this sometimes unless you restart the
apache server, so I did that.


On Mon, Jan 6, 2014 at 6:12 AM, Travis Scrimshaw tsc...@ucdavis.edu wrote:

 See http://trac.sagemath.org/ticket/15637.


 On Monday, January 6, 2014 1:58:01 AM UTC-8, Volker Braun wrote:

 Andrew assured me that he had fixed that bug about 5 hours ago... maybe
 you can email him with the stack trace thats on the error page.



 On Sunday, January 5, 2014 11:25:18 PM UTC-10, Jean-Pierre Flori wrote:

 Hi all,

 I'm getting
 
 Oops…
 *Trac detected an internal error:*

 TypeError: object of type 'listreverseiterator' has no len()


 There was an internal error in Trac. It is recommended that you notify
 your local Trac administrator with the information needed to reproduce the
 issue.

 To that end, you could  a ticket.

 The action that triggered the error was:

 POST: /ticket/15316
 

 on ticket #15316 when trying to set the branch to u/jpflori/ticket/15316.
 Any idea of what's going wrong?

 Best,
 JP

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Re: [sage-devel] Guys, it takes one minute to load every single page of trac. We have to do something about it.

[R. Andrew Ohana]

Ok, I just deployed the rewritten sage plugin, and removed all usage of the
trac git plugin. There are bound to be a few bugs, but hopefully trac will
be much faster now.


On Fri, Jan 3, 2014 at 10:26 AM, Nathann Cohen nathann.co...@gmail.comwrote:

 Yooo !

  Don't thank me yet, you must have just had good luck. I'm planning on
 working on this today.

 Really ? You must have scared it, then. Something happened, I am sure ! :-P

 Nathann

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Re: [sage-devel] Guys, it takes one minute to load every single page of trac. We have to do something about it.

[R. Andrew Ohana]

On Fri, Jan 3, 2014 at 3:29 AM, Nathann Cohen nathann.co...@gmail.comwrote:

 Andrew, I don't know which part of your soul you had to sell for what you
 did, but Trac seems to be Much faster now. Thank you S much
 !!!


Don't thank me yet, you must have just had good luck. I'm planning on
working on this today.


 Nathann


 On Wednesday, January 1, 2014 12:10:34 PM UTC+1, R. Andrew Ohana wrote:

 I think the main culprit is the git trac plugin (as it seems to have
 gotten much much worse in the last couple weeks as we have finally made the
 changeover). One of my goals at Sage Days 56 is to completely remove our
 usage of this plugin.


 On Wed, Jan 1, 2014 at 2:43 AM, Nathann Cohen nathan...@gmail.comwrote:

 As the title says. It takes a lifetime to load a ticket's page. It takes
 a lifetime to click on reply to answer a comment.

 Guys in my lab request funding by listing computational problems for
 which we have no efficient algorithm and they say that they will fix it. I
 don't think that any part of Trac is involved though, and I'm pretty sure
 that today's computer can handle out git history.

 What can we do ? How can I help ? If I have to spend nights trying to
 make this thing work I will. But we have to do something O_O

 Nathann

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Re: [sage-devel] Guys, it takes one minute to load every single page of trac. We have to do something about it.

[R. Andrew Ohana]

I think the main culprit is the git trac plugin (as it seems to have gotten
much much worse in the last couple weeks as we have finally made the
changeover). One of my goals at Sage Days 56 is to completely remove our
usage of this plugin.


On Wed, Jan 1, 2014 at 2:43 AM, Nathann Cohen nathann.co...@gmail.comwrote:

 As the title says. It takes a lifetime to load a ticket's page. It takes a
 lifetime to click on reply to answer a comment.

 Guys in my lab request funding by listing computational problems for which
 we have no efficient algorithm and they say that they will fix it. I don't
 think that any part of Trac is involved though, and I'm pretty sure that
 today's computer can handle out git history.

 What can we do ? How can I help ? If I have to spend nights trying to make
 this thing work I will. But we have to do something O_O

 Nathann

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Re: [sage-devel] Cannot add ssh key in trac prefs

[R. Andrew Ohana]

Please try again. This should now be fixed.


On Wed, Jan 1, 2014 at 12:29 PM, Jean-Pierre Flori jpfl...@gmail.comwrote:

 I'm getting an error:
 *Trac detected an internal error:*

 IOError: [Errno 13] Permission denied: 
 u'/home/www-data/gitolite/keydir/03/jpflori.pub'


 Did I do something wrong?

