Re: [sage-devel] Import issue for Sage when using the system's Python (e.g. Debian)

2019-01-10 Thread 'Julien Puydt' via sage-devel

Le 10/01/2019 à 22:03, Jeroen Demeyer a écrit :

On 2019-01-10 21:51, 'Julien Puydt' via sage-devel wrote:

Didn't François mention changing SAGE_ROOT wasn't needed?


He said

SAGE_ROOT should only be needed for the packaging system
and possibly the doctests. I regard any needs for SAGE_ROOT at runtime
a bug.


In other words: it is still needed, but that's a bug. And I agree with 
that.



https://trac.sagemath.org/ticket/27040


JP

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Re: [sage-devel] Import issue for Sage when using the system's Python (e.g. Debian)

2019-01-10 Thread François Bissey



> On 11/01/2019, at 09:48, Jeroen Demeyer  wrote:
> 
> On 2019-01-10 20:46, 'Julien Puydt' via sage-devel wrote:
>> 
>> 
>> Le 10/01/2019 à 20:07, François Bissey a écrit :
>>> I have recently made the following change in sage-on-gentoo’s env.py
>>> _add_variable_or_fallback('SAGE_LOCAL',  
>>> sysconfig.get_config_var("prefix”))
>>> 
>>> which means SAGE_LOCAL is now pulled from the system rather than
>>> a seeded value (as it was before).
>>> 
>> 
>> Perhaps upstream would accept such a trivial change?
> 
> If you make a ticket for it, sure. But it won't help with SAGE_ROOT.
> 
> By the way, why sysconfig.get_config_var("prefix”) instead of sys.prefix?

Because at least on gentoo sys.prefix (while correct) is a bit weird. It is 
defined
relative to the real python executable which ends up being a strange location on
Gentoo due to the system to support multiple python.
/usr/lib/python-exec/python{2.7,3.6}/../../..

This is the right place but a bit confusing, sysconfig on the other hand always 
return 
something clearly understandable. There is another reason, SAGE_LOCAL is not 
the 
only thing I set using sysconfig

SINGULAR_SO = sysconfig.get_config_var("LIBDIR")+"/libSingular.”+extension

I used to have all those weird mechanism to deal with lib/lib64 (and who knows 
what
is needed in debian). But really I have nothing against sys.prefix.

SAGE_ROOT is not needed at runtime for distros but it is definitely not the same
thing for “vanilla” as things stands. Since vanilla still insists on integration
with the build system and completely removing it, is hard in some parts.
Also it is quite deliberately set to None (and SAGE_LOCAL too) in vanilla - 
probably
so you can’t run sage outside of a sage set environment.

François

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Re: [sage-devel] Import issue for Sage when using the system's Python (e.g. Debian)

2019-01-10 Thread Jeroen Demeyer

On 2019-01-10 21:51, 'Julien Puydt' via sage-devel wrote:

Didn't François mention changing SAGE_ROOT wasn't needed?


He said

SAGE_ROOT should only be needed for the packaging system
and possibly the doctests. I regard any needs for SAGE_ROOT at runtime
a bug.


In other words: it is still needed, but that's a bug. And I agree with that.

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Re: [sage-devel] Import issue for Sage when using the system's Python (e.g. Debian)

2019-01-10 Thread 'Julien Puydt' via sage-devel

Hi,

Le 10/01/2019 à 21:48, Jeroen Demeyer a écrit :

On 2019-01-10 20:46, 'Julien Puydt' via sage-devel wrote:

Perhaps upstream would accept such a trivial change?


If you make a ticket for it, sure. But it won't help with SAGE_ROOT.


Didn't François mention changing SAGE_ROOT wasn't needed?

JP

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Re: [sage-devel] Import issue for Sage when using the system's Python (e.g. Debian)

2019-01-10 Thread Jeroen Demeyer

On 2019-01-10 20:46, 'Julien Puydt' via sage-devel wrote:



Le 10/01/2019 à 20:07, François Bissey a écrit :

I have recently made the following change in sage-on-gentoo’s env.py
_add_variable_or_fallback('SAGE_LOCAL',  sysconfig.get_config_var("prefix”))

which means SAGE_LOCAL is now pulled from the system rather than
a seeded value (as it was before).



