[sage-devel] Workaround for missing link to MacTex for MacOS Sage app

[Michael Frey]

I found that when trying to access LATeX (MacTeX) calls in a Sage notebook 
via MatPlotLib or directly Sage would report that it could not find some 
TeX function.  It appears that the PATH variable being used by the Sage app 
is pointing to /usr/texbin, not /Library/TeX/texbin.  As a workaround I 
modified src/mac-app/start-sage.sh and added:

if test -d /Library/TeX/texbin

then

export PATH=$PATH:/Library/TeX/texbin

fi


After rebuilding the Sage app dmg, Sage works as expected when accessing 
TeX calls.


There may be a better way, but I could not find one searching through the 
Sage source.


I am not sure how proceed with getting this corrected so users do not have 
the manually edit the start-sage.sh file.


Regards,


Mike

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Re: [sage-devel] Re: Python3?

[Jeroen Demeyer]

On 2017-01-19 17:44, William Stein wrote:

On Thu, Jan 19, 2017 at 9:39 AM, Jeroen Demeyer  wrote:

On 2017-01-19 17:17, William Stein wrote:


... and presumably what we already decided is now completely
impossible to implement and banned from Python3?



I don't think we ever decided anything. For Parents, we use Robert
Bradshaw's implementation from 2008 but it's not documented what it does or
why it does things that way. For example, there is a doctest

sage: ZZ < QQ
True

but I doubt that this is the right thing to do.


Let me rewrite the above: ... and presumably what we already
**implemented** is now completely
impossible to implement and banned from Python3?


It's mostly possible. However, what's the point of trying to reverse 
engineer the current code when it probably doesn't do the right thing? 
Since we have to change comparison code anyway for Python 3, we should 
use this opportunity to properly define how comparison should work.


Secondly, Python 3 has different "best practices" for comparison 
compared to Python 2. Example:


Python 2.7.5:
>>> 1 < "x"
True

Python 3.4.1:
>>> 1 < "x"
Traceback (most recent call last):
  File "", line 1, in 
TypeError: unorderable types: int() < str()

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Re: [sage-devel] Re: Python3?

[Jeroen Demeyer]

On 2017-01-19 19:18, Travis Scrimshaw wrote:

I thought Frédéric actually removed that test (at my insistence)?


Maybe in a ticket which is not merged yet? In any case, that test is 
still there in 7.5.1.


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Re: [sage-devel] Re: Python3?

['Julien Puydt' via sage-devel]

Hi,

On 19/01/2017 18:44, William Stein wrote:

On Thu, Jan 19, 2017 at 9:39 AM, Jeroen Demeyer  wrote:

On 2017-01-19 17:17, William Stein wrote:


... and presumably what we already decided is now completely
impossible to implement and banned from Python3?



I don't think we ever decided anything. For Parents, we use Robert
Bradshaw's implementation from 2008 but it's not documented what it does or
why it does things that way. For example, there is a doctest

sage: ZZ < QQ
True

but I doubt that this is the right thing to do.


Let me rewrite the above: ... and presumably what we already
**implemented** is now completely
impossible to implement and banned from Python3?


Well, if it is implemented but doesn't really make sense, is it that big 
a problem to drop it for the transition to Python 3 ?


Snark on #debian-science

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Re: [sage-devel] Re: Python3?

[Travis Scrimshaw]

For the cmp problem, Jeroen as suggested implementing our own cmp function. 
Thus, we just add this to the imports of every file that we don't want to 
go to rich comparisons (i.e., that needs it), which tries calling __cmp__ 
then falls back to ordering. This should at least get all of Sage to 
compile (when I said this before, I was thinking only of Cython files and 
forgot that we actually compile python files [in a different sense]), but 
it pushes the problem under the rug.

Best,
Travis


On Thursday, January 19, 2017 at 11:39:13 AM UTC-6, Jeroen Demeyer wrote:
>
> On 2017-01-19 17:17, William Stein wrote: 
> > ... and presumably what we already decided is now completely 
> > impossible to implement and banned from Python3? 
>
> I don't think we ever decided anything. For Parents, we use Robert 
> Bradshaw's implementation from 2008 but it's not documented what it does 
> or why it does things that way. For example, there is a doctest 
>
> sage: ZZ < QQ 
> True 
>
> but I doubt that this is the right thing to do. 
>

I thought Frédéric actually removed that test (at my insistence)?