 Best,
 JP

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Re: Re: [sage-devel] The Annual Sage on Python 3 Thread

[R. Andrew Ohana]

On Mon, Dec 30, 2013 at 10:14 AM, William Stein wst...@gmail.com wrote:

 This discussion on Hacker News is relevant to The Annual Sage on
 Python 3 Thread

https://news.ycombinator.com/item?id=6985207

http://alexgaynor.net/2013/dec/30/about-python-3/

 1. Argument against switching now:

 One quote from the HN discussion: My last few Python projects have
 started out as Python 3, but ended up as 2 due to missing library
 support.The takeaway for me is that even if we could easily just
 switch Sage to Python 3, it's not 100% clear that we actually should
 do so today.   Doing so could alienate users, and restrict the
 third-party code and packages that can be installed into Sage. For
 example, we might see I started out using Sage (which uses Python 3),
 but had to switch to Numpy/Scipy/etc. and Python 2 due to missing
 library support.Anyway, I wanted to point this out loud and clear
 in case anybody on the list has been silently worrying about this.

 2. Argument for switching now:

 On the other hand, the main suggestion in the discussion there for how
 to fix this situation is to get all the popular Linux distros to
 switch to Python3.   Sage is like a linux distro, in that if we switch
 it would help move things along.Also, Sage isn't meant to be
 mainly a python platform, but an alternative to Mathematica/etc.
 platform.

 To me personally, a killer feature I really like in Python3 is the
 massively improved unicode support.  I don't personally use it, but I
 think it makes Sage much, much more palatable to the international
 community, who like to write code like the following, which was sent
 to me by Ширшов Андрей in Russia, who just one first prize in a
 contest there for applying Sage to ship-building:

 #Sage variable names can be only in Latin characters
 numbers=[1,2,3.5]
 strings=[alpha, beta, gamma]
 names=[Зоя, Яна, Кит]

 второе_имя=Яна

 print(numbers)
 print(strings)
 print(names)
 if второе_имя in names:
 print(Второе имя в списке %s % второе_имя)


 According to
 http://stackoverflow.com/questions/2649544/unicode-identifiers-in-python
  this will never work in Python2 no matter what you do, but it does
 work fine with python3.  So you can put the above in a file cyr.py,
 and type python3 cyr.py, and it works.

 I look at analytics a lot, and the distribution of Sage users is very
 world-wide, with a lot from non-native-English countries, and some of
 them would really appreciate being able to name their variables using
 their own language.In Mathematica (I just checked), there's no
 problem at all with unicode identifiers, so far as I can tell. So
 from the Sage mission statement -- create a viable alternative to the
 Ma's -- it seems critical to our goals to switch to Python 3.

 William


I don't think that we are quite there with switching. For starters we need
both scons and polybori to be updated to support python 3, but beyond that,
the Sage library needs a massive amount of work to make it Python 3
compatible. Moreover, I don't think we have to force the switch, it should
be perfectly possible to support both python 2 and python 3 for a period of
time.

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Re: Re: [sage-devel] The Annual Sage on Python 3 Thread

[R. Andrew Ohana]

On Mon, Dec 30, 2013 at 1:04 PM, William Stein wst...@gmail.com wrote:

 On Mon, Dec 30, 2013 at 12:47 PM, Nils Bruin nbr...@sfu.ca wrote:
  On Monday, December 30, 2013 12:35:37 PM UTC-8, R. Andrew Ohana wrote:
 
  Moreover, I don't think we have to force the switch, it should be
  perfectly possible to support both python 2 and python 3 for a period of
  time.
 
 
  What's the benefit of that? The sage process itself will be running on
 one
  python process. We can't be hybrid with that. So either you make the
 whole
  sage library Py3-capable or not. We could ship both Py2 and Py3 so that
 we
  can run some scripts under Py3 and the sage process under Py2 (or vice
  versa), but having two pythons seems a lot of admin for very little
 benefit.
  I could see a development version that for a while has both to aid
 debugging
  adapting the sage library, but outside of that I don't see a benefit of
  having both.

 The benefit is that we could switch to python3 by default; however, if
 somebody runs into a show-stopper issue, we can tell them: heh, just
 do 'sage --py2' to start your copy of Sage up using python2 instead.
  It directly addresses the main argument that I made against switching
 above.  It sounds technically difficult, but it is certainly possible.


