Re: [sage-support] Sage Crash Report

[Isuru Fernando]

Ah, that package was marked broken. conda-forge and defaults channels are
not ABI compatible, (it'll be in a month or so once the conda-forge rebuild
is done)
You should prioritize conda-forge over defaults and see what happens. Let
me know if it doesn't work and I'll send you the env file for a new
environment.

Isuru

On Sun, Nov 18, 2018 at 4:20 PM Kolen Cheung 
wrote:

> Interesting, it failed.
>
> sage ❯❯❯ conda env create -f env.yml
> Solving environment: failed
>
> ResolvePackageNotFound:
>   - sagenb==1.0.3=py_0
>
> Searching it on https://anaconda.org/conda-forge/sagenb/files shows it
> doesn’t exist. Has it been removed?
>
> Another question, I noticed that you prioritize conda-forge over defaults,
> why?
>
> Thanks.
> ​
>
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Re: [sage-support] plot3d doesn't work in jupyterlab / jupyter notebook

[Antonio Rojas]

El domingo, 18 de noviembre de 2018, 4:24:58 (UTC+1), Kolen Cheung escribió:
>
> Currently it's like this: on an ArchLinux machine, install sage through 
> pacman, and install the sagemath kernel to my jupyterlab hub. And then 
> through the jupyterlab-hub I remote it and use the sagemath kernel and 
> typed the above commands.
>
> I'm guessing it requires some widgets to be installed in jupyter for them 
> to work. Since I'm not using the Sage notebook interface but a 
> Jupyterlab-hub instance that has the sagemath kernel installed.
>
> ​
>>>
>>
The three.js version shipped by Arch is too new and not supported by Sage. 
Either use jsmol (which is still the default), or use the online version of 
three.js (viewer='threejs', online=True) (with sagemath 8.4-4, in previous 
versions the online version doesn't work either)

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Re: [sage-support] plot3d doesn't work in jupyterlab / jupyter notebook

[Enrique Artal]

If I am not wrong it works from a terminal and also if one uses either sage 
-m jupyter or sage -n jupyterlab. 
It is possible to use it directly from jupyter or jupyter lab if the 
sagemath kernel is availabe to jupyter, e.g. at 
/usr/local/share/jupyter/kernels or .local/share/jupyter/kernels, and the 
nbextensions (jsmol,mathjax threejs) linked should not interfere your 
jupyter installation.. 
It may be more complicated using jupyterhub; at least for threejs, if I am 
not wrong something must be changed in order to look for the non-found 
files in external places since jupyterhub is not able to find them locally. 
At some point I was able to use it changing some sage files but I do not 
know how to do it properly.

El lunes, 19 de noviembre de 2018, 3:38:49 (UTC+1), Kolen Cheung escribió:
>
> I tried to install threejs by jupyter labextension install jupyter-threejs 
> but it still doesn’t work. I tried on both jupyter and jupyterlab. I didn’t 
> tried symlinking the directories you mentioned though, because I don’t want 
> to mess up the virtual environments created by conda (my jupyterlab 
> environment is created using conda.)
> ​
>

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Re: [sage-support] plot3d doesn't work in jupyterlab / jupyter notebook

[Enrique Artal]

If I am not wrong it works from a terminal and also if one uses either sage 
-m jupyter or sage -n jupyterlab. 
It is possible to use it directly from jupyter or jupyter lab if the 
sagemath kernel is availabe to jupyter, e.g. at 
/usr/local/share/jupyter/kernels or .local/share/jupyter/kernels, and the 
nbextensions (jsmol,mathjax threejs) linked should not interfere your 
jupyter installation.. 
It may be more complicated using jupyterhub; at least for threejs, if I am 
not wrong something must be changed in order to look for the non-found 
files in external places since jupyterhub is not able to find them locally. 
At some point I was able to use it changing some sage files but I do not 
know how to do it properly.

El lunes, 19 de noviembre de 2018, 3:38:49 (UTC+1), Kolen Cheung escribió:
>
> I tried to install threejs by jupyter labextension install jupyter-threejs 
> but it still doesn’t work. I tried on both jupyter and jupyterlab. I didn’t 
> tried symlinking the directories you mentioned though, because I don’t want 
> to mess up the virtual environments created by conda (my jupyterlab 
> environment is created using conda.)
> ​
>

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Re: [sage-support] Quaternions, how to speed up computation

[Kolen Cheung]

Hi, I’m trying to translate this Sage syntax to Python syntax (i.e. using 
sage as a Python library.) But I got stuck even on the first command.