Best,
Travis

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[sage-devel] Re: R fails to compile

[Rob Gross]

Hi,

A bit more clarification.  I upgraded to 7.5.1 using sage --upgrade.  There 
is a copy of libiconv in /usr/local/lib and one that the Mac OS installs in 
/usr/lib.  The command "sage -installed" reports that iconv is installed.

This is obviously a minor problem, given that no one else has reported it, 
and I'm happy to use the Mac where the upgraded ran flawlessly until the 
next upgrade, which might clear up the problem.--Rob

On Wednesday, January 18, 2017 at 7:15:33 PM UTC-5, Samuel Lelievre wrote:
>
>
>
> Tue 2017-01-17 02:24:54 UTC, Rob Gross:
>
> > I tried to upgrade to 7.5.1 on several different Macs which I thought 
> had identical software.
> >
> > However, on one of them, R failed to compile, with the error:
> >
> >   installing 'sysdata.rda'
> > dyld: Symbol not found: __libiconv_version
> >   Referenced from: 
> /Users/gross/sage-7.0/local/var/tmp/sage/build/r-3.2.4-revised.p0/src/lib/libR.dylib
> >   Expected in: flat namespace
> >  in 
> /Users/gross/sage-7.0/local/var/tmp/sage/build/r-3.2.4-revised.p0/src/lib/libR.dylib
> > /bin/sh: line 1: 22794 Doneecho 
> "tools:::sysdata2LazyLoadDB(\"./R/sysdata.rda\",\"../../../library/tools/R\")"
> >  22795 Abort trap: 6   | R_DEFAULT_PACKAGES=NULL LC_ALL=C 
> ../../../bin/R --vanilla --slave
> >
> > Any ideas?
> >
> > Thanks.--Rob
>
> Just to make sure, you are working in a directory called
>
>  /Users/gross/sage-7.0
>
> but you have checked out the sources for version 7.5.1 using git,
> is that right?
>

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[sage-devel] GSoC 2017 kickoff

[Harald Schilly]

Hello, this year's Google Summer of Code 2017 just started.

I assume we will try again to be part of it, and therefore I've
started the registration process.

The most important aspect is to have mentors and project proposals.
For that, I've started this year's wiki page as a copy of last year:

https://wiki.sagemath.org/GSoC/2017 (compare with 2016)

The deadline for the application is Feb. 9th and I'm again working on
this like in the past 5 years.

-- Harald

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Re: [sage-devel] Re: Python3?

[William Stein]

On Thu, Jan 19, 2017 at 9:39 AM, Jeroen Demeyer  wrote:
> On 2017-01-19 17:17, William Stein wrote:
>>
>> ... and presumably what we already decided is now completely
>> impossible to implement and banned from Python3?
>
>
> I don't think we ever decided anything. For Parents, we use Robert
> Bradshaw's implementation from 2008 but it's not documented what it does or
> why it does things that way. For example, there is a doctest
>
> sage: ZZ < QQ
> True
>
> but I doubt that this is the right thing to do.

Let me rewrite the above: ... and presumably what we already
**implemented** is now completely
impossible to implement and banned from Python3?

 -- William

>
>
> --
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Re: [sage-devel] Re: Python3?

[Jeroen Demeyer]

On 2017-01-19 17:17, William Stein wrote:

... and presumably what we already decided is now completely
impossible to implement and banned from Python3?


I don't think we ever decided anything. For Parents, we use Robert 
Bradshaw's implementation from 2008 but it's not documented what it does 
or why it does things that way. For example, there is a doctest


sage: ZZ < QQ
True

but I doubt that this is the right thing to do.

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Re: [sage-devel] Re: Python3?

[William Stein]

On Thu, Jan 19, 2017 at 9:08 AM, Jeroen Demeyer  wrote:
> On 2017-01-19 07:47, Frédéric Chapoton wrote:
>>
>> For 1C), the cmp problem has not been considered yet, but it is *huge*.
>
>
> An important part of the cmp() problem is that we need to decide *how*
> comparison of Sage objects should work.

... and presumably what we already decided is now completely
impossible to implement and banned from Python3?