This would certainly be very nice, but

Alternatively, we could have a build flag that determines whether
 everything gets built with py3 or py2.


this would probably be much easier.

It all sounds like a lot of extra pain and work, but it is possible
 and addresses the main argument against switching.


I don't think it is that much work to maintain, as for most python code
there isn't that large of a difference between python 2 and 3. There will
of course be some trickier bits, but how we deal with most of these issues
should occur during the initial porting process.


 Your main argument against this is for very little benefit --
 however, given that only 2% of download from PyPi are for py3, and in
 light of the discussions I linked to, evidence suggests there's
 potentially substantial real benefit to continuing to support the
 python2 ecosystem, at least for now.

  -- William


 
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Re: [sage-devel] Re: Why is patchbot installing stuff?

[R. Andrew Ohana]

On Mon, Dec 30, 2013 at 3:28 PM, Robert Bradshaw 
rober...@math.washington.edu wrote:

 For performance reasons, the patchbot always installs ccache. However,
 this shouldn't fail...


This line in the log looks suspicious:

tee: /tmp/tmp4Y_0j9-sage-git-temp-11630/logs/install.log: No such file
or directory

I don't know who's running this patchbot, but it may be a configuration
error.

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Re: [sage-devel] git trac command

[R. Andrew Ohana]

On Wed, Dec 25, 2013 at 12:36 PM, Volker Braun vbraun.n...@gmail.comwrote:

I've been working on a git trac subcommand to complement the git suite
 with trac integration instead of the separate UI that the sage -dev scripts
 present. This project is the basis for my release management scripts, so I
 have been eating my own dog food for a while now. I think it is now in a
 state where it would be useful to others, so I propose to integrate it as a
 standard spkg. Obligatory vote:

 [ ]  Yes, please
 [X ]  Make it optional
 [ ]  No, you stink

 http://trac.sagemath.org/ticket/15587


IMO, I think for developers who are using git directly that they should be
installing this under /usr/local (or some other prefix that they include in
their paths). In particular, I think it is a very bad idea to integrate the
codebase into the sage codebase for two reasons:

1. It will make it more difficult to get to install the tools in /usr/local
(e.g.), as you will have to hunt down in the sage source code to find the
appropriate setup.py.
2. We will run into the issue of the tools suddenly having a different
feature set while switching between branches (this was incredibly
frustrating for the dev scripts).

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Re: Re: [sage-devel] The Annual Sage on Python 3 Thread

[R. Andrew Ohana]

I disagree with the sentiment that we should make python package X a
standard package because it is useful for Y. At that rate, every
(compatibly licensed) mathematics and science python package will be a
standard part of sage. Because pycrypto is not truly a dependency of the
sage library (i.e. used in a non-trivial manner), nor is it nicely
integrated into to sage (you have to `from pycrypto import foo`), to me it
clearly falls into this boat.

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Re: [sage-devel] Re: Error with trac

[R. Andrew Ohana]

Ok, the issue should hopefully be fixed now.


On Fri, Dec 20, 2013 at 7:41 AM, John Cremona john.crem...@gmail.comwrote:

 I have a variation: I successfully pushed a new commit to #15554, then
 went onto trac to enter the commit hash manually, but get the error
 message


Although in your case, you haven't actually pushed to the branch yet. I've
added a nop (instead of error) if the commit field is invalid (this should
only happen if someone enters the commit field manually -- which no one
should ever have to do).

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Re: [sage-devel] Re: Error with trac

[R. Andrew Ohana]

Yes, sorry. I'll try to look into this sometime this weekend.


On Fri, Dec 20, 2013 at 5:23 PM, Volker Braun vbraun.n...@gmail.com wrote:

 Its a bug in our trac plugin. I'm pretty sure Andrew will fix it when he
 has some time ;-)




 On Saturday, December 21, 2013 12:25:07 AM UTC, John H Palmieri wrote:

 Yes, same for me with #14993. Any ideas what to do about it?

   John

 On Friday, December 20, 2013 2:21:10 AM UTC-8, Frédéric Chapoton wrote:

 I have the same problem with #15550. Quite displeasant.

 Frédéric

 Le vendredi 20 décembre 2013 04:18:37 UTC+1, Travis Scrimshaw a écrit :

 I'm getting the following error anytime I try to attach a new branch to
 a ticket which previously didn't have one (in particular #12453 and #9280):

 *Trac detected an internal error:*

 TypeError: 'unicode' object is not callable

 There was an internal error in Trac. It is recommended that you notify
 your local Trac administrator with the information needed to reproduce the
 issue.

