Re: Please choose a free license for fasta3 components

[Alex Mestiashvili]

this one got bounced, one more is following :)

Alex

Please choose a free license for fasta3 components

[Alex Mestiashvili]

Hi,

I'm writing you on behalf of the Debian Med team which is a group inside
Debian with the objective to package free software with relevance in
biology and medicine for official Debian. We are about to create a
debian package from fasta3 as you can see on our so called tasks biology
page[1].

According to the Debian Free Software Guidelines[2] which are widely
accepted as Open Source definition the current license of some files
such as src/smith_waterman_sse2.c and src/glo[bc]al_sse2.[ch] is not
free since it forbids free use of the software in commercial products.

I wonder whether you might consider changing the licensing to some free
license like GPL, BSD or MPL - just anything that has no such
restriction to non-commercial use and use of modified code.  You might
like to know that several other authors of biologic software recently
switched to free licenses (may be most prominently phylib).  The
advantage for you inside Debian would be a higher visibility of fasta3
(since we distribute it with metapackages) and a way better quality
assurance since Debian is running several tools to automatically detect
problems inside the distributed software.


Kind regards and thanks for your cooperation

Alex

[1] http://blends.debian.org/med/tasks/bio#fasta3
[2] https://www.debian.org/social_contract#guidelines

Please choose a free license for fasta3 components

[Alex Mestiashvili]

Hi,

I'm writing you on behalf of the Debian Med team which is a group inside
Debian with the objective to package free software with relevance in
biology and medicine for official Debian. We are about to create a
debian package from fasta3 as you can see on our so called tasks biology
page[1].

According to the Debian Free Software Guidelines[2] which are widely
accepted as Open Source definition the current license of some files
such as src/smith_waterman_sse2.c and src/glo[bc]al_sse2.[ch] is not
free since it forbids free use of the software in commercial products.

I wonder whether you might consider changing the licensing to some free
license like GPL, BSD or MPL - just anything that has no such
restriction to non-commercial use and use of modified code.  You might
like to know that several other authors of biologic software recently
switched to free licenses (may be most prominently phylib).  The
advantage for you inside Debian would be a higher visibility of fasta3
(since we distribute it with metapackages) and a way better quality
assurance since Debian is running several tools to automatically detect
problems inside the distributed software.


Kind regards and thanks for your cooperation

Alex

[1] http://blends.debian.org/med/tasks/bio#fasta3
[2] https://www.debian.org/social_contract#guidelines

Re: Freeing fasta3 (Was: fasta3_36.3.8g-1_amd64.changes is NEW)

[Andreas Tille]

On Thu, Apr 19, 2018 at 03:16:50PM +0200, Steffen Möller wrote:
> 
> I propose to just let it continue its course into Debian.

I'm fine to leave it in new - may be it takes some time to reach
and convince the authors.

Kind regards

  Andreas.

-- 
http://fam-tille.de

Re: Freeing fasta3 (Was: fasta3_36.3.8g-1_amd64.changes is NEW)

[Steffen Möller]

On 4/19/18 3:07 PM, Alex Mestiashvili wrote:
> On 04/19/2018 02:44 PM, Steffen Möller wrote: >> >> On 4/19/18 1:43 PM, 
> Andreas Tille wrote: >>> Hi, >>> >>> On Thu,
Apr 19, 2018 at 10:19:31AM +, Debian FTP Masters wrote: 
binary:fasta3 is NEW.  binary:fasta3-doc is NEW. 
binary:fasta3-doc is NEW.  binary:fasta3 is NEW.  source:fasta3
is NEW.   Your package has been put into the NEW queue, which
requires manual action  from the ftpteam to process. The upload was
otherwise valid (it had a good  OpenPGP signature and file hashes
are valid), so please be patient. >>> nice. Did anybody checked the only
reason for making this package non-free: >>> >>> >>> Files:
src/glo[bc]al_sse2.[ch] >>> src/smith_waterman_sse2.c >>> Copyright:
2006,2010 Michael Farrar  >>> License:
Academics-only >>> This program may not be sold or incorporated into a
commercial product, >>> in whole or in part, without written consent of
Michael Farrar. For >>> further information regarding permission for use
or reproduction, please >>> contact: Michael Farrar at
farrar.mich...@gmail.com. >>> >>> >>> I think chances to get 8 year old
software freed from the restriction >>> are worth trying. It would be
nice if you could do so and record your >>> attempt here[1]. >>> >>> [1]
https://wiki.debian.org/DebianMed/SoftwareLiberation >> >> I agree,
Andreas. It should be well in the interest of the other authors >> to
have >> that "academics only" constraint removed. They may even not be
aware of it. >> >> Alex kindly helped out (and nicely improved the
packaging!) with his >> sponsoring. >> I had asked for it since it was
nagging badly on the bottom of a long >> todo list >> and do not want
open any extra mental slot for it. So, someone else please >> address
such follow-ups. >> >> Many thanks, >> >> Steffen >> >> > > Hi Steffen
and Andreas, > > Wouldn't it be better to dcut it now (if not too late),
try to resolve > the issue and re-upload ? > > Thanks, > Alex
The package can move any time from non-free to main once upstream
decides to free also the last bit of their software.

I propose to just let it continue its course into Debian.

Best,

Steffen

Re: Freeing fasta3 (Was: fasta3_36.3.8g-1_amd64.changes is NEW)

[Alex Mestiashvili]

On 04/19/2018 02:44 PM, Steffen Möller wrote:
> 
> On 4/19/18 1:43 PM, Andreas Tille wrote:
>> Hi,
>>
>> On Thu, Apr 19, 2018 at 10:19:31AM +, Debian FTP Masters wrote:
>>> binary:fasta3 is NEW.
>>> binary:fasta3-doc is NEW.
>>> binary:fasta3-doc is NEW.
>>> binