[sage-devel] Re: OS X build failure: "Error installing package gfortran-7.2.0"

[Michael Frey]

I get the same error with MAcOS Mojave and Xcode 10.0.  The release notes 
for Xcode 10 state that /usr/include is being relocated to 
/Library/Developer//CommandLineTools/SDKs/MacOSX.sdk/usr/include/. 
 See the Xcode 10 release notes: 
https://developer.apple.com/documentation/xcode_release_notes/xcode_10_release_notes.
 
 There is a temporary workaround by installing 
/Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg.


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Re: [sage-devel] Re: Smith Normal Form over ZZ seriously slow

[William Stein]

On Wed, Oct 10, 2018 at 3:29 PM Travis Scrimshaw  wrote:
>
> So the bulk of the time is spent converting the Pari object back into a Sage 
> object; mainly, this line:
>
> U = self.matrix_space(ncols = self._nrows)([v[0][i,j] for i in 
> xrange(self._nrows-1,-1,-1) for j in xrange(self._nrows)])
>
> which has 1000x1000 calls to extra the data and then has to be reconstituted 
> into a matrix object. I am not sure if there is a way around this. It might 
> just be a by-product of outsourcing the computation.
>

Thanks for boiling this down to the bottleneck.  It can probably be
made much faster.   Instead of doing

v[0][i,j],

which  probably involves at least two complicated pari calls, is there
a way to convert v[0] to a Python list in one call? If not, one could
add an optimized way to do so.  Then convert that list to a matrix in
sage.

> Best,
> Travis
>
>
> On Thursday, October 11, 2018 at 5:58:04 AM UTC+10, John Cremona wrote:
>>
>> The method smith_form() for matrices over ZZ uses  pari's matsnf() but is 
>> vastly slower.  Compare these:
>>
>> sage: M=MatrixSpace(ZZ,1000,5).random_element()
>> sage: %timeit S=M.smith_form(transformation=True)
>> 1 loop, best of 3: 2.57 s per loop
>> sage: pM=pari(M)
>> sage: %timeit S=pM.matsnf(1)
>> 10 loops, best of 3: 49.5 ms per loop
>>
>> That's a factor of 50.  There's something to be done in the interface 
>> because pari's convention is opposite to Sage's so one has to reverse the 
>> order of rows/columns in the output from pari, but still...
>>
>> John
>
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[sage-devel] Re: Remove sagenb documentation from the reference manual?

[Travis Scrimshaw]

+1 to the proposal on #25382.

Best,
Travis


On Wednesday, October 10, 2018 at 3:27:59 PM UTC+10, John H Palmieri wrote:
>
> At https://trac.sagemath.org/ticket/25382 
> ,
>  
> it is being proposed to remove the documentation for the legacy Sage 
> notebook, a.k.a. sagenb, from the reference manual. Some reasons for this:
>
> - sagenb does not work with Python 3, nor does its documentation, so if we 
> want the docs to build with Python 3, we need to delete it.
> - Indeed, sagenb is not really being developed, as far as I can tell. 
> Maintained to some extent, but not developed. Please correct me if this is 
> incorrect.
> - Some distributions remove this from the reference manual already (as far 
> as I understand).
> - The reference manual should be for Sage proper, not for its components. 
> The reference manual doesn't include documentation for IPython or the 
> Jupyter notebook. It does include links to them, and the proposal would be 
> to give as good a link as possible to sagenb.
>
> Some reasons against this:
>
> - sagenb used to be part of Sage, so its role is different from other 
> components like IPython, etc.
>
> By the way, it is straightforward to remove the sagenb documentation 
> completely. It is more complicated and kind of ugly, but possible, to 
> include the docs in the reference manual conditionally on whether Sage is 
> built with Python 2 or Python 3. This is discussed on the ticket.
>
> Any comments?
>
> -- 
> John
>
>

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[sage-devel] Re: Smith Normal Form over ZZ seriously slow

[Travis Scrimshaw]

So the bulk of the time is spent converting the Pari object back into a 
Sage object; mainly, this line:

U = self.matrix_space(ncols = self._nrows)([v[0][i,j] for i in xrange(self.
_nrows-1,-1,-1) for j in xrange(self._nrows)])

which has 1000x1000 calls to extra the data and then has to be 
reconstituted into a matrix object. I am not sure if there is a way around 
this. It might just be a by-product of outsourcing the computation.

