[sage-devel] Re: Help : best way to compile a package sphinx's documentation during spkg-install

2019-01-31 Thread Sébastien Labbé


On Thursday, January 31, 2019 at 8:47:17 PM UTC+1, Simon King wrote:
>
> Hi Sébastien, 
>
>
Hi Simon,
 

> On 2019-01-31, Sébastien Labbé > wrote: 
> > I do not know if this helps, but I do it this way in my optional 
> package: 
> > 
> > doc: 
> > cd docs && sage -sh -c "make html" 
> > 
> > doc-pdf: 
> > cd docs && sage -sh -c "make latexpdf" 
>
> Interesting. Isn't the spkg installation happening in a Sage shell 
> anyway? 
>

Well, I am sure I do not follow the good way of doing it...

I build the documentation always aside of anything else. So I do make doc 
in the root repository of my package.


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[sage-devel] Re: Help : best way to compile a package sphinx's documentation during spkg-install

2019-01-31 Thread Simon King
Hi Sébastien,

On 2019-01-31, Sébastien Labbé  wrote:
> I do not know if this helps, but I do it this way in my optional package:
>
> doc:
> cd docs && sage -sh -c "make html"
>
> doc-pdf:
> cd docs && sage -sh -c "make latexpdf"

Interesting. Isn't the spkg installation happening in a Sage shell
anyway?

Best regards,
Simon

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Re: [sage-devel] Help : best way to compile a package sphinx's documentation during spkg-install

2019-01-31 Thread Sébastien Labbé
I do not know if this helps, but I do it this way in my optional package:

doc:
cd docs && sage -sh -c "make html"

doc-pdf:
cd docs && sage -sh -c "make latexpdf"


On Thursday, January 31, 2019 at 12:05:03 PM UTC+1, Vincent Klein wrote:
>
> Thanks for your answer.
> I don't know exactly why it works with sagenb but doing the same with 
> pplpy doesn't work
> #spkg-install
>
> cd src && sdh_pip_install .
>
> cd docs
> $MAKE html
>
>
> Result in this :
>
> [pplpy-0.8.2b0] reading sources... [100%] index
> [pplpy-0.8.2b0] 
> [pplpy-0.8.2b0] WARNING: autodoc: failed to import module u'ppl'; the 
> following exception was raised:
> [pplpy-0.8.2b0] No module named ppl
> [pplpy-0.8.2b0] WARNING: autodoc: failed to import module 
> u'ppl.constraint'; the following exception was raised:
> [pplpy-0.8.2b0] No module named ppl.constraint
> [pplpy-0.8.2b0] WARNING: autodoc: failed to import module 
> u'ppl.linear_algebra'; the following exception was raised:
> [pplpy-0.8.2b0] No module named ppl.linear_algebra
> [pplpy-0.8.2b0] WARNING: autodoc: failed to import module 
> u'ppl.generator'; the following exception was raised:
> [pplpy-0.8.2b0] No module named ppl.generator
> [pplpy-0.8.2b0] WARNING: autodoc: failed to import module 
> u'ppl.polyhedron'; the following exception was raised:
> [pplpy-0.8.2b0] No module named ppl.polyhedron
> [pplpy-0.8.2b0] WARNING: autodoc: failed to import module 
> u'ppl.mip_problem'; the following exception was raised:
> [pplpy-0.8.2b0] No module named ppl.mip_problem
>
> Le jeudi 31 janvier 2019 10:56:46 UTC+1, Dima Pasechnik a écrit :
>>
>> Have a look at 
>>
>> build/pkgs/sagenb/spkg-install 
>>
>> which does what you are looking for, in one go, I think. 
>>
>> On Thu, Jan 31, 2019 at 8:49 AM Vincent Klein  wrote: 
>> > 
>> > Hi, 
>> > 
>> > I am looking for a good way  to compile a package sphinx's 
>> documentation during a spkg-install execution. 
>> > After doing a sdh_pip_install the compiled files are still in a 
>> temporary directory ($SAGE_DESTDIR_LOCAL/lib/python2.7/site-packages), a 
>> therefore a simple sphinx "make html" will fail to find your package's 
>> compiled files. 
>> > I am looking for a generic way for the /lib/python2.7/site-packages 
>> part. I haven't find an environment variable for that (I think this path is 
>> given/constructed by distutils). 
>> > 
>> > This question comes from ticket 
>> https://trac.sagemath.org/ticket/23024#comment:106. 
>> > 
>> > The current workaround we have is doing an "inplace" build before 
>>  generating the documentation (
>> https://git.sagemath.org/sage.git/commit/?id=ef8997834f73c34d983260c0ba782041d0966a02)
>>  
>>
>> > 
>> > Any help is welcomed 
>> > 
>> > Vincent K. 
>> > 
>> > -- 
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>> > For more options, visit https://groups.google.com/d/optout. 
>>
>