 To that end, you could  a ticket.

 The action that triggered the error was:

 POST: /ticket/9280


 


 Any ideas?


 Thanks,

 Travis


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Re: [sage-devel] The Annual Sage on Python 3 Thread

[R. Andrew Ohana]

I've made #15530 to track the progress on supporting python3 (and there is
already a good amount there that is up for review).


Also, other than the trivial usage in sage.monoids.string_monoid(_element),
I'm not finding any real usage of pycrypto. Am I missing something? If not,
I would elect to make it an optional package.


On Wed, Dec 11, 2013 at 3:48 PM, Dan Drake ddr...@math.wisc.edu wrote:

 On Wed, 11 Dec 2013 at 02:53AM -0800, R. Andrew Ohana wrote:
  But this time with a report!
 
  Broken spkgs:
 
  sagetex (maybe?)

 Why the maybe? What happens if you try to use Py3?

 In January I might be able to update SageTeX to Python 3. It should be
 easy. (Famous last words?)


 Dan

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 ---




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Re: [sage-devel] Re: Ticket #12555 has invalid state

[R. Andrew Ohana]

The problem was the commit messages that had non-ascii characters were not
being properly decoded as utf8 (in this case there was a zero-width space
in one of the commit messages).


On Sun, Dec 15, 2013 at 3:01 PM, Jeroen Demeyer jdeme...@cage.ugent.bewrote:

 On 2013-12-15 23:49, Volker Braun wrote:

 Did you just change it? Because it is displaying fine for me...

 Works now, I guess Andrew fixed it.


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[sage-devel] The Annual Sage on Python 3 Thread

[R. Andrew Ohana]

But this time with a report!

Broken spkgs:

PIL
setuptools (really distribute)
sympy
pycrypto
pynac
rpy2
pexpect
gdmodule
sqlalchemy
networkx
mpmath
zn_poly
sagenb
sagetex (maybe?)
scons
(almost certainly polybori -- it depends on scons)

and a number of others that use python 2 spkg-install scripts, or need
other minor updates.

Of these, setuptools, sympy, rpy2, sqlalchemy, networkx, mpmath, and
pycrypto should be fixed with simple updates (see #15510, #15511, and
#15512 for the first 3). For the others:

gdmodule, PIL, sqlalchemy -- do we use these anywhere? (I don't see any
imports, or even tests of these libraries in our test suite, although I
could be missing something) If not, I think would vote that we should
change these to optional spkgs; reduce the bloat of the base distribution.

PIL -- If we keep this a standard package, we should switch to Pillow, as
upstream PIL is dead.

pynac -- I have a small patch that makes this build against python3, and
hopefully this will be sufficient to make it work.

pexpect, zn_poly -- 2to3 seems to be sufficient for these

scons -- there is on going work to port to python3 (seems likely to come
with the next release)

polybori -- no clue


This leaves a very short list of what packages we are waiting on:
sagenb
scons
polybori
sagetex?
sage library + scripts

In other words, almost everything upstream is ready for Python 3.

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Re: [sage-devel] Re: OS X Mavericks

[R. Andrew Ohana]

They don't supply a Fortran compiler, which we need. Also as of Xcode 5
they no longer supply gcc (the gcc in PATH is actually clang) and some
packages we include depend explicitly on having gcc as our c compiler.

If anything we need our own compiler now more than before, and this
situation doesn't look like it will be changing given Apple's decisions.

Andrew
On Nov 22, 2013 7:47 PM, Stefan stefanvanz...@gmail.com wrote:

 Just wondering... has Apple's compiler by any chance improved enough so we
 can stop building our own GCC?

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Re: [sage-devel] OS X Mavericks

[R. Andrew Ohana]

FYI, this is up for review now.


On Sun, Nov 17, 2013 at 11:51 PM, R. Andrew Ohana andrew.oh...@gmail.comwrote:

 I've opened #15433 to trac porting to 10.9.