Best,
Travis


On Thursday, October 11, 2018 at 5:58:04 AM UTC+10, John Cremona wrote:
>
> The method smith_form() for matrices over ZZ uses  pari's matsnf() but is 
> vastly slower.  Compare these:
>
> sage: M=MatrixSpace(ZZ,1000,5).random_element()
> sage: %timeit S=M.smith_form(transformation=True)
> 1 loop, best of 3: 2.57 s per loop
> sage: pM=pari(M)
> sage: %timeit S=pM.matsnf(1)
> 10 loops, best of 3: 49.5 ms per loop
>
> That's a factor of 50.  There's something to be done in the interface 
> because pari's convention is opposite to Sage's so one has to reverse the 
> order of rows/columns in the output from pari, but still...
>
> John
>

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[sage-devel] Re: Remove sagenb documentation from the reference manual?

[Volker Braun]

+1 to unconditional removal. Really its just sending confusing messages to 
users looking for help. If you are new to Sage in 2018 you should never 
start sagenb.



On Wednesday, October 10, 2018 at 7:27:59 AM UTC+2, John H Palmieri wrote:
>
> At https://trac.sagemath.org/ticket/25382, it is being proposed to remove 
> the documentation for the legacy Sage notebook, a.k.a. sagenb, from the 
> reference manual. Some reasons for this:
>
> - sagenb does not work with Python 3, nor does its documentation, so if we 
> want the docs to build with Python 3, we need to delete it.
> - Indeed, sagenb is not really being developed, as far as I can tell. 
> Maintained to some extent, but not developed. Please correct me if this is 
> incorrect.
> - Some distributions remove this from the reference manual already (as far 
> as I understand).
> - The reference manual should be for Sage proper, not for its components. 
> The reference manual doesn't include documentation for IPython or the 
> Jupyter notebook. It does include links to them, and the proposal would be 
> to give as good a link as possible to sagenb.
>
> Some reasons against this:
>
> - sagenb used to be part of Sage, so its role is different from other 
> components like IPython, etc.
>
> By the way, it is straightforward to remove the sagenb documentation 
> completely. It is more complicated and kind of ugly, but possible, to 
> include the docs in the reference manual conditionally on whether Sage is 
> built with Python 2 or Python 3. This is discussed on the ticket.
>
> Any comments?
>
> -- 
> John
>
>

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[sage-devel] Smith Normal Form over ZZ seriously slow

[John Cremona]

The method smith_form() for matrices over ZZ uses  pari's matsnf() but is
vastly slower.  Compare these:

sage: M=MatrixSpace(ZZ,1000,5).random_element()
sage: %timeit S=M.smith_form(transformation=True)
1 loop, best of 3: 2.57 s per loop
sage: pM=pari(M)
sage: %timeit S=pM.matsnf(1)
10 loops, best of 3: 49.5 ms per loop

That's a factor of 50.  There's something to be done in the interface
because pari's convention is opposite to Sage's so one has to reverse the
order of rows/columns in the output from pari, but still...

John

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Re: [sage-devel] Re: Remove sagenb documentation from the reference manual?

[William Stein]

Hi,

I wrote much of sagenb and am why sagenb is currently not optional.
I'm fine with removing it from sage and/or making it optional.

