[sage-devel] Re: Invitation to Participate in Survey: Governance and Community building

[jplab]

Hello everyone,

This is a reminder to fill out the survey before August 1st.

Thanks a lot to the people that took the time to answer!

Best regards,

The SageMath Code of Conduct Committee

Le lundi 1 juillet 2024 à 22:44:00 UTC-4, tcsc...@gmail.com a écrit :

> Thank you for taking the time to make and review the results of this 
> survey.
>
> Best,
> Travis
>
> On Friday, June 28, 2024 at 1:08:02 PM UTC+9 Anne Schilling wrote:
>
>> Thank you for taking the initiative!
>>
>> Best wishes,
>>
>> Anne
>>
>> On Thursday, June 27, 2024 at 4:46:21 AM UTC-7 Sébastien Labbé wrote:
>>
>>> Good idea! I will take the time to answer the survey soon.
>>>
>>> Sébastien
>>>
>>>

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Re: [sage-devel] Re: ask.sagemath.org issues - do we need it?

[jplab]

Hello,

Jumping in here...

1) I remember discussions from the past while the (Anything)overflow era 
was booming, there was ideas to create the Sageoverflow database of Q 
For me, the main reason not to go is *ownership of the data* and *hosting*. 
As Sébastien perfectly illustrated, the immense heritage of the answers 
there carries a *huge value* and should not be lost. Be it only for the 
sake of the time spent answering questions. How to make sure that Q 
remain in our hands and that we do not depend on the good will of hosting 
platforms? Having ask-sage as it is currently satisfies this, and I am 
happy about that.

2) I myself use it very very often to find answers, and I do not always 
logging to add my thumbs up (and probably many users do the same...), *so 
seeing that there aren't many upvotes might not be a fair indication of 
value here*. There are also answers with many upvotes...

3) I just come back from a Summer School (ECCO 2024) in Colombia where I 
taught Sage to 130 students, and I do mention that AskSage exists and they 
can ask their questions there. Yes, the 0 year bug is annoying, but a user 
doesn't care: they care about getting the answer quickly, period. Meanwhile 
I asked the students that know about Sage where they get their knowledge 
from, and many told me that asksage is a very useful ressource to get the 
answers they need: asksage is well-known to the Sage-user base. So again, I 
think that a simple-and-stupid Q webpage has its value. The simpler it is 
for the user, the better.

Side question: what is necessary to host such a webpage? I could ask my IT 
about the possibilities to host such a page at my department.

Best,
Jean-Philippe





Le jeudi 4 juillet 2024 à 11:13:12 UTC-4, kcrisman a écrit :

> Thank you Sébastien for standing up for users, for distinguishing between 
> users and developers, and for recognizing that those two groups have 
> different needs.  May your Karma increase exponentially!
>
>
>
> This is the point which we must keep hammering home.  Sage users and 
> developers are not the same thing.  This is often in tension (as has also 
> been pointed out numerous times) with the limited, unpaid, developer time 
> issue, and that one is also important.  However, the latter issue gets a 
> lot more screen time.
>
> With respect to Discourse specifically, I just played with it a little 
> bit, and though I was open to it given the import option, unfortunately it 
> seems a lot more like Discord (Slack?) than a pure Q site.  I think the 
> problem isn't going to be so much not having karma (though I admit that 
> when I had time to be very active on it that was some motivation) for 
> contributors, as that it's sort of like the hoops I had to jump through 
> getting help when I built a computer with my kids.
>
> The help forum was on Discord.  Okay, so first I have to sign up.  Then I 
> have to figure out what "channels" are, and where my question belongs.  And 
> then there are "welcome" things, and so on and so forth.  While Discourse 
> seems to have different names for these things, the level of complexity is 
> still there.  That's what makes Q sites (not just ask, or the Stack* 
> sites, but also Quora or whatever) popular.  There is ONE thing they do, 
> and that's what you do.  You ask questions, you get answers.  
>
> I'll be the first to admit that ask.sagemath looks a bit dated, and that 
> the "0 years" bug is annoying, and that there are plenty of questions not 
> followed up on.  (That's also the case for Sage questions on 
> Stackoverflow.)  And I am impressed that there are still users helping each 
> other with Sage and CoCalc stuff on the CoCalc Discord, which has long 
> since been *officially* abandoned by CoCalc (though William checks once in 
> a great while). Infrastructure/hosting has been a problem too, as noted at 
> various points in the thread.
>
> However, ask.sagemath seems stable enough right now in terms of actual 
> functionality, and is just very easy for people to sign up for and use.  I 
> think the community should be very hesitant to add additional barriers to 
> participation by *users*, some of which (as is clear if you read enough 
> posts) definitely are not going to be engaging in a more Discourse-like 
> option.  Or, if we have to do something like that, it would be almost 
> better to archive ask.sagemath and point people to Zulip, which seems (to 
> the laity such as myself) to be pretty much like Discourse, except that 
> there is already a (somewhat?) thriving number of Sage people using it!   
>
> Still, the first thing should be to figure out if anyone has contacted the 
> askbot developer to ask the relevant questions.  I see that he still 
> participates regularly on his own forum, though (annoyingly) didn't respond 
> to the questions Samuel L. asked recently.  
>
> Not-as-random-as-you-think links:
> * https://stackshare.io/stackups/discourse-vs-zulip (because they do seem 
> similar)
> * 
> 

[sage-devel] Invitation to Participate in Survey: Governance and Community building

[jplab]

Dear SageMath Community,

As most of you are likely aware, our communication platforms surrounding 
the development of Sagemath have unfortunately been the scene of 
inappropriate behavior, which has impacted our progress and overall 
community atmosphere. In light of this, and as part of our ongoing efforts 
to improve and move our project forward, the Code of Conduct Committee is 
conducting a survey to gather insight and feedback from our community 
members. Your input is crucial in shaping the future of SageMath, and we 
kindly invite you to participate.

In order to encourage open and honest feedback, the Code of Conduct 
Committee will evaluate the responses to the survey and present them in an 
anonymized way to the community. One question asks for your name, but this 
is optional. Giving your name allows us to ask for clarification if needed. 
If you want to submit some answers with your name attached and others 
anonymously, feel free to submit multiple responses to the survey. This 
initiative is meant to foster a supportive and constructive dialogue that 
should not take place as a response to this message, but rather in a 
regulated, open forum once the survey has been completed.

By participating, you will contribute to a comprehensive understanding of 
our community's needs. Your voice matters, and we are eager to hear your 
thoughts and suggestions.

Please click on the link below to access the survey:

https://forms.gle/Nj8fcS9wNDJReZvc9

The survey will remain open until August 1st, and we encourage you to share 
your views before this date. Thank you for your time and for being an 
integral part of our community.

Best regards,

The SageMath Code of Conduct Committee

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Re: [sage-devel] Urgent: Please vote on these "disputed" PRs

[jplab]

Dear all,

The Code of Conduct Committee considered the issue and found no need for 
David to recuse himself as requested.


We would like to use this opportunity to clarify that messages sent by any 
of us and signed as “The Code of Conduct Committee” have been approved by 
the entire committee. The person sending that message is just the 
messenger, the one who volunteered to send the message at an agreed time.


Sincerely,

The Code of Conduct Committee


Le vendredi 12 avril 2024 à 15:00:51 UTC-4, Matthias Koeppe a écrit :

> I have asked David Roe to recuse himself from any further 
> discussions/actions involving me in the CoCC.
>
> The persistent refusal to make a distinction between *abusive conduct* and 
> *calling out abuse* has caused too much damage already.
>
> Matthias
>
> On Wednesday, April 10, 2024 at 9:28:40 PM UTC-7 David Roe wrote:
>
> We have received messages from several people that the level of discord on 
> display between Dima and Matthias makes them feel uncomfortable 
> participating on this email list. To protect the community from this 
> acrimony, we are for now restricting Dima and Matthias to moderated 
> contributions on sage-devel.  We are sad in taking this step, and are 
> continuing to work privately with both Dima and Matthias to resolve this 
> conflict.
> David
> for the sage-conduct committee
>
> On Wed, Apr 10, 2024 at 7:30 PM Matthias Koeppe  
> wrote:
>
> Reported.
>
> On Wednesday, April 10, 2024 at 3:39:56 PM UTC-7 Dima Pasechnik wrote:
>
> On Wed, Apr 10, 2024 at 6:14 PM Matthias Koeppe  
> wrote:
>
> On Wednesday, April 10, 2024 at 6:49:11 AM UTC-7 julian...@fsfe.org wrote:
>
> We have carefully reviewed [...]
>
> We therefore disagree with characterizing opposing opinions as “artificial 
> friction”, “hostile demands”, or an “attempt to sabotage”.
> Such allegations will have no effect other than to antagonize the other 
> party. This is not helpful in fostering constructive debate.
>
>
> Julian, please, that's highly inappropriate. I'm not characterizing 
> opposing *opinions*.
>
>
> Matthias, you keep characterizing my input into discussions as "persistent 
> abusive conduct", see e.g. your
> https://github.com/sagemath/sage/pull/36676#issuecomment-2048352139
>
> I demand a public apology, and a lift of the block on GitHub.
> Else Matthias should be banned from SageMath for a while, if not 
> permanently. Enough is enough. 
>
> Dima
>
>
> With this terminology I'm describing the modes of existing, persistent, 
> non-constructive *actions* on these PRs by others. 
>
>
> These are not "allegations"; what I am describing has been happening in 
> plain sight, is fully documented, and has been reported to the sage-abuse 
> and CoCC committees. As you know, some of these have already led to 
> sanctions by the committees, while I am still waiting for acknowledgment 
> (and clear actions) regarding numerous reported violations of our code of 
> conduct (and reviewing code) by the current committee.
>
> I do understand that the new committee is still learning how to recognize 
> and handle abuse; it's a complicated and challenging topic to master. In 
> the meantime, as I have asked the committee in private already, more 
> thoughtful restraint in issuing public reprimands is necessary.
>
>

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[sage-devel] MSC-2020 -- Class 52: Convex and Discrete Geometry -- CAS Citations from 2000 to 2021

[jplab]

Dear all,

During the Summer, I was curious to know more about the impact of Sage in 
my research area (MSC2020-52: Convex and Discrete Geometry).

If I recall correctly, around 2010-11 was the integration of ppl as a 
backend for polyhedral computations, and it more or less also corresponds 
to the first citation of Sagemath in MSC2020-52. Ten years after, how were 
Sagemath and other software cited? Can Sage be considered a trusted and 
used software for research in Convex and Discrete Geometry?

TL;DR: In 10 years, Sagemath went from 0% share of the CAS citations to 33% 
in 2021 and seems to continue growing as of 2022.

I take this opportunity to thank the Sage community and the developers of 
related softwares integrated for this Huge effort and to let you know of 
the positive comments that I receive form the research community in MSC-52. 
THANK YOU SO MUCH!

If you are interested in a deeper analysis, I produced detailed graphics 
and provide the raw data in a Jupyter notebook on my webpage:

https://jplab.github.io/sage_cite.html

Best wishes,
J-P

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[sage-devel] Re: Error while compiling -- ecl-21.2.1 on Debian 11

[jplab]

Hallo,

Ok, by brute forcing i.e. removing Brew, the sage installation proceeded 
without problems (and still compiling as of now, if I don't reply later, it 
means it worked).