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[sage-devel] Re: Location of ecl packages

2019-01-31 Thread Nils Bruin


On Thursday, January 31, 2019 at 8:11:26 AM UTC-8, mmarco wrote:
>
> I am working in a Kenzo interface/optional package. I managed to load 
> through the ecl interface, but using asdf, but in order to do that I had to 
> have it installed in my ~/common-lisp/ directory. As an optional package, 
> it should be located in some directory of the sage install, that must be 
> found by ecl's asdf.
>
> Does someone know where should I put it?
>

I suspect

$SAGE_LOCAL/lib/ecl/ 

should do it. That's where "maxima.fas" is placed, and (require 'maxima) 
works.

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Re: [sage-devel] Location of ecl packages

2019-01-31 Thread Dima Pasechnik
On Thu, Jan 31, 2019 at 4:11 PM mmarco  wrote:
>
> I am working in a Kenzo interface/optional package. I managed to load through 
> the ecl interface, but using asdf, but in order to do that I had to have it 
> installed in my ~/common-lisp/ directory. As an optional package, it should 
> be located in some directory of the sage install, that must be found by ecl's 
> asdf.
>
> Does someone know where should I put it?

I think it should be SAGE_LOCAL/lib/ecl/.
That's where various *.asd and *.fas files live.


>
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Re: [sage-devel] sage crash report

2019-01-31 Thread Vincent Delecroix

Thank you for the report. The error invokes some write access
errror:

OSError: [Errno 13] Permission denied: '/home/a/.sage/db'

Which most probably means that you did something wrong at
installation time.

Could you send the output of the following command

 $ ls -ld /home/a/.sage

And could you precise

* How did you install SageMath? (describe very precisely all steps)
* How did you launch SageMath for the first time?

Vincent

Le 31/01/2019 à 14:37, Aranka a écrit :

Ubuntu 16.04 LTS
I was simply trying to open sage from the terminal. Haven't even been
asking it to perform any actual actions yet.
Also simply e-mailing to sage-supp...@googlegroups.com as suggested in the
terminal after a crash does not work as indicated. One gets back an e-mail
that it's not possible to post to the group.



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[sage-devel] Location of ecl packages

2019-01-31 Thread mmarco
I am working in a Kenzo interface/optional package. I managed to load 
through the ecl interface, but using asdf, but in order to do that I had to 
have it installed in my ~/common-lisp/ directory. As an optional package, 
it should be located in some directory of the sage install, that must be 
found by ecl's asdf.

Does someone know where should I put it?

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[sage-devel] Re: Help : best way to compile a package sphinx's documentation during spkg-install

2019-01-31 Thread Simon King
On 2019-01-31, Vincent Klein  wrote:
> Thanks for your answer.
> I don't know exactly why it works with sagenb but doing the same with pplpy 
> doesn't work
> #spkg-install
>
> cd src && sdh_pip_install .
>
> cd docs
> $MAKE html

I would like to know it, too. With p_group_cohomology, if I recall
correctly, I also had the problem that during package installation the
documentation won't build, whereas it does build when doing it manually.
I didn't check the latest version, though.