William
On Wed, Oct 10, 2018 at 10:43 AM Timo Kaufmann  wrote:
>
> I'm also in favor. Besides being more complicated, I think doing something 
> different here for python2 and python3 would be a bad idea.
>
> Am Mittwoch, 10. Oktober 2018 07:27:59 UTC+2 schrieb John H Palmieri:
>>
>> At https://trac.sagemath.org/ticket/25382, it is being proposed to remove 
>> the documentation for the legacy Sage notebook, a.k.a. sagenb, from the 
>> reference manual. Some reasons for this:
>>
>> - sagenb does not work with Python 3, nor does its documentation, so if we 
>> want the docs to build with Python 3, we need to delete it.
>> - Indeed, sagenb is not really being developed, as far as I can tell. 
>> Maintained to some extent, but not developed. Please correct me if this is 
>> incorrect.
>> - Some distributions remove this from the reference manual already (as far 
>> as I understand).
>> - The reference manual should be for Sage proper, not for its components. 
>> The reference manual doesn't include documentation for IPython or the 
>> Jupyter notebook. It does include links to them, and the proposal would be 
>> to give as good a link as possible to sagenb.
>>
>> Some reasons against this:
>>
>> - sagenb used to be part of Sage, so its role is different from other 
>> components like IPython, etc.
>>
>> By the way, it is straightforward to remove the sagenb documentation 
>> completely. It is more complicated and kind of ugly, but possible, to 
>> include the docs in the reference manual conditionally on whether Sage is 
>> built with Python 2 or Python 3. This is discussed on the ticket.
>>
>> Any comments?
>>
>> --
>> John
>>
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[sage-devel] Re: Remove sagenb documentation from the reference manual?

[Timo Kaufmann]

I'm also in favor. Besides being more complicated, I think doing something 
different here for python2 and python3 would be a bad idea.

Am Mittwoch, 10. Oktober 2018 07:27:59 UTC+2 schrieb John H Palmieri:
>
> At https://trac.sagemath.org/ticket/25382, it is being proposed to remove 
> the documentation for the legacy Sage notebook, a.k.a. sagenb, from the 
> reference manual. Some reasons for this:
>
> - sagenb does not work with Python 3, nor does its documentation, so if we 
> want the docs to build with Python 3, we need to delete it.
> - Indeed, sagenb is not really being developed, as far as I can tell. 
> Maintained to some extent, but not developed. Please correct me if this is 
> incorrect.
> - Some distributions remove this from the reference manual already (as far 
> as I understand).
> - The reference manual should be for Sage proper, not for its components. 
> The reference manual doesn't include documentation for IPython or the 
> Jupyter notebook. It does include links to them, and the proposal would be 
> to give as good a link as possible to sagenb.
>
> Some reasons against this:
>
> - sagenb used to be part of Sage, so its role is different from other 
> components like IPython, etc.
>
> By the way, it is straightforward to remove the sagenb documentation 
> completely. It is more complicated and kind of ugly, but possible, to 
> include the docs in the reference manual conditionally on whether Sage is 
> built with Python 2 or Python 3. This is discussed on the ticket.
>
> Any comments?
>
> -- 
> John
>
>

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Re: [sage-devel] Re: Remove sagenb documentation from the reference manual?

[Dima Pasechnik]

Anyhow, I am for removal these docs from Sage proper,
(and making sagenb optional)
On Wed, Oct 10, 2018 at 9:09 AM Frédéric Chapoton  wrote:
>
> This is the alternative : what would need to be done to fix the same problem 
> in another way.
>
> Le mercredi 10 octobre 2018 10:08:00 UTC+2, Dima Pasechnik a écrit :
>>
>>
>>
>> On Wed, 10 Oct 2018, 08:16 Frédéric Chapoton,  wrote:
>>>
>>> I agree with and support strongly this proposal of removal of sagenb doc, 
>>> which is a step towards having "make" (and not only "make build") being 
>>> working with python3.
>>>
>>> The alternative would require a lot of work on sagenb itself :
>>>
>>> * merge the deprecation pull request there
>>> * release a new sagenb
>>> * make a ticket for upgrading the sagenb in sage
>>> * and then the doc may still be broken as sagenb is not 100% 
>>> python3-compatible (some issues with email remains)
>>
>>
>> I believe this is independent of removal of sagenb docs from Sage proper, no?
>>>
>>>
>>> Frédéric
>>>
>>>
>>> Le mercredi 10 octobre 2018 07:27:59 UTC+2, John H Palmieri a écrit :

