Re: [sage-devel] Science Code Manifesto

[Dima Pasechnik]

I'm trying to avoid Elsevier and Springer, if at all possible :(
Blame the lawyers...
You could have contacted the editors, and explained the situation. They 
have 
their leeway with the publisher.

AFAIK, CMU would still allow you to put this text up on your homepage.
At least, if you look up homepages of CMU CS people, they have their 
articles there.

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[sage-devel] Re: Proposal for "3-D" logo for Sage...

[Jonathan]

On Oct 16, 4:52 pm, Benjamin Jones  wrote:

> Very cool. Are you willing to post the code that produces it? (just
> out of curiosity about how you made it..)

Of course...Actually, my intent is to generate a function in Sage that
will produce it so that others can manipulate it and improve upon it.
First we have to chase some bugs out of Jmol.  I had to do a little
fussing to make this work.

Jonathan

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Re: [sage-devel] Proposal for "3-D" logo for Sage...

[Benjamin Jones]

On Sun, Oct 16, 2011 at 3:16 PM, Jonathan  wrote:
> I was preparing a poster for a Univ. Wisc. System Chemistry meeting
> and was playing with Jmol.  I mocked up a 3-D version of the Sage logo
> which can be rotated in Jmol [also found a bug in Jmol by doing
> this ;)].  Anyway, I thought a static version might be useful as an
> update to the Sage logo.  I've posted it to the logo section of the
> Sage Wiki.  What do people think?  You can see it at this link:
>
> http://wiki.sagemath.org/logos?action=AttachFile&do=view&target=Sage+logo+3D.png
>
> Jonathan
>


Very cool. Are you willing to post the code that produces it? (just
out of curiosity about how you made it..)

--
Benjamin Jones

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[sage-devel] Proposal for "3-D" logo for Sage...

[Jonathan]

I was preparing a poster for a Univ. Wisc. System Chemistry meeting
and was playing with Jmol.  I mocked up a 3-D version of the Sage logo
which can be rotated in Jmol [also found a bug in Jmol by doing
this ;)].  Anyway, I thought a static version might be useful as an
update to the Sage logo.  I've posted it to the logo section of the
Sage Wiki.  What do people think?  You can see it at this link:

http://wiki.sagemath.org/logos?action=AttachFile&do=view&target=Sage+logo+3D.png

Jonathan

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Re: [sage-devel] Science Code Manifesto

[daly]

Oh, and as another aside, I left CMU in February (I'm now
unemployed) but the last effort we had was to release our
6 year research project as open source. That effort is tied
up in legal somewhere and has been since January. Since I'm
no longer there I expect the code will never see the light
of day. Which implies that I cannot use my last 6 years of
work. Technically I cannot complain as I knew the rules
while I worked there but it really does seem like a waste
of good research. Nobody will be able to build on the results,
which is a fundamental principle of scientific progress.

Tim Daly

On Sun, 2011-10-16 at 15:42 -0400, daly wrote:
> Hmmm. I did work at CMU last year on a Journal article.
> It was based on about 3 years of research work. The article
> was completed, submitted for review, and accepted. CMU
> required that I sign over the copyright to them. Springer
> required that I sign over the copyright to them, despite
> an agreement between CMU and Springer. It turned out that
> the agreement was between CMU and Springer USA but the
> Journal is published by Springer Europe. 
> 
> Ultimately the two lawyers could not agree and my Journal
> article was withdrawn during production. CMU now holds the
> copyright. Three years of work and I have nothing, no rights
> and no publication.
> 
> As a major advocate of Literate Programming I was hoping to
> publish a follow-on paper that included the actual source
> code. Why bother?
> 
> Tim Daly
> 
> 
> On Sun, 2011-10-16 at 12:20 -0700, William Stein wrote:
> > 
> > 
> > On Sunday, October 16, 2011, Dima Pasechnik  wrote:
> > > Bill,
> > > are you sure that you have signed away to your employer rights to
> > your ideas ?
> > 
> > Technically Bill only said that Uni's consider employee work
> > intellectual property, but he did not say they consider it *their*
> > intellectual property...
> > 
> > > While some not so great universities are just degree-selling
> > businesses, 
> > > last time I had to obtain a permission from my employer for
> > publishing something, was still in Soviet Union!
> > > So I really don't see how results of work done by a faculty member
> > are university property. 
> > >  
> > >
> > > --
> > > To post to this group, send an email to sage-devel@googlegroups.com
> > > To unsubscribe from this group, send an email to sage-devel
> > +unsubscr...@googlegroups.com
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> > http://groups.google.com/group/sage-devel
> > > URL: http://www.sagemath.org
> > >
> > 
> > -- 
> > William Stein
> > Professor of Mathematics
> > University of Washington
> > http://wstein.org
> > 
> > 
> > 
> > -- 
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> > URL: http://www.sagemath.org
> 