Cheers,
Simon

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[sage-devel] sage crash report

2019-01-31 Thread Aranka
Ubuntu 16.04 LTS
I was simply trying to open sage from the terminal. Haven't even been 
asking it to perform any actual actions yet.
Also simply e-mailing to sage-supp...@googlegroups.com as suggested in the 
terminal after a crash does not work as indicated. One gets back an e-mail 
that it's not possible to post to the group.

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***

IPython post-mortem report

{'commit_hash': u'033ab93c7',
 'commit_source': 'installation',
 'default_encoding': 'UTF-8',
 'ipython_path': '/opt/SageMath/local/lib/python2.7/site-packages/IPython',
 'ipython_version': '5.8.0',
 'os_name': 'posix',
 'platform': 'Linux-4.15.0-43-generic-x86_64-with-debian-stretch-sid',
 'sys_executable': '/opt/SageMath/local/bin/python2',
 'sys_platform': 'linux2',
 'sys_version': '2.7.15 (default, Jan 18 2019, 04:23:03) \n[GCC 7.2.0]'}

***



***

Crash traceback:

---
---
OSError  Python 2.7.15: /opt/SageMath/local/bin/python2
   Thu Jan 31 14:24:29 2019
A problem occurred executing Python code.  Here is the sequence of function
calls leading up to the error, with the most recent (innermost) call last.
/opt/SageMath/src/bin/sage-ipython in ()
  1 #!/usr/bin/env sage-python23
  2 # -*- coding: utf-8 -*-
  3 """
  4 Sage IPython startup script.
  5 """
  6 
  7 # Display startup banner. Do this before anything else to give the user
  8 # early feedback that Sage is starting.
  9 from sage.misc.banner import banner
 10 banner()
 11 
 12 from sage.repl.interpreter import SageTerminalApp
 13 
 14 app = SageTerminalApp.instance()
---> 15 app.initialize()
global app.initialize = >
 16 app.start()

 in initialize(self=, argv=None)

/opt/SageMath/local/lib/python2.7/site-packages/traitlets/config/application.pyc
 in catch_config_error(method=, 
app=, *args=(None,), **kwargs={})
 72 TRAITLETS_APPLICATION_RAISE_CONFIG_FILE_ERROR = False
 73 else:
 74 raise ValueError("Unsupported value for environment variable: 
'TRAITLETS_APPLICATION_RAISE_CONFIG_FILE_ERROR' is set to '%s' which is none of 
 {'0', '1', 'false', 'true', ''}."% _envvar )
 75 
 76 
 77 @decorator
 78 def catch_config_error(method, app, *args, **kwargs):
 79 """Method decorator for catching invalid config 
(Trait/ArgumentErrors) during init.
 80 
 81 On a TraitError (generally caused by bad config), this will print 
the trait's
 82 message, and exit the app.
 83 
 84 For use on init methods, to prevent invoking excepthook on invalid 
input.
 85 """
 86 try:
---> 87 return method(app, *args, **kwargs)
method = 
app = 
args = (None,)
kwargs = {}
 88 except (TraitError, ArgumentError) as e:
 89 app.print_help()
 90 app.log.fatal("Bad config encountered during initialization:")
 91 app.log.fatal(str(e))
 92 app.log.debug("Config at the time: %s", app.config)
 93 app.exit(1)
 94 
 95 
 96 class ApplicationError(Exception):
 97 pass
 98 
 99 
100 class LevelFormatter(logging.Formatter):
101 """Formatter with additional `highlevel` record
102 

/opt/SageMath/local/lib/python2.7/site-packages/IPython/terminal/ipapp.pyc in 
initialize(self=, argv=None)
301 
302 return super(TerminalIPythonApp, self).parse_command_line(argv)
303 
304 @catch_config_error
305 def initialize(self, argv=None):
306 """Do actions after construct, but before starting the app."""
307 super(TerminalIPythonApp, self).initialize(argv)
308 if self.subapp is not None:
309 # don't bother initializing further, starting subapp
310 return
311 # print self.extra_args
312 if self.extra_args and not self.something_to_run:
313 self.file_to_run = self.extra_args[0]
314 self.init_path()
315 # create the shell
--> 316 self.init_shell()
self.init_shell = >
317 # and draw the banner
318 self.init_banne