>
> For example, it seems that we cannot really agree on what should happen with
> "x != y" when x and y cannot be coerced to a common parent.
>
> The same with things like "ZZ < QQ".
>
>
> --
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Re: [sage-devel] Re: Python3?

[Jeroen Demeyer]

On 2017-01-19 07:47, Frédéric Chapoton wrote:

For 1C), the cmp problem has not been considered yet, but it is *huge*.


An important part of the cmp() problem is that we need to decide *how* 
comparison of Sage objects should work.


For example, it seems that we cannot really agree on what should happen 
with "x != y" when x and y cannot be coerced to a common parent.


The same with things like "ZZ < QQ".

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Re: [sage-devel] Re: Our SSL serial drama-cum-cliffhanger

[Dima Pasechnik]

Are you able to build Sage under/in homebrew?

On Thursday, January 19, 2017 at 3:01:49 PM UTC, Kosta wrote:
>
> Right now (pre-ticket) if you try to build sage on OSX Sierra and above, 
> it will be built without
> OpenSSL support. I'm not sure what happens if you download a prebuilt 
> package but somehow I assumed
> that if you don't have OpenSSL installed, then you can't use OpenSSL 
> (otherwise I don't understand
> the whole discussion re GPL/OpenSSL). My comment regarding installing sage 
> via homebrew is with this
> in mind, since right now it simply automatically installs the prebuilt 
> package.
>
> The ticket addresses the building issue - it looks for the headers in a 
> user specified location (in an environment variable) if it is defined, and 
> otherwise in the location that homebrew installs to.
>
> -- 
> Konstantin Kliakhandler
> http://slumpy.org
>   )°) )°( (°(
>
> On 18 January 2017 at 20:56, Dima Pasechnik  > wrote:
>
>>
>>
>> On Wednesday, January 18, 2017 at 1:20:20 PM UTC, Emmanuel Charpentier 
>> wrote:
>>>
>>> I'm not sure to understand the ticket. Does that means that OS X Sage 
>>> will depend on Apple's SSL library ? Or depend on a systemwide OpenSSL ? Or 
>>> am I mistaken entirely ?
>>>
>>> Apple still sneakily ships OpenSSL headers in XCode, for some sort of 
>> upgrading tools, I guess.
>> The location is unstable, though, it chnages from one version of XCode to 
>> another :-)
>>
>> Using homebrew to build Sage on OSX isn't well-explored, IMHO. It might 
>> work, given some effort is made.
>>
>>  
>>
>>> --
>>> Emmanuel Charpentier
>>>
>>> Le lundi 16 janvier 2017 21:07:40 UTC+1, Kosta a écrit :

 Regarding OSX, take a look at ticket 21944 
  [basically a way to either 
 specify where to find the openssl headers or to use the homebrew headers 
 if 
 available].

 The homebrew package can be made to depend on the openssl package. 
 Finally, regarding packaged .app - I don't know. I think it would be 
 reasonable to prompt the user about this issue if the dynamic library is 
 not found. I may be wrong, but I think that in recent years homebrew has 
 become the de-facto package manager and in older OS versions openssl was 
 present, so it would be fairly reasonable to just prompt the user to 
 install homebrew and then install via homebrew.

 Cheers,
 Kosta

 -- 
 Konstantin Kliakhandler
 http://slumpy.org
   )°) )°( (°(

 On 15 January 2017 at 15:51, Emmanuel Charpentier <
 emanuel.c...@gmail.com> wrote:

> A first step  towards a 
> solution awaits your comments and review.
>
> Plan :
>
>1. Document OpenSSL dependency, mention the possibility of 
>compiling againts GnuTLS (with drawbacks)
>2. Get OpenSSL development libs on the machines producing Unix 
>binary tarballs/packages.
>3. (To be discussed) : create a standard "SSL" package serving as 
>a backup, allowing compilation on OpenSSL-less machines. As done for 
> git, 
>this package should do nothing if OpenSSL is installed systemwide.
>4. Complete curl as a standard package, which would allow :
>5. Upgrade R. Pffwww...
>
> Unsolved problem : What about Macs (I don't have a Mac and can't 
> contribute).
>
> To be discussed : Cygwin (advoce from Erik Bray keenly awaited...).
>
> HTH,
>
> --
> Emmanuel Charpentier
>
> Le dimanche 1 janvier 2017 02:55:42 UTC+1, Emmanuel Charpentier a 
> écrit :
>>
>> Dear list,
>>
>> We have three separate, but interacting, difficulties with SSL/TLS 
>> support in Sage. I'll summarize the results of the efforts of several 
>> people who tracked them, and propose a couple of solutions.
>>
>> *I) Python now (discreetly) depends on Open SSL.*
>>
>> Their license page  states :
>>
>>> The modules hashlib 
>>> , 
>>> posix , 
>>> ssl , crypt 
>>>  use the 
>>> OpenSSL library for added performance if made available by the 
>>> operating system. Additionally, the Windows and Mac OS X installers for 
>>> Python may include a copy of the OpenSSL libraries, so we include a 
>>> copy of 
>>> the OpenSSL license here:
>>>
>> followed by the bizarre OpenSSL license. For our purpose, the 
>> important statement is *"use the OpenSSL library for added 
>> performance if made available by the operating system."*.
>>
>> "Added performance, my 

Re: [sage-devel] Re: Python3?

[Erik Bray]

On Thu, Jan 19, 2017 at 8:47 AM, Frédéric Chapoton  wrote:
> Hello,
>
> let me try to summarize : we are still quite far from being python3
> compatible.
>
> There are two main milestones we must reach:
>
> 1)  being able to build sage with python3 ;
> (with substeps: 1A) being able to cythonize all pyx files / 1B) being able
> to compile all pyx files) 1C) being able to build all py files.
>
> 2) having all doctests pass
>
> Currently, progress is very slowly being made on 1) and some changes are
> made in parallel (in a blind way) for 2)
>
> Concerning 1), I would say cmp and unicode are the main remaining problems.
> Integer division has almost been tackled, but not quite.
>
> The problem with cmp is quite hard, and it seems that every instance of
> cmp() must be handled separately. I have gained some experience on the
> subject, but given the lack of reviewers, this implies a very slow pace.
> This cmp problem should be the last remaining thing to handle before
> reaching 1A) and maybe even 1B)
>
> For 1C), the cmp problem has not been considered yet, but it is huge.
>
> Unicode problem has almost not been looked at either. I just had a quick
> look at #14153.
>
> Concerning having doctests pass 2), some work has already been done, but
> given that we are not able to build, this is done without any check, which
> is bad. Here, we are trying (in the dark) to prepare things for when build
> will happen.
>
> Some general comments : I have been told to make progress by small steps, so
> using many tickets. This is maybe better for stability, but implies that
> every single move takes a long time to enter sage: review and closing may
> take months. Very often, I must stop working on python3, because there are
> already many positively reviewed tickets, and only much later they willl be
> closed. I need them to be cleaned up to have a clear view of the situation.
>
> Another problem is regression. I have made patchbot plugins to try and
> prevent incompatible code to enter sage again. This is not sufficient. We
> need to have the doctest framework itself check that there is no bad print
> and a few other solved issues. I have required help to do that, but nobody
> stepped in.
>
> I would like to thank here the people that have been tirelessly refering so
> many of the python3 tickets, in particular Travis, Jeroen and Jori. If some
> other people are interested, reviewing tickets would be helpful. Or even
> working on the remaining issues. I did not want to do all this just me
> alone...

I am hoping to help more with this especially once the Cygwin
situation is wrapped up a bit more neatly and I have the Cygwin
built-bot up and running.  I can especially help with string-related
issues as I have a lot of experience with Python 3 porting, and
especially as it relates to that.

I can't be of much help with the cmp stuff since it seems to rely on
knowledge of how various objects in Sage are expected to work that I
don't have a firm grasp on.  As you say, it needs to be handled on a
case-by-case basis and it would probably be a big help to you (and
Sage in general) to have a bugbash on that.

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Re: [sage-devel] Re: Our SSL serial drama-cum-cliffhanger

[Konstantin Kliakhandler]

Right now (pre-ticket) if you try to build sage on OSX Sierra and above, it
will be built without
OpenSSL support. I'm not sure what happens if you download a prebuilt
package but somehow I assumed
that if you don't have OpenSSL installed, then you can't use OpenSSL
(otherwise I don't understand
the whole discussion re GPL/OpenSSL). My comment regarding installing sage
via homebrew is with this
in mind, since right now it simply automatically installs the prebuilt
package.

