Re: Worth packaging bio_assembly_refinement?

[Sascha Steinbiss]

Hi Afif,

first of all thanks for looking at Circlator, which was on my list as well :)

>> I'm looking into packaging Circlator, which depends on the Sanger
>> program bio_assembly_refinement. Looking into it, I'm wondering whether
>> this is a tool that will just get folded into circlator eventually. Do
>> you think it's worth packaging it separately?
> 
> I should add that the alternative would be to bundle it into the
> circlator package as a multi-orig tarball. The question is better
> rephrased as whether it's worth packaging bio_assembly_refinement
> /separately/.

Yes, I noticed the dependency on bio_assembly_refinement as well and I was’t 
sure what part of it is really needed, since it’s description sounded a bit 
similar to Circlator itself. I didn’t have the time yet to look into it in more 
detail yet.
I have cc’d Martin Hunt, the Circlator author, and Nishadi de Silva, the 
bio_assembly_refinement author, on this email and they might be able to say 
more.

Many thanks,
Sascha

Re: RFS: python-typing

[Mattia Rizzolo]

On Mon, Mar 07, 2016 at 06:33:24PM +0100, Michael Crusoe wrote:
> Thanks!
> 
> git+ssh://git.debian.org/git/debian-med/python-typing.git

As you wrote in the ITP, are you still interested in this?

FYI, I'm a supporter of starting dropping python2 bits when possible;
removing py2 will be painful enough also without more new packages...

-- 
regards,
Mattia Rizzolo

GPG Key: 66AE 2B4A FCCF 3F52 DA18  4D18 4B04 3FCD B944 4540  .''`.
more about me:  http://mapreri.org  : :'  :
Launchpad user: https://launchpad.net/~mapreri  `. `'`
Debian QA page: https://qa.debian.org/developer.php?login=mattia  `-


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Bug#817056: ITP: python-typing -- Type Hints for Python

[Michael R. Crusoe]

See
https://www.python.org/dev/peps/pep-0484/#suggested-syntax-for-python-2-7-and-straddling-code
Pe 8 mar. 2016 06:24, "Brian May"  a scris:

> "Michael R. Crusoe"  writes:
>
> >  This is a backport of the standard library typing module to Python
> >  versions older than 3.5.
>
> Not sure what the point of this is; doesn't typing hinting require PEP
> 3107, which isn't in Python 2.x?
> --
> Brian May 
>

Re: Worth packaging bio_assembly_refinement?

[Afif Elghraoui]

On الإثنين  7 آذار 2016 21:48, Afif Elghraoui wrote:
> Hi, Sascha,
> I'm looking into packaging Circlator, which depends on the Sanger
> program bio_assembly_refinement. Looking into it, I'm wondering whether
> this is a tool that will just get folded into circlator eventually. Do
> you think it's worth packaging it separately?
> 

I should add that the alternative would be to bundle it into the
circlator package as a multi-orig tarball. The question is better
rephrased as whether it's worth packaging bio_assembly_refinement
/separately/.

Thanks and regards
Afif

-- 
Afif Elghraoui | عفيف الغراوي
http://afif.ghraoui.name

Worth packaging bio_assembly_refinement?

[Afif Elghraoui]

Hi, Sascha,
I'm looking into packaging Circlator, which depends on the Sanger
program bio_assembly_refinement. Looking into it, I'm wondering whether
this is a tool that will just get folded into circlator eventually. Do
you think it's worth packaging it separately?

Thanks and regards
Afif

-- 
Afif Elghraoui | عفيف الغراوي
http://afif.ghraoui.name

Bug#817056: ITP: python-typing -- Type Hints for Python

[Brian May]

"Michael R. Crusoe"  writes:

>  This is a backport of the standard library typing module to Python
>  versions older than 3.5.

Not sure what the point of this is; doesn't typing hinting require PEP
3107, which isn't in Python 2.x?
-- 
Brian May 

Re: Can "PDB" license be considered free ?

[Bas Wijnen]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

On Mon, Mar 07, 2016 at 04:38:55PM -0600, Don Armstrong wrote:
> On Mon, 07 Mar 2016, Peter Rice wrote:
> > The conclusion was that scientific data (SwissProt, PDB, etc.) are
> > scientific facts and it is not reasonable to require permission to
> > change them.
> 
> This isn't true; there are loads of reasons to change sequences and
> structural models of proteins. Protein sequences are just based on
> references which have inaccuracies and do not represent ancestral
> sequences or the true variation present in real populations; in my lab
> we modify UniProt sequences and redistribute those modifications in
> publications all of the time.