 On Sat, Nov 16, 2013 at 10:18 PM, R. Andrew Ohana 
 andrew.oh...@gmail.comwrote:

 Ok, I've successfully built a fully working copy of sage on 10.9 (i.e.
 passes all
 doctests with 3 exceptions, see below).

 polybori: I stopped experiencing the issue others are having (and still
 have not
 been able to figure out what resolved it for me)

 scipy: This seems like more or less the same issue that we had with 10.8
 -- see
 #13309. An easy work around until scipy is updated is to add
 -D__ACCELERATE__ to the CPPFLAGS.

 r: links against CoreData, which in turn links against sqlite.
 Unfortunately, it
 seems like CoreData now requires the extra modules Apple has included in
 the
 system copy of sqlite. As I see it we have 2 options:
 1) include these extra modules to support CoreData
 2) switch to using the system sqlite on osx
 I would vote for the 2nd, as I think it would reduce future headache (and
 it isn't
 crucial for our purposes to have the most recent version of sqlite).
 Doing this
 currently produces 3 doctests errors that explicitly test our copy of
 sqlite

 sage library: the system cblas won't pretend it is atlas anymore, so set
 BLAS2 to 'cblas'

 gcc: at least for me, I was finding that the resulting libstdc++ was
 missing some
 symbols. I haven't looked into this yet (I instead used homebrew's gcc).

 --
 Andrew




 --
 Andrew




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Re: [sage-devel] OS X Mavericks

[R. Andrew Ohana]

I've uploaded a binary to
http://boxen.math.washington.edu/home/ohanar/builds/sage-5.13.beta3-x86_64-Darwin.dmg--
no promises it will work for you.


On Sun, Nov 17, 2013 at 11:51 PM, R. Andrew Ohana andrew.oh...@gmail.comwrote:

 I've opened #15433 to trac porting to 10.9.


 On Sat, Nov 16, 2013 at 10:18 PM, R. Andrew Ohana 
 andrew.oh...@gmail.comwrote:

 Ok, I've successfully built a fully working copy of sage on 10.9 (i.e.
 passes all
 doctests with 3 exceptions, see below).

 polybori: I stopped experiencing the issue others are having (and still
 have not
 been able to figure out what resolved it for me)

 scipy: This seems like more or less the same issue that we had with 10.8
 -- see
 #13309. An easy work around until scipy is updated is to add
 -D__ACCELERATE__ to the CPPFLAGS.

 r: links against CoreData, which in turn links against sqlite.
 Unfortunately, it
 seems like CoreData now requires the extra modules Apple has included in
 the
 system copy of sqlite. As I see it we have 2 options:
 1) include these extra modules to support CoreData
 2) switch to using the system sqlite on osx
 I would vote for the 2nd, as I think it would reduce future headache (and
 it isn't
 crucial for our purposes to have the most recent version of sqlite).
 Doing this
 currently produces 3 doctests errors that explicitly test our copy of
 sqlite

 sage library: the system cblas won't pretend it is atlas anymore, so set
 BLAS2 to 'cblas'

 gcc: at least for me, I was finding that the resulting libstdc++ was
 missing some
 symbols. I haven't looked into this yet (I instead used homebrew's gcc).

 --
 Andrew




 --
 Andrew




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Re: [sage-devel] OS X Mavericks

[R. Andrew Ohana]

I've opened #15433 to trac porting to 10.9.


On Sat, Nov 16, 2013 at 10:18 PM, R. Andrew Ohana andrew.oh...@gmail.comwrote:

 Ok, I've successfully built a fully working copy of sage on 10.9 (i.e.
 passes all
 doctests with 3 exceptions, see below).

 polybori: I stopped experiencing the issue others are having (and still
 have not
 been able to figure out what resolved it for me)

 scipy: This seems like more or less the same issue that we had with 10.8
 -- see
 #13309. An easy work around until scipy is updated is to add
 -D__ACCELERATE__ to the CPPFLAGS.

 r: links against CoreData, which in turn links against sqlite.
 Unfortunately, it
 seems like CoreData now requires the extra modules Apple has included in
 the
 system copy of sqlite. As I see it we have 2 options:
 1) include these extra modules to support CoreData
 2) switch to using the system sqlite on osx
 I would vote for the 2nd, as I think it would reduce future headache (and
 it isn't
 crucial for our purposes to have the most recent version of sqlite). Doing
 this
 currently produces 3 doctests errors that explicitly test our copy of
 sqlite

 sage library: the system cblas won't pretend it is atlas anymore, so set
 BLAS2 to 'cblas'

 gcc: at least for me, I was finding that the resulting libstdc++ was
 missing some
 symbols. I haven't looked into this yet (I instead used homebrew's gcc).

