Re: [sage-devel] how to log sage output for long running program

2019-03-15 Thread 'Justin C. Walker' via sage-devel 


> On Mar 15, 2019, at 21:46 , Ai Bo  wrote:
> 
> I am running a long running program. I would like to log the output.
> I have tried: 
>  ../sage-8.6/sage test.sage > test.log &
> 
> There is nothing written in test.log before the program finishes. 
> I tried to use tee, same problem.
> 
> I tried to add:
> f = open('test.log', 'w')
> 
> in my test.sage program, still nothing is written before the program finishes.
> 
> How to log a long running program?

The problem, I think, is that python uses buffered output.  I assume that you 
are using print statements, so (without knowing more), I would use
  sys.stdout.flush()
after each print, or after points in your program where the state is useful for 
debugging.

If I’ve made the wrong assumptions, let us know.

HTH

Justin

--
Justin C. Walker
Curmudgeon at Large
Director
Institute for the Enhancement of the Director's Income
--
Build a man a fire and he'll be warm
 for a night.
Set a man on fire and he'll be warm
 for the rest of his life.



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[sage-devel] how to log sage output for long running program

2019-03-15 Thread Ai Bo 
I am running a long running program. I would like to log the output.
I have tried: 
 ../sage-8.6/sage test.sage > test.log &

There is nothing written in test.log before the program finishes. 
I tried to use tee, same problem.

I tried to add:
f = open('test.log', 'w')

in my test.sage program, still nothing is written before the program 
finishes.

How to log a long running program?

Thanks,

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Re: [sage-devel] Re: internet tests failing

2019-03-15 Thread Dima Pasechnik 
On Fri, Mar 15, 2019 at 10:17 PM Dima Pasechnik  wrote:
>
>
>
> On Friday, March 15, 2019 at 5:58:15 PM UTC, John H Palmieri wrote:
>>
>>
>>
>> On Friday, March 15, 2019 at 3:31:33 AM UTC-7, Dima Pasechnik wrote:
>>>
>>> On Thu, Mar 14, 2019 at 7:51 PM John H Palmieri  wrote:
>>> >
>>> > I'm seeing the same failure on a Mac running the most recent OS X. I have 
>>> > openssl 1.1.1a installed on this machine, and I see the error in Sage. 
>>> > Then I did './sage -i openssl' and './sage -f python2', and I still see 
>>> > the error. The Python 2 log file does not list ssl among the modules 
>>> > which were not built, so it looks like it was built with ssl support.
>>>
>>> Can you use Sage's pip on packages from external repos, or is this also
>>> broken?
>>
>>
>> $ ./sage --pip install pylatex
>>
>> works just fine: finds the file, downloads it using https, etc. Is that the 
>> sort of thing you mean?
>
>
> OK, so apparently pip is less picky here. Unrolling this thing about oeis() 
> function, it boils down to
> Python's
>
> >>> from urllib import urlopen
> >>> f=urlopen("https://oeis.org/";)
>
> that fails with   CERTIFICATE_VERIFY_FAILED

I can reproduce this on Sage 8.6 with included openssl installed.

This is how to fix it, assuming you install your openssl from Sage
spkg, basically using a slightly adjusted script from Python.org
python 2.7.16 installer.

Change to your SAGE_ROOT
start ./sage -sh

mkdir local/openssl

run the attached Python script (which will install certificates module
via pip and pull the needed certs for the local openssl)

We perhaps should add this to pyopenssl Sage spkg.

Dima
>
> See more on this in the sub-thread here:
> https://groups.google.com/d/msg/sage-devel/f443LhVnyKc/JLLZrQOWBgAJ
>
>
>>
>>
>>
>>>
>>>
>>> Looking at how Homebrew installs openssl 1.1.1b, one sees that it does
>>> some post_install involving system's keychains and certs:
>>> https://github.com/Homebrew/homebrew-core/blob/master/Formula/open...@1.1.rb
>>>
>>> So it could be that Sage's openssl spkg must dance this dance too.
>>>
>>> It looks like a need for a blocker trac ticket on this, then...
>>>
>>>
>>>
>>>
>>> >
>>> >
>>> >
>>> > On Thursday, March 14, 2019 at 11:19:37 AM UTC-7, Volker Braun wrote:
>>> >>
>>> >> I'm guessing you run this on an oldish mac, those have an outdated 
>>> >> openssl that doesn't support TLS12. More and more sites are switching 
>>> >> that on. Building Sage's openssl should fix that.
>>> >>
>>> >>
>>> >>
>>> >> On Thursday, March 14, 2019 at 7:09:50 PM UTC+1, kcrisman wrote:
>>> >>>
>>> >>> This could be just me.  But I am getting a lot of this when I try 
>>> >>> running optional internet tests for e.g. src/sage/databases/oeis.py or 
>>> >>> src/sage/symbolic/integration/external.py  Internet clearly works if 
>>> >>> you can read this message, but apparently it doesn't work from within 
>>> >>> Sage, because I get this message when I try it in the Sage command line 
>>> >>> as well with e.g. this command.  Any ideas - do I need to rebuild Sage 
>>> >>> with additional SSL support or something?  That should be mentioned 
>>> >>> somewhere.  Thanks!
>>> >>>
>>> >>> - kcrisman
>>> >>>
>>> >>> w = oeis(7540) ; w
>>> >>>
>>> >>>
>>> >>> URLError: >> >>> certificate verify failed (_ssl.c:726)>
>>> >
>>> > --
>>> > You received this message because you are subscribed to the Google Groups 
>>> > "sage-devel" group.
>>> > To unsubscribe from this group and stop receiving emails from it, send an 
>>> > email to sage-devel+...@googlegroups.com.
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>>> > Visit this group at https://groups.google.com/group/sage-devel.
>>> > For more options, visit https://groups.google.com/d/optout.