Note that this text only says that if you modify things, you're required to
change the name.  In other words, they are protecting the terminology, so when
you use a certain code, everyone is always talking about the same thing.  This
is a very reasonable thing to require; without it, the database would be much
less useful.

> All of that said, because PDB and UniProt files are not works of
> authorship, they likely do not qualify for copyright protection in the
> US, so the licensing terms can largely be ignored. However, that may not
> be true of other jurisdictions.

The text that was quoted doesn't really talk about IP; it just says that it
isn't about that: as a user, you must find the license and abide by it.  This
is annoying (because it means you must find those licenses before you know if
you can use the data), but I don't blame them.

On the other hand, if you are correct (I have no idea about this data) that it
is not copyrightable, then you also don't need a license, so that solves that
problem.

The question would probably have been better asked on -legal though, so I'm
sending it there.  For those reading there without seeing the thread before, it
starts here: https://lists.debian.org/debian-devel/2016/03/msg00091.html

Thanks,
Bas
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Re: Can "PDB" license be considered free ?

[Don Armstrong]

On Mon, 07 Mar 2016, Peter Rice wrote:
> We had this discussion some years back about SwissProt protein
> sequence entries included as test data in EMBOSS. We also have PDB
> files in the EMBOSS test data.
> 
> The conclusion was that scientific data (SwissProt, PDB, etc.) are
> scientific facts and it is not reasonable to require permission to
> change them.

This isn't true; there are loads of reasons to change sequences and
structural models of proteins. Protein sequences are just based on
references which have inaccuracies and do not represent ancestral
sequences or the true variation present in real populations; in my lab
we modify UniProt sequences and redistribute those modifications in
publications all of the time.

PDB files are also just the current model of a particular
crystallization of a particular set of molecules. It's pretty standard
practice to modify them using simulations to account for different
binding partners and assemblies. [I've published the PDB files
containing these modifications, for example.]

All of that said, because PDB and UniProt files are not works of
authorship, they likely do not qualify for copyright protection in the
US, so the licensing terms can largely be ignored. However, that may not
be true of other jurisdictions.

-- 
Don Armstrong  http://www.donarmstrong.com

It is easier to build strong children than to repair broken men.
 -- Frederick Douglass

Bug#817056: ITP: python-typing -- Type Hints for Python

[Michael R. Crusoe]

That was my plan. Though I just realized that I don't need this if I switch
to building only the Python 3 version of schema-salad-tool so I am likely
to close this ITP.

The package is at git+ssh://git.debian.org/git/debian-med/python-typing.git
if anyone is interested.

On Mon, Mar 7, 2016 at 7:38 PM, Scott Kitterman 
wrote:

> On Monday, March 07, 2016 09:01:30 AM Michael R. Crusoe wrote:
> > Package: wnpp
> > Severity: wishlist
> > Owner: Debian Med team 
> >
> > * Package name: python-typing
> >   Version : 3.5.0.1
> >   Upstream Author : Guido van Rossum, Jukka Lehtosalo, Łukasz Langa
> >  * URL :
> > https://docs.python.org/3.5/library/typing.html * License :
> Python
> > 2.0
> >   Programming Lang: Python
> >   Description : Type Hints for Python
> >
> >  This is a backport of the standard library typing module to Python
> >  versions older than 3.5.
> >
> >  Typing defines a standard notation for Python function and variable
> >  type annotations. The notation can be used for documenting code in a
> >  concise, standard format, and it has been designed to also be used by
> >  static and runtime type checkers, static analyzers, IDEs and other
> >  tools.
> >
> > This is a new dependency for python-schema-salad, and will be for any
> other
> > Py2/Py3 package that contains typing hints. It will be maintained by the
> > Debian-Med team but I'm happy to hand it over to other interested
> parties.
>
> Please only package this for python(2).  We are in the process of dropping
> python3.4, so a python3 package isn't needed.
>
> Scott K
>



-- 
Michael R. Crusoe CWL Community Engineer cru...@ucdavis.edu
Common Workflow Language projectUniversity of California, Davis
https://impactstory.org/MichaelRCrusoe http://twitter.com/biocrusoe

Re: Can "PDB" license be considered free ?