 --
 Andrew




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Re: [sage-devel] OS X Mavericks

[R. Andrew Ohana]

Ok, I've successfully built a fully working copy of sage on 10.9 (i.e.
passes all
doctests with 3 exceptions, see below).

polybori: I stopped experiencing the issue others are having (and still
have not
been able to figure out what resolved it for me)

scipy: This seems like more or less the same issue that we had with 10.8 --
see
#13309. An easy work around until scipy is updated is to add
-D__ACCELERATE__ to the CPPFLAGS.

r: links against CoreData, which in turn links against sqlite.
Unfortunately, it
seems like CoreData now requires the extra modules Apple has included in the
system copy of sqlite. As I see it we have 2 options:
1) include these extra modules to support CoreData
2) switch to using the system sqlite on osx
I would vote for the 2nd, as I think it would reduce future headache (and
it isn't
crucial for our purposes to have the most recent version of sqlite). Doing
this
currently produces 3 doctests errors that explicitly test our copy of sqlite

sage library: the system cblas won't pretend it is atlas anymore, so set
BLAS2 to 'cblas'

gcc: at least for me, I was finding that the resulting libstdc++ was
missing some
symbols. I haven't looked into this yet (I instead used homebrew's gcc).

-- 
Andrew

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[sage-devel] Re: [sage-git] cython cache and speeding up rebuild

[R. Andrew Ohana]

On Sat, Nov 16, 2013 at 10:08 PM, Robert Bradshaw rober...@gmail.comwrote:

 On Sat, Nov 16, 2013 at 9:10 AM, Volker Braun vbraun.n...@gmail.com
 wrote:
  Can somebody remind me of the status of the cython compiler cache?

 Discussion at http://trac.sagemath.org/ticket/13031 , but it may have
 been fixed since then.


I'm pretty sure the issues that were encountered were because of bugs in
the dependency checking (which I believe are largely resolved at this
point). I think
the issue was that there was a lot of opposition to enabling a cache --
which could
easily be resolved with some environment/configuration variable.

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Re: [sage-devel] Re: OS X Mavericks

[R. Andrew Ohana]

Has anyone else been looking into this?

Where I've gotten:

scipy:
  easy fix, just add -D__ACCELERATE__ to CPPFLAGS

polybori:
  this is a phantom bug that I can no longer reproduce (and I don't know
what changed in my environment)

r:
  seems less like an issue with r, than with sqlite -- in particular it
seems CoreData relies more heavily on sqlite now, and the version we build
is missing some stuff that it needs (this is an unfortunate side-effect of
setting DYLD_LIBRARY_PATH)

sage library:
  chokes on -latlas, although setting BLAS2=cblas seems to resolve the
issue

other:
  upon startup, the sage runtime crashes -- the copy of libstdc++ we build
can't seem to find some stuff


On Wed, Nov 6, 2013 at 2:39 PM, William Stein wst...@gmail.com wrote:

 -BEGIN PGP SIGNED MESSAGE-
 Hash: SHA1



 On 11/6/13, 2:34 PM, Jean-Pierre Flori wrote:
 
 
  On Wednesday, November 6, 2013 11:20:00 PM UTC+1, William wrote:
 
  On Mon, Nov 4, 2013 at 5:56 PM, Mike Zabrocki
  mike.z...@gmail.comjavascript: wrote:
  [...] After I installed the new command line tools then I was
  able to build
  from
  source also for about 3 hours and then I encountered the same
  errors
  that
  others are seeing here.
 
  Hi,
 
  In the interest of porting Sage to OS X 10.9, I dug up a macbook
  pro laptop, did a clean install of OS X 10.9 and dev tools on it,
  and put
 
 
  When I get a little more time, I'll try to install Mavericks into a
  virtual machine (if possible, Lion was quite easy) and give it a
  shot as well.
 
  Best,

 Well I just added you to the Sagemath Cloud project, in the hopes you
 can't resist taking a look



 https://cloud.sagemath.com/projects/4148c5ce-7a49-43fd-b558-359172738584/files/

  JP
 
 -BEGIN PGP SIGNATURE-
 Version: GnuPG/MacGPG2 v2.0.22 (Darwin)
 Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/

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 -END PGP SIGNATURE-

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Re: [sage-devel] Re: trac email config

[R. Andrew Ohana]

There could also be an issue with the digital signature if the public key
did not get transferred to the new and configuration.
On Oct 19, 2013 11:18 AM, Volker Braun vbraun.n...@gmail.com wrote:

 I get the following from spamassasin:

 X-Spam-hits: BAYES_00 -1.9, MISSING_HEADERS 1.021, RDNS_NONE 0.793,
  REPLYTO_WITHOUT_TO_CC 1.552, LANGUAGES en, BAYES_USED user, SA_VERSION
 3.3.2

 First, there used to be a Cc: sage-t...@googlegroups.com that is not
 present any more, this is
 REPLYTO_WITHOUT_TO_CC

 Second, reverse dns doesn't work. This nets us a RDNS_NONE penalty:

 $ host trac.sagemath.org
 trac.sagemath.org is an alias for trac.sagedev.org.
 trac.sagedev.org has address 128.208.178.249
 $ host 128.208.178.249
 Host 249.178.208.128.in-addr.arpa. not found: 3(NXDOMAIN)



 On Saturday, October 19, 2013 7:05:22 PM UTC+1, Frédéric Chapoton wrote:

 Hello,

 since the new trac server introduced last week, the trac emails are
 classified as spam in my mailbox. This is very inconvenient. Am I the only
 one observing this ? If not, maybe this could be caused by a
 misconfiguration of the new trac machine ?

 Frédéric

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Re: [sage-devel] Need help with optional spkgs

[R. Andrew Ohana]

On Mon, Oct 7, 2013 at 1:44 PM, Volker Braun vbraun.n...@gmail.com wrote:

 Do you know where in the library the large cremona database is used?
 Grepping for cremona.db doesn't find anything.


It is at sage.databases.cremona, although everything in the library should
be already be up to date (e.g. the small cremona database that is included
as a standard package uses the same underlying code and that still works).

SAGE_DATA in the current mercurial releases is just an alias for
SAGE_LOCAL/share and SAGE_ROOT/data is similarly just a symlink, at this
point it really is just the database install scripts that are using the old
directory.

On Monday, October 7, 2013 9:00:05 PM UTC+1, John Cremona wrote:

 On 7 October 2013 13:58, Volker Braun vbrau...@gmail.com wrote:
  Databases go to SAGE_LOCAL/share. Thats an easy change.

 I hope so. All that database_cremona_ellcurve does is to put one file
 into the right place, which cannot be hard.  Of course the library
 code has to know where that palce is.

 John

 
 
  On Monday, October 7, 2013 1:48:52 PM UTC+1, Martin Albrecht wrote:
 
  It seems to me the database_* packages fail because there is no
  $SAGE_ROOT/data any more. Where should databases be installed to now?
 
 
  On 7 October 2013 12:52, Volker Braun vbrau...@gmail.com wrote:
 
  We need to make sure that the optional spkg still work with the new
 git
  directory layout. I've tried to build all optional spkgs and the
 following
  ran into problems installing. Some failures may be trivial, but some
 spkgs
  will need updating. If you care about one of these, please check the
 build
  log and help transition it to the new directory layout. If it turns
 out that
  nobody cares then we will move the spkg to experimental.
 
  brian
  cunningham_tables
  database_cremona_ellcurve
  database_jones_numfield
  database_kohel
  database_odlyzko_zeta
  database_sloane_oeis
  database_stein_watkins_mini.p0
  database_symbolic_data
  fricas
  fricasaldor
  jsmath_image_fonts
  libcocoa
  libtheora
  mpi4py
  openssl
  p_group_cohomology
  PyQt_x11
  TOPCOM
  valgrind
 
  Logfiles are here:
  http://boxen.math.washington.edu/home/vbraun/Sage/Testing/optional/
 
  The corresponding trac ticket is http://trac.sagemath.org/ticket/14962
 
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[sage-devel] SPKG policy

[R. Andrew Ohana]

I'm trying to review #7539 which aims to include the small primesieve
library in Sage, but I'm not quite up to date on what the current policy is
on including new SPKGs. I thought at one point it was decided that all new
SPKGs needed to be optional for a period before becoming standard, however
there are several fairly recent cases that ignored this policy.

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Re: [sage-devel] Re: New Trac Server

[R. Andrew Ohana]

Yup, this is again the issue of needing more space on the trac server. I
cleared out some more stuff while we continue to wait to get some more disk
space on the system.


On Sun, Jul 21, 2013 at 7:41 AM, Travis Scrimshaw tsc...@ucdavis.eduwrote:

 Hey Andrew,
Somethings wrong with the new trac server:

 OperationalError: could not extend file base/30560/30652: No space left on 
 device
 HINT:  Check free disk space.