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#!/usr/bin/env python
# install_certifi.py
#
# sample script to install or update a set of default Root Certificates
# for the ssl module.  Uses the certificates provided by the certifi package:
#   https://pypi.python.org/pypi/certifi

import os
import os.path
import ssl
import stat
import subprocess
import sys

STAT_0o775 = ( stat.S_IRUSR | stat.S_IWUSR | stat.S_IXUSR
 | stat.S_IRGRP | stat.S_IWGRP | stat.S_IXGRP
 | stat.S_IROTH |stat.S_IXOTH )

def main():
openssl_dir, openssl_cafile = os.path.split(
ssl.get_default_verify_paths().openssl_cafile)

print(" -- pip install --upgrade certifi")
subprocess.check_call([sys.executable,
"-E", "-s", "-m", "pip", "install", "--upgrade", "certifi"])

import certifi

# change working directory to the default

Re: [sage-devel] Re: internet tests failing

2019-03-15 Thread Dima Pasechnik 


On Friday, March 15, 2019 at 5:58:15 PM UTC, John H Palmieri wrote:
>
>
>
> On Friday, March 15, 2019 at 3:31:33 AM UTC-7, Dima Pasechnik wrote:
>>
>> On Thu, Mar 14, 2019 at 7:51 PM John H Palmieri  
>> wrote: 
>> > 
>> > I'm seeing the same failure on a Mac running the most recent OS X. I 
>> have openssl 1.1.1a installed on this machine, and I see the error in Sage. 
>> Then I did './sage -i openssl' and './sage -f python2', and I still see the 
>> error. The Python 2 log file does not list ssl among the modules which were 
>> not built, so it looks like it was built with ssl support. 
>>
>> Can you use Sage's pip on packages from external repos, or is this also 
>> broken? 
>>
>
> $ ./sage --pip install pylatex
>
> works just fine: finds the file, downloads it using https, etc. Is that 
> the sort of thing you mean?
>

OK, so apparently pip is less picky here. Unrolling this thing about oeis() 
function, it boils down to
Python's

>>> from urllib import urlopen 
>>> f=urlopen("https://oeis.org/";) 

that fails with   CERTIFICATE_VERIFY_FAILED

See more on this in the sub-thread here:
https://groups.google.com/d/msg/sage-devel/f443LhVnyKc/JLLZrQOWBgAJ



>
>  
>
>>
>> Looking at how Homebrew installs openssl 1.1.1b, one sees that it does 
>> some post_install involving system's keychains and certs: 
>>
>> https://github.com/Homebrew/homebrew-core/blob/master/Formula/open...@1.1.rb 
>>
>> So it could be that Sage's openssl spkg must dance this dance too. 
>>
>> It looks like a need for a blocker trac ticket on this, then... 
>>
>>
>>
>>
>> > 
>> > 
>> > 
>> > On Thursday, March 14, 2019 at 11:19:37 AM UTC-7, Volker Braun wrote: 
>> >> 
>> >> I'm guessing you run this on an oldish mac, those have an outdated 
>> openssl that doesn't support TLS12. More and more sites are switching that 
>> on. Building Sage's openssl should fix that. 
>> >> 
>> >> 
>> >> 
>> >> On Thursday, March 14, 2019 at 7:09:50 PM UTC+1, kcrisman wrote: 
>> >>> 
>> >>> This could be just me.  But I am getting a lot of this when I try 
>> running optional internet tests for e.g. src/sage/databases/oeis.py or 
>> src/sage/symbolic/integration/external.py  Internet clearly works if you 
>> can read this message, but apparently it doesn't work from within Sage, 
>> because I get this message when I try it in the Sage command line as well 
>> with e.g. this command.  Any ideas - do I need to rebuild Sage with 
>> additional SSL support or something?  That should be mentioned somewhere. 
>>  Thanks! 
>> >>> 
>> >>> - kcrisman 
>> >>> 
>> >>> w = oeis(7540) ; w 
>> >>> 
>> >>> 
>> >>> URLError: > certificate verify failed (_ssl.c:726)> 
>> > 
>> > -- 
>> > You received this message because you are subscribed to the Google 
>> Groups "sage-devel" group. 
>> > To unsubscribe from this group and stop receiving emails from it, send 
>> an email to sage-devel+...@googlegroups.com. 
>> > To post to this group, send email to sage-...@googlegroups.com. 
>> > Visit this group at https://groups.google.com/group/sage-devel. 
>> > For more options, visit https://groups.google.com/d/optout. 
>>
>

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Re: [sage-devel] Re: Computing determinants of obviously singular matrices

2019-03-15 Thread dimpase 
On Fri, Mar 15, 2019 at 02:59:05PM -0700, Kwankyu Lee wrote:
> 
> If the determinant is obviously zero, then you don't need to run the 
> computation. If a preprocessing to check zero rows or columns is added, 
> then the determinant computation would become slower for usual nontrivial 
> cases.

I would not be so categorical here. It makes a perfect sense to add a
parameter to the determinant function that would switch such a check on.
Similarly, one can think of adding a check for rows with just one non-0,
as they can be used for a very effcient reduction...

Dima

> 
> 
> Cheers. 
> 
> On Saturday, March 16, 2019 at 2:15:06 AM UTC+9, Maximilian Jaroschek wrote:
> >
> > Hello, 
> >
> > I'm using the current developer version of sage and noticed that when 
> > computing determinants of matrices over polynomial rings and rational 
> > functions, cases where the determinant is easily seen to be zero due to 
> > zero rows or columns can take an unreasonable long time to compute. I 
> > compared the timings with the same computation over other domains.
> >
> > sage: L.=PolynomialRing(QQ)
> > sage: MS=MatrixSpace(L,100)
> > sage: time _=MS.zero().determinant()
> > CPU times: user 13.4 s, sys: 19.6 ms, total: 13.5 s
> > Wall time: 13.5 s
> > sage: MS=MatrixSpace(L.fraction_field(),100)
> > sage: time _=MS.zero().determinant()
> > CPU times: user 200 ms, sys: 0 ns, total: 200 ms
> > Wall time: 200 ms
> > sage: MS=MatrixSpace(ZZ,100)
> > sage: time _=MS.zero().determinant()
> > CPU times: user 563 盜, sys: 5 盜, total: 568 盜
> > Wall time: 573 盜
> > sage: MS=MatrixSpace(L,40)
> > sage: M=MS.random_element(3)
> > sage: M=M.with_rescaled_row(0,0)
> > sage: M.rows()[0]==0
> > True
> > sage: time _=M.determinant()
> > CPU times: user 35.2 s, sys: 8.06 ms, total: 35.2 s
> > Wall time: 35.2 s
> > sage: MS=MatrixSpace(L.fraction_field(),10)
> > sage: M=MS.random_element(3)
> > sage: M=M.with_rescaled_row(0,0)
> > sage: M.rows()[0]==0
> > True
> > sage: time _=M.determinant()
> > CPU times: user 1min 56s, sys: 300 ms, total: 1min 56s
> > Wall time: 1min 56s
> > sage: MS=MatrixSpace(ZZ,500)
> > sage: M=MS.random_element(2^40)
> > sage: M=M.with_rescaled_row(0,0)
> > sage: M.rows()[0]==0
> > True
> > sage: time _=M.determinant()
> > CPU times: user 67.6 ms, sys: 0 ns, total: 67.6 ms
> > Wall time: 67.9 ms
> > sage: 
> >
> > Probably a preprocessing step could help that looks for zero rows or 
> > columns before running the actual algorithm.
> >
> >
> > Best,
> > Maximilian
> >
> 
> -- 
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[sage-devel] Re: Computing determinants of obviously singular matrices