In Sage,

>>> R. = QQ[]>>> type(R)



Then I thought I can import it in Python like this:

import sage.rings
# OK

sage.rings.polynomial.polynomial_ring.PolynomialRing_field
# AttributeError

sage.rings.polynomial.polynomial_ring.PolynomialRing_field_with_category

How would you write the same program in Python using sage as a library? And 
in general I see many unfamiliar syntax (from Python’s point of view) like 
R., QQ[], (0..20), etc. Do you think it is realistic to use sage as a 
Python library and completely not using sage (as an interpreter) itself?

c.f. Documentation on using sage as a library? 


Thanks.
​

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Re: [sage-support] plot3d doesn't work in jupyterlab / jupyter notebook

[Kolen Cheung]

I tried to install threejs by jupyter labextension install jupyter-threejs 
but it still doesn’t work. I tried on both jupyter and jupyterlab. I didn’t 
tried symlinking the directories you mentioned though, because I don’t want 
to mess up the virtual environments created by conda (my jupyterlab 
environment is created using conda.)
​

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Re: [sage-support] plot3d doesn't work in jupyterlab / jupyter notebook

[Nils Bruin]

It depends a little bit on how you install the sage kernel into your 
jupyter notebook server, but chances are you have to do some extra work to 
install some notebook extensions.

In the sage install, in "/local/share" there are 3 subdirs 
"jsmol, "mathjax", "threejs". These need to be findable as "nbextensions" 
by your jupyter. Having them symlinked in, say, 
/usr/local/share/jupyter/nbextensions should do the trick [if your sage 
kernel lives in .../kernels/sagemath , you would probably want to symlink 
these extensions from .../nbextensions ] 

On Sunday, November 18, 2018 at 2:25:43 PM UTC-8, Kolen Cheung wrote:
>
> sage: y = var('y')
> sage: plot3d(x * y, (x, -1, 1), (y, -1, 1), viewer='threejs')
> Launched html viewer for Graphics3d Object
>
> I didn’t see anything since I’m remote ssh. I tried both ssh -X and ssh -Y 
> but they doesn’t work.
>
> I don’t have a local machine that has a working sage yet. So can’t test 
> that.
>
> Thanks.
> ​
>

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Re: [sage-support] plot3d doesn't work in jupyterlab / jupyter notebook

[Kolen Cheung]

sage: y = var('y')
sage: plot3d(x * y, (x, -1, 1), (y, -1, 1), viewer='threejs')
Launched html viewer for Graphics3d Object

I didn’t see anything since I’m remote ssh. I tried both ssh -X and ssh -Y 
but they doesn’t work.

I don’t have a local machine that has a working sage yet. So can’t test 
that.

Thanks.
​

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Re: [sage-support] Sage Crash Report

[Kolen Cheung]

Interesting, it failed.

sage ❯❯❯ conda env create -f env.yml
Solving environment: failed

ResolvePackageNotFound: 
  - sagenb==1.0.3=py_0

Searching it on https://anaconda.org/conda-forge/sagenb/files shows it 
doesn’t exist. Has it been removed?

Another question, I noticed that you prioritize conda-forge over defaults, 
why?

Thanks.
​

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Re: [sage-support] Sage Crash Report

[Dima Pasechnik]