 I get this by going to view tickets - tickets needing review. I also get 
 an error message on the view tickets page in the Bugs subheader and trying to 
 view other larger groups of tickets.


 Best,

 Travis


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Re: [sage-devel] Trac server: positive review report broken

[R. Andrew Ohana]

Ok, trac has been updated. Please let me know if you continue to experience
this issue.


On Sun, Jul 21, 2013 at 2:43 PM, R. Andrew Ohana andrew.oh...@gmail.comwrote:

 This was reported upstream and is reported to be fixed. I'll see about
 pulling in the latest source and updating trac.


 On Sun, Jul 21, 2013 at 2:35 PM, Jeroen Demeyer jdeme...@cage.ugent.bewrote:

 On 07/21/2013 11:14 PM, Jeroen Demeyer wrote:

 I must admit that I haven't read the whole thread about the new Trac,
 but it's very annoying that the positive review report is broken:

 http://trac.sagemath.org/sage_**trac/report/40http://trac.sagemath.org/sage_trac/report/40

 ProgrammingError: column reference id is ambiguous
 LINE 9: ...RE ((COALESCE(t.status,'')='**positive_review')) OR id in
 (147...
   ^


 This errors only occurs after making some changes to positive_review
 tickets and then refreshing the page.


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Re: [sage-devel] Trac server: positive review report broken

[R. Andrew Ohana]

This was reported upstream and is reported to be fixed. I'll see about
pulling in the latest source and updating trac.


On Sun, Jul 21, 2013 at 2:35 PM, Jeroen Demeyer jdeme...@cage.ugent.bewrote:

 On 07/21/2013 11:14 PM, Jeroen Demeyer wrote:

 I must admit that I haven't read the whole thread about the new Trac,
 but it's very annoying that the positive review report is broken:

 http://trac.sagemath.org/sage_**trac/report/40http://trac.sagemath.org/sage_trac/report/40

 ProgrammingError: column reference id is ambiguous
 LINE 9: ...RE ((COALESCE(t.status,'')='**positive_review')) OR id in
 (147...
   ^


 This errors only occurs after making some changes to positive_review
 tickets and then refreshing the page.


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Re: [sage-devel] Re: New Trac Server

[R. Andrew Ohana]

On Fri, Jul 19, 2013 at 12:05 AM, John Cremona john.crem...@gmail.comwrote:

 Now when I login (ssh trac) I get

 PTY allocation request failed on channel 0
 hello anonymous, this is git@trac running gitolite3 (unknown) on git
 1.7.9.5

  R W sage
 Connection to trac.sagemath.org closed.


Try again, it should recognize you as cremona. The trac server hard disk
got saturated, but I cleared out some stuff until Keith adds some more
storage to the machine.


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Re: [sage-devel] Re: New Trac Server

[R. Andrew Ohana]

On Fri, Jul 19, 2013 at 12:19 AM, R. Andrew Ohana andrew.oh...@gmail.comwrote:

 On Fri, Jul 19, 2013 at 12:05 AM, John Cremona john.crem...@gmail.comwrote:

 Now when I login (ssh trac) I get

 PTY allocation request failed on channel 0
 hello anonymous, this is git@trac running gitolite3 (unknown) on git
 1.7.9.5

  R W sage
 Connection to trac.sagemath.org closed.


 Try again, it should recognize you as cremona. The trac server hard disk
 got saturated, but I cleared out some stuff until Keith adds some more
 storage to the machine.


Which, I should say, is why the changes didn't propagate.

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Re: [sage-devel] Re: New Trac Server

[R. Andrew Ohana]

On Thu, Jul 18, 2013 at 3:58 PM, Dima Pasechnik dimp...@gmail.com wrote:

 can it be a bit more detailed? I have no idea how to get a working Sage
 git tree to begin with. Is it documented anywhere?


Ok, I've updated https://github.com/sagemath/sage/wiki. Let me know if
there is anything that is still unclear.

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Re: [sage-devel] Re: New Trac Server

[R. Andrew Ohana]

On Wed, Jul 17, 2013 at 11:44 PM, P Purkayastha ppu...@gmail.com wrote:

 The new trac looks good! Almost every link has a square box next to it. Is
 that intentional?


Looking at the front page of trac it appears to indicate links that leave
trac, so I imagine yes, it was an intentional change made upstream. No clue
on if it is configurable or not.

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