2019-03-15 Thread Kwankyu Lee 
Hi,

If the determinant is obviously zero, then you don't need to run the 
computation. If a preprocessing to check zero rows or columns is added, 
then the determinant computation would become slower for usual nontrivial 
cases.


Cheers. 

On Saturday, March 16, 2019 at 2:15:06 AM UTC+9, Maximilian Jaroschek wrote:
>
> Hello, 
>
> I'm using the current developer version of sage and noticed that when 
> computing determinants of matrices over polynomial rings and rational 
> functions, cases where the determinant is easily seen to be zero due to 
> zero rows or columns can take an unreasonable long time to compute. I 
> compared the timings with the same computation over other domains.
>
> sage: L.=PolynomialRing(QQ)
> sage: MS=MatrixSpace(L,100)
> sage: time _=MS.zero().determinant()
> CPU times: user 13.4 s, sys: 19.6 ms, total: 13.5 s
> Wall time: 13.5 s
> sage: MS=MatrixSpace(L.fraction_field(),100)
> sage: time _=MS.zero().determinant()
> CPU times: user 200 ms, sys: 0 ns, total: 200 ms
> Wall time: 200 ms
> sage: MS=MatrixSpace(ZZ,100)
> sage: time _=MS.zero().determinant()
> CPU times: user 563 µs, sys: 5 µs, total: 568 µs
> Wall time: 573 µs
> sage: MS=MatrixSpace(L,40)
> sage: M=MS.random_element(3)
> sage: M=M.with_rescaled_row(0,0)
> sage: M.rows()[0]==0
> True
> sage: time _=M.determinant()
> CPU times: user 35.2 s, sys: 8.06 ms, total: 35.2 s
> Wall time: 35.2 s
> sage: MS=MatrixSpace(L.fraction_field(),10)
> sage: M=MS.random_element(3)
> sage: M=M.with_rescaled_row(0,0)
> sage: M.rows()[0]==0
> True
> sage: time _=M.determinant()
> CPU times: user 1min 56s, sys: 300 ms, total: 1min 56s
> Wall time: 1min 56s
> sage: MS=MatrixSpace(ZZ,500)
> sage: M=MS.random_element(2^40)
> sage: M=M.with_rescaled_row(0,0)
> sage: M.rows()[0]==0
> True
> sage: time _=M.determinant()
> CPU times: user 67.6 ms, sys: 0 ns, total: 67.6 ms
> Wall time: 67.9 ms
> sage: 
>
> Probably a preprocessing step could help that looks for zero rows or 
> columns before running the actual algorithm.
>
>
> Best,
> Maximilian
>

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Re: [sage-devel] Re: internet tests failing

2019-03-15 Thread John H Palmieri 


On Friday, March 15, 2019 at 3:31:33 AM UTC-7, Dima Pasechnik wrote:
>
> On Thu, Mar 14, 2019 at 7:51 PM John H Palmieri  > wrote: 
> > 
> > I'm seeing the same failure on a Mac running the most recent OS X. I 
> have openssl 1.1.1a installed on this machine, and I see the error in Sage. 
> Then I did './sage -i openssl' and './sage -f python2', and I still see the 
> error. The Python 2 log file does not list ssl among the modules which were 
> not built, so it looks like it was built with ssl support. 
>
> Can you use Sage's pip on packages from external repos, or is this also 
> broken? 
>

$ ./sage --pip install pylatex

works just fine: finds the file, downloads it using https, etc. Is that the 
sort of thing you mean?


 

>
> Looking at how Homebrew installs openssl 1.1.1b, one sees that it does 
> some post_install involving system's keychains and certs: 
>
> https://github.com/Homebrew/homebrew-core/blob/master/Formula/open...@1.1.rb 
>
> So it could be that Sage's openssl spkg must dance this dance too. 
>
> It looks like a need for a blocker trac ticket on this, then... 
>
>
>
>
> > 
> > 
> > 
> > On Thursday, March 14, 2019 at 11:19:37 AM UTC-7, Volker Braun wrote: 
> >> 
> >> I'm guessing you run this on an oldish mac, those have an outdated 
> openssl that doesn't support TLS12. More and more sites are switching that 
> on. Building Sage's openssl should fix that. 
> >> 
> >> 
> >> 
> >> On Thursday, March 14, 2019 at 7:09:50 PM UTC+1, kcrisman wrote: 
> >>> 
> >>> This could be just me.  But I am getting a lot of this when I try 
> running optional internet tests for e.g. src/sage/databases/oeis.py or 
> src/sage/symbolic/integration/external.py  Internet clearly works if you 
> can read this message, but apparently it doesn't work from within Sage, 
> because I get this message when I try it in the Sage command line as well 
> with e.g. this command.  Any ideas - do I need to rebuild Sage with 
> additional SSL support or something?  That should be mentioned somewhere. 
>  Thanks! 
> >>> 
> >>> - kcrisman 
> >>> 
> >>> w = oeis(7540) ; w 
> >>> 
> >>> 
> >>> URLError:  certificate verify failed (_ssl.c:726)> 
> > 
> > -- 
> > You received this message because you are subscribed to the Google 
> Groups "sage-devel" group. 
> > To unsubscribe from this group and stop receiving emails from it, send 
> an email to sage-devel+...@googlegroups.com . 
> > To post to this group, send email to sage-...@googlegroups.com 
> . 
> > Visit this group at https://groups.google.com/group/sage-devel. 
> > For more options, visit https://groups.google.com/d/optout. 
>

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Re: [sage-devel] Re: schedule for 8.7 rc and final release

2019-03-15 Thread Volker Braun 
PS: The openssl master branch is already Apache 
licensed: 
https://github.com/openssl/openssl/commit/151333164ece49fdba3fe5c4bbdccd9ae66d.
 