Perhaps upstream would accept such a trivial change?


If you make a ticket for it, sure. But it won't help with SAGE_ROOT.

By the way, why sysconfig.get_config_var("prefix”) instead of sys.prefix?

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Re: [sage-devel] Import issue for Sage when using the system's Python (e.g. Debian)

2019-01-10 Thread 'Julien Puydt' via sage-devel




Le 10/01/2019 à 20:07, François Bissey a écrit :

I have recently made the following change in sage-on-gentoo’s env.py
_add_variable_or_fallback('SAGE_LOCAL',  sysconfig.get_config_var("prefix”))

which means SAGE_LOCAL is now pulled from the system rather than
a seeded value (as it was before).



Perhaps upstream would accept such a trivial change?

JP

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Re: [sage-devel] Import issue for Sage when using the system's Python (e.g. Debian)

2019-01-10 Thread François Bissey



> On 11/01/2019, at 05:04, E. Madison Bray  wrote:
> 
> If you want to look-before-you-leap you could also check if
> `SAGE_ROOT` and `SAGE_LOCAL` are set to something reasonable in
> `os.environ`. 

Just SAGE_LOCAL. SAGE_ROOT should only be needed for the packaging system
and possibly the doctests. I regard any needs for SAGE_ROOT at runtime
a bug.

> I have mentioned elsewhere (e.g. on
> https://trac.sagemath.org/ticket/22652) that the sage.env module ought
> to be fixed upstream (that is, in the main Sage sources) so that it
> can actually work properly without having to set any special
> environment variables.

I have recently made the following change in sage-on-gentoo’s env.py 
_add_variable_or_fallback('SAGE_LOCAL',  sysconfig.get_config_var("prefix”))

which means SAGE_LOCAL is now pulled from the system rather than
a seeded value (as it was before). 

François

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Re: [sage-devel] Import issue for Sage when using the system's Python (e.g. Debian)

2019-01-10 Thread Nathan Dunfield
On Thursday, January 10, 2019 at 9:58:56 AM UTC-6, E. Madison Bray wrote:
>
> > On archlinux that also uses system Python for Sage the 
> > situation is better: importing sage.all in Python2 does work! Even 
> > though the configuration constants are not in the environment! They 
> > are set up properly in sage_env.py that is part of the SageMath 
> > installation. And more precisely $SAGE_LOCAL fallsback to the default 
> > "/usr" which is what it is intend to be on archlinux. 
> > 
> > I don't understand why on Debian $SAGE_LOCAL is set to None and 
> > managed by environment variables. 
>
> I have mentioned elsewhere (e.g. on 
> https://trac.sagemath.org/ticket/22652) that the sage.env module ought 
> to be fixed upstream (that is, in the main Sage sources) so that it 
> can actually work properly without having to set any special 
> environment variables.  Even if it has to guess in some cases, and has 
> to raise a RuntimeError if it can't reasonably guess the correct 
> values for some variables, in most cases it should be possible to 
> design this in such a way that it *just works* from a normal python 
> interpreter with no additional variables set. 
>

Fixing upstream is always best, but in the meantime is there some reason 
that the Debian package doesn't just patch "sage/env.py" like Arch does?  
Looking at the Arch approach, I checked that the following 3-line patch 
causes 'python -c "import sage.all"' to succeed on Debian Sid with SageMath 
8.4. 

Best,

Nathan

--- env.py.orig 2019-01-03 05:15:59.0 -0600
+++ env.py 2019-01-10 12:28:13.0 -0600
@@ -118,10 +118,10 @@
 _add_variable_or_fallback('LOCAL_IDENTIFIER','$HOSTNAME.%s'%os.getpid())
 
 # bunch of sage directories and files
-_add_variable_or_fallback('SAGE_ROOT',   None)
-_add_variable_or_fallback('SAGE_LOCAL',  None)
+_add_variable_or_fallback('SAGE_ROOT',   '/usr/share/sagemath')
+_add_variable_or_fallback('SAGE_LOCAL',  '/usr')
 _add_variable_or_fallback('SAGE_ETC',opj('$SAGE_LOCAL', 'etc'))
-_add_variable_or_fallback('SAGE_SCRIPTS_DIR',opj('$SAGE_LOCAL', 'bin'))
+_add_variable_or_fallback('SAGE_SCRIPTS_DIR',opj('$SAGE_ROOT', 'bin'))
 _add_variable_or_fallback('SAGE_INC',opj('$SAGE_LOCAL', 'include'))
 _add_variable_or_fallback('SAGE_SHARE',  opj('$SAGE_LOCAL', 'share'))