 At https://trac.sagemath.org/ticket/25382, it is being proposed to remove 
 the documentation for the legacy Sage notebook, a.k.a. sagenb, from the 
 reference manual. Some reasons for this:

 - sagenb does not work with Python 3, nor does its documentation, so if we 
 want the docs to build with Python 3, we need to delete it.
 - Indeed, sagenb is not really being developed, as far as I can tell. 
 Maintained to some extent, but not developed. Please correct me if this is 
 incorrect.
 - Some distributions remove this from the reference manual already (as far 
 as I understand).
 - The reference manual should be for Sage proper, not for its components. 
 The reference manual doesn't include documentation for IPython or the 
 Jupyter notebook. It does include links to them, and the proposal would be 
 to give as good a link as possible to sagenb.

 Some reasons against this:

 - sagenb used to be part of Sage, so its role is different from other 
 components like IPython, etc.

 By the way, it is straightforward to remove the sagenb documentation 
 completely. It is more complicated and kind of ugly, but possible, to 
 include the docs in the reference manual conditionally on whether Sage is 
 built with Python 2 or Python 3. This is discussed on the ticket.

 Any comments?

 --
 John

>>> --
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Re: [sage-devel] Re: Remove sagenb documentation from the reference manual?

[Frédéric Chapoton]

This is the alternative : what would need to be done to fix the same 
problem in another way.

Le mercredi 10 octobre 2018 10:08:00 UTC+2, Dima Pasechnik a écrit :
>
>
>
> On Wed, 10 Oct 2018, 08:16 Frédéric Chapoton,  > wrote:
>
>> I agree with and support strongly this proposal of removal of sagenb doc, 
>> which is a step towards having "make" (and not only "make build") being 
>> working with python3.
>>
>> The alternative would require a *lot of work* on sagenb itself :
>>
>> * merge the deprecation pull request there
>> * release a new sagenb
>> * make a ticket for upgrading the sagenb in sage
>> * and then the doc may still be broken as sagenb is not 100% 
>> python3-compatible (some issues with email remains)
>>
>
> I believe this is independent of removal of sagenb docs from Sage proper, 
> no?
>
>>
>> Frédéric
>>
>>
>> Le mercredi 10 octobre 2018 07:27:59 UTC+2, John H Palmieri a écrit :
>>>
>>> At https://trac.sagemath.org/ticket/25382, it is being proposed to 
>>> remove the documentation for the legacy Sage notebook, a.k.a. sagenb, from 
>>> the reference manual. Some reasons for this:
>>>
>>> - sagenb does not work with Python 3, nor does its documentation, so if 
>>> we want the docs to build with Python 3, we need to delete it.
>>> - Indeed, sagenb is not really being developed, as far as I can tell. 
>>> Maintained to some extent, but not developed. Please correct me if this is 
>>> incorrect.
>>> - Some distributions remove this from the reference manual already (as 
>>> far as I understand).
>>> - The reference manual should be for Sage proper, not for its 
>>> components. The reference manual doesn't include documentation for IPython 
>>> or the Jupyter notebook. It does include links to them, and the proposal 
>>> would be to give as good a link as possible to sagenb.
>>>
>>> Some reasons against this:
>>>
>>> - sagenb used to be part of Sage, so its role is different from other 
>>> components like IPython, etc.
>>>
>>> By the way, it is straightforward to remove the sagenb documentation 
>>> completely. It is more complicated and kind of ugly, but possible, to 
>>> include the docs in the reference manual conditionally on whether Sage is 
>>> built with Python 2 or Python 3. This is discussed on the ticket.
>>>
>>> Any comments?
>>>
>>> -- 
>>> John
>>>
>>> -- 
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Re: [sage-devel] Re: Remove sagenb documentation from the reference manual?