Though no release yet.

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Re: [sage-devel] Re: schedule for 8.7 rc and final release

2019-03-15 Thread Volker Braun 
On Friday, March 15, 2019 at 5:12:59 PM UTC+1, Dima Pasechnik wrote:
>
> 1) As Python.org now ships 2.7.16 with pre-build openssl, then why 
> don't we do the same? 
>

Because Python is not GPL licensed, of course
 

> (IMHO Sage should not try to out-saint the pope, and stick to "we 
> don't ship openssl orthodoxy") 
>

I'm fine with packaging the cert bundle, installing it, switch the osx 
binary build to include it, and test that on a variety of older macs. It 
would definitely be a improvement for the mac users. But we shouldn't delay 
Sage 8.7 for that.

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[sage-devel] Computing determinants of obviously singular matrices

2019-03-15 Thread Maximilian Jaroschek 
Hello, 

I'm using the current developer version of sage and noticed that when 
computing determinants of matrices over polynomial rings and rational 
functions, cases where the determinant is easily seen to be zero due to 
zero rows or columns can take an unreasonable long time to compute. I 
compared the timings with the same computation over other domains.

sage: L.=PolynomialRing(QQ)
sage: MS=MatrixSpace(L,100)
sage: time _=MS.zero().determinant()
CPU times: user 13.4 s, sys: 19.6 ms, total: 13.5 s
Wall time: 13.5 s
sage: MS=MatrixSpace(L.fraction_field(),100)
sage: time _=MS.zero().determinant()
CPU times: user 200 ms, sys: 0 ns, total: 200 ms
Wall time: 200 ms
sage: MS=MatrixSpace(ZZ,100)
sage: time _=MS.zero().determinant()
CPU times: user 563 µs, sys: 5 µs, total: 568 µs
Wall time: 573 µs
sage: MS=MatrixSpace(L,40)
sage: M=MS.random_element(3)
sage: M=M.with_rescaled_row(0,0)
sage: M.rows()[0]==0
True
sage: time _=M.determinant()
CPU times: user 35.2 s, sys: 8.06 ms, total: 35.2 s
Wall time: 35.2 s
sage: MS=MatrixSpace(L.fraction_field(),10)
sage: M=MS.random_element(3)
sage: M=M.with_rescaled_row(0,0)
sage: M.rows()[0]==0
True
sage: time _=M.determinant()
CPU times: user 1min 56s, sys: 300 ms, total: 1min 56s
Wall time: 1min 56s
sage: MS=MatrixSpace(ZZ,500)
sage: M=MS.random_element(2^40)
sage: M=M.with_rescaled_row(0,0)
sage: M.rows()[0]==0
True
sage: time _=M.determinant()
CPU times: user 67.6 ms, sys: 0 ns, total: 67.6 ms
Wall time: 67.9 ms
sage: 

Probably a preprocessing step could help that looks for zero rows or 
columns before running the actual algorithm.


Best,
Maximilian

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Re: [sage-devel] Re: schedule for 8.7 rc and final release

2019-03-15 Thread Dima Pasechnik 
On Fri, Mar 15, 2019 at 3:55 PM E. Madison Bray  wrote:
>
> On Fri, Mar 15, 2019 at 4:47 PM Dima Pasechnik  wrote:
> >
> > On Fri, Mar 15, 2019 at 3:35 PM E. Madison Bray  
> > wrote:
> > >
> > > On Fri, Mar 15, 2019 at 3:31 PM Dima Pasechnik  wrote:
> > > >
> > > > It appears that Sage's openssl package is broken on MacOS nowadays.
> > > > Should this be a blocker?
> > >
> > > How is SSL support currently handled in MacOS?  I have not kept up
> > > with that issue.  Are OSX users still not able to do something as
> > > simple as pip install?
> > >
> >
> > current Sage 8.6 MacOS binary installer comes with urllib that cannot
> > work with https.
> > I presume this is precisely what we see reported here, as it's exactly
> > what oeis() function of Sage needs.
> >
> > However, 2.7.16 binary installer of Python from python.org comes with a 
> > script
> > Install\ Certificates.command , which says inside
> >
> > # install_certifi.py
> > # sample script to install or update a set of default Root Certificates
> > # for the ssl module.  Uses the certificates provided by the certifi 
> > package:
> > #   https://pypi.python.org/pypi/certifi
> >
> > and which, after you run it, allows  urllib to function properly.
> > (but not before - perhaps it's launched automatically if you open some
> > Python GUI that comes in that installer)
> >
> > Perhaps we should do something like this...
>
> That appears to be a separate issue.  What do you mean by "binary
> installer comes with urllib that cannot work with https"?

Indeed, it's one of the two issues we saw recently here. And this one,
with binary 8.6 it is indeed that
"import ssl" fails. But even if people install Sage's optional openssl
package on MacOS, it won't be enough, still.

>
> Because if there is no _ssl module included in Python then it can't
> use HTTPS anyways.  But if `import _ssl` works then there is a working
> SSL library included, whatever it may be.
>
> The other issue is just a question of whether or not the SSL library
> has up-to-date root certificates to verify connections with.  If it
> doesn't, then HTTPS connections will fail with some
> SSL_CERTIFICATE_VERIFY_FAILED
Yes, this is exactly what I saw when I tried Python.org's 2.7.16
without running that script:

>>> from urllib import urlopen
>>> f=urlopen("https://oeis.org/";)

Traceback (most recent call last):
  File "", line 1, in 
  File 
"/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib.py",
line 87, in urlopen
return opener.open(url)
  File 
"/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib.py",
line 213, in open
return getattr(self, name)(url)
  File 
"/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib.py",
line 443, in open_https
h.endheaders(data)
  File 
"/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/httplib.py",
line 1038, in endheaders
self._send_output(message_body)
  File 
"/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/httplib.py",
line 882, in _send_output
self.send(msg)
  File 
"/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/httplib.py",
line 844, in send
self.connect()
  File 
"/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/httplib.py",
line 1263, in connect
server_hostname=server_hostname)
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/ssl.py",
line 369, in wrap_socket
_context=self)
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/ssl.py",
line 599, in __init__
self.do_handshake()
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/ssl.py",
line 828, in do_handshake
self._sslobj.do_handshake()
IOError: [Errno socket error] [SSL: CERTIFICATE_VERIFY_FAILED]
certificate verify failed (_ssl.c:727)


>  which can be worked around in a number
> of different ways (including installing up-to-date root CA certs from
> a presumed "trusted" source into a location that Python's urllib knows
> where to look).

The bottom line is two-fold:

1) As Python.org now ships 2.7.16 with pre-build openssl, then why
don't we do the same?
(IMHO Sage should not try to out-saint the pope, and stick to "we
don't ship openssl orthodoxy")

2) It's not sufficient to have an up to date openssl package, it also
needs some further blessing
with certs on MacOS.

Dima

>
>
> > > > On Thu, Mar 14, 2019 at 4:49 PM Volker Braun  
> > > > wrote:
> > > > >
> > > > > Feel free to fix the Cygwin-related bugs, but some of these are 
> > > > > longstanding issues that should be discussed with upstream first; 
> > > > > Realistically thats not going to make it to the next Sage version.
> > > > >
> > > > >
> > > > >
> > > > > On Thursday, March 14, 2019 at 2:36:29 PM UTC+1, E. Madison Bray 
> > > > > wrote:
> > > > >>
> > > > >> Hi Volker,
> > > > >>
> > > > >> I don't think there should be a release candidate at least until most
> > > > >> of the blocker issues [1] are resolved;

Re: [sage-devel] Re: schedule for 8.7 rc and final release

2019-03-15 Thread E. Madison Bray 
On Fri, Mar 15, 2019 at 4:47 PM Dima Pasechnik  wrote:
>
> On Fri, Mar 15, 2019 at 3:35 PM E. Madison Bray  wrote:
> >
> > On Fri, Mar 15, 2019 at 3:31 PM Dima Pasechnik  wrote:
> > >
> > > It appears that Sage's openssl package is broken on MacOS nowadays.
> > > Should this be a blocker?
> >
> > How is SSL support currently handled in MacOS?  I have not kept up
> > with that issue.  Are OSX users still not able to do something as
> > simple as pip install?
> >
>
> current Sage 8.6 MacOS binary installer comes with urllib that cannot
> work with https.
> I presume this is precisely what we see reported here, as it's exactly
> what oeis() function of Sage needs.
>
> However, 2.7.16 binary installer of Python from python.org comes with a script
> Install\ Certificates.command , which says inside
>
> # install_certifi.py
> # sample script to install or update a set of default Root Certificates
> # for the ssl module.  Uses the certificates provided by the certifi package:
> #   https://pypi.python.org/pypi/certifi
>
> and which, after you run it, allows  urllib to function properly.
> (but not before - perhaps it's launched automatically if you open some
> Python GUI that comes in that installer)
>
> Perhaps we should do something like this...

That appears to be a separate issue.  What do you mean by "binary
installer comes with urllib that cannot work with https"?

Because if there is no _ssl module included in Python then it can't
use HTTPS anyways.  But if `import _ssl` works then there is a working
SSL library included, whatever it may be.

The other issue is just a question of whether or not the SSL library
has up-to-date root certificates to verify connections with.  If it
doesn't, then HTTPS connections will fail with some
SSL_CERTIFICATE_VERIFY_FAILED which can be worked around in a number
of different ways (including installing up-to-date root CA certs from
a presumed "trusted" source into a location that Python's urllib knows
where to look).


> > > On Thu, Mar 14, 2019 at 4:49 PM Volker Braun  
> > > wrote:
> > > >
> > > > Feel free to fix the Cygwin-related bugs, but some of these are 
> > > > longstanding issues that should be discussed with upstream first; 
> > > > Realistically thats not going to make it to the next Sage version.
> > > >
> > > >
> > > >
> > > > On Thursday, March 14, 2019 at 2:36:29 PM UTC+1, E. Madison Bray wrote:
> > > >>
> > > >> Hi Volker,
> > > >>
> > > >> I don't think there should be a release candidate at least until most
> > > >> of the blocker issues [1] are resolved; in particular the four that
> > > >> are already either positively reviewed or are in-progress.
> > > >>
> > > >> Thanks
> > > >>
> > > >>
> > > >> [1] 
> > > >> https://trac.sagemath.org/query?priority=blocker&status=needs_info&status=needs_review&status=needs_work&status=new&status=positive_review&milestone=sage-8.7&group=status&col=id&col=summary&col=priority&col=owner&col=type&col=component&col=time&order=priority
> > > >>
> > > >> On Thu, Mar 14, 2019 at 2:25 PM Volker Braun  
> > > >> wrote:
> > > >> >
> > > >> > Next develop release will be rc0
> > > >> >
> > > >> > IMHO changes to gmpy2 should wait until the next version to give it 
> > > >> > some time to test out.
> > > >> >
> > > >> > --
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> > > >> > Groups "sage-devel" group.
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Re: [sage-devel] Re: schedule for 8.7 rc and final release

2019-03-15 Thread Dima Pasechnik 
On Fri, Mar 15, 2019 at 3:35 PM E. Madison Bray  wrote:
>
> On Fri, Mar 15, 2019 at 3:31 PM Dima Pasechnik  wrote:
> >
> > It appears that Sage's openssl package is broken on MacOS nowadays.
> > Should this be a blocker?
>
> How is SSL support currently handled in MacOS?  I have not kept up
> with that issue.  Are OSX users still not able to do something as
> simple as pip install?
>

current Sage 8.6 MacOS binary installer comes with urllib that cannot
work with https.
I presume this is precisely what we see reported here, as it's exactly
what oeis() function of Sage needs.