I guess the place to report such issues is here:
https://github.com/conda-forge/sage-feedstock
On Sun, Nov 18, 2018 at 10:58 AM Kolen Cheung  wrote:
>
> I actually tried a whole bunch of combinations. Build with and without the 
> intel channel, with python 2 or 3, on 3 different systems (macOS, ArchLinux, 
> and SUSE), all through conda. They all have some problems (that upon `sage` 
> there's an error, but this is the only one I reported so they can in 
> principle be all not working for a different reason.
>
> But may be a more general question, is the conda-forge formula really works? 
> If so are there a reproducible build that is tested to be working? If so, can 
> the environment be shared (like the environment.yml I generated above.)
>
> Among the supported installation methods, conda is preferred, because it is 
> reproducible and extensible and isolated. And conda is designed to handle 
> exactly the situation like Sage, that has a lot of non-python dependencies, 
> and conda has a lot of compiler stacks as well.
>
> Who's maintaining the conda-forge formula? May be they can take a look at 
> this?
>
> Regards,
> Kolen
> On Nov 18, 2018, 1:56 AM -0800, Dima Pasechnik , wrote:
>
> Oh, wait, these are all Python3 libraries, correct? This looks fishy
> to me. As well,
> Sage's libgd does not link ICU libraries (all these libicu*),
> fontconfig and webp, all these must be conda-forge
> modifications.
> So that's not something we could realistically fix without conda people.
>
> The usual suggestion - build Sage from source...
>
> On Sun, Nov 18, 2018 at 1:41 AM Kolen Cheung  
> wrote:
>
>
> sage ~ ❯❯❯ ls -alh 
> /home/sage/.conda/envs/sage/lib/python3.6/site-packages/sage/matrix/../../../../libgd.so.3
> lrwxrwxrwx 1 sage sage 14 Nov 17 17:34 
> /home/sage/.conda/envs/sage/lib/python3.6/site-packages/sage/matrix/../../../../libgd.so.3
>  -> libgd.so.3.0.5
> sage ~ ❯❯❯ ldd 
> /home/sage/.conda/envs/sage/lib/python3.6/site-packages/sage/matrix/../../../../libgd.so.3
> linux-vdso.so.1 (0x7ffd5f589000)
> libm.so.6 => /usr/lib/libm.so.6 (0x7f0a078fe000)
> libpng16.so.16 => 
> /home/sage/.conda/envs/sage/lib/python3.6/site-packages/sage/matrix/../../../.././libpng16.so.16
>  (0x7f0a076c3000)
> libz.so.1 => 
> /home/sage/.conda/envs/sage/lib/python3.6/site-packages/sage/matrix/../../../.././libz.so.1
>  (0x7f0a074a8000)
> libfontconfig.so.1 => 
> /home/sage/.conda/envs/sage/lib/python3.6/site-packages/sage/matrix/../../../.././libfontconfig.so.1
>  (0x7f0a07263000)
> libfreetype.so.6 => 
> /home/sage/.conda/envs/sage/lib/python3.6/site-packages/sage/matrix/../../../.././libfreetype.so.6
>  (0x7f0a06f87000)
> libjpeg.so.9 => 
> /home/sage/.conda/envs/sage/lib/python3.6/site-packages/sage/matrix/../../../.././libjpeg.so.9
>  (0x7f0a06d49000)
> libtiff.so.5 => 
> /home/sage/.conda/envs/sage/lib/python3.6/site-packages/sage/matrix/../../../.././libtiff.so.5
>  (0x7f0a06acf000)
> libwebp.so.6 => 
> /home/sage/.conda/envs/sage/lib/python3.6/site-packages/sage/matrix/../../../.././libwebp.so.6
>  (0x7f0a06831000)
> libpthread.so.0 => /usr/lib/libpthread.so.0 (0x7f0a0681)
> libc.so.6 => /usr/lib/libc.so.6 (0x7f0a0664c000)
> /usr/lib64/ld-linux-x86-64.so.2 (0x7f0a07d04000)
> libxml2.so.2 => 
> /home/sage/.conda/envs/sage/lib/python3.6/site-packages/sage/matrix/../../../../././libxml2.so.2
>  (0x7f0a062e5000)
> libdl.so.2 => /usr/lib/libdl.so.2 (0x7f0a062de000)
> libicui18n.so.58 => 
> /home/sage/.conda/envs/sage/lib/python3.6/site-packages/sage/matrix/../../../../././libicui18n.so.58
>  (0x7f0a05e69000)
> libicuuc.so.58 => 
> /home/sage/.conda/envs/sage/lib/python3.6/site-packages/sage/matrix/../../../../././libicuuc.so.58
>  (0x7f0a05abb000)
> libicudata.so.58 => 
> /home/sage/.conda/envs/sage/lib/python3.6/site-packages/sage/matrix/../../../../././libicudata.so.58
>  (0x7f0a03fbb000)
> liblzma.so.5 => 
> /home/sage/.conda/envs/sage/lib/python3.6/site-packages/sage/matrix/../../../../././liblzma.so.5
>  (0x7f0a03d8d000)
> librt.so.1 => /usr/lib/librt.so.1 (0x7f0a03d83000)
> libstdc++.so.6 => 
> /home/sage/.conda/envs/sage/lib/python3.6/site-packages/sage/matrix/../../../.././././libstdc++.so.6
>  (0x7f0a03c4)
> libgcc_s.so.1 => 
> /home/sage/.conda/envs/sage/lib/python3.6/site-packages/sage/matrix/../../../.././././libgcc_s.so.1
>  (0x7f0a03c2b000)
>
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Re: [sage-support] Sage Crash Report

[Dima Pasechnik]

Oh, wait, these are all Python3 libraries, correct? This looks fishy
to me. As well,
Sage's libgd does not link ICU libraries (all these libicu*),
fontconfig and webp, all these must be conda-forge
modifications.
So that's not something we could realistically fix  without conda people.