[Dima Pasechnik]

On Wed, 10 Oct 2018, 08:16 Frédéric Chapoton,  wrote:

> I agree with and support strongly this proposal of removal of sagenb doc,
> which is a step towards having "make" (and not only "make build") being
> working with python3.
>
> The alternative would require a *lot of work* on sagenb itself :
>
> * merge the deprecation pull request there
> * release a new sagenb
> * make a ticket for upgrading the sagenb in sage
> * and then the doc may still be broken as sagenb is not 100%
> python3-compatible (some issues with email remains)
>

I believe this is independent of removal of sagenb docs from Sage proper,
no?

>
> Frédéric
>
>
> Le mercredi 10 octobre 2018 07:27:59 UTC+2, John H Palmieri a écrit :
>>
>> At https://trac.sagemath.org/ticket/25382, it is being proposed to
>> remove the documentation for the legacy Sage notebook, a.k.a. sagenb, from
>> the reference manual. Some reasons for this:
>>
>> - sagenb does not work with Python 3, nor does its documentation, so if
>> we want the docs to build with Python 3, we need to delete it.
>> - Indeed, sagenb is not really being developed, as far as I can tell.
>> Maintained to some extent, but not developed. Please correct me if this is
>> incorrect.
>> - Some distributions remove this from the reference manual already (as
>> far as I understand).
>> - The reference manual should be for Sage proper, not for its components.
>> The reference manual doesn't include documentation for IPython or the
>> Jupyter notebook. It does include links to them, and the proposal would be
>> to give as good a link as possible to sagenb.
>>
>> Some reasons against this:
>>
>> - sagenb used to be part of Sage, so its role is different from other
>> components like IPython, etc.
>>
>> By the way, it is straightforward to remove the sagenb documentation
>> completely. It is more complicated and kind of ugly, but possible, to
>> include the docs in the reference manual conditionally on whether Sage is
>> built with Python 2 or Python 3. This is discussed on the ticket.
>>
>> Any comments?
>>
>> --
>> John
>>
>> --
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[sage-devel] Re: Remove sagenb documentation from the reference manual?

[Frédéric Chapoton]

I agree with and support strongly this proposal of removal of sagenb doc, 
which is a step towards having "make" (and not only "make build") being 
working with python3.

The alternative would require a *lot of work* on sagenb itself :

* merge the deprecation pull request there
* release a new sagenb
* make a ticket for upgrading the sagenb in sage
* and then the doc may still be broken as sagenb is not 100% 
python3-compatible (some issues with email remains)

Frédéric


Le mercredi 10 octobre 2018 07:27:59 UTC+2, John H Palmieri a écrit :
>
> At https://trac.sagemath.org/ticket/25382, it is being proposed to remove 
> the documentation for the legacy Sage notebook, a.k.a. sagenb, from the 
> reference manual. Some reasons for this:
>
> - sagenb does not work with Python 3, nor does its documentation, so if we 
> want the docs to build with Python 3, we need to delete it.
> - Indeed, sagenb is not really being developed, as far as I can tell. 
> Maintained to some extent, but not developed. Please correct me if this is 
> incorrect.
> - Some distributions remove this from the reference manual already (as far 
> as I understand).
> - The reference manual should be for Sage proper, not for its components. 
> The reference manual doesn't include documentation for IPython or the 
> Jupyter notebook. It does include links to them, and the proposal would be 
> to give as good a link as possible to sagenb.
>
> Some reasons against this:
>
> - sagenb used to be part of Sage, so its role is different from other 
> components like IPython, etc.
>
> By the way, it is straightforward to remove the sagenb documentation 
> completely. It is more complicated and kind of ugly, but possible, to 
> include the docs in the reference manual conditionally on whether Sage is 
> built with Python 2 or Python 3. This is discussed on the ticket.
>
> Any comments?
>
> -- 
> John
>
>

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