However, 2.7.16 binary installer of Python from python.org comes with a script
Install\ Certificates.command , which says inside

# install_certifi.py
# sample script to install or update a set of default Root Certificates
# for the ssl module.  Uses the certificates provided by the certifi package:
#   https://pypi.python.org/pypi/certifi

and which, after you run it, allows  urllib to function properly.
(but not before - perhaps it's launched automatically if you open some
Python GUI that comes in that installer)

Perhaps we should do something like this...






> > On Thu, Mar 14, 2019 at 4:49 PM Volker Braun  wrote:
> > >
> > > Feel free to fix the Cygwin-related bugs, but some of these are 
> > > longstanding issues that should be discussed with upstream first; 
> > > Realistically thats not going to make it to the next Sage version.
> > >
> > >
> > >
> > > On Thursday, March 14, 2019 at 2:36:29 PM UTC+1, E. Madison Bray wrote:
> > >>
> > >> Hi Volker,
> > >>
> > >> I don't think there should be a release candidate at least until most
> > >> of the blocker issues [1] are resolved; in particular the four that
> > >> are already either positively reviewed or are in-progress.
> > >>
> > >> Thanks
> > >>
> > >>
> > >> [1] 
> > >> https://trac.sagemath.org/query?priority=blocker&status=needs_info&status=needs_review&status=needs_work&status=new&status=positive_review&milestone=sage-8.7&group=status&col=id&col=summary&col=priority&col=owner&col=type&col=component&col=time&order=priority
> > >>
> > >> On Thu, Mar 14, 2019 at 2:25 PM Volker Braun  wrote:
> > >> >
> > >> > Next develop release will be rc0
> > >> >
> > >> > IMHO changes to gmpy2 should wait until the next version to give it 
> > >> > some time to test out.
> > >> >
> > >> > --
> > >> > You received this message because you are subscribed to the Google 
> > >> > Groups "sage-devel" group.
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> > >> > an email to sage-devel+...@googlegroups.com.
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> > >> > Visit this group at https://groups.google.com/group/sage-devel.
> > >> > For more options, visit https://groups.google.com/d/optout.
> > >
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Re: [sage-devel] Re: schedule for 8.7 rc and final release

2019-03-15 Thread E. Madison Bray 
On Fri, Mar 15, 2019 at 3:31 PM Dima Pasechnik  wrote:
>
> It appears that Sage's openssl package is broken on MacOS nowadays.
> Should this be a blocker?

How is SSL support currently handled in MacOS?  I have not kept up
with that issue.  Are OSX users still not able to do something as
simple as pip install?

> On Thu, Mar 14, 2019 at 4:49 PM Volker Braun  wrote:
> >
> > Feel free to fix the Cygwin-related bugs, but some of these are 
> > longstanding issues that should be discussed with upstream first; 
> > Realistically thats not going to make it to the next Sage version.
> >
> >
> >
> > On Thursday, March 14, 2019 at 2:36:29 PM UTC+1, E. Madison Bray wrote:
> >>
> >> Hi Volker,
> >>
> >> I don't think there should be a release candidate at least until most
> >> of the blocker issues [1] are resolved; in particular the four that
> >> are already either positively reviewed or are in-progress.
> >>
> >> Thanks
> >>
> >>
> >> [1] 
> >> https://trac.sagemath.org/query?priority=blocker&status=needs_info&status=needs_review&status=needs_work&status=new&status=positive_review&milestone=sage-8.7&group=status&col=id&col=summary&col=priority&col=owner&col=type&col=component&col=time&order=priority
> >>
> >> On Thu, Mar 14, 2019 at 2:25 PM Volker Braun  wrote:
> >> >
> >> > Next develop release will be rc0
> >> >
> >> > IMHO changes to gmpy2 should wait until the next version to give it some 
> >> > time to test out.
> >> >
> >> > --
> >> > You received this message because you are subscribed to the Google 
> >> > Groups "sage-devel" group.
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> >> > an email to sage-devel+...@googlegroups.com.
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> >
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Re: [sage-devel] Re: Remove sagenb documentation from the reference manual?

2019-03-15 Thread dimpase 
On Thu, Mar 07, 2019 at 07:12:29AM -0800, kcrisman wrote:
> >
> > http://doc.sagemath.org/html/en/reference/repl/sage/repl/ipython_kernel/interact.html
> > http://doc.sagemath.org/html/en/prep/Quickstarts/Interact.html
> >
> >
> Thanks; I knew about the second one, since I wrote it :-) but the first one 
> is good to have on hand.
> 
> Unfortunately, that means the only really complete documentation for 
> interact is still in something like Dima's
> 
> file:///mnt/opt/Sage/sage-dev/local/share/doc/sagenb/notebook/interact.html 
> 
> Harald, is there some equivalent to this possible on the website?  Google 
> may otherwise have this old stale one around forever.

It is perfectly possible to link all these 
file:///mnt/opt/Sage/sage-dev/local/share/doc/sagenb/notebook/interact.html 

in the main Reference manual index.rst file; e.g the following
--
--- a/src/doc/en/reference/index.rst
+++ b/src/doc/en/reference/index.rst
@@ -15,6 +15,7 @@ User Interface
 * :doc:`Command Line Interface (REPL) `
 * For the Jupyter notebook interface, visit `its documentation 
`_.
 * For the legacy notebook interface, which is no longer actively maintained, 
visit the `source repository `_.
+* `SageNB `_

 Graphics
 
--

provides this. It's annoying that one must put full paths to the files
there, and not relative ones (cause one cannot get above "sphinx root"
with the relative links :-( )

I searched in vain for a Sphinx solution to this---it's really silly
that one cannot do things like 
`SageNB <$SAGE_LOCAL/share/doc/sagenb/index.html>`_

A good solution should be via autoconf then. We'll have index.rst.in
template to be filled in. I've opened #27495 to handle this.