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Re: [sage-devel] Science Code Manifesto

[daly]

Hmmm. I did work at CMU last year on a Journal article.
It was based on about 3 years of research work. The article
was completed, submitted for review, and accepted. CMU
required that I sign over the copyright to them. Springer
required that I sign over the copyright to them, despite
an agreement between CMU and Springer. It turned out that
the agreement was between CMU and Springer USA but the
Journal is published by Springer Europe. 

Ultimately the two lawyers could not agree and my Journal
article was withdrawn during production. CMU now holds the
copyright. Three years of work and I have nothing, no rights
and no publication.

As a major advocate of Literate Programming I was hoping to
publish a follow-on paper that included the actual source
code. Why bother?

Tim Daly


On Sun, 2011-10-16 at 12:20 -0700, William Stein wrote:
> 
> 
> On Sunday, October 16, 2011, Dima Pasechnik  wrote:
> > Bill,
> > are you sure that you have signed away to your employer rights to
> your ideas ?
> 
> Technically Bill only said that Uni's consider employee work
> intellectual property, but he did not say they consider it *their*
> intellectual property...
> 
> > While some not so great universities are just degree-selling
> businesses, 
> > last time I had to obtain a permission from my employer for
> publishing something, was still in Soviet Union!
> > So I really don't see how results of work done by a faculty member
> are university property. 
> >  
> >
> > --
> > To post to this group, send an email to sage-devel@googlegroups.com
> > To unsubscribe from this group, send an email to sage-devel
> +unsubscr...@googlegroups.com
> > For more options, visit this group at
> http://groups.google.com/group/sage-devel
> > URL: http://www.sagemath.org
> >
> 
> -- 
> William Stein
> Professor of Mathematics
> University of Washington
> http://wstein.org
> 
> 
> 
> -- 
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Re: [sage-devel] Re: Science Code Manifesto

[John Cremona]

I think Bill is unduly pessimistic about the attitude of our employer
(University of Warwick, UK).  I did actually consult my previous
employer's intellectual property people before putting GPL onto my
code (eclib) before handing it over to William to include in Sage.
They were quite happy.

On the other hand, I have heard that the U of Sydney has much more
strict ideas about who owns the rights to any work done by its staff
*and visitors*, which is one reason why we cannot expect Magma to
become free soon.

John

On Sun, Oct 16, 2011 at 7:44 PM, Dima Pasechnik  wrote:
> Bill,
> are you sure that you have signed away to your employer rights to your ideas
> ?
> While some not so great universities are just degree-selling businesses,
> last time I had to obtain a permission from my employer for publishing
> something, was still in Soviet Union!
> So I really don't see how results of work done by a faculty member are
> university property.
>
>
> --
> To post to this group, send an email to sage-devel@googlegroups.com
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> URL: http://www.sagemath.org
>

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Re: [sage-devel] Science Code Manifesto

[William Stein]

On Sunday, October 16, 2011, Dima Pasechnik  wrote:
> Bill,
> are you sure that you have signed away to your employer rights to your
ideas ?

Technically Bill only said that Uni's consider employee work intellectual
property, but he did not say they consider it *their* intellectual
property...

> While some not so great universities are just degree-selling businesses,
> last time I had to obtain a permission from my employer for publishing
something, was still in Soviet Union!
> So I really don't see how results of work done by a faculty member are
university property.
>
>
> --
> To post to this group, send an email to sage-devel@googlegroups.com
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> For more options, visit this group at
http://groups.google.com/group/sage-devel
> URL: http://www.sagemath.org
>

-- 
William Stein
Professor of Mathematics
University of Washington
http://wstein.org

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[sage-devel] Re: Science Code Manifesto

[Dima Pasechnik]

Bill,
are you sure that you have signed away to your employer rights to your ideas 
?