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Re: [sage-devel] Import issue for Sage when using the system's Python (e.g. Debian)

2019-01-10 Thread Nathan Dunfield
On Thursday, January 10, 2019 at 9:38:15 AM UTC-6, vdelecroix wrote:
>
> Could you repeat the order in which things are broken. 
>

Any of the following sequences of commands will install both the SnapPy 
Python package and SageMath without producing any errors:

0) install python2 and python-pip 
1) install snappy via pip 
2) install sagemath via apt 

and 

1) install sagemath via apt 
2) install snappy via pip

and 

1) install sagemath via apt 
2) source sage-env and install snappy via pip 

Independent of which route one takes above both of the following commands 
will succeed:

A) sage -python -c "import snappy"
B) source  /usr/share/sagemath/bin/sage-env; python -c "import snappy"

and this will always fail:

C) python -c "import snappy"

Best,

Nathan



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Re: [sage-devel] Import issue for Sage when using the system's Python (e.g. Debian)

2019-01-10 Thread E. Madison Bray
On Thu, Jan 10, 2019 at 4:47 AM Nathan Dunfield  wrote:
>
> I am a developer of the Python package "snappy" which acquires extra features 
> when imported inside of Sage. Some of our Linux users have recently reported 
> difficulties with SnapPy on machines where Sage was installed by the standard 
> package manger making use of the system libraries and in particular the 
> system python.  I have reproduced the problem on Debian Sid but it also 
> manifests itself on Fedora 28 [1].  The root of our problem is that in this 
> situation:
>
> python -c "import sage.all"
>
> results the error:
>
> Traceback (most recent call last):
>   File "", line 1, in 
>   File "/usr/lib/python2.7/dist-packages/sage/all.py", line 71, in 
> from sage.env import SAGE_ROOT, SAGE_SRC, SAGE_DOC_SRC, SAGE_LOCAL, 
> DOT_SAGE, SAGE_ENV
>   File "/usr/lib/python2.7/dist-packages/sage/env.py", line 123, in 
> _add_variable_or_fallback('SAGE_ETC',opj('$SAGE_LOCAL', 'etc'))
>   File "/usr/lib/python2.7/dist-packages/sage/env.py", line 103, in 
> _add_variable_or_fallback
> value = sep.join(components)
> TypeError: sequence item 0: expected string, NoneType found
>
> whereas
>
> sage -python -c "import sage.all"
>
> works as expected.  Currently, our Python package tests for whether it is 
> running in SageMath by:
>
> _within_sage = False
> try:
> import sage.all
> _within_sage = True
> except ImportError:
> pass
>
> One solution for us (I think) would be to simply catch and ignore all types 
> of exceptions in the above block, but I was wondering if the current behavior 
> of 'python -c "import sage.all"' was expected or is this possibly a bug?  Or 
> perhaps there is a work-around of some kind?

It's expected (see my previous reply) but obviously not great.  For
now I would just rewrite your above test to catch Exception, instead
of just ImportError.  This is a nitpick but instead of _within_sage I
would name that variable something like "_have_sage" instead: It's
just a test whether or not sage can be imported.

If you want to look-before-you-leap you could also check if
`SAGE_ROOT` and `SAGE_LOCAL` are set to something reasonable in
`os.environ`.  Those are the two environment variables that currently
need to be set at a minimum for that module to work properly.  But
even with that it would still be wise to catch exceptions anyways.

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Re: [sage-devel] Import issue for Sage when using the system's Python (e.g. Debian)

2019-01-10 Thread E. Madison Bray
On Thu, Jan 10, 2019 at 1:57 PM Vincent Delecroix
<20100.delecr...@gmail.com> wrote:
>
> (side note)
>
> On archlinux that also uses system Python for Sage the
> situation is better: importing sage.all in Python2 does work! Even
> though the configuration constants are not in the environment! They
> are set up properly in sage_env.py that is part of the SageMath
> installation. And more precisely $SAGE_LOCAL fallsback to the default
> "/usr" which is what it is intend to be on archlinux.
>
> I don't understand why on Debian $SAGE_LOCAL is set to None and
> managed by environment variables.