The above tickets seem to head in the right direction: it seems odd that 
sage would detect automatically that brew is the package manager on debian 
if installed... Thankfully, the configure logs are a charm to figure that 
out! :)

Thanks for the help!

JP

Le mercredi 4 mai 2022 à 15:34:39 UTC-4, Matthias Koeppe a écrit :

> From your config.log:
>
> configure:84048: checking for the package system in use configure:84051: 
> result: homebrew 
>
> It looks like you have linuxbrew installed (sorry, I didn't see that 
> before when I looked at your log). 
>
> This is an untested configuration. See 
> https://trac.sagemath.org/ticket/29159 and 
> https://trac.sagemath.org/ticket/32753
>
>
> On Wednesday, May 4, 2022 at 11:51:07 AM UTC-7 jplab wrote:
>
>> Hello,
>>
>> I tried with:
>> ~sage$ sudo apt-get -y autoremove --purge ecl
>> ~sage$ which ecl
>> ~sage$ make distclean
>> ~sage$ ./configure
>> ~sage$ make
>>
>> I get the same error, and then also discovered that givaro in my system 
>> is detected but then fflas fails to install because the version of my 
>> system's givaro is too old... Hmm.
>>
>> Le mercredi 4 mai 2022 à 14:04:29 UTC-4, Matthias Koeppe a écrit :
>>
>>> Try if it goes away if you uninstall the ecl system package
>>>
>>> On Wednesday, May 4, 2022 at 10:05:37 AM UTC-7 jplab wrote:
>>>
>>>> Here they are.
>>>>
>>>> Le mercredi 4 mai 2022 à 12:26:02 UTC-4, Matthias Koeppe a écrit :
>>>>
>>>>> Top-level config.log and full ecl build log please
>>>>>
>>>>> On Wednesday, May 4, 2022 at 9:11:22 AM UTC-7 jplab wrote:
>>>>>
>>>>>> Hello,
>>>>>>
>>>>>> I haven't compiled sage for too long (shame on me...). I have a fresh 
>>>>>> installation of Debian bullseye, and the compilation fails at 
>>>>>> ecl-21.2.1. 
>>>>>> The relevant log mentions:
>>>>>>
>>>>>> Building ecl_min...
>>>>>>  25 ./ecl_min: error while loading shared libraries: libffi.so.8: 
>>>>>> cannot open shared object file: No such file or directory
>>>>>>  24 make[6]: *** [Makefile:99: bin/ecl] Error 127
>>>>>>  23 make[5]: *** [Makefile:65: all] Error 2
>>>>>>
>>>>>> I have libffi 7 installed:
>>>>>>
>>>>>> ~/sage$ find /usr/lib -name "libffi.so*"
>>>>>> /usr/lib/x86_64-linux-gnu/libffi.so.7
>>>>>> /usr/lib/x86_64-linux-gnu/libffi.so
>>>>>> /usr/lib/x86_64-linux-gnu/libffi.so.7.1.0
>>>>>>
>>>>>> The ecl available in the stable release of Debian seems not to be 
>>>>>> recent enough so the sage configure sets it to install ecl-21.2.1. I 
>>>>>> also 
>>>>>> tried to install ecl using brew instead, but then, the sage compilation 
>>>>>> failed to install maxima... So, I'm trying to start from the "first" 
>>>>>> problem...
>>>>>>
>>>>>> Any idea on how to proceed would be great!
>>>>>>
>>>>>> Thanks in advance!
>>>>>>
>>>>>> JP
>>>>>>
>>>>>

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[sage-devel] Error while compiling -- ecl-21.2.1 on Debian 11

[jplab]

Hello,

I haven't compiled sage for too long (shame on me...). I have a fresh 
installation of Debian bullseye, and the compilation fails at ecl-21.2.1. 
The relevant log mentions:

Building ecl_min...
 25 ./ecl_min: error while loading shared libraries: libffi.so.8: cannot 
open shared object file: No such file or directory
 24 make[6]: *** [Makefile:99: bin/ecl] Error 127
 23 make[5]: *** [Makefile:65: all] Error 2

I have libffi 7 installed:

~/sage$ find /usr/lib -name "libffi.so*"
/usr/lib/x86_64-linux-gnu/libffi.so.7
/usr/lib/x86_64-linux-gnu/libffi.so
/usr/lib/x86_64-linux-gnu/libffi.so.7.1.0

The ecl available in the stable release of Debian seems not to be recent 
enough so the sage configure sets it to install ecl-21.2.1. I also tried to 
install ecl using brew instead, but then, the sage compilation failed to 
install maxima... So, I'm trying to start from the "first" problem...

Any idea on how to proceed would be great!

Thanks in advance!

JP

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Re: [sage-devel] Re: ask.sagemath.org issues - do we need it?

[jplab]

Hello,

I think it is a fair question to consider whether we need AskSage. This 
discussion reminded me of a previous thread in the group which I think is 
still worth reading today:
Sage Stack Exchange Site: 
https://groups.google.com/g/sage-devel/c/hwEhxaetakk/m/XSWWUYS9LCwJ

While the discussion certainly dates from a different era of Sage, I think 
that certain arguments didn't change, in particular that "a fully free QA 
site was more consistent with the values of the Sage community" rather than 
a StackExchange hosting [Niles Johnson, from the above discussion].

+1 for a fully free QA page that lets people easily ask questions from a 
broad range of subscriptions platforms (google, facebook, name-it,... 
somehow I also do believe that average users like this better than a 
minimal forum).

Best,
J-P



Le samedi 11 décembre 2021 à 16:39:04 UTC-5, dim...@gmail.com a écrit :

>
>
> On Sat, 11 Dec 2021, 17:58 Emmanuel Charpentier,  
> wrote:
>
>> Discourse is somewhat nosy : I have to use it for questions related to 
>> Stan ...
>>
>
> Nosy? Discourse can be self-hosted.
>
> While askbot promises a new version in February, it's obviously a small 
> platform.
>
>
>>
>>
>>
>> Le samedi 11 décembre 2021 à 18:52:34 UTC+1, Matthias Koeppe a écrit :
>>
>>> On Saturday, December 11, 2021 at 7:00:54 AM UTC-8 kcrisman wrote:
>>>
  As for sage-support, it's always surprising to me how many "customers" 
 simply disappear as soon as you mention asking a question there - somehow 
 they either want a Q site, or to ask on Facebook, or whatever.  I don't 
 really know why this happens, but clearly the Q sites (in toto) are 
 necessary.


>>> Another option may be to move to Discourse. Many projects use it, 
>>> including https://discuss.python.org/ and 
>>> https://discourse.julialang.org/
>>>
>>>
>>> https://meta.discourse.org/t/easy-way-to-migrate-askbot-to-discourse/148677
>>>
>>>  
>>>
>> -- 
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>> https://groups.google.com/d/msgid/sage-devel/8da2cc03-032a-483d-9d44-5de4a4c4e3d2n%40googlegroups.com
>>  
>> 
>> .
>>
>

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[sage-devel] missing configure.ac? in binary of 9.2 Debian 64 bits.

[jplab]

Hello!

I have downloaded the sage9.2 Debian binary to be used on a cluster.
I have untarred it and then simply run ./sage to do a sanity check. Then it 
runs the relocate-once.py script, but fails at the file "config.status" 
since it is not there.

I could fix this by taking my own configure.ac file and execute ./configure 
on the cluster and then rerun sage. Which then gave me this dirt at the end 
of the script:

patching /home/labbe/sage/SageMath/src/sage/ext/interpreters/wrapper_rr.pxd
patching /home/labbe/sage/SageMath/src/sage/ext/interpreters/wrapper_rr.pyx
┌┐
│ SageMath version 9.2, Release Date: 2020-10-24 │
│ Using Python 3.8.5. Type "help()" for help.│
└┘
/home/labbe/sage/SageMath/local/lib/python3.8/site-packages/traitlets/config/loader.py:795:
 
SyntaxWarning: "is" with a literal. Did you mean "=="?
  if len(key) is 1:
/home/labbe/sage/SageMath/local/lib/python3.8/site-packages/traitlets/config/loader.py:804:
 
SyntaxWarning: "is" with a literal. Did you mean "=="?
  if len(key) is 1:
/home/labbe/sage/SageMath/local/lib/python3.8/site-packages/psutil/_pslinux.py:551:
 
DeprecationWarning: invalid escape sequence \d
  search = re.compile('cpu\d')
/home/labbe/sage/SageMath/local/lib/python3.8/site-packages/psutil/_pslinux.py:1468:
 
DeprecationWarning: invalid escape sequence \s
  _private_re=re.compile(b"Private.*:\s+(\d+)"),
/home/labbe/sage/SageMath/local/lib/python3.8/site-packages/psutil/_pslinux.py:1469:
 
DeprecationWarning: invalid escape sequence \s
  _pss_re=re.compile(b"Pss.*:\s+(\d+)"),
/home/labbe/sage/SageMath/local/lib/python3.8/site-packages/psutil/_pslinux.py:1470:
 
DeprecationWarning: invalid escape sequence \s
  _swap_re=re.compile(b"Swap.*:\s+(\d+)")):
/home/labbe/sage/SageMath/local/lib/python3.8/site-packages/psutil/_pslinux.py:1583:
 
DeprecationWarning: invalid escape sequence \d
  def num_ctx_switches(self, 
_ctxsw_re=re.compile(b'ctxt_switches:\t(\d+)')):
/home/labbe/sage/SageMath/local/lib/python3.8/site-packages/psutil/_pslinux.py:1596:
 
DeprecationWarning: invalid escape sequence \d
  def num_threads(self, _num_threads_re=re.compile(b'Threads:\t(\d+)')):
/home/labbe/sage/SageMath/local/lib/python3.8/site-packages/psutil/_pslinux.py:1652:
 
DeprecationWarning: invalid escape sequence \d
  self, _re=re.compile(b"Cpus_allowed_list:\t(\d+)-(\d+)")):
/home/labbe/sage/SageMath/local/lib/python3.8/site-packages/psutil/_pslinux.py:1814:
 
DeprecationWarning: invalid escape sequence \d
  def uids(self, _uids_re=re.compile(b'Uid:\t(\d+)\t(\d+)\t(\d+)')):
/home/labbe/sage/SageMath/local/lib/python3.8/site-packages/psutil/_pslinux.py:1820:
 
DeprecationWarning: invalid escape sequence \d
  def gids(self, _gids_re=re.compile(b'Gid:\t(\d+)\t(\d+)\t(\d+)')):
/home/labbe/sage/SageMath/local/lib/python3.8/site-packages/sage/calculus/functional.py:57:
 
DeprecationWarning: invalid escape sequence \d
  """
sage: 
1+1 
   

2
sage: P = 
Polyhedron()
   

sage: 
P   
   

The empty polyhedron in ZZ^0
sage: 
quit
   

Exiting Sage (CPU time 0m1.28s, Wall time 2m0.29s).
labbe@ cluster:~/sage/SageMath$ ./sage
┌┐
│ SageMath version 9.2, Release Date: 2020-10-24 │
│ Using Python 3.8.5. Type "help()" for help.│
└┘
sage: quit

So, it seems that Sage is running "ok". But that does not seem to be right 
to assume that everything went fine...

Is there something that I am missing here?

Greetings,
J-P

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[sage-devel] Re: Proposal to add "tox" as a standard package - entry point for testing and linting

[jplab]

Hi!