Re: [sage-devel] Re: documentation of SageMath (Python) packages

2019-01-31 Thread Vincent Delecroix

Le 31/01/2019 à 14:01, E. Madison Bray a écrit :

On Tue, Jan 29, 2019 at 9:38 PM Nathan Dunfield  wrote:


  Vincent,


Imagine I have a Python module, typically hosted on PyPI and depending
on SageMath, that provides documentation in some form (e.g. a pdf file,
a sphinx repo, etc).

1) When a user performs `sage -pip install X`, should the documentation
 be compiled and installed?



I can tell you what we do with SnapPy, which has both Sphinx-generated docs and some PDF files. 
When building the sdist tarballs and wheels for posting on PyPI, we use Sphinx to compile the docs 
into HTML and then put the resulting HTML files as well as a few random PDFs into the Python 
package as "package data".   There are convenience functions such as 
"spherogram.pdf_docs()" which open the docs in a webrowser or pdfviewer as appropriate. 
As we support vanilla Python as well as SageMath, we can't assume that Sphinx is installed.


+1 to this approach.  It's definitely easier if the docs are
pre-generated by the developer and included in the source tarball.


This is definitely easy and doable. But what should be done with it by
default? Would you advice to do as Nathan did with Snappy: copy
the documentation inside the installed Python package?

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Re: [sage-devel] spkgs dependencies graph

2019-01-31 Thread E. Madison Bray
On Tue, Jan 29, 2019 at 7:45 PM Dima Pasechnik  wrote:
>
> Has anyone written code to compute it?
> (and create a Sage graph out of it, maybe)

I actually have in the past, though I don't remember if I've kept it
anywhere.  It's easy to do though.

Btw I did make a Sage Graph out of it and tried plotting it and boy
was that a mess (it worked, but it was pretty unreadable :)

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Re: [sage-devel] Re: documentation of SageMath (Python) packages

2019-01-31 Thread E. Madison Bray
On Tue, Jan 29, 2019 at 9:38 PM Nathan Dunfield  wrote:
>
>  Vincent,
>
>> Imagine I have a Python module, typically hosted on PyPI and depending
>> on SageMath, that provides documentation in some form (e.g. a pdf file,
>> a sphinx repo, etc).
>>
>> 1) When a user performs `sage -pip install X`, should the documentation
>> be compiled and installed?
>
>
> I can tell you what we do with SnapPy, which has both Sphinx-generated docs 
> and some PDF files. When building the sdist tarballs and wheels for posting 
> on PyPI, we use Sphinx to compile the docs into HTML and then put the 
> resulting HTML files as well as a few random PDFs into the Python package as 
> "package data".   There are convenience functions such as 
> "spherogram.pdf_docs()" which open the docs in a webrowser or pdfviewer as 
> appropriate. As we support vanilla Python as well as SageMath, we can't 
> assume that Sphinx is installed.

+1 to this approach.  It's definitely easier if the docs are
pre-generated by the developer and included in the source tarball.

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Re: [sage-devel] py3: issue with round

2019-01-31 Thread E. Madison Bray
If you have any insight to share on the rationale of Sage's existing
built-in round() behavior it would also be very appreciated,
especially for this ticket: https://trac.sagemath.org/ticket/25827

To summarize the discussion thus far:

* Sage currently has its own `round()` function defined in
sage.misc.functional , which in the global namespace of the Sage
interpreter replaces the Python built-in `round()`; the main reason
for this appears to be that it was not possible in the past to
override how `round()` acts on arbitrary types: It would just convert
them to floats first if they have a `__float__()` method, and then
round that value.

* However, Python 3 introduces a `__round__(self, n=0)` special method
that types can implement to be called when `round()` is called on
instances of that type.

* Here, I proposed a new `__round__()` method for MPFR reals that
takes into account the rounding mode of the parent field (e.g. RNDU,
RNDN, etc.)  This seems to work, but would be a change in behavior
over the old `.round()` method on that class.

* It's not clear why the old `.round()` method ignored the rounding
mode and whether or not there's a good reason for that.  It's also not
clear if we even need to replace the built-in `round()` on Python 3 if
types can implement `__round__()`.  These are two separate questions
though, at least I think.

On Thu, Jan 31, 2019 at 8:42 AM David Coudert  wrote:
>
> Does anyone know a suitable way to fix the following issue with round in 
> Python3 ?
>
> sage: G = Graph([(0, 1)])
> sage: f = g._build_flow_graph({(0, 1): 1}, True)
> ---
> TypeError Traceback (most recent call last)
>  in ()
> > 1 f = g._build_flow_graph({(Integer(0), Integer(1)): Integer(1)}, True)
>
> /Users/dcoudert/sage3/sage/local/lib/python3.6/site-packages/sage/graphs/generic_graph.py
>  in _build_flow_graph(self, flow, integer)
>9094 g.delete_edge(u, v)
>9095 else:
> -> 9096 g.set_edge_label(u, v, int(round(l)))
>9097
>9098 # returning a graph with the same embedding, the 
> corresponding name, etc ...
>
> TypeError: type sage.rings.integer.Integer doesn't define __round__ method
> sage:
> sage: f = g._build_flow_graph({(0, 1): 1.0}, True)
> ---
> TypeError Traceback (most recent call last)
>  in ()
> > 1 f = g._build_flow_graph({(Integer(0), Integer(1)): 
> RealNumber('1.0')}, True)
>
> /Users/dcoudert/sage3/sage/local/lib/python3.6/site-packages/sage/graphs/generic_graph.py
>  in _build_flow_graph(self, flow, integer)
>9094 g.delete_edge(u, v)
>9095 else:
> -> 9096 g.set_edge_label(u, v, int(round(l)))
>9097
>9098 # returning a graph with the same embedding, the 
> corresponding name, etc ...
>
> TypeError: type sage.rings.real_mpfr.RealLiteral doesn't define __round__ 
> method
>
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Re: [sage-devel] Help : best way to compile a package sphinx's documentation during spkg-install

2019-01-31 Thread Vincent Klein
Thanks for your answer.
I don't know exactly why it works with sagenb but doing the same with pplpy 
doesn't work
#spkg-install

cd src && sdh_pip_install .

cd docs
$MAKE html


Result in this :

[pplpy-0.8.2b0] reading sources... [100%] index
[pplpy-0.8.2b0] 
[pplpy-0.8.2b0] WARNING: autodoc: failed to import module u'ppl'; the 
following exception was raised:
[pplpy-0.8.2b0] No module named ppl
[pplpy-0.8.2b0] WARNING: autodoc: failed to import module 
u'ppl.constraint'; the following exception was raised:
[pplpy-0.8.2b0] No module named ppl.constraint
[pplpy-0.8.2b0] WARNING: autodoc: failed to import module 
u'ppl.linear_algebra'; the following exception was raised:
[pplpy-0.8.2b0] No module named ppl.linear_algebra
[pplpy-0.8.2b0] WARNING: autodoc: failed to import module u'ppl.generator'; 
the following exception was raised:
[pplpy-0.8.2b0] No module named ppl.generator
[pplpy-0.8.2b0] WARNING: autodoc: failed to import module 
u'ppl.polyhedron'; the following exception was raised:
[pplpy-0.8.2b0] No module named ppl.polyhedron
[pplpy-0.8.2b0] WARNING: autodoc: failed to import module 
u'ppl.mip_problem'; the following exception was raised:
[pplpy-0.8.2b0] No module named ppl.mip_problem

Le jeudi 31 janvier 2019 10:56:46 UTC+1, Dima Pasechnik a écrit :
>
> Have a look at 
>
> build/pkgs/sagenb/spkg-install 
>
> which does what you are looking for, in one go, I think. 
>
> On Thu, Jan 31, 2019 at 8:49 AM Vincent Klein  > wrote: 
> > 
> > Hi, 
> > 
> > I am looking for a good way  to compile a package sphinx's documentation 
> during a spkg-install execution. 
> > After doing a sdh_pip_install the compiled files are still in a 
> temporary directory ($SAGE_DESTDIR_LOCAL/lib/python2.7/site-packages), a 
> therefore a simple sphinx "make html" will fail to find your package's 
> compiled files. 
> > I am looking for a generic way for the /lib/python2.7/site-packages 
> part. I haven't find an environment variable for that (I think this path is 
> given/constructed by distutils). 
> > 
> > This question comes from ticket 
> https://trac.sagemath.org/ticket/23024#comment:106. 
> > 
> > The current workaround we have is doing an "inplace" build before 
>  generating the documentation (
> https://git.sagemath.org/sage.git/commit/?id=ef8997834f73c34d983260c0ba782041d0966a02)
>  
>
> > 
> > Any help is welcomed 
> > 
> > Vincent K. 
> > 
> > -- 
> > You received this message because you are subscribed to the Google 
> Groups "sage-devel" group. 
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>

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[sage-devel] Re: py3: issue with round

2019-01-31 Thread David Coudert
Thanks, it's working well.

Le jeudi 31 janvier 2019 08:45:37 UTC+1, Frédéric Chapoton a écrit :
>
> You could add (at the price of some speed)
>
> from sage.misc.functional import round
>
>>
>>

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Re: [sage-devel] Help : best way to compile a package sphinx's documentation during spkg-install

2019-01-31 Thread Dima Pasechnik
Have a look at

build/pkgs/sagenb/spkg-install

which does what you are looking for, in one go, I think.

On Thu, Jan 31, 2019 at 8:49 AM Vincent Klein  wrote:
>
> Hi,
>
> I am looking for a good way  to compile a package sphinx's documentation 
> during a spkg-install execution.
> After doing a sdh_pip_install the compiled files are still in a temporary 
> directory ($SAGE_DESTDIR_LOCAL/lib/python2.7/site-packages), a therefore a 
> simple sphinx "make html" will fail to find your package's compiled files.
> I am looking for a generic way for the /lib/python2.7/site-packages part. I 
> haven't find an environment variable for that (I think this path is 
> given/constructed by distutils).
>
> This question comes from ticket 
> https://trac.sagemath.org/ticket/23024#comment:106.
>
> The current workaround we have is doing an "inplace" build before  generating 
> the documentation 
> (https://git.sagemath.org/sage.git/commit/?id=ef8997834f73c34d983260c0ba782041d0966a02)
>
> Any help is welcomed
>
> Vincent K.
>
> --
> 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+unsubscr...@googlegroups.com.
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> Visit this group at https://groups.google.com/group/sage-devel.
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[sage-devel] Help : best way to compile a package sphinx's documentation during spkg-install

2019-01-31 Thread Vincent Klein
Hi,

I am looking for a good way  to compile a package sphinx's documentation 
during a spkg-install execution.
After doing a sdh_pip_install the compiled files are still in a temporary 
directory ($SAGE_DESTDIR_LOCAL/lib/python2.7/site-packages), a therefore a 
simple sphinx "make html" will fail to find your package's compiled files.
I am looking for a generic way for the /lib/python2.7/site-packages part. I 
haven't find an environment variable for that (I think this path is 
given/constructed by distutils). 

This question comes from 
ticket https://trac.sagemath.org/ticket/23024#comment:106.

The current workaround we have is doing an "inplace" build before  
generating the documentation 
(https://git.sagemath.org/sage.git/commit/?id=ef8997834f73c34d983260c0ba782041d0966a02)

Any help is welcomed

Vincent K.

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