While some not so great universities are just degree-selling businesses, 
last time I had to obtain a permission from my employer for publishing 
something, was still in Soviet Union!
So I really don't see how results of work done by a faculty member are 
university property. 
 

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[sage-devel] Re: Bug in symbolic expression simplification?

[Simon King]

Bump.

On 13 Okt., 08:43, Simon King  wrote:
> ...
>   sage: q1 = SR(p1)
>   sage: q2 = SR(p2)
>   sage: q3 = SR(p3)
>   sage: q4 = SR(p4)
>   sage: q5 = SR(p5)
>   sage: q = ((q1/q2+q3)^2+(q3/(q4+q5)))/((q3/(q4+q5/(q1+q2)))+q2)
>   sage: q.simplify()
>   Traceback (most recent call last):
>   ...
>   TypeError:

Do you agree that an error in simplifying a simple arithmetic
expression of polynomial symbolic expressions is a bug? Do you agree
that a naked type error (that gives no hint on what's wrong) is
another bug?

Cheers,
Simon

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[sage-devel] Re: Science Code Manifesto

[Nathann Cohen]

>
> It is important to realise that Universities are businesses. They do 
> not fundamentally care about the advancement of science. 


O_O 

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[sage-devel] Re: Science Code Manifesto

[Bill Hart]

On Oct 14, 10:12 am, Maarten Derickx 
wrote:
> Altough I agree with what they say in the manifesto, I would say that what
> they say there is really a bare minimum. For example they do not even insist
> that the source code should be licenced in such a way that you can use it
> for scientific purposes.

Universities consider work done by their employees as intellectual
property. Therefore making the code available for others to use under
an open license is tantamount to giving away the competitive edge they
currently have.

It is important to realise that Universities are businesses. They do
not fundamentally care about the advancement of science.

The manifesto represents a complete failure of imagination. They
cannot imagine a future in which widespread exposure of the ideas in
code will be just as important as the widespread exposure of the ideas
in the written paper. However, fortunately history does not remember
the name of the guy who developed Pythagoras' theorem in secret and
refused to share the details with his colleagues for personal gain.

Bill.

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[sage-devel] Error configuring R when compiling sage in Ubuntu 11.10

[Khương Huỳnh]

 Original Message 
Subject:Error configuring R when compiling sage in Ubuntu 11.10
Date:   Sun, 16 Oct 2011 21:27:20 +0900
From:   Khương Huỳnh 
To: sage-devel@googlegroups.com



Dear Sage-team,

My name is Khuong. I tried to compile Sage in Ubuntu 11.10 64 bit in a 
Dell N4010.
The compiling stopped when configuring R. I am a newbie in using sage 
and linux.
Could you please explain me what happen and how to solve the issue ? 
Parts of the install.log file are included below.


Best,

Khuong


"
_Configuring R with ATLAS_
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
loading site script './config.site'
loading build-specific script './config.site'
...
 checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for cos in -lm... yes
checking for sin in -lm... yes
checking for dlopen in -ldl... yes
checking readline/history.h usability... yes
checking readline/history.h presence... yes
checking for readline/history.h... yes
checking readline/readline.h usability... yes
checking readline/readline.h presence... yes
checking for readline/readline.h... yes
checking for rl_callback_read_char in -lreadline... no
checking for main in -lncurses... yes
checking for rl_callback_read_char in -lreadline... no
checking for history_truncate_file... no
_configure: error: --with-readline=yes (default) and headers/libs are 
not available_

_Configuring R with fallback options_
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
loading site script './config.site'




checking how to hardcode library paths into programs... immediate
checking for cos in -lm... yes
checking for sin in -lm... yes
checking for dlopen in -ldl... yes
checking readline/history.h usability... yes
checking readline/history.h presence... yes
checking for readline/history.h... yes
checking readline/readline.h usability... yes
checking readline/readline.h presence... yes
checking for readline/readline.h... yes
checking for rl_callback_read_char in -lreadline... no
checking for main in -lncurses... yes
checking for rl_callback_read_char in -lreadline... no
checking for history_truncate_file... no
_configure: error: --with-readline=yes (default) and headers/libs are 
not available

Error configuring R.
_
real0m10.495s
user0m3.692s
sys0m2.064s
sage: An error occurred while installing r-2.10.1.p4
"

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Re: [sage-devel] Re: Options for sage -pkg

[Keshav Kini]

I think what Leif meant was that most compression formats (including gzip 
and bz2) implement good enough error detection to obviate md5 hashing. See this 
post  on trac #329 
(not sure what trac #352, "error in matrix creation options", has to do with 
anything).