I have mentioned elsewhere (e.g. on
https://trac.sagemath.org/ticket/22652) that the sage.env module ought
to be fixed upstream (that is, in the main Sage sources) so that it
can actually work properly without having to set any special
environment variables.  Even if it has to guess in some cases, and has
to raise a RuntimeError if it can't reasonably guess the correct
values for some variables, in most cases it should be possible to
design this in such a way that it *just works* from a normal python
interpreter with no additional variables set.



> Le 10/01/2019 à 04:47, Nathan Dunfield a écrit :
> > I am a developer of the Python package "snappy" which acquires extra
> > features when imported inside of Sage. Some of our Linux users have
> > recently reported difficulties with SnapPy on machines where Sage was
> > installed by the standard package manger making use of the system libraries
> > and in particular the system python.  I have reproduced the problem on
> > Debian Sid but it also manifests itself on Fedora 28 [1].  The root of our
> > problem is that in this situation:
> >
> > python -c "import sage.all"
> >
> > results the error:
> >
> > Traceback (most recent call last):
> >File "", line 1, in 
> >File "/usr/lib/python2.7/dist-packages/sage/all.py", line 71, in 
> >  from sage.env import SAGE_ROOT, SAGE_SRC, SAGE_DOC_SRC, SAGE_LOCAL,
> > DOT_SAGE, SAGE_ENV
> >File "/usr/lib/python2.7/dist-packages/sage/env.py", line 123, in 
> > 
> >  _add_variable_or_fallback('SAGE_ETC',opj('$SAGE_LOCAL', 'etc'))
> >File "/usr/lib/python2.7/dist-packages/sage/env.py", line 103, in
> > _add_variable_or_fallback
> >  value = sep.join(components)
> > TypeError: sequence item 0: expected string, NoneType found
> >
> > whereas
> >
> > sage -python -c "import sage.all"
> >
> > works as expected.  Currently, our Python package tests for whether it is
> > running in SageMath by:
> >
> > _within_sage = False
> > try:
> >  import sage.all
> >  _within_sage = True
> > except ImportError:
> >  pass
> >
> > One solution for us (I think) would be to simply catch and ignore all types
> > of exceptions in the above block, but I was wondering if the current
> > behavior of 'python -c "import sage.all"' was expected or is this possibly
> > a bug?  Or perhaps there is a work-around of some kind?
> >
> > Thanks,
> >
> > Nathan
> >
> > P.S. In the Debian package "sage" does not accept the "-pip" flag, even
> > though installing the "sagemath" package does pull in "pip" (tested on a
> > clear Sid Docker container).  Why is this?  I ask because our current
> > instructions for installing SnapPy into SageMath use "sage -pip".
> >
> >
> > [1] See the second comment, not the original report, on
> > https://bitbucket.org/t3m/snappy/issues/14/
> >
>
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Re: [sage-devel] Import issue for Sage when using the system's Python (e.g. Debian)

2019-01-10 Thread Vincent Delecroix

Le 10/01/2019 à 16:01, Nathan Dunfield a écrit :




On Thursday, January 10, 2019 at 6:47:33 AM UTC-6, vdelecroix wrote:


Le 10/01/2019 à 04:47, Nathan Dunfield a écrit :


P.S. In the Debian package "sage" does not accept the "-pip" flag, even
though installing the "sagemath" package does pull in "pip" (tested on a
clear Sid Docker container).  Why is this?  I ask because our current
instructions for installing SnapPy into SageMath use "sage -pip".


The sage script in Debian is indeed a restricted version of the
original sage script (to avoid messing up with the system). You
can just use the pip from the system. That works fine if you
source the environment variables first:

$ source /usr/share/sagemath/bin/sage-env
$ pip install surface_dynamics --user



Yes, snappy installs fine with the system pip (even without sourcing
sage-env), though as you know from writing the flatsurf docs, this
distinction rather complicates the installation instructions.