This looks like a great new feature! I discovered it by surprise when the 
command "pep8 -v some_file.py" was not returning anything anymore, while 
typically it returns hundreds of lines...

Looking a bit around, I guess that one should add a few of the typical PEP8 
errors in tox.ini? Does that make sense? It seems that the lines 
responsible for that are:

[pycodestyle]   

   

# Check for the following issues:
# E401: multiple imports on one line
# E701: multiple statements on one line (colon)
# E702: multiple statements on one line (semicolon)
# W605: invalid escape sequence ‘x’
# See https://pycodestyle.pycqa.org/en/latest/intro.html#error-codes
select = E401,E701,E702,W605
max-line-length = 160

I'm thinking about the usual "Empty line contains whitespaces", and 
similar... should they all be listed here?

If I understood correctly, this likely affects everyone using pep8 while 
coding and linting... What should be the Sage-9.2-method/command to get 
something that looks like the good old "pep8 -v" output?

Le mercredi 9 septembre 2020 à 19:05:44 UTC+2, Matthias Koeppe a écrit :

> On Monday, September 7, 2020 at 2:18:34 PM UTC-7, Matthias Koeppe wrote:
>
>> tox (https://tox.readthedocs.io/en/latest/) is a popular package that is 
>> used by a large number of Python projects as the standard entry point for 
>> testing and linting.
>>
> [...] 
>>
> I propose to make "tox" a standard package of the Sage distribution so 
>> that this functionality becomes available by default.
>>
>> By convention, this requires a vote here on sage-devel.
>>
>>
> Thanks everyone. This is now https://trac.sagemath.org/ticket/30416 
> , needs review
>
>
>

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[sage-devel] Re: https://wiki.sagemath.org/ReleaseTours/sage-9.2

[jplab]

Great!

I added a Section about the Polyhedral Geometry related new things.

Best',

Le samedi 8 août 2020 20:10:17 UTC+2, Matthias Koeppe a écrit :
>
> Let's prepare the release tour for the upcoming 9.2 release by 
> collaborative editing.
>
> https://wiki.sagemath.org/ReleaseTours/sage-9.2
>
>
>
>

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[sage-devel] Re: Want to add generalised Newton's method for solving a nonlinear systems of equations to Sage

[jplab]

Hello Daniel,

I am not very familiar with the numerical newton methods in Sage. Have you 
looked in numpy?

Concerning the contribution process, you may appreciate the following 
answer given on AskSage

https://ask.sagemath.org/question/50630/how-to-contribute-to-sage-in-less-than-20-easy-steps/

which complements the Developers Manual:

https://doc.sagemath.org/html/en/developer/

Best,
J-P

Le samedi 2 mai 2020 00:09:34 UTC+2, Daniel Khodabakhsh a écrit :
>
> Hello,
>
> I have a generalised implementation of Newton's method for solving a 
> nonlinear system of equations that I want to add to Sage.
> This would be my first potential contribution so I had a few questions 
> before I can move forward.
>
> Questions #1:
> The reason I wrote an implementation was because I couldn't find this 
> algorithm in Sage. Before I proceed, could someone confirm that this indeed 
> doesn't already exist?
>
> Questions #2:
> If it really isn't part of Sage yet, which module should I add this to?
>
> Once I get this information I'll work on integrating it into the 
> recommended module and create a new ticket on https://trac.sagemath.org/
>
> If I have the process wrong please let me know!
>
>

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Re: [sage-devel] Renaming `affine_hull` for polyhedra

[jplab]

>
>
>> in #29326. 
>>
>> Do you have thoughts about it? Does anyone have a better name? Opinions 
>> are welcome.
>>
>
> affine_hull_projection
>
+1 for affine_hull_projection

At one moment, I thought something called "make_full_dimensional" or would 
be a very straightforward name. One could think of eventually add such an 
alias, but I would be already happy with "affine_hull_projection".

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[sage-devel] Re: Optional and experimental packages

[jplab]

Hi,

Le lundi 28 octobre 2019 23:02:23 UTC+1, John H Palmieri a écrit :
>
>
>
> *Experimental:*
>
> - the following failed to build:
>
> autotools
> cocoalib
> libtheora
> polymake
> qepcad
> scipoptsuite
> surf
> valgrind
>
> - the following succeeded:
>
> gap3
> lie
> modular_decomposition
> perl_term_readline_gnu
>
> polymake succeeded but only after installing the perl JSON package. (Why 
> is jupymake optional and polymake experimental? jupymake has polymake as a 
> dependency, and optional packages should not depend on experimental 
> packages.)
>
>
This problem should be addressed here: 
https://trac.sagemath.org/ticket/27763 .

I do not know how jupymake ended up being optional while it depends on an 
experimental package. Nevertheless, I know that there was the idea of 
making polymake optional now that it has a more stable installation and 
portability.

See the ticket: https://trac.sagemath.org/ticket/22710 for more information 
about the development of polymake package and interface.

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[sage-devel] Re: Problems launching jupyter browser window and threejs browser window

[jplab]

>
>> Then, a Firefox browser window opens with Firefox's "pingponging ball of 
>> Death" of an eternally loading window...
>>
>>
>
> Works for me (on the same ticket branch). This is with Ubuntu 18.04 + 
> Firefox 70.0. What is your system? 
>

Ok... After some thoughts when you asked about my firefox version, it made 
me realize that I do not restart my firefox often. 
Some time ago I updated it without restarting (which I am surprised it did 
not crash, which is the typical behavior...).

In any case, the classical "turning firefox on and off" made everything 
work again. (facepalm)

Just for the record: I have debian buster running Firefox 68.2.0esr.

Thanks for prompting me to realize that!

Best,
J-P

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Re: [sage-devel] Problems launching jupyter browser window and threejs browser window

[jplab]

Hi,

Le dimanche 27 octobre 2019 20:10:11 UTC+1, Dima Pasechnik a écrit :
>
> On Sun, Oct 27, 2019 at 4:36 PM jplab > 
> wrote: 
> > 
> > Hi everyone, 
> > 
> > I wanted to test the following ticket on sage 9.0beta2: 
> > 
> > https://trac.sagemath.org/ticket/28658 
> > 
> > So I wrote the following in the terminal: 
> > 
> > sage: p = polytopes.icosahedron() 
> > sage: p.plot() 
> > Launched html viewer for Graphics3d Object 
> > 
> > Then, a Firefox browser window opens with Firefox's "pingponging ball of 
> Death" of an eternally loading window... 
> > 
> > The same thing occurs with 
> > 
> > sage -notebook 
> > 
> > Previously, I've been having problems with launching jupyter, but 
> copy-pasting 
> > the link given in the terminal in the address bar always worked, so I 
> had my workaround. 
> > But I have grown tired of this workaround and I thought maybe someone 
> knew how to solve this? 
> > 
> > I've just done a "make distclean" for another reason, have a freshly 
> compiled sage and moved ".sage" to ".sage_old" to see if 
> > this changes anything: Nope. 
> > 
> > I am running debian buster with firefox being my default browser. 
> > 
> > Any ideas would be appreciated! 
> > 
> > While we are here, on another train of thoughts: is it me or viewing 
> polyhedron with threejs does not show the edges? 
>
> I too don't see the edges of the icosahedron while viewin the in 
> jupyter notebook. 
> Could you open a ticket for this? 
>

Yes, this is now #28662: https://trac.sagemath.org/ticket/28662

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[sage-devel] Problems launching jupyter browser window and threejs browser window

[jplab]

Hi everyone,

I wanted to test the following ticket on sage 9.0beta2:

https://trac.sagemath.org/ticket/28658

So I wrote the following in the terminal:

sage: p = polytopes.icosahedron()
sage: p.plot()
Launched html viewer for Graphics3d Object

Then, a Firefox browser window opens with Firefox's "pingponging ball of 
Death" of an eternally loading window...

The same thing occurs with

sage -notebook

Previously, I've been having problems with launching jupyter, but 
copy-pasting 
the link given in the terminal in the address bar always worked, so I had 
my workaround.
But I have grown tired of this workaround and I thought maybe someone knew 
how to solve this?

I've just done a "make distclean" for another reason, have a freshly 
compiled sage and moved ".sage" to ".sage_old" to see if 
this changes anything: Nope.

I am running debian buster with firefox being my default browser.

Any ideas would be appreciated!

While we are here, on another train of thoughts: is it me or viewing 
polyhedron with threejs does not show the edges?

J-P

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[sage-devel] Re: Need help testing #27122 and #27103

[jplab]

Which platforms need testing precisely? and which platforms were tested?

J-P

Le vendredi 25 octobre 2019 22:28:03 UTC+2, Jonathan Kliem a écrit :
>
> Hi, I would appreciate some help testing #27122 
>  and possibly on top of that 
> #27103 .
>
> Both tickets have instructions for testing in their description, which are 
> hopefully helpful. The first ticket adds a compile argument to optimize 
> sage for the current machine (unless SAGE_FAT_BINARIES is set).
> Naturally, the behavior depends very much on the machine and we need a 
> variety of tests, to see if it is ok. The compile argument `-march=native` 
> is supposed to change things only for the better, but who knows what will 
> or can happen.
>
> The second ticket makes use of the first and is also very much platform 
> dependent.
>
> Thank you,
>
> Jonathan
>

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[sage-devel] Re: Switch to Python 3 by default

[jplab]

+1

Le dimanche 27 octobre 2019 01:58:23 UTC+2, Volker Braun a écrit :
>
> Maybe I missed it, but I didn't find a ticket for that. I think now would 
> be a good time to flip the switch, though. Any thoughts?
>

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[sage-devel] Re: what is the correct defintion of a vertex graph for polyhedra with lines?

[jplab]

Hi Jonathan,

Could you be more precise with what you mean with "projection"?

What is the status quo? (Please provide a minimal reproducible working 
example that shows the contrast along with the proposed wished change that 
you have in mind, otherwise we are left to guess what you mean and that is 
leaving the door open to a lot of misunderstanding)

What is the proposed changed?

What is the assumption in the mentioned doctest?

For computational aid, when no vertices exists (i.e. there is a lineality 
space) the current implementation creates an appropriate vertex. I guess we 
have to deal with this eventhough the object does not have a 0-dimensional 
face in reality. This is to have consistency between H- and 
V-representations. In order to have a consistent V-representation, you need 
an anchor point, otherwise just having rays and lines does not determine 
uniquely the object.

That said, if you are interested in making a vertex-graph for unbounded 
polyhedra, then, edges should have two vertices.

One way is to ask to keep only bounded edges in the definition, and the 
default behavior gives the vertex graph on bounded edges. If one wants the 
full graph with a point at infinity that compactifies the full vertex 
graph, then one could do so by adding an optional parameter 
"unbounded=False/True". Where the default would be False and return only 
compact edges and True would return one more vertex "the vertex at 
infinity".

To me this seems to be the most reasonable behavior. I don't know if this 
answer your question.

Le vendredi 18 octobre 2019 12:09:53 UTC+2, Jonathan Kliem a écrit :
>
> In #28626  I want to use 
> `CombinatorialPolyhedron` to obtain the vertex graph of polyhedra.
>
> However, I seem to have a different opinion of a vertex graph than is 
> currently implemented in sage.
>
> Should the vertex graph of an unpointed polyhedron return the vertex graph 
> of the projection or should it be empty?
>
> As of now the method `vertices` returns the defining vertices, which are 
> the proper vertices except for unpointed polyhedra.
>
> I don't think this ambiguous meaning of vertex should continue for the 
> vertex graph.
>
> However the current behavior is at the moment assumed in a strange doctest 
> of `combinatorial_automorphism_group`.
> (E.g. the order of the combinatorial automorphism group does not change 
> when you add lines.)
>

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[sage-devel] Re: Poll: three.js as the default 3d viewer in Sage

[jplab]

+1 to make threejs the default viewer.

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Re: [sage-devel] Polyhedron -- make constructions respect backend

[jplab]

Hi Jonathan,

Le lundi 3 juin 2019 23:31:29 UTC+2, vdelecroix a écrit :
>
> To my mind: 
>
>   * backend and base ring should be preserved by default. Of course 
> it should make sense: a translation by sqrt(2) would break the 
> base ring QQ. 
>

+1


>   * no need to create one ticket for each method if this is mostly 
> the same action to be done for each of them. If some method needs 
> special care or give rise to discussions, a specific ticket could 
> be open. 
>

+1


Le 03/06/2019 à 23:25, 'Jonathan Kliem' via sage-devel a écrit : 
> > At the moment the backend setting is lost, when constructing a pyramid 
> of a 
> > Polyhedron. 
> > 
> > Same holds for all other constructions. 
>

If you are ready to go through the construction to make them consistent 
with the above convention: great!

> Any thoughts on this? 
> > 
> > Also I think the base ring should be respected as well (as is done in 
> > Polyhedron.translation). 
> > At the moment it can happen, that the base ring shrinks, when 
> constructing 
> > a pyramid for example 
> > (if the user forced base ring QQ, there might have been good reason for 
> > doing so, and I would say it is not nice, if one has to change base ring 
> > again along the way). 
>

It is hard to make sense of "If the user forced base ring QQ" after the 
object got created. 
How should we know if that keyword was given when looking at the object?

The reason I ask this question is because I do not believe that the usage 
of the keyword 
"base_ring" is "to force the base ring used", but rather to help the 
constructor to build the 
desired object in a specific base ring: the input is converted in that base 
ring (if possible) 
once things are constructed. Then, as Vincent mentioned, and I agree, the 
base ring 
should be kept as long as it is possible.

On the other hand, a user "forcing QQ"  can be thought as a peculiar thing 
to do. Every 
rational polyhedron has an integer H-representation, so if one looks at the 
H-representation, 
QQ is not necessary to write the H-representation. The distinction comes 
from the 
V-representation and has consequences on the related objects (Ehrhart 
quasi-polynomial 
vs Ehrhart polynomial and any method that makes use of integer 
arithmetic...). So, yes 
there should be a distinction between the two base rings ZZ and QQ. That 
said, I believe that internally, 
it should always try to take the "simplest" base ring possible. If the user 
then wants a 
different ring, then Sage will give the object back in that one, but may do 
computations with a 
different ring. So now again, does "forcing a base ring" makes sense?

That said, as explained in the tutorial

http://doc.sagemath.org/html/en/thematic_tutorials/geometry/polyhedra_tutorial.html

A clean way to work with polyhedron is to have the objects already be in a 
common base ring already.
If this is not possible and one gives different types in the input, then it 
will go on and figure out a 
proper base ring. But, since this might take a while, the keyword "base 
ring" helps in this regards.

So, one should be careful in using this keyword... For example, after 
#25097 is merged, this will become possible:

sage: sqrt_2s = sqrt(2)
sage: cbrt_2s = 2^(1/3)
sage: P1 = Polyhedron(vertices = [[sqrt_2s, 0], [0, cbrt_2s]]);P1
Traceback (most recent call last):
...
ValueError: no appropriate backend for computations with Symbolic Ring

sage: P2 = Polyhedron(vertices = [[sqrt_2s, 0], [0, cbrt_2s]],backend=
'normaliz');P2
A 1-dimensional polyhedron in (Symbolic Ring)^2 defined as the convex hull 
of 2 vertices

sage: Polyhedron(vertices = [[sqrt_2s, 0], [0, cbrt_2s]],backend='field')
Traceback (most recent call last):
...
ValueError: the 'field' backend for polyhedron can not be used with non-exact 
fields

The object P2's base ring is the Symbolic Ring, but the computations are 
done in the normaliz field accessible with the method `_normaliz_field`.  

J-P

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[sage-devel] Re: polymake 3.1 package failing install on SageMath 8.7

[jplab]

Hi Stefan,

Polymake had some issues with gcc 7 in the past. I do not know if the 
following could help you:

https://forum.polymake.org/viewtopic.php?f=10=579

The latest version (3.4) of polymake is very close to be in Sage:

https://trac.sagemath.org/ticket/24905

Compilation was tested on macOS Mojave, debian stable and ArchLinux. It 
would be great if you could test this 
branch on your computer and let us know if it worked on your OS (either 
here or on the ticket discussion page).

Best regards,
Jean-Philippe


Le mardi 7 mai 2019 00:03:10 UTC+2, stefan...@gmail.com a écrit :
>
> Hi,
>
> I'm looking at the sagemath package called "polymake".
>
> I tried to install it in SageMath 8.7 and it pulled polymake 3.1
>
> I'm attaching the log. I believe the relevant portion is this:
>
> reference to an undeclared variable $err_prefix at 
> /home/user/SageMath/local/share/polymake/perllib/Polymake/utils.pl line 
> 198. 
> Compilation failed in require at 
> /home/user/SageMath/local/share/polymake/perllib/Polymake.pm line 61.
> Compilation failed in require at /home/user/SageMath/local/bin/polymake 
> line 162. 
>
>
> Most of the build goes through rather well, but at the end, this perl 
> build script seems to fail.
> I tried to skim through the referenced files utils.pl (line 198) and 
> Polymake.pm (line 61) and apparently
> it implements a custom way of declaring variables through a keyword that's 
> called "declare" which is
> not part of the Perl language and is custom-built for polymake's build 
> system.
>
> I wasn't able to figure out the problem, but I'm writing here so others 
> can have a look.
> Does this package build for someone else?
>
> Thanks,
> Stefan
>

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Re: [sage-devel] Polyhedron.vertices() function call behaviour

[jplab]

I have created a ticket here:

https://trac.sagemath.org/ticket/27709

and now made the vector method output a copy.

Le mercredi 17 avril 2019 07:44:22 UTC+2, vdelecroix a écrit :
>
> Le 16/04/2019 à 09:58, jplab a écrit : 
> > 
> > 
> > Le vendredi 12 avril 2019 06:41:50 UTC+2, John H Palmieri a écrit : 
> >> 
> >> Can you provide details of how you created the polyhedron? As David 
> said, 
> >> Q.vertices() should make a copy before returning the result, and I 
> would 
> >> like to recreate this so I can fix it. 
> >> 
> >> +1 
> > 
>
> sage: C = polytopes.cube() 
> sage: C.vertices()[0].vector()[0] = 3 
> sage: C.vertices() 
> (A vertex at (3, -1, -1), 
> ... 
>

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Re: [sage-devel] Error installing latte_int

[jplab]

Making the suggested changes seemed to have solved the issue. I guess this 
should become a patch upstream or a patch in the sage package...

Le mercredi 17 avril 2019 15:41:57 UTC+2, Dima Pasechnik a écrit :
>
> this looks like
> https://github.com/mkoeppe/LiDIA/issues/1
>
> to me.
> there is a workaround suggested there.
>
> On Wed, 17 Apr 2019 15:35 Sophia Elia, > 
> wrote:
>
>> I tried to install latte_int using sage -i latte_int and received an 
>> error installing the lidia package. I am using mac and running os 10.14.4. 
>> My log file is attached.
>>
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Re: [sage-devel] Polyhedron.vertices() function call behaviour

[jplab]

Le vendredi 12 avril 2019 06:41:50 UTC+2, John H Palmieri a écrit :
>
> Can you provide details of how you created the polyhedron? As David said, 
> Q.vertices() should make a copy before returning the result, and I would 
> like to recreate this so I can fix it.
>
> +1

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[sage-devel] Re: Cernay 2019: math software developers workshop: Sage, GAP, ...

[jplab]

Great!! My schedule is finally flexible enough this year!

Looking forward to the dates. Is there going to be funding avaialble for 
students, postdoc from ODK?

Best,
J-P

Le dimanche 17 mars 2019 09:02:05 UTC+1, Nicolas M. Thiéry a écrit :
>
>Hello, 
>
> I am planning to organize this Spring one of our regular math software 
> developers workshop in Cernay (near Paris), in the the spirit of our 
> previous ones, including: 
>
> - Sage Days 77: Sage developer days on packaging, portability, 
> documentation tools (2016) 
>   https://wiki.sagemath.org/days77 
>   Sage & GAP days 85: packaging, portability, documentation tools (2017) 
> - https://wiki.sagemath.org/days85 
> - Workshop on interfacing (math) software with low level libraries (2018) 
>   https://github.com/OpenDreamKit/OpenDreamKit/issues/251 
>
> Themes will include packaging, portability, interfaces between 
> systems; more themes and projects are welcome; please edit the page: 
>
> https://hackmd.io/j5FzB173Q4uaExUw-6Glpg 
>
> If you are tentatively interested in participating, please fill in the 
> date poll before March 21st (next Thursday): 
>
> https://framadate.org/EemimQr2YPZJlNnx 
>
> Please forward to the relevant mailing lists (GAP, Oscar, Pari/GP, 
> Singular, Polymake, ...) or people. 
>
> Once the date is fixed, I'll send an official announcement. 
>
> Cheers, 
> Nicolas 
> -- 
> Nicolas M. Thiéry "Isil" > 
> http://Nicolas.Thiery.name/ 
>

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[sage-devel] Re: Sage 8.4 has broken Hilbert polynomials

[jplab]

This still does not work in Sage version 8.7.beta7.

I have created a ticket located at

https://trac.sagemath.org/ticket/27483

Best regards,


Le lundi 5 novembre 2018 18:55:25 UTC+1, john_perry_usm a écrit :
>
> This code works in Sage 8.3, but not in Sage 8.4.
>
> P. = PolynomialRing(QQ)
> I = Ideal([x^3, x*y^2, y^4, x^2*y*z, y^3*z, x^2*z^2, x*y*z^2, x*z^3])
> I.hilbert_polynomial()
>
> I haven't yet dug into the cause, but the error it reports is,
>
> AttributeError: 'sage.rings.rational.Rational' object has no 
> attribute 'leading_coefficient'
>
>
>

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[sage-devel] Re: polymake-3.1 build fails with std::__::numeric_limits<...>

[jplab]

Dear Harly Hallikas,

This error seems to be in polymake source code. You could report this 
compilation error to the polymake development team here:

https://forum.polymake.org/

to see if this fixed in the current version. The current version is 3.3 
available here:

https://polymake.org/doku.php/download/start

Which planned to be updated in the ticket:

https://trac.sagemath.org/ticket/24905

which should be ready soon (hopefully!).

Looking at the release page of polymake, it seems that they do not yet have 
a bundle for 10.14, so I do not know if it can work out of the box in this 
case.

As Dima said, this is an experimental package and any such report is very 
welcome to improve it!

Best,
Jean-Philippe



Le mercredi 13 mars 2019 12:52:01 UTC+1, Harly Hallikas a écrit :
>
> I'm not really C++ specialist, therefore, I'm not even trying to fix it 
> myself. 
>
> Looks like the numeric_types are already defined in stdlib.
>
> Attached the log file..
>
>
> Computer 2018 MacBookPro (Core i9), macOS Mojave Version 10.14.3 (18D109)
>

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[sage-devel] #27071: Recommendations on naming convention and _repr_

[jplab]

Hello,

In the ticket:

https://trac.sagemath.org/ticket/27071

We implement the method `ambient_V_indices` for faces of polyhedron to get 
a grip of the indices of faces of polyhedron, which were not yet easily 
accessible.

At the same time, I suggest a change to the `_repr_` function to make it 
more informative:

From:

sage: P = polytopes.cube()
sage: TwoFace = P.faces(2)[0]
sage: TwoFace
<0,1,2,3>


-> This could represent a 2-dimensional square and also a 3-dimensional 
simplex.

To:

sage: TwoFace
A 2-dimensional face of a Polyhedron in ZZ^3 defined as the convex hull of 4 
vertices


which is essentially a fusion of the current situation for face of lattice 
polytopes and the representation string of Polyhedron objects.

For the user interested in the indices, one can now get them by:

sage: TwoFace.ambient_V_indices()
(0, 1, 2, 3)


Is such a change to `_repr_` reasonable?

Another question:

is there a preferred convention in sage for "number of ...". For Polyhedra 
they start with `n_` while for graphs they start with `num_`

Thanks,
J-P

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[sage-devel] Re: Real algebraic varieties

[jplab]

Dear Thierry,

I have to solve polynomial systems of equations on a regular basis and 
would be happy to see sage improve in this respect.

My strategy is to use numerical algorithms.

There is Bertini (I glued together my own customized interface to it 4-5 
years ago). They now migrated to C code and are available on github:

https://github.com/bertiniteam/b2

Bertini can guarantee "with probability 1" that it found _all_ isolated 
solutions (under the right circumstances). 

Then, using some degree bounds and solving the system around an isolated 
solution to get enough decimal places, it is possible to get back the 
actually minimal polynomial for the algebraic solution. This method was 
successfully used for example in:

https://page.mi.fu-berlin.de/moritz/papers/t2-diss.html
https://page.mi.fu-berlin.de/moritz/papers/j002-computing-maximal-copies.html

Reading about Bertini, I learned about PHCpack, which is apparently 
partially available in Sage:

http://doc.sagemath.org/html/en/reference/interfaces/sage/interfaces/phc.html
http://homepages.math.uic.edu/~jan/download.html
http://homepages.math.uic.edu/~jan/PHCpack/phcpack.html

There is also a recent development in julia, developed in Berlin, where one 
of the long term goal is to improve polyhedral homotopies for such systems. 
Apparently, they can beat bertini in instances of 0-dimensional cases.

https://www.juliahomotopycontinuation.org/

That's my bit of knowledge in this area. I know that it is 'numerical' but, 
as far as applications go, they often help a lot and it is a very active 
field of research and algorithmic development...

Best,
JP

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Re: [sage-devel] Tools to compute Hilbert Poincaré series

[jplab]

Hi Simon,

Le samedi 1 septembre 2018 22:59:12 UTC+2, Simon King a écrit :
>
>
>
> The question in all cases (frobby, Normaliz, LattE, CoCoA) is whether the 
> conversion 
> from Singular is efficient. 
>
>
Normaliz can compute the Hilbert series of monomial ideals given different 
gradings. 
With Matthias Koeppe, Winfried Bruns, and Sebastian Gutsche, we are working 
on 
interfacing normaliz to sage through pynormaliz:

sage -i normaliz
sage -i pynormaliz

https://trac.sagemath.org/ticket/25090
https://trac.sagemath.org/ticket/25091

and use it through polyhedron objects.

Normaliz also interact with cocoa inside (but do not know the details, 
Winfried Bruns 
would be the one to ask). Normaliz is already an optional package, but not 
all its 
features are accessible 25090 and 25091 are there for that.

Grüße,
Jean-Philippe

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[sage-devel] Re: document and doctest constructing polyhedra over number fields

[jplab]

Good Morning,

This issue is reported here also (4 years ago, yes, ages ago): 

https://trac.sagemath.org/ticket/17197

The fresh thematic tutorial on polyhedra contains the remedy material you 
are looking for:

http://doc.sagemath.org/html/en/thematic_tutorials/geometry/polyhedra_tutorial.html

Best,
Jean-Philippe

Le vendredi 17 août 2018 09:11:18 UTC+2, Dima Pasechnik a écrit :
>
> While I appreciate dark humour, this is my morning What the Hell moment: 
> illustrating a feature by showing how it does not work, but not by how it 
> works:
> see
> https://trac.sagemath.org/ticket/26077
>
> 
>

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[sage-devel] Re: talk

[jplab]

Hi,

It is great to have a recent snapshot of the status of Sage and a wishlist!

This summer marks the 10th year when my brother showed me Sage for 
the first time at the beginning of my master (So happy I did not need to 
use Maple or Matematica any more...). It is awesome to see it so 
lively and to be able to participate in improving it!

On the number of contribution graph, it seems that the number increased 
since the move to git in around 2014? Is that accurate?

About moving trac to github, I have been aware of gitlab, an "open-core" 
competitor of gitlab. My institution uses it instead of github as its 
platform 
for internal collaborations. As I am not an expert in this respect, but I 
find 
it interesting to consider, as you mention that your computer was 100% 
open source apart from Magma. Here's a letter from the CEO of gitlab, 
from 2 years ago last week:

https://about.gitlab.com/2016/07/20/gitlab-is-open-core-github-is-closed-source/

which ends by:

"In conclusion (TLDR), GitLab has an open core business model and ships 
both open and closed source software. GitHub hosts most open source 
projects but ships closed source software."

For what it's worth, I thought I would mention it here...

JP

Le mardi 24 juillet 2018 21:18:32 UTC+2, William a écrit :
>
> Hi, 
>
> I just wrote a short talk that I'm about to give at ICMS 2018 about a 
> sort of Sage status report and wishlist: 
>
> https://goo.gl/qNycb3 
>
> -- 
> William (http://wstein.org) 
>

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Re: [sage-devel] SCIP integration into sage

[jplab]

Hi,

Maybe I just give my basic knowledge about SCIP and ZIB.

Le vendredi 13 avril 2018 11:20:25 UTC+2, bluescarni a écrit :
>
> http://scip.zib.de/academic.txt
>
> """
> 1. This license applies to you only if you are a member of a noncommercial 
>and academic institution, e.g., a university. The license expires as
>soon as you are no longer a member of this institution. 
> """
>
>
Perhaps including the very first sentence of the license would put a bit 
more context:

''This license for ZIB software is designed to guarantee freedom to share and 
change software for academic use, but restricting commercial firms
from exploiting your knowhow for their benefit.''


... this somehow reminds me of some long discussions I've seen pass by on 
sage-devel. Anyhow, the 
discussion here is about announcing that it would now be possible to use 
SCIP inside Sage. I think this is 
a good news. As far as I know, it has been possible to use other Ma's 
softwares inside Sage, and I don't 
see why it couldn't be the same with SCIP.

According to Gurobi, they are the best non-proprietary LP optimization 
package that you can get. [see p.17 of 
http://www.gurobi.com/pdfs/benchmarks.pdf]

So basically these acedemics, I imagine funded with taxpayers' money, are 
> preventing the general public to use software they paid for?
>

As for ZIB, in 2016, it had almost 8M€ in third party funding, see 
http://www.zib.de/institute/zib-in-numbers 
If you go in the Research section, and you know that it is a German based 
institute, you may guest some companies that fund them.

That said, of course, the publish "Publish or Perish" has a role to play in 
the choice of license. But since I 
don't want to spend time rewriting an optimization package, I will gladly 
cite them and say  that I used their 
software.

My 2 cents...

JP

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[sage-devel] Re: Question about number_field_elements_from_algebraics (Ticket 20181)

[jplab]

Haha! That could be a good Easter egg...

... and I would not mind if some algebraists had a look at the NumberField 
elements that come out either from this adapted function either!

Le mardi 10 avril 2018 11:02:38 UTC+2, Dima Pasechnik a écrit :
>
> I misread this as "getting_number_field_elements_from_algebraists"...
>
> On Monday, April 9, 2018 at 5:10:07 PM UTC+1, jplab wrote:
>>
>> Dear all,
>>
>> In order to get algebraic polyhedra using the normaliz backend [1], we 
>> modify the function
>>
>> number_field_elements_from_algebraics of qqbar.py to give embedded number 
>> fields and also accept a larger class of algebraic numbers, say coming from 
>> cyclotomic fields [2].
>>
>> For example, this is now possible:
>>
>> sage: UCF = UniversalCyclotomicField()
>> sage: E = UCF.gen(5)
>> sage: L. = NumberField(x^2-189*x+16, embedding=200)
>> sage: my_nums = [-52*E - 136*E^2 - 136*E^3 - 52*E^4, 
>> L.gen()._algebraic_(AA),sqrt(2)]
>> sage: aa_my_nums = [AA(_) for _ in my_nums]
>> sage: res = number_field_elements_from_algebraics(aa_my_nums,embedded=True)
>> sage: res
>> (Number Field in a with defining polynomial y^8 - 35670*y^6 + 476899047*y^4 
>> - 2832410271650*y^2 + 6305298701739921,
>>  [2310/26212773509*a^7 - 185432947/78638320527*a^5 + 
>> 1652517502195/78638320527*a^3 - 4904676315215467/78638320527*a + 94,
>>   -1238/2803377488467023*a^7 + 185460719/11213509953868092*a^5 - 
>> 2754936849443/11213509953868092*a^3 + 8180694680816975/3737836651289364*a + 
>> 189/2,
>>   -1979/1887160880826*a^7 + 26472586/943580440413*a^5 - 
>> 235822245043/943580440413*a^3 + 466325019915415/629053626942*a],
>>  Ring morphism:
>>From: Number Field in a with defining polynomial y^8 - 35670*y^6 + 
>> 476899047*y^4 - 2832410271650*y^2 + 6305298701739921
>>To:   Algebraic Real Field
>>Defn: a |--> 96.9475535136628?)
>> sage: res[0].gen_embedding()
>> 96.9475535136628?
>>
>>
>> The ticket 2018 needs review and it would be nice to have the opinion of 
>> experts on number fields in Sage... 
>>
>> For example, there is currently one failing doctest where it seems that 
>> the newer version is smarter, so that the test is not necessary anymore.
>>
>> [1] https://trac.sagemath.org/ticket/25097
>> [2] https://trac.sagemath.org/ticket/20181
>>
>

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[sage-devel] Question about number_field_elements_from_algebraics (Ticket 20181)

[jplab]

Dear all,

In order to get algebraic polyhedra using the normaliz backend [1], we 
modify the function

number_field_elements_from_algebraics of qqbar.py to give embedded number 
fields and also accept a larger class of algebraic numbers, say coming from 
cyclotomic fields [2].

For example, this is now possible:

sage: UCF = UniversalCyclotomicField()
sage: E = UCF.gen(5)
sage: L. = NumberField(x^2-189*x+16, embedding=200)
sage: my_nums = [-52*E - 136*E^2 - 136*E^3 - 52*E^4, 
L.gen()._algebraic_(AA),sqrt(2)]
sage: aa_my_nums = [AA(_) for _ in my_nums]
sage: res = number_field_elements_from_algebraics(aa_my_nums,embedded=True)
sage: res
(Number Field in a with defining polynomial y^8 - 35670*y^6 + 476899047*y^4 - 
2832410271650*y^2 + 6305298701739921,
 [2310/26212773509*a^7 - 185432947/78638320527*a^5 + 
1652517502195/78638320527*a^3 - 4904676315215467/78638320527*a + 94,
  -1238/2803377488467023*a^7 + 185460719/11213509953868092*a^5 - 
2754936849443/11213509953868092*a^3 + 8180694680816975/3737836651289364*a + 
189/2,
  -1979/1887160880826*a^7 + 26472586/943580440413*a^5 - 
235822245043/943580440413*a^3 + 466325019915415/629053626942*a],
 Ring morphism:
   From: Number Field in a with defining polynomial y^8 - 35670*y^6 + 
476899047*y^4 - 2832410271650*y^2 + 6305298701739921
   To:   Algebraic Real Field
   Defn: a |--> 96.9475535136628?)
sage: res[0].gen_embedding()
96.9475535136628?


The ticket 2018 needs review and it would be nice to have the opinion of 
experts on number fields in Sage... 

For example, there is currently one failing doctest where it seems that the 
newer version is smarter, so that the test is not necessary anymore.

[1] https://trac.sagemath.org/ticket/25097
[2] https://trac.sagemath.org/ticket/20181

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Re: [sage-devel] Proposal : Add pplpy and gmpy2 as standard packages.

[jplab]

Hi all,

Allow me to jump in the discussion as a daily "Sage user" of code using the 
ppl backend in the Polyhedron class. 
I put the "Sage user" in quotes, because it seems that it was used for 
different types of users.

What's in for the normal strictly routine not-developing user?

Well, IMHO more transparency about libraries used. Basically, I just 
figured out where the wrapper for ppl was(!). 
Ok, perhaps I'm ignorant or stupid; but to me, it seems like making pplpy 
and gmpy2 standard packages 
is not a revolutionary idea that is going to break everything, or is it? 
Further, 

- no Standard Sage user is asked to know or use gmpy2 or pplpy. 
>These are respectively used as gmp data transition and backend 
>for polyhedra 
>

Further, I believe that the strictly routine not-developing user will not 
notice the difference as the vast majority 
(of the users of sage that I know) are not even aware that there is such a 
thing as a "python integer" and a 
"Sage integer" and they keep on using Sage despite some of its 
incongruities. So if we speak of those users, 
I can not really see how any smelly unpleasantness would be laid down on 
their heads by making ppl available 
through a standard library as opposed to being Cython wrapped.

I am aware that I do not have a full overview of the changes implied by 
making the transition smooth, but since I felt 
concerned as an indirect daily user of ppl, I wanted to express my opinion 
on the matter:

Propose to replace `sage.libs.ppl` by the standalone pplpy 
> . This require to have pplpy as a 
> standard package. 

As pplpy use gmpy2 the latter should be stantard too.


+1 

As Vincent pointed out:

- pplpy currently includes more ppl features than sage.libs.ppl 
>

and could always be improved by a larger user/developer base being a 
python2&3 package.

Jean-Philippe

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Re: [sage-devel] Re: changelogs missing in http://www.sagemath.org/changelogs/index.html

[jplab]

This would indeed be fantastic as I am writing an application for funding 
for a future SageDays 
and it would be great to have an order of magnitude of how many active 
contributors there are 
to the latest Sage releases!

Le jeudi 28 septembre 2017 14:59:50 UTC+2, kcrisman a écrit :
>
>
>
>
> I'll try to have a look today. 
>>
>
> That would be fantastic if this could be back up, granted the definitely 
> nontrivial work involved getting it going again.
>

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[sage-devel] Re: Polyhedron plot bug

[jplab]

Dear Fidel,

Thank you for your bug report. I have created the ticket

https://trac.sagemath.org/ticket/23555

for this issue.

Best,
Jean-Philippe

Le samedi 22 juillet 2017 19:02:07 UTC+2, fidelbc a écrit :
>
> Hello all,
>
> A question [1] at the CoCalc group is related to the following issue while 
> plotting a polyhedron.
>
> If a polyhedron P that is "far" from the origin is constructed, then 
> P.plot() displays the origin. Thus making the actual polyhedron relatively 
> small, see [2] for an example.
>
> The culprit seems to be line 1248 of sage/geometry/polyhedron/plot.py, 
> where Graphics3d() is constructed. The bounding box of Graphics3d() is 
> actually ((0,0,0),(0,0,0)) and is therefore included as part of the 
> projection to be plotted.
>
> Thanks,
> fidel
>
> [1]: https://groups.google.com/d/msg/cocalc/YQQHboBCwPw/d8-NlOS8BwAJ
>

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Re: [sage-devel] Why do Polyhedron objects inherit from "Element"?

[jplab]

> 
> > The reason to wonder is that it seems to provide methods to a polyhedron 
> > object which make no sense: 
> > 
> > 
> > .is_idempotent() 
> > .is_zero() 
> > .n() 
> > .numerical_approx() 
> > .subs() 
> > .substitute() 
>
> This is a *mess* that should actually be removed from Element! 
>
>
Okay, that explains somehow the origin of that. So, among all the classes 
that inherit from Element, such scenario repeats itself I guess?

Hmm... Hopefully none require such methods... Should this be a ticket then?
 

> Element is good when you want coercion to be involved. Such coercion 
> might be useful for polyhdera when considering for example 
>
>   scalar x polyhedron 
>   scalar + polyhedron 
>   matrix x polyhedron 
>   (polyhedron over R1) + (polyhedron over R2) 
>
>
True. That's good to have!

Thanks for enlightening me!

JP 

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[sage-devel] Why do Polyhedron objects inherit from "Element"?

[jplab]

Dear all,

Some time ago, during the Sage Days 84 in Olot, 

https://wiki.sagemath.org/days84

some participants (including myself) wondered why would Polyhedron objects 
inherit from the "Element" class.

The reason to wonder is that it seems to provide methods to a polyhedron 
object which make no sense:


.is_idempotent()
.is_zero()
.n()
.numerical_approx()
.subs()
.substitute()

Although 3 methods seem fair to have:

.cartesian_product()   (Well...)
.rename()
.reset_name()

So, the question is: what is good in inheriting from "Element" for a 
polyhedron object?

Is there something important to inherit from "Element" that I am not aware 
of?

Otherwise, perhaps it would make sense to remove this inheritance (and 
check that nothing breaks...)?




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[sage-devel] Re: making a reset() makes it impossible to "quit"

[jplab]

Thanks for the pointer!

Le jeudi 30 mars 2017 11:37:32 UTC+2, Frédéric Chapoton a écrit :
>
> https://trac.sagemath.org/ticket/22529
>
> Le jeudi 30 mars 2017 11:07:22 UTC+2, jplab a écrit :
>>
>>
>>
>> Le mercredi 29 mars 2017 19:48:57 UTC+2, John H Palmieri a écrit :
>>>
>>> It looks like a bug to me.
>>>
>>>
>> Should I open a ticket then? 
>>
>

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[sage-devel] Re: making a reset() makes it impossible to "quit"

[jplab]

Le mercredi 29 mars 2017 19:48:57 UTC+2, John H Palmieri a écrit :
>
> It looks like a bug to me.
>
>
Should I open a ticket then? 

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[sage-devel] making a reset() makes it impossible to "quit"

[jplab]

Hi,

Is the following normal:

sage: a=2; a
2
sage: reset()
sage: a
Traceback (most recent call last):
...
NameError: name 'a' is not defined
sage: quit
Traceback (most recent call last):
...
NameError: name 'quit' is not defined


See the question on AskSage:

https://ask.sagemath.org/question/9643/clearing-all-user-defined-variables-from-current-session/

It not really practical then...

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[sage-devel] Re: sphinx_tikz() in the documentation?

[jplab]

>
>
> Le lundi 6 mars 2017 05:12:29 UTC+1, Travis Scrimshaw a écrit :
>>
>> Are you not able to do it by putting the tikz code in a .. MATH:: block?
>>
>>
> Haven't tried! Will do! 
>

Actually, after a second thought, I do not think it will work. Here is what 
I want to do in a simple example.

.. PLOT::

P = polytopes.icosahedron()
Img = P.projection().tikz()  # Img contains a LatexExpr
sphinx_tikz(Img)

Then sphinx_tikz would process the tikz code to show a .png picture. I do 
not want to show tikz/latex code per se, but rather the picture that it 
actually represents.


 

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[sage-devel] Re: sphinx_tikz() in the documentation?

[jplab]

Le lundi 6 mars 2017 05:12:29 UTC+1, Travis Scrimshaw a écrit :
>
> Are you not able to do it by putting the tikz code in a .. MATH:: block?
>
>
Haven't tried! Will do! 

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[sage-devel] sphinx_tikz() in the documentation?

[jplab]

Hi all,

It is now possible to add plots in the documentation via the command 
sphinx_plot, see for example:

http://doc.sagemath.org/html/en/reference/plotting/sage/plot/plot.html

I would like to know about how to implement a similar function which would 
do a similar job with a `Latex_Expr` object that contains a tikzpicture.

For a potential use case, see here:

http://doc.sagemath.org/html/en/thematic_tutorials/polytope_tikz.html

Something like tikz2png. After googling, I found this:

https://pypi.python.org/pypi/sphinxcontrib-tikz

Could that be helpful? If one follows a similar strategy as it was used for 
sphinx_plot, would that work (with or without the above package)?

I am aware that this is probably a time consuming task, but perhaps the 
time invested in sphinx_plot could be useful here?

I would be happy to get some input!

JP

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[sage-devel] Sage Days 79 in Jerusalem, November 2016 -- Second announcement

[jplab]

Dear all,

The *Sage Days 79* are going to take place for the first time in Israel on 

*November 21st to 24th 2016* 

on the Givat Ram Campus of the Hebrew University of Jerusalem.

The aim of the meeting will be to introduce the software to students and 
mathematicians in the region, with further emphasis on (but not limited to) 
*geometric 
combinatorics* and *symbolic dynamics*. It will be a great occasion to 
learn more about the software and for advanced developers to present and 
improve current tools.

The workshop receives funding from the European Research Council (ERC) 
grant entitled "*Avenues in Probabilistic and Geometric Combinatorics*", 
which can support student participants' accomodation during the workshop 
and/or travel to Jerusalem.

The deadline for funding is *September 30th 2016*.

For all the information concerning the event and registration see:
https://wiki.sagemath.org/days79

Cordially,
Jean-Philippe Labbé
Postdoctoral Fellow of the Einstein Institute of Mathematics at the Hebrew 
University of Jerusalem

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[sage-devel] First SageDays in Israel (SageDays79)

[jplab]

Hi everyone,

I am pleased to let you know that the first SageDays in Israel are going to 
take place in *November 21 to 25* 2016!

https://wiki.sagemath.org/days79

The aim of the SageDays will be to gather the users of the region for the 
first time and hopefully create new collaborations with more advanced 
developers from outside Israel. The workshop will also be accessible to new 
users, students and professors alike.

For any information about the workshop feel free to contact me.

Jean-Philippe

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Re: [sage-devel] Re: Methods for polyhedron are ring dependant?

[jplab]

Hi everyone,

Out of the discussion I could conclude the following:

-it would be a good idea to warn the user if some results may be wrong due 
to the used ring. Perhaps this deserves a ticket on its own.
-use is_positive for non exact ring

and I suggest:

-Perhaps containment should be done combinatorially in the case of an 
inexact ring (looking at the incidence matrix) and using the canonical 
ordering of vertices and facets?

Would that make sense?

I'm also fine with providing RDF polyhedra as they are, but for some 
methods I realized that it makes a difference in the way to implement them, 
which is good to know. In the case of barycentric subdivision it makes a 
huge difference in the computation time, the algorithmic method, and the 
truth of the results...

JP

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[sage-devel] Methods for polyhedron are ring dependant?

[jplab]

Hi everyone,

Currently, I am working on the ticket:

http://trac.sagemath.org/ticket/18442

which implements a barycentric subdivision of a polytope. For this I use 
the containment check. In the tests, it works fine for a regular pentagon 
over AA but not over RDF. The problem can be seen with the following code:

sage: P = polytopes.regular_polygon(5)
sage: a_vertex = P.vertices()[0]
sage: for facet in P.Hrepresentation(): print facet.contains(a_vertex), 
facet.interior_contains(a_vertex)

True False
True True
True False
True True
True True
sage: P = polytopes.regular_polygon(5, base_ring=RDF)
sage: a_vertex = P.vertices()[0]
sage: for facet in P.Hrepresentation(): print facet.contains(a_vertex), 
facet.interior_contains(a_vertex) 
True True
True True
True True
True True
True True

(The first output is as expected: the vertex is not contained in the 
interior of exactly 2 facets. This is not the case in RDF)

Right now, I have the following question in mind: Does it make sense to 
have polyhedron over RDF? By which I mean: it can not even deal with 
containment of faces properly. Reasonably, the user knows that and will use 
a different ring... But what if?

I know that it is practical to have polyhedron defined over RDF for 
different reasons, but there is a fundamental change in the results (and 
pretty much any method doing computations) if the ring changes. I'm NOT 
asking to remove RDF as a possible ring. The reason I'm asking is that I 
have to use such containment check to implement the method barycentric 
subdivision for polyhedron, but then it breaks for polyhedron defined on 
RDF because of that. So there are methods that simply do not work when the 
ring is RDF.

Maybe this analogy could explain my thoughts:

If we compute the eigenvalues of a matrix defined over RDF, sage warns us 
that the results may go bad. It doesn't if the matrix is rational... Could 
such a warning be issued when working with RDF? And then put NotImplemented 
whenever it is known that RDF could cause trouble (and then fix it for that 
specific ring?).

I could simply set the barycentric subdivision for polyhedron over RDF not 
to be implemented, but I feel this would not answer the problem raised 
anyway.

Thanks!

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[sage-devel] Re: Bug in hilbert numerator of a big ideal?

[jplab]

Hi!

So, the workaround I found was to wrap cocoa using a subprocess... It works 
quite ok for my purposes...

Thanks for your help!
JP

Le samedi 23 mai 2015 08:05:51 UTC+3, john_perry_usm a écrit :


 Ok, I'll have a look at frobby! Just to check, I installed Macaulay2 and 
 did the same computation and it gave me the right answer... 


 CoCoA might also compute the correct answer, as I believe CoCoA switches 
 silently to bigint whenever it notices the need. I don't think Sage 
 supports CoCoA anymore though. (I'd like to fix that one day, but there are 
 lots of things I'd like to do one day...)
  

 So I could interface my code, but this is not the optimal way. If it is a 
 bug, it should be looked at and repaired...


 I'm willing to be corrected here, but my reaction is that this is not a 
 bug. Sage uses Singular as its commutative algebra engine, and Singular 
 advertises this limitation. As an analogy, it's not a bug if a computer 
 algebra system that cautions users that it works only modulo a prime p 
 gives you 1-2=p-1 instead of -1.

 That doesn't mean we can't address it. Hilbert series  polynomials work 
 with int, so maybe a workaround would be to check output from Singular, and 
 see if 2^32 divides it; if so, cancel the corresponding term. I don't know 
 if we can guarantee that this is always correct.

 Alternately, we can ask upstream.

 john perry


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[sage-devel] Re: Bug in hilbert numerator of a big ideal?

[jplab]

Dear John,

Ok, I'll have a look at frobby! Just to check, I installed Macaulay2 and 
did the same computation and it gave me the right answer... So I could 
interface my code, but this is not the optimal way. If it is a bug, it 
should be looked at and repaired...

Best,
Jean-Philippe


Le jeudi 21 mai 2015 23:38:02 UTC+3, john_perry_usm a écrit :

 Actually, there seems to be a convenient frobby.hilbert() function which 
 does what you want, though I don't know if it's happy with larger 
 coefficients.

 john perry

 On Thursday, May 21, 2015 at 3:35:23 PM UTC-5, john_perry_usm wrote:

 Hi

 I factored this polynomial and found out that the number:

 4294967296 (which should ring a bell)

 is a factor of the polynomial!


 It didn't ring a bell for me, but factor(4294967296) enlightens me. :-)
  

 It seems that the hilbert numerator uses singular. Can that be that 
 singular can not deal with very big integers?? Or with too many variables?


 I *think* the first sentence on this page is related to your question:

 http://www.singular.uni-kl.de/Manual/latest/sing_90.htm#SEC129


 In principle you could get around it using another Hilbert function. You 
 could try frobby, which is actually in Sage (in mine, anyway), but I've 
 never used it, so I can't be more helpful, sorry.

 john perry



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[sage-devel] Re: trac broken (/tmp/ is full)

[jplab]

Hi,

This happened to me yesterday with #18442 and a few hours later it was back 
and ok...

JP

Le jeudi 21 mai 2015 14:28:08 UTC+3, vdelecroix a écrit :

 Hello, 

 Again trac does not show many tickets. Going to 

 http://trac.sagemath.org/ticket/15456 

 I got 

 Trac detected an internal error: 

  OSError: [Errno 2] No such file or directory: '/tmp/tmp_1iGR1' 

 Vincent 


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[sage-devel] Bug in hilbert numerator of a big ideal?

[jplab]

Hi everyone,

I encountered a weird behavior while computing the hilbert numerator of 
certain Stanley-Reisner ideals 
http://en.wikipedia.org/wiki/Stanley%E2%80%93Reisner_ring.

It is difficult to give a short, self-contained, correct example since the 
smallest example I can obtain that 
produces the bug involves an ideal with ~2500 generators (of degree 2) on 
around ~70 variables.

Eventhough the ideal is relatively big, I know what it should look like (i 
know the simplicial complex it comes from). 
So I remove from the obtained hilbert numerator the correct solution and I 
find a non-zero polynomial.

I factored this polynomial and found out that the number:

4294967296 (which should ring a bell)

is a factor of the polynomial!

I produced different examples and this number always comes up when I do not 
get the expected hilbert numerator.

It seems that the hilbert numerator uses singular. Can that be that 
singular can not deal with very big integers?? Or with too many variables?
Thanks,
JP

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[sage-devel] Re: Please review ticket #18128 -- Face truncation of polyhedron

[jplab]

Hi again,

The ticket is again ready for review!

http://trac.sagemath.org/ticket/18128

Thanks!!
JP

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[sage-devel] timeit in the cloud vs terminal

[jplab]

Hi!

Compare the following code in the command line and the cloud:

In the terminal:

sage: t=timeit('factor(ZZ.random_element(10^40))', seconds=True)
sage: t
0.019134044647216797
sage: type(t)
type 'float'

In the cloud:

sage: t=timeit('factor(ZZ.random_element(10^40))', seconds=True)
0.0210275173187
sage: type(t)
type 'NoneType'

Is that normal that the timeit in the file sage_salvus.py does not return a 
float when the keyword seconds is set to True?

Thank you very much!


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[sage-devel] Re: The high memory cost of creating many Polyhedron objects

[jplab]

Hi,

I had not noticed that Polyhedron created a Poset, and if so that 'makes 
 sense'. I had the same problem with both classes: it makes it very hard to 
 create a lot of Polyhedron objects, or many posets (and this, in turns, 
 makes it hard to write a routine that enumerates posets up to isomorphism) 
 :-/


Yes, this is really bad. At the time, I had to create loads of relatively 
small polyhedral cones and discard them but the computation was hitting the 
RAM limit way too fast.

Is the related poset problem really difficult to fix?

I believe that trying to have a workaround for polyhedron to avoid the 
usage of the face lattice is

1) a lot of work
2) not clear how fast it could be

Of course, once the face lattice is computed many combinatorial data is 
stored there, so it's logic to use this data structure. So a workaround is 
not really ideal anyway.

JP

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[sage-devel] Re: The high memory cost of creating many Polyhedron objects

[jplab]

One thing could be to see how much of the information of the face lattice 
is required for some specific methods...

Perhaps some of them could be implemented without using the face lattice in 
certain cases and be just as fast...

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[sage-devel] Please review ticket #18128 -- Face truncation of polyhedron

[jplab]

Hi,

Please review #18128 http://trac.sagemath.org/ticket/18128.

This ticket implements the method face truncation for polyhedron. The 
method edge_truncation is renamed simply truncation.

Thanks!!!
Jean-Philippe

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[sage-devel] Re: The high memory cost of creating many Polyhedron objects

[jplab]

Hi Nathann,

Have a look at the thread Memory leak in Polyhedron object 
https://groups.google.com/forum/#!searchin/sage-devel/Memory$20leak$20in$20Polyhedron/sage-devel/ka_T52z_i5A/nVG7-V-4ubkJ
.

Would that be the problem for you? In this case, the problem is the ticket 
#14356.

Best,
JP

Le mardi 17 février 2015 16:55:35 UTC+2, Nathann Cohen a écrit :

 Hello everybody, 

 I am trying to compute a couple of things on polyhedra, and for that I 
 need to generate and test a lot of them, each at a time. While I never 
 store them in any way my code stops after a while because of lack of 
 memory: would somebody know if this is caused by same reason as for 
 Posets ? 

 Have fun, 

 Nathann 


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[sage-devel] Re: ipython-notebook: show picture in notebook (e.g. latex-tikz)

[jplab]

Hi!

I just want to say that this is a very nice feature!!

Jean-Philippe

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[sage-devel] Re: Sage logo -- Proposal

[jplab]

Dear Harald,

Thank you very much the detailed answer! This is pretty much what I was 
looking for!

Indeed, it seems like a big decision to change the logo just like that. 
It is good to know 
about the whole story behind the logo.

Of course, the point that logos develop a certain signature for a product 
and that it takes 
a lot of work, time and effort for people to instinctively recognize it... 
Nevertheless,
sometimes logos evolve 
https://www.google.co.il/search?q=logo+evolutionnum=20safe=offsource=lnmstbm=ischsa=Xei=MusjVaLfLcipsgGcj4GgDAved=0CAcQ_AUoAQbiw=1280bih=672...
 
Perhaps it is not time for Sagemath yet. Maybe eventually, it 
may influence the choice of a next version of the logo...

Best,
JP

Le jeudi 2 avril 2015 11:40:37 UTC+3, Harald Schilly a écrit :



 On Sunday, March 29, 2015 at 5:23:53 PM UTC+2, jplab wrote:

 What do you think?


 Hi, sorry to spoil the party. I'm strongly against changing the logo in 
 such a substantial way.  I'm happy with slight adoptions or creating 
 doodles (temporary modifications with a specific theme) but not a change 
 like that. 

 There are two main reasons for me:
 The logo itself is the work of a professional designer. It's crucial to 
 get all details right for such an important piece of graphics, and that's 
 the reason why the logo works on display, as a small App Icon (IOS or 
 Android) or as large as a poster printout. Just using the generic output of 
 any graphics engine might look nice on first glance, but details do matter 
 and it would need some manual work to fix it. That's why there exists the 
 profession graphics designer on its own, where talented people learn how 
 to do this properly. (Mathematican's wouldn't want any lay person to make 
 proofs which just look neat but are nonsense, either). Concretely for the 
 logo above, the outer ring of the dots do not align with the lines, there 
 is no 3D effect (varying dot sizes and line thicknesses) and the dashed 
 background lines might cause troubles at smaller scale.

 The second reason is, that after more than 6 years (I think?) it is 
 already pretty iconic and many can identify it. It has been used in many 
 places, sticker, poster, apps, and even advertisements in academic 
 journals. A change like that would kill all this.

 ... and finally, it has already been mentioned that there are others who 
 have a semi-transparent icosahedron as their logo. I know about the AMS, 
 but I'm sure there might be others.

 And besides all that, would you be the maintainer of the logo? In the last 
 years I got quite a few emails about the logo, where some wanted it in a 
 special variation, a size, needed handholding for some adoptions / 
 file-format changes or other (rather fuzzy) requests. So, it's much more 
 than just replacing it on a couple of places, but an ongoing task. Just a 
 warning ;-)

 -- harald




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[sage-devel] Re: Sage logo -- Proposal

[jplab]

Interestingly, I just noticed that on the sagetrac webpage, the logo is 
different than the usual one:

http://trac.sagemath.org/

It seems that this is actually the real picture behind Sagemath logo. 
Could that be?

This would be that the logo is actually some sort of Schlegel diagram of a 
higher dimensional polytope?

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[sage-devel] Re: We can now have pictures in our documentation

[jplab]

This looks very powerful!!!

Thank you very much!!

I have a few questions (you probably see me coming with these...):

- Can this be used to show pdf pictures obtained by (tikz) latex code?

- In general, can sage show a pdf picture as a plot option? (Something in 
the vain of 
http://www.liafa.univ-paris-diderot.fr/~labbe/blogue/2012/11/using-sage-graphviz-dot2tex-tikz-tikz2pdf-to-draw-a-graph/)

If both is possible, the documentation would benefit greatly!

JP

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[sage-devel] Where to put a tutorial to draw polytopes in Tikz?

[jplab]

Hi,

Recently, I wrote a small tutorial describing how to draw polytopes in TikZ 
using sage. It is currently on my webpage [1]. It would be better to have 
it somewhere in the sage documentation, but where exactly, and in which 
format?

Best,
Jean-Philippe

[1] http://page.mi.fu-berlin.de/labbe/polytope.html

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[sage-devel] Where is the long_element (or w0) method of Coxeter groups gone?

[jplab]

Hi,

I had some older code using Coxeter groups. Since I was running the code on 
machines with different version of Sage, I was handling manually if whether 
it had CoxeterGroup or not (I used WeylGroup when needed). 

Now I'm rebasing my code to the latest version of Sage, and to my surprise, 
there seems not to have a method to get the longest element anymore?

For WeylGroup, I can get .longest_element_hardcoded(). Nevertheless, I do 
not want to work with WeylGroups since I also need several things about 
Coxeter groups.

What happened to the method formerly known as .w0?

Thank you,
Jean-Philippe

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[sage-devel] Memory leak in Polyhedron objects

[jplab]

Hey Sage-devel!

I've been experiencing memory issues dealing with Polyhedron objects for a 
while now... Perhaps it is time to look if something could be done.

Here is a simple code reproducing the (what I believe to be a) memory leak.

First, I use the garbage collector to force the cleaning of memory and then 
look if the python command grows in memory in a top.

sage: while True:   
P=Polyhedron(vertices=[[1,0,0],[0,1,0],[0,0,1]])
eq=P.equations()
del P, eq
gc.collect()
: 
63
31
31
31
31
...

It constantly collects garbage, which is to be expected, and on the long 
run, the python command does not increase in memory usage. While, on the 
contrary:

sage: while True:
: P=Polyhedron(vertices=[[1,0,0],[0,1,0],[0,0,1]])
: fv=P.f_vector()
: del P, fv
: gc.collect()
: 
0
0
0
...

Which not to be expected I guess. Then, when one waits enough, one sees in 
the top that the memory of python increases steadily... This is bad!

I have observed the same behavior with the following functions:

adjacency_matrix
f_vector
face_lattice
facet_adjacency_matrix
facial_adjacencies
graph
is_simple
vertex_adjacencies (although deprecated, also in the new method to produce 
the output)
vertex_adjacency_matrix
vertex_graph

Someone has an idea?

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[sage-devel] Re: Memory leak in Polyhedron objects

[jplab]

Le lundi 16 juin 2014 16:53:45 UTC+2, Volker Braun a écrit :

 The problem is in posets, so you get it in all methods that construct the 
 face lattice:

 http://trac.sagemath.org/ticket/14356


Ok! Good to know! Thanks for the quick reply! 

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[sage-devel] Please review #15547 -- Drawing polytopes using TikZ

[jplab]

This ticket fixes two small errors in the plotting of polyhedron.

http://trac.sagemath.org/ticket/15547

This makes it possible to draw polytope using TikZ code.

See http://page.mi.fu-berlin.de/labbe/Gallery.html for a few drawing 
examples.

Thanks a lot!

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[sage-devel] Multiplication of matrices in a cyclotomic field seems to be slow

[jplab]

Hi,

I posted a ticket this morning about some profiling I did on product of 
matrices (see http://trac.sagemath.org/ticket/16116). Here is a minimal 
example:

sage: PR=PolynomialRing(QQ,[x])
 sage: I=Ideal(x^2 - 1/2*x - 1/4) 

sage: Q=PR.quotient(I) 

sage: elmt_uni=matrix(Q,[[-2*x, 1, 6*x + 2],[-2*x, 2*x, 4*x + 1],[0,0,1]]) 

sage: %timeit elmt_uni*elmt_uni 

1000 loops, best of 3: 1.46 ms per loop  


 sage: CF.F=CyclotomicField(2*5) 

sage: f5=(F+~F)/2 

sage: m=matrix(CF,[[-2*f5, 1, 6*f5 + 2],[-2*f5, 2*f5, 4*f5 + 1],[0,0,1]]) 

sage: type(m) type 'sage.matrix.matrix_cyclo_dense.Matrix_cyclo_dense' 

sage: m.parent() 

Full MatrixSpace of 3 by 3 dense matrices over Cyclotomic Field of order 10 
 and degree 4 

sage: %timeit m*m 100 loops, best of 3: 1.98 ms per loop


Both computation seems to take the same time although more complicated 
example show that the first method is faster. Then, I disactivated the 
verification on cyclotomic fields on line 962 of the file 
/src/sage/matrix/matrix_space.py to get a matrix_generic_dense instead of 
matrix_cyclo_dense.

It gives me:

sage: CF.F=CyclotomicField(2*5)

 sage: f5=(F+~F)/2 

 sage: m=matrix(CF,[[-2*f5, 1, 6*f5 + 2],[-2*f5, 2*f5, 4*f5 + 1],[0,0,1]]) 

 sage: m.parent()

 Full MatrixSpace of 3 by 3 dense matrices over Cyclotomic Field of order 10 
 and degree 4

 sage: type(m)

 type 'sage.matrix.matrix_generic_dense.Matrix_generic_dense'

 sage: %timeit m*m

 1000 loops, best of 3: 251 µs per loop


The question is now: what is the method *_matrix_times_matrix_,* located in 
the module *matrix_cyclo_dense.pyx*, doing so that it takes so much time 
compared to the usual generic multiplication of the module 
matrix_generic_dense? Is there a known use case when the multiplication in 
matrix_cyclo_dense is faster than the generic one?

Thanks,
JPLab


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[sage-devel] Re: polymake wrapper

[jplab]

Hi,

This is just to connect discussions. Here is the link to pypolymake
discussion on the forum of polymake:

http://forum.polymake.org/viewtopic.php?f=9t=178

Cheers,
J-P

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[sage-devel] Polymake/ Are the Sage polytope constructors (too) slow?

[jplab]

My message is in two parts.

The first one is more about Polymake vs Sage. The second is about how
polytopes are constructed in Sage.



For a couple of weeks now, I need to work with polytopes and the
Polyhedron class.

I'm a student currently at Techniche Universität Berlin, so Polymake
is quite the most popular software when dealing with polytopes as it
was created here some years ago. I went through the threads about
Polymake in Sage-devel... if I may summarize what I understood:

-Polymake is an extensive software for anything dealing with polytope
theory;
-Its licence is not completely compatible with Sage, which makes it
impossible to distribute Polymake within Sage;
-It could still be added as a experimental sage-package;
-The sage package is now broken;
-It seems to be a pain to make in work with sage, on all platforms;
-Polyhedron.py includes more and more simple functions that polymake
offers;

Was that all true?

If I understood correctly, the trend now would be to implement
gradually functions of polymake in native sage? Or there would still
be an interest to include somehow Polymake in Sage?

I looked a bit at Polymake and using only Sage would make my life (and
hopefully the life of others here) easier. If anyone is interested by
Polymake/Sage, I would be interested to know what's your opinion, as I
might like to collaborate to the Polyhedron class at some point!

---

Next week, I give a talk about Sage in our research group. I will
present the history and the basics... And also I want to show what
Sage can do with polytopes. So I started by constructing some simple
polytopes, and it seems that Sage is not so fast to construct bigger
examples:

The 3-dimensional permutahedron is fine.

sage: time polytopes.permutahedron(4)
CPU times: user 0.06 s, sys: 0.01 s, total: 0.07 s
Wall time: 0.24 s
A 3-dimensional polyhedron in QQ^3 defined as the convex hull of 24
vertices.

At the 4-dim. permutahedron, things are getting really slowed down.
This is a rather simple polytope which Polymake deals with in no time.

sage: time polytopes.permutahedron(5)
CPU times: user 0.39 s, sys: 0.02 s, total: 0.41 s
Wall time: 7.52 s
A 4-dimensional polyhedron in QQ^4 defined as the convex hull of 120
vertices.

I have a MacBook Pro OSX.6.5 2.4Ghz and I don't see any reason for
Sage taking that much time. I know it's the Wall time that is long,
but I have nothing else running and looking at my Activity Monitor,
the process cdd_both_reps_gmp remains there for a few seconds after
the process python disappeared. Am I wrong?

This also happens for polytopes.cyclic_polytope(10,13),
polytopes.n_cube(7) and bigger values...

Does anyone think that could be improved? I need to show that Sage
could be a viable choice to work with polytopes! ;-)

Thanks,
Jean-Philippe Labbé

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[sage-devel] Re: proposal to remove dsage from sage

[jplab]

Hello everyone,

I worked during months with my computer lab director trying to make
dsage work... We managed once to make it work properly.

In dsage:
-Documentation is anemic;
-Many not implemented functions;
-Bizarre behaviours
-...

My vote is:

[x] - Remove dSage from Sage and use something else instead.

We resign from using dsage and we now use xgrid on Mac. I found that
Parallel Python could do the job too... I don't know much about this
library, but could it be added to sage some day? I would be glad to
help if we can add it to sage.

Jean-Philippe Labbé
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