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[sage-devel] .hgignore

[Keshav Kini]

Hi all,

I was browsing through $SAGE_ROOT/devel/sage/.hgignore and noticed that some 
specific filenames are mentioned which don't seem to exist in my 
installation of Sage (4.7.2.alpha3 built from source). Might these files 
come into being some time in the future if I install certain SPKGs or 
something, or are they cruft which should be removed from the .hgignore 
file? I notice the .hgignore file hasn't been changed since 2009, and hasn't 
been changed by any more than a few lines here and there since 2007, which 
makes me suspect the latter, but I'm not sure, hence this post.

-Keshav


Join us in #sagemath on irc.freenode.net !

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[sage-devel] Re: twisted 11

[Dima Pasechnik]

by the way, here is a problem I was hitting while trying to doctest 
twisted-11 + flack-nb.
Any idea what is happening there? It's quite weird:


File 
"/usr/local/src/sage/sage-4.7.1/devel/rkirov-flask/sagenb/notebook/notebook.py",
line 1238:
   sage: nb.html_worksheet_revision_list('admin', W)
Exception raised:
   Traceback (most recent call last):
 File "/usr/local/src/sage/sage-4.7.1/local/bin/ncadoctest.py",
line 1231, in run_one_test
   self.run_one_example(test, example, filename, compileflags)
 File "/usr/local/src/sage/sage-4.7.1/local/bin/sagedoctest.py",
line 38, in run_one_example
   OrigDocTestRunner.run_one_example(self, test, example,
filename, compileflags)
 File "/usr/local/src/sage/sage-4.7.1/local/bin/ncadoctest.py",
line 1172, in run_one_example
   compileflags, 1) in test.globs
 File "", line 1, in 
   nb.html_worksheet_revision_list('admin', W)###line 1238:
   sage: nb.html_worksheet_revision_list('admin', W)
 File 
"/usr/local/src/sage/sage-4.7.1/devel/rkirov-flask/sagenb/notebook/notebook.py",
line 1246, in html_worksheet_revision_list
   username = username)
 File 
"/usr/local/src/sage/sage-4.7.1/devel/rkirov-flask/sagenb/notebook/template.py",
line 155, in template
   r = tmpl.render(**context)
 File 
"/usr/local/src/sage/sage-4.7.1/local/lib/python2.6/site-packages/Jinja2-2.5.5-py2.6.egg/jinja2/environment.py",
line 892, in render
   return self.environment.handle_exception(exc_info, True)
 File 
"/usr/local/src/sage/sage-4.7.1/devel/rkirov-flask/sagenb/data/sage/html/notebook/worksheet_revision_list.html",
line 9, in top-level template code
   {% set select = "revisions" %}
 File 
"/usr/local/src/sage/sage-4.7.1/devel/rkirov-flask/sagenb/data/sage/html/notebook/base_aux.html",
line 1, in top-level template code
   {% extends "html/notebook/base.html" %}
 File 
"/usr/local/src/sage/sage-4.7.1/devel/rkirov-flask/sagenb/data/sage/html/notebook/base.html",
line 11, in top-level template code
   {% set system_names = worksheet.notebook().system_names() %}
 File 
"/usr/local/src/sage/sage-4.7.1/devel/rkirov-flask/sagenb/data/sage/html/base_authenticated.html",
line 1, in top-level template code
   {% extends "html/base.html" %}
 File 
"/usr/local/src/sage/sage-4.7.1/devel/rkirov-flask/sagenb/data/sage/html/base.html",
line 26, in top-level template code
   {% block body %}
 File 
"/usr/local/src/sage/sage-4.7.1/devel/rkirov-flask/sagenb/data/sage/html/base.html",
line 28, in block "body"
   {% block header %}
 File 
"/usr/local/src/sage/sage-4.7.1/devel/rkirov-flask/sagenb/data/sage/html/base.html",
line 32, in block "header"
   {{ gettext('The Sage Notebook') }}
   UndefinedError: 'gettext' is undefined
*

thanks,
Dima

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