Indeed. And this have to be discussed with Debian distribution as
Dima pointed out. The (long term) answer will probably be: make
snappy a proper Debian package in two versions "snappy" and
"snappy-sagemath".


Our issue reports have actually come from people who installed SnapPy in
their system Python with pip only to have it crash when starting the
SnapPy app because they had also previously installed Sage via their
package manager.  In other words, our "installing SnapPy in Linux (no
Sage)" instructions will fail if user has previously installed Sage in a
particular way.


Could you repeat the order in which things are broken. Is this

1) install snappy via pip
2) install sagemath via apt
3) launch python and load snappy

or/and

1) install sagemath via apt
2) install snappy via pip

I believe the following should work

1) install sagemath via apt
2) source sage-env and install snappy via pip
3) launch sage and load snappy

But might be broken when loading from python.

Vincent

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Re: [sage-devel] Import issue for Sage when using the system's Python (e.g. Debian)

2019-01-10 Thread Nathan Dunfield



On Thursday, January 10, 2019 at 6:47:33 AM UTC-6, vdelecroix wrote:
>
> Le 10/01/2019 à 04:47, Nathan Dunfield a écrit : 
> > 
> > P.S. In the Debian package "sage" does not accept the "-pip" flag, even 
> > though installing the "sagemath" package does pull in "pip" (tested on a 
> > clear Sid Docker container).  Why is this?  I ask because our current 
> > instructions for installing SnapPy into SageMath use "sage -pip". 
>
> The sage script in Debian is indeed a restricted version of the 
> original sage script (to avoid messing up with the system). You 
> can just use the pip from the system. That works fine if you 
> source the environment variables first: 
>
> $ source /usr/share/sagemath/bin/sage-env 
> $ pip install surface_dynamics --user 
>

Yes, snappy installs fine with the system pip (even without sourcing 
sage-env), though as you know from writing the flatsurf docs, this 
distinction rather complicates the installation instructions.

Our issue reports have actually come from people who installed SnapPy in 
their system Python with pip only to have it crash when starting the 
SnapPy app because they had also previously installed Sage via their 
package manager.  In other words, our "installing SnapPy in Linux (no 
Sage)" instructions will fail if user has previously installed Sage in a 
particular way.  

Nathan

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Re: [sage-devel] Import issue for Sage when using the system's Python (e.g. Debian)

2019-01-10 Thread Vincent Delecroix

(side note)

On archlinux that also uses system Python for Sage the
situation is better: importing sage.all in Python2 does work! Even
though the configuration constants are not in the environment! They
are set up properly in sage_env.py that is part of the SageMath
installation. And more precisely $SAGE_LOCAL fallsback to the default
"/usr" which is what it is intend to be on archlinux.

I don't understand why on Debian $SAGE_LOCAL is set to None and
managed by environment variables.

Le 10/01/2019 à 04:47, Nathan Dunfield a écrit :

I am a developer of the Python package "snappy" which acquires extra
features when imported inside of Sage. Some of our Linux users have
recently reported difficulties with SnapPy on machines where Sage was
installed by the standard package manger making use of the system libraries
and in particular the system python.  I have reproduced the problem on
Debian Sid but it also manifests itself on Fedora 28 [1].  The root of our
problem is that in this situation:

python -c "import sage.all"

results the error:

Traceback (most recent call last):
   File "", line 1, in 
   File "/usr/lib/python2.7/dist-packages/sage/all.py", line 71, in 
 from sage.env import SAGE_ROOT, SAGE_SRC, SAGE_DOC_SRC, SAGE_LOCAL,
DOT_SAGE, SAGE_ENV
   File "/usr/lib/python2.7/dist-packages/sage/env.py", line 123, in 
 _add_variable_or_fallback('SAGE_ETC',opj('$SAGE_LOCAL', 'etc'))
   File "/usr/lib/python2.7/dist-packages/sage/env.py", line 103, in
_add_variable_or_fallback
 value = sep.join(components)
TypeError: sequence item 0: expected string, NoneType found

whereas

sage -python -c "import sage.all"

works as expected.  Currently, our Python package tests for whether it is
running in SageMath by:

_within_sage = False
try:
 import sage.all
 _within_sage = True
except ImportError:
 pass

One solution for us (I think) would be to simply catch and ignore all types
of exceptions in the above block, but I was wondering if the current
behavior of 'python -c "import sage.all"' was expected or is this possibly
a bug?  Or perhaps there is a work-around of some kind?