The usual suggestion - build Sage from source...

On Sun, Nov 18, 2018 at 1:41 AM Kolen Cheung  wrote:
>
> sage ~ ❯❯❯ ls -alh 
> /home/sage/.conda/envs/sage/lib/python3.6/site-packages/sage/matrix/../../../../libgd.so.3
> lrwxrwxrwx 1 sage sage 14 Nov 17 17:34 
> /home/sage/.conda/envs/sage/lib/python3.6/site-packages/sage/matrix/../../../../libgd.so.3
>  -> libgd.so.3.0.5
> sage ~ ❯❯❯ ldd 
> /home/sage/.conda/envs/sage/lib/python3.6/site-packages/sage/matrix/../../../../libgd.so.3
> linux-vdso.so.1 (0x7ffd5f589000)
> libm.so.6 => /usr/lib/libm.so.6 (0x7f0a078fe000)
> libpng16.so.16 => 
> /home/sage/.conda/envs/sage/lib/python3.6/site-packages/sage/matrix/../../../.././libpng16.so.16
>  (0x7f0a076c3000)
> libz.so.1 => 
> /home/sage/.conda/envs/sage/lib/python3.6/site-packages/sage/matrix/../../../.././libz.so.1
>  (0x7f0a074a8000)
> libfontconfig.so.1 => 
> /home/sage/.conda/envs/sage/lib/python3.6/site-packages/sage/matrix/../../../.././libfontconfig.so.1
>  (0x7f0a07263000)
> libfreetype.so.6 => 
> /home/sage/.conda/envs/sage/lib/python3.6/site-packages/sage/matrix/../../../.././libfreetype.so.6
>  (0x7f0a06f87000)
> libjpeg.so.9 => 
> /home/sage/.conda/envs/sage/lib/python3.6/site-packages/sage/matrix/../../../.././libjpeg.so.9
>  (0x7f0a06d49000)
> libtiff.so.5 => 
> /home/sage/.conda/envs/sage/lib/python3.6/site-packages/sage/matrix/../../../.././libtiff.so.5
>  (0x7f0a06acf000)
> libwebp.so.6 => 
> /home/sage/.conda/envs/sage/lib/python3.6/site-packages/sage/matrix/../../../.././libwebp.so.6
>  (0x7f0a06831000)
> libpthread.so.0 => /usr/lib/libpthread.so.0 (0x7f0a0681)
> libc.so.6 => /usr/lib/libc.so.6 (0x7f0a0664c000)
> /usr/lib64/ld-linux-x86-64.so.2 (0x7f0a07d04000)
> libxml2.so.2 => 
> /home/sage/.conda/envs/sage/lib/python3.6/site-packages/sage/matrix/../../../../././libxml2.so.2
>  (0x7f0a062e5000)
> libdl.so.2 => /usr/lib/libdl.so.2 (0x7f0a062de000)
> libicui18n.so.58 => 
> /home/sage/.conda/envs/sage/lib/python3.6/site-packages/sage/matrix/../../../../././libicui18n.so.58
>  (0x7f0a05e69000)
> libicuuc.so.58 => 
> /home/sage/.conda/envs/sage/lib/python3.6/site-packages/sage/matrix/../../../../././libicuuc.so.58
>  (0x7f0a05abb000)
> libicudata.so.58 => 
> /home/sage/.conda/envs/sage/lib/python3.6/site-packages/sage/matrix/../../../../././libicudata.so.58
>  (0x7f0a03fbb000)
> liblzma.so.5 => 
> /home/sage/.conda/envs/sage/lib/python3.6/site-packages/sage/matrix/../../../../././liblzma.so.5
>  (0x7f0a03d8d000)
> librt.so.1 => /usr/lib/librt.so.1 (0x7f0a03d83000)
> libstdc++.so.6 => 
> /home/sage/.conda/envs/sage/lib/python3.6/site-packages/sage/matrix/../../../.././././libstdc++.so.6
>  (0x7f0a03c4)
> libgcc_s.so.1 => 
> /home/sage/.conda/envs/sage/lib/python3.6/site-packages/sage/matrix/../../../.././././libgcc_s.so.1
>  (0x7f0a03c2b000)
>
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