[Gert Wollny]

Hi, 

> * The user assumes all responsibility for insuring that intellectual
> property claims associated with any data set deposited in the PDB
> archive are honored.  It should be understood that the PDB data files
> do not contain any information  on intellectual property claims with
> the exception in some cases of a reference for a patent involving the
> structure.

I.e. on one hand the user would have to hunt down the IP information to
see whether she can use the pdb files at all, and on the other had,
there seem to be parts that are covered by patents for which a user
would probably need to acquire an additional license.

Would this not conflict with the DFSG 7? 

"The rights attached to the program must apply to all to whom the
program is redistributed without the need for execution of an
additional license by those parties."

Best, 
Gert 

https://www.debian.org/social_contract

Re: Can "PDB" license be considered free ?

[Peter Rice]

Hi Riley,

On 07/03/2016 19:20, Riley Baird wrote:

The distribution of modified PDB data including the records HEADER, CAVEAT,
REVDAT, SPRSDE, DBREF, SEQADV, and MODRES in PDB format and their mmCIF and
XML equivalents is not allowed.


I'm not sure what the PDB format is, so I might be wrong, but my
intuition is that trying to stop people from distributing data in a
certain file format would be non-free.


We had this discussion some years back about SwissProt protein sequence 
entries included as test data in EMBOSS. We also have PDB files in the 
EMBOSS test data.


The conclusion was that scientific data (SwissProt, PDB, etc.) are 
scientific facts and it is not reasonable to require permission to 
change them.


The license says you may not alter the entries in the PDB database (text 
file) and redistribute it in any of its original formats - because PDB 
releases must only come from the curators of the database.


It may help to consider an equivalent in another field. Imagine an open 
source package that included a copy of the Declaration of Independence. 
It would not be reasonable to insist on permission to change the text, 
for example to add a phrase from Animal Farm ... "but some are more 
equal than others"


Hope that helps,

Peter Rice

Re: Can "PDB" license be considered free ?

[Riley Baird]

> The distribution of modified PDB data including the records HEADER, CAVEAT, 
> REVDAT, SPRSDE, DBREF, SEQADV, and MODRES in PDB format and their mmCIF and 
> XML equivalents is not allowed.

I'm not sure what the PDB format is, so I might be wrong, but my
intuition is that trying to stop people from distributing data in a
certain file format would be non-free.


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Bug#817056: ITP: python-typing -- Type Hints for Python

[Scott Kitterman]

On Monday, March 07, 2016 09:01:30 AM Michael R. Crusoe wrote:
> Package: wnpp
> Severity: wishlist
> Owner: Debian Med team 
> 
> * Package name: python-typing
>   Version : 3.5.0.1
>   Upstream Author : Guido van Rossum, Jukka Lehtosalo, Łukasz Langa
>  * URL :
> https://docs.python.org/3.5/library/typing.html * License : Python
> 2.0
>   Programming Lang: Python
>   Description : Type Hints for Python
> 
>  This is a backport of the standard library typing module to Python
>  versions older than 3.5.
> 
>  Typing defines a standard notation for Python function and variable
>  type annotations. The notation can be used for documenting code in a
>  concise, standard format, and it has been designed to also be used by
>  static and runtime type checkers, static analyzers, IDEs and other
>  tools.
> 
> This is a new dependency for python-schema-salad, and will be for any other
> Py2/Py3 package that contains typing hints. It will be maintained by the
> Debian-Med team but I'm happy to hand it over to other interested parties.

Please only package this for python(2).  We are in the process of dropping 
python3.4, so a python3 package isn't needed.

Scott K

Re: Can "PDB" license be considered free ?

[Ben Finney]

Alex Mestiashvili  writes:

> I am going to package a software with pdb files in the test suite and
> I wonder if the license below can be considered free.

For reference in the discussion and for later reference, it helps to
have the license text directly in a message.

>  ftp://ftp.wwpdb.org/pub/pdb/advisory.txt

At the time of this message, that URL responds with the following text:

=
   ADVISORY NOTICE FOR USE OF THE PDB ARCHIVE

By using the materials available in this archive, the user agrees to abide
by the following conditions:

* The archival data files in the PDB archive are made freely available 
to all users. Data files within the archive may be redistributed in original 
form without restriction. Redistribution of modified data files using the same 
file name as is on the FTP server is prohibited. The rules for file names are 
detailed at http://www.wwpdb.org/wwpdb_charter.html.