The ticket addresses the building issue - it looks for the headers in a
user specified location (in an environment variable) if it is defined, and
otherwise in the location that homebrew installs to.

-- 
Konstantin Kliakhandler
http://slumpy.org
  )°) )°( (°(

On 18 January 2017 at 20:56, Dima Pasechnik  wrote:

>
>
> On Wednesday, January 18, 2017 at 1:20:20 PM UTC, Emmanuel Charpentier
> wrote:
>>
>> I'm not sure to understand the ticket. Does that means that OS X Sage
>> will depend on Apple's SSL library ? Or depend on a systemwide OpenSSL ? Or
>> am I mistaken entirely ?
>>
>> Apple still sneakily ships OpenSSL headers in XCode, for some sort of
> upgrading tools, I guess.
> The location is unstable, though, it chnages from one version of XCode to
> another :-)
>
> Using homebrew to build Sage on OSX isn't well-explored, IMHO. It might
> work, given some effort is made.
>
>
>
>> --
>> Emmanuel Charpentier
>>
>> Le lundi 16 janvier 2017 21:07:40 UTC+1, Kosta a écrit :
>>>
>>> Regarding OSX, take a look at ticket 21944
>>>  [basically a way to either
>>> specify where to find the openssl headers or to use the homebrew headers if
>>> available].
>>>
>>> The homebrew package can be made to depend on the openssl package.
>>> Finally, regarding packaged .app - I don't know. I think it would be
>>> reasonable to prompt the user about this issue if the dynamic library is
>>> not found. I may be wrong, but I think that in recent years homebrew has
>>> become the de-facto package manager and in older OS versions openssl was
>>> present, so it would be fairly reasonable to just prompt the user to
>>> install homebrew and then install via homebrew.
>>>
>>> Cheers,
>>> Kosta
>>>
>>> --
>>> Konstantin Kliakhandler
>>> http://slumpy.org
>>>   )°) )°( (°(
>>>
>>> On 15 January 2017 at 15:51, Emmanuel Charpentier <
>>> emanuel.c...@gmail.com> wrote:
>>>
 A first step  towards a
 solution awaits your comments and review.

 Plan :

1. Document OpenSSL dependency, mention the possibility of
compiling againts GnuTLS (with drawbacks)
2. Get OpenSSL development libs on the machines producing Unix
binary tarballs/packages.
3. (To be discussed) : create a standard "SSL" package serving as a
backup, allowing compilation on OpenSSL-less machines. As done for git,
this package should do nothing if OpenSSL is installed systemwide.
4. Complete curl as a standard package, which would allow :
5. Upgrade R. Pffwww...

 Unsolved problem : What about Macs (I don't have a Mac and can't
 contribute).

 To be discussed : Cygwin (advoce from Erik Bray keenly awaited...).

 HTH,

 --
 Emmanuel Charpentier

 Le dimanche 1 janvier 2017 02:55:42 UTC+1, Emmanuel Charpentier a
 écrit :
>
> Dear list,
>
> We have three separate, but interacting, difficulties with SSL/TLS
> support in Sage. I'll summarize the results of the efforts of several
> people who tracked them, and propose a couple of solutions.
>
> *I) Python now (discreetly) depends on Open SSL.*
>
> Their license page  states :
>
>> The modules hashlib
>> ,
>> posix ,
>> ssl , crypt
>>  use the
>> OpenSSL library for added performance if made available by the
>> operating system. Additionally, the Windows and Mac OS X installers for
>> Python may include a copy of the OpenSSL libraries, so we include a copy 
>> of
>> the OpenSSL license here:
>>
> followed by the bizarre OpenSSL license. For our purpose, the
> important statement is *"use the OpenSSL library for added
> performance if made available by the operating system."*.
>
> "Added performance, my a^htired foot : Thierry has checked the
> possibilities of an OpenSSL-less Sage, and I have further checked other
> possibilities. Our trials conclusively demonstrate that Gnu TLS can't be
> substituted to OpenSSL for at least the following reasons :
>
>- Sage's pip is non-functionnal when 

Re: [sage-devel] Sage runs in Window's 10's new Unix subsystem

[GK]

On Thursday, January 12, 2017 at 2:00:37 PM UTC+3, David Joyner wrote:
>
> On Thu, Jan 12, 2017 at 3:43 AM, GK  
> wrote: 
> > 
> >> 
> >> I am not having any problem starting the notebook. You might genuinely 
> be 
> >> out of memory, or hard drive space. 
> >> 
> > 
> > I am not having trouble starting the notebook either, but I can not do 
> > anything with it, also, no, I am not running out of memory nor hard disk 
> > space. 
> > 
>
> I've tested the notebook out at work where there's a windows machine. 
> (a) It doesn't seem to work in IE. 
> (b) In chrome and FF, the initial command is very slow. Maybe 15 
> seconds or more. After that, it speeds up but is never snappy like the 
> CLI. 
> (c) I only tried the CLI once in windows and it seems to work fine. I 
> don't remember it being slow. 
>
> GK: Does your experience match this? 
>

Dear David,

(a) I haven't tried IE or Chrome, I tried FF and Edge and did not notice 
any difference between the browsers.
(b) Even when it was working, the notebook indeed needed a lot of time to 
load, just as you describe. After that, the speed was OK.
(c) Although I haven't done any complex work on the CLI, it does indeed 
seem to work normally and snappy.
 

>
> > I have increased the amount of virtual memory usable by windows to a 
> > ridiculous amount and I am running everything and monitoring my system 
> at 
> > the same time and memory/hard disk space do not run out. Perhaps the 
> amount 
> > of memory or hard disk space allocated by windows to the linux subsystem 
> > does actually run out, but I do not know how to check that. I related 
> the 
> > problem with the windows update, as exactly before the update everything 
> ran 
> > smoothly and right after the update sage never ran again. I do not think 
> > this is a coincidence... 
> > 
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[sage-devel] Re: Closing wontfix-tickets

[Frédéric Chapoton]

+1, please

Le jeudi 19 janvier 2017 09:48:58 UTC+1, Jori Mäntysalo a écrit :
>
> Could someone close all 49 wontfix-positive_review -tickets? 
>
> IMO it would be nice to have this done after every stable release. 
>
> -- 
> Jori Mäntysalo 
>

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Re: [sage-devel] Python3?

[Jeroen Demeyer]

On 2017-01-19 04:17, Travis Scrimshaw wrote:

Frédéric has been working on getting stuff Python3 compatible. When he
wakes up, he probably will give us an assessment. I believe he is able
to get Sage to compile with Python3 with perhaps a few small tickets.


Note the word "compile", which is not the same as actually functioning.

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[sage-devel] Closing wontfix-tickets

[Jori Mäntysalo]

Could someone close all 49 wontfix-positive_review -tickets?

IMO it would be nice to have this done after every stable release.

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Jori Mäntysalo

Re: [sage-devel] Re: Python3?

[Frédéric Chapoton]

There is no summary page for the cmp situation anywhere.

You can look at #16537 and #17175

To know how this was solved in some cases, look at the tickets here:

https://trac.sagemath.org/query?component=python3

having cmp in the title. Almost every case is different, because it can be 
either pyx_file/py_file, cython_class/python_class, coercion/no_coercion, 
and so on.

To get rid of the call to cmp(), one often has to replace __cmp__ or _cmp_ 
by something else, and the something depends very much on the context.

But maybe I am just saying nonsense. Jeoren, please correct me.

Frederic


Le jeudi 19 janvier 2017 08:58:24 UTC+1, Snark a écrit :
>
> Hi, 
>
> On 19/01/2017 08:47, Frédéric Chapoton wrote: 
>
> > The problem with cmp is quite hard, and it seems that every instance of 
> > cmp() must be handled separately. I have gained some experience on the 
> > subject, but given the lack of reviewers, this implies a very slow pace. 
> > This cmp problem should be the last remaining thing to handle before 
> > reaching 1A) and maybe even 1B) 
>
> is there some place with a good summary of the cmp situation, and can 
> you point at some patches showing how the matter is fixed? 
>
> Thanks, 
>
> Snark on #debian-science 
>

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