Dima

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Re: [sage-devel] Re: schedule for 8.7 rc and final release

2019-03-15 Thread Volker Braun 
Is openssl compiled into the macos binary? Technically we wouldn't be 
allowed to distribute that


On Friday, March 15, 2019 at 3:58:17 PM UTC+1, Dima Pasechnik wrote:
>
> On Fri, Mar 15, 2019 at 2:53 PM Volker Braun  > wrote: 
> > 
> > We don't build it by default, so imho the answer is no. Not every 
> optional package works on every supported platform, even if we strive for 
> that. 
>
>
> Are we going to ship broken MacOS binaries then? 
>
> > 
> > On Friday, March 15, 2019 at 3:31:36 PM UTC+1, Dima Pasechnik wrote: 
> >> 
> >> It appears that Sage's openssl package is broken on MacOS nowadays. 
> >> Should this be a blocker? 
> >> 
> >> On Thu, Mar 14, 2019 at 4:49 PM Volker Braun  
> wrote: 
> >> > 
> >> > Feel free to fix the Cygwin-related bugs, but some of these are 
> longstanding issues that should be discussed with upstream first; 
> Realistically thats not going to make it to the next Sage version. 
> >> > 
> >> > 
> >> > 
> >> > On Thursday, March 14, 2019 at 2:36:29 PM UTC+1, E. Madison Bray 
> wrote: 
> >> >> 
> >> >> Hi Volker, 
> >> >> 
> >> >> I don't think there should be a release candidate at least until 
> most 
> >> >> of the blocker issues [1] are resolved; in particular the four that 
> >> >> are already either positively reviewed or are in-progress. 
> >> >> 
> >> >> Thanks 
> >> >> 
> >> >> 
> >> >> [1] 
> https://trac.sagemath.org/query?priority=blocker&status=needs_info&status=needs_review&status=needs_work&status=new&status=positive_review&milestone=sage-8.7&group=status&col=id&col=summary&col=priority&col=owner&col=type&col=component&col=time&order=priority
>  
> >> >> 
> >> >> On Thu, Mar 14, 2019 at 2:25 PM Volker Braun  
> wrote: 
> >> >> > 
> >> >> > Next develop release will be rc0 
> >> >> > 
> >> >> > IMHO changes to gmpy2 should wait until the next version to give 
> it some time to test out. 
> >> >> > 
> >> >> > -- 
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> Groups "sage-devel" group. 
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>

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Re: [sage-devel] Re: schedule for 8.7 rc and final release

2019-03-15 Thread Dima Pasechnik 
On Fri, Mar 15, 2019 at 2:53 PM Volker Braun  wrote:
>
> We don't build it by default, so imho the answer is no. Not every optional 
> package works on every supported platform, even if we strive for that.


Are we going to ship broken MacOS binaries then?

>
> On Friday, March 15, 2019 at 3:31:36 PM UTC+1, Dima Pasechnik wrote:
>>
>> It appears that Sage's openssl package is broken on MacOS nowadays.
>> Should this be a blocker?
>>
>> On Thu, Mar 14, 2019 at 4:49 PM Volker Braun  wrote:
>> >
>> > Feel free to fix the Cygwin-related bugs, but some of these are 
>> > longstanding issues that should be discussed with upstream first; 
>> > Realistically thats not going to make it to the next Sage version.
>> >
>> >
>> >
>> > On Thursday, March 14, 2019 at 2:36:29 PM UTC+1, E. Madison Bray wrote:
>> >>
>> >> Hi Volker,
>> >>
>> >> I don't think there should be a release candidate at least until most
>> >> of the blocker issues [1] are resolved; in particular the four that
>> >> are already either positively reviewed or are in-progress.
>> >>
>> >> Thanks
>> >>
>> >>
>> >> [1] 
>> >> https://trac.sagemath.org/query?priority=blocker&status=needs_info&status=needs_review&status=needs_work&status=new&status=positive_review&milestone=sage-8.7&group=status&col=id&col=summary&col=priority&col=owner&col=type&col=component&col=time&order=priority
>> >>
>> >> On Thu, Mar 14, 2019 at 2:25 PM Volker Braun  wrote:
>> >> >
>> >> > Next develop release will be rc0
>> >> >
>> >> > IMHO changes to gmpy2 should wait until the next version to give it 
>> >> > some time to test out.
>> >> >
>> >> > --
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Re: [sage-devel] Re: schedule for 8.7 rc and final release

2019-03-15 Thread Volker Braun 
We don't build it by default, so imho the answer is no. Not every optional 
package works on every supported platform, even if we strive for that.


On Friday, March 15, 2019 at 3:31:36 PM UTC+1, Dima Pasechnik wrote:
>
> It appears that Sage's openssl package is broken on MacOS nowadays. 
> Should this be a blocker? 
>
> On Thu, Mar 14, 2019 at 4:49 PM Volker Braun  > wrote: 
> > 
> > Feel free to fix the Cygwin-related bugs, but some of these are 
> longstanding issues that should be discussed with upstream first; 
> Realistically thats not going to make it to the next Sage version. 
> > 
> > 
> > 
> > On Thursday, March 14, 2019 at 2:36:29 PM UTC+1, E. Madison Bray wrote: 
> >> 
> >> Hi Volker, 
> >> 
> >> I don't think there should be a release candidate at least until most 
> >> of the blocker issues [1] are resolved; in particular the four that 
> >> are already either positively reviewed or are in-progress. 
> >> 
> >> Thanks 
> >> 
> >> 
> >> [1] 
> https://trac.sagemath.org/query?priority=blocker&status=needs_info&status=needs_review&status=needs_work&status=new&status=positive_review&milestone=sage-8.7&group=status&col=id&col=summary&col=priority&col=owner&col=type&col=component&col=time&order=priority
>  
> >> 
> >> On Thu, Mar 14, 2019 at 2:25 PM Volker Braun  
> wrote: 
> >> > 
> >> > Next develop release will be rc0 
> >> > 
> >> > IMHO changes to gmpy2 should wait until the next version to give it 
> some time to test out. 
> >> > 
> >> > -- 
> >> > You received this message because you are subscribed to the Google 
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> >> > For more options, visit https://groups.google.com/d/optout. 
> > 
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Re: [sage-devel] Re: schedule for 8.7 rc and final release

2019-03-15 Thread Dima Pasechnik 
It appears that Sage's openssl package is broken on MacOS nowadays.
Should this be a blocker?