Thanks,

Nathan

P.S. In the Debian package "sage" does not accept the "-pip" flag, even
though installing the "sagemath" package does pull in "pip" (tested on a
clear Sid Docker container).  Why is this?  I ask because our current
instructions for installing SnapPy into SageMath use "sage -pip".


[1] See the second comment, not the original report, on
https://bitbucket.org/t3m/snappy/issues/14/



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Re: [sage-devel] Import issue for Sage when using the system's Python (e.g. Debian)

2019-01-10 Thread Vincent Delecroix

Le 10/01/2019 à 04:47, Nathan Dunfield a écrit :


P.S. In the Debian package "sage" does not accept the "-pip" flag, even
though installing the "sagemath" package does pull in "pip" (tested on a
clear Sid Docker container).  Why is this?  I ask because our current
instructions for installing SnapPy into SageMath use "sage -pip".


The sage script in Debian is indeed a restricted version of the
original sage script (to avoid messing up with the system). You
can just use the pip from the system. That works fine if you
source the environment variables first:

$ source /usr/share/sagemath/bin/sage-env
$ pip install surface_dynamics --user

Best wishes
Vincent

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Re: [sage-devel] Import issue for Sage when using the system's Python (e.g. Debian)

2019-01-10 Thread Vincent Delecroix

Dear Nathan,

I think that the cause of the trouble is that in Debian if you
start Python and try "import sage" it will fail. You first need
to set up some environment variables via

$ source /usr/share/sagemath/bin/sage-env

Best
Vincent

PS: I ran into that with surface_dynamics
https://gitlab.com/videlec/surface_dynamics

Le 10/01/2019 à 04:47, Nathan Dunfield a écrit :

I am a developer of the Python package "snappy" which acquires extra
features when imported inside of Sage. Some of our Linux users have
recently reported difficulties with SnapPy on machines where Sage was
installed by the standard package manger making use of the system libraries
and in particular the system python.  I have reproduced the problem on
Debian Sid but it also manifests itself on Fedora 28 [1].  The root of our
problem is that in this situation:

python -c "import sage.all"

results the error:

Traceback (most recent call last):
   File "", line 1, in 
   File "/usr/lib/python2.7/dist-packages/sage/all.py", line 71, in 
 from sage.env import SAGE_ROOT, SAGE_SRC, SAGE_DOC_SRC, SAGE_LOCAL,
DOT_SAGE, SAGE_ENV
   File "/usr/lib/python2.7/dist-packages/sage/env.py", line 123, in 
 _add_variable_or_fallback('SAGE_ETC',opj('$SAGE_LOCAL', 'etc'))
   File "/usr/lib/python2.7/dist-packages/sage/env.py", line 103, in
_add_variable_or_fallback
 value = sep.join(components)
TypeError: sequence item 0: expected string, NoneType found

whereas

sage -python -c "import sage.all"

works as expected.  Currently, our Python package tests for whether it is
running in SageMath by:

_within_sage = False
try:
 import sage.all
 _within_sage = True
except ImportError:
 pass

One solution for us (I think) would be to simply catch and ignore all types
of exceptions in the above block, but I was wondering if the current
behavior of 'python -c "import sage.all"' was expected or is this possibly
a bug?  Or perhaps there is a work-around of some kind?

Thanks,

Nathan

P.S. In the Debian package "sage" does not accept the "-pip" flag, even
though installing the "sagemath" package does pull in "pip" (tested on a
clear Sid Docker container).  Why is this?  I ask because our current
instructions for installing SnapPy into SageMath use "sage -pip".


[1] See the second comment, not the original report, on
https://bitbucket.org/t3m/snappy/issues/14/



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Re: [sage-devel] Import issue for Sage when using the system's Python (e.g. Debian)

2019-01-09 Thread Dima Pasechnik
I've forwarded this to sage-packaging, and the relevant Debian list,
as more appropriate forums for this issue.

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