* Data files containing PDB content may incorporate the PDB 4-letter entry 
name (e.g. 1ABC) in standard PDB records only if they are exactly the same 
as what is residing in the PDB archive. This does not prevent databases 
from including PDB entry_id's as cross-references where it is clear that 
they refer to the PDB archive. PDB records refer to the standard PDB format. 
The distribution of modified PDB data including the records HEADER, CAVEAT, 
REVDAT, SPRSDE, DBREF, SEQADV, and MODRES in PDB format and their mmCIF and 
XML equivalents is not allowed.

* The user assumes all responsibility for insuring that intellectual property 
claims associated with any data set deposited in the PDB archive are honored. 
It should be understood that the PDB data files do not contain any information 
on intellectual property claims with the exception in some cases of a reference
for a patent involving the structure.

* Any opinion, findings, and conclusions expressed in the PDB archive by the 
authors/contributors do not necessarily reflect the views of the wwPDB.

* The data in the PDB archive are provided on an "as is" basis.  The wwPDB
nor its comprising institutions cannot be held liable to any party for direct, 
indirect, special, incidental, or consequential damages, including lost 
profits, arising from the use of PDB materials.

* Resources on this site are provided without warranty of any kind, either
expressed or implied. This includes but is not limited to merchantability or 
fitness for a particular purpose. The institutions managing this site make 
no representation that these resources will not infringe any patent or other 
proprietary right.
=

-- 
 \ “Facts do not cease to exist because they are ignored.” —Aldous |
  `\Huxley |
_o__)  |
Ben Finney

Can "PDB" license be considered free ?

[Alex Mestiashvili]

Hi All,

I am going to package a software with pdb files in the test suite and
I wonder if the license below can be considered free.

 ftp://ftp.wwpdb.org/pub/pdb/advisory.txt

 
http://www.rcsb.org/pdb/static.do?p=general_information/about_pdb/policies_references.html

Thank you,
Alex

RFS: python-typing

[Michael Crusoe]

Thanks!

git+ssh://git.debian.org/git/debian-med/python-typing.git

-- 
Michael R. Crusoe

Bug#817056: ITP: python-typing -- Type Hints for Python

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
Owner: Debian Med team 

* Package name: python-typing
  Version : 3.5.0.1
  Upstream Author : Guido van Rossum, Jukka Lehtosalo, Łukasz Langa 

* URL : https://docs.python.org/3.5/library/typing.html
* License : Python 2.0
  Programming Lang: Python
  Description : Type Hints for Python

 This is a backport of the standard library typing module to Python
 versions older than 3.5.
 
 Typing defines a standard notation for Python function and variable
 type annotations. The notation can be used for documenting code in a
 concise, standard format, and it has been designed to also be used by
 static and runtime type checkers, static analyzers, IDEs and other
 tools.

This is a new dependency for python-schema-salad, and will be for any other
Py2/Py3 package that contains typing hints. It will be maintained by the
Debian-Med team but I'm happy to hand it over to other interested parties.

Re: bamtools_2.4.0+dfsg-4_amd64.changes REJECTED

[Michael Crusoe]

Thanks!

On Mon, Mar 7, 2016 at 8:26 AM Mattia Rizzolo  wrote:

> uploaded.
>
> On Mon, Mar 7, 2016 at 6:55 AM Michael Crusoe 
> wrote:
>
>> My apologies; I've updated Git
>>
>> On Sun, Mar 6, 2016 at 10:50 AM, Afif Elghraoui 
>> wrote:
>>
>>> Hi, Michael,
>>>
>>> On السبت  5 آذار 2016 11:22, Michael R. Crusoe wrote:
>>>
 Can I get bamtools 2.4.0+dfsg-4 sponsored? I split the library
 documentation into a separate package so I can't upload on my own.


>>> I don't see the latest changes in git. Could you push what you have?
>>>
>>> Thanks and regards
>>> Afif
>>>
>>> --
>>> Afif Elghraoui | عفيف الغراوي
>>> http://afif.ghraoui.name
>>>
>>>
>>