On Thu, Mar 14, 2019 at 4:49 PM Volker Braun  wrote:
>
> Feel free to fix the Cygwin-related bugs, but some of these are longstanding 
> issues that should be discussed with upstream first; Realistically thats not 
> going to make it to the next Sage version.
>
>
>
> On Thursday, March 14, 2019 at 2:36:29 PM UTC+1, E. Madison Bray wrote:
>>
>> Hi Volker,
>>
>> I don't think there should be a release candidate at least until most
>> of the blocker issues [1] are resolved; in particular the four that
>> are already either positively reviewed or are in-progress.
>>
>> Thanks
>>
>>
>> [1] 
>> https://trac.sagemath.org/query?priority=blocker&status=needs_info&status=needs_review&status=needs_work&status=new&status=positive_review&milestone=sage-8.7&group=status&col=id&col=summary&col=priority&col=owner&col=type&col=component&col=time&order=priority
>>
>> On Thu, Mar 14, 2019 at 2:25 PM Volker Braun  wrote:
>> >
>> > Next develop release will be rc0
>> >
>> > IMHO changes to gmpy2 should wait until the next version to give it some 
>> > time to test out.
>> >
>> > --
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>
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[sage-devel] Re: Error with Parallelism, case of nproc>1

2019-03-15 Thread Eric Gourgoulhon 
The bug seems to be triggered by the use of a symbolic function (the one 
created by function('chi')). 
It is now tracked at 
https://trac.sagemath.org/ticket/27492


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[sage-devel] Re: pretty print latex doctest error

2019-03-15 Thread kcrisman 


> I see a different but I guess related error, arising like this:
>

I wonder if this is what causes our errors to be different:

This is XeTeX, Version 3.14159265-2.6-0.9 (TeX Live 2018) (preloaded 
format=xelatex)

Also, my error in command line only occurs once - I guess because it's a 
warning, not an error per se. 

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Re: [sage-devel] Re: internet tests failing

2019-03-15 Thread kcrisman 
As another data point from Mac, with a DIFFERENT set of errors, 
see https://groups.google.com/d/msg/sage-release/KYiD_QSJjBs/ApfxGOXjBwAJ 
and the there-attached failures which look like this:

  File 
"/Users/Sage/sage-8.7.beta7/local/lib/python2.7/site-packages/sage/databases/oeis.py",
 line 196, in _fetch
raise IOError("%s\nError fetching %s." % (msg, url))
IOError: 
Error fetching 
https://oeis.org/search?q=3%2C+7%2C+15%2C+1&start=0&fmt=text&n=4.

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Re: [sage-devel] Re: internet tests failing

2019-03-15 Thread Dima Pasechnik 
On Thu, Mar 14, 2019 at 7:51 PM John H Palmieri  wrote:
>
> I'm seeing the same failure on a Mac running the most recent OS X. I have 
> openssl 1.1.1a installed on this machine, and I see the error in Sage. Then I 
> did './sage -i openssl' and './sage -f python2', and I still see the error. 
> The Python 2 log file does not list ssl among the modules which were not 
> built, so it looks like it was built with ssl support.

Can you use Sage's pip on packages from external repos, or is this also
broken?

Looking at how Homebrew installs openssl 1.1.1b, one sees that it does
some post_install involving system's keychains and certs:
https://github.com/Homebrew/homebrew-core/blob/master/Formula/open...@1.1.rb

So it could be that Sage's openssl spkg must dance this dance too.

It looks like a need for a blocker trac ticket on this, then...




>
>
>
> On Thursday, March 14, 2019 at 11:19:37 AM UTC-7, Volker Braun wrote:
>>
>> I'm guessing you run this on an oldish mac, those have an outdated openssl 
>> that doesn't support TLS12. More and more sites are switching that on. 
>> Building Sage's openssl should fix that.
>>
>>
>>
>> On Thursday, March 14, 2019 at 7:09:50 PM UTC+1, kcrisman wrote:
>>>
>>> This could be just me.  But I am getting a lot of this when I try running 
>>> optional internet tests for e.g. src/sage/databases/oeis.py or 
>>> src/sage/symbolic/integration/external.py  Internet clearly works if you 
>>> can read this message, but apparently it doesn't work from within Sage, 
>>> because I get this message when I try it in the Sage command line as well 
>>> with e.g. this command.  Any ideas - do I need to rebuild Sage with 
>>> additional SSL support or something?  That should be mentioned somewhere.  
>>> Thanks!
>>>
>>> - kcrisman
>>>
>>> w = oeis(7540) ; w
>>>
>>>
>>> URLError: >> verify failed (_ssl.c:726)>
>
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[sage-devel] Re: Error with Parallelism, case of nproc>1

2019-03-15 Thread Eric Gourgoulhon 
Thanks for the report. I confirm the bug in Sage 8.7.beta7. 
What is strange is that ddChi seems a perfectly valid symbolic expression:
sage: ddChi = ddChi.expand(); ddChi
2*diff(chi(r, theta, phi), r)/r + cos(theta)*diff(chi(r, theta, phi), theta
)/(r^2*sin(theta)) + diff(chi(r, theta, phi), theta, theta)/r^2 + diff(chi(r
, theta, phi), phi, phi)/(r^2*sin(theta)^2) + diff(chi(r, theta, phi), r, r)
sage: (ddChi - 2*diff(chi(r, theta, phi), r)/r).simplify()
cos(theta)*diff(chi(r, theta, phi), theta)/(r^2*sin(theta)) + diff(chi(r, 
theta, phi), theta, theta)/r^2 + diff(chi(r, theta, phi), phi, phi)/(r^2*sin
(theta)^2) + diff(chi(r, theta, phi), r, r)

and yet
sage: ddChi.coefficient(diff(chi(r, theta, phi), r), 1)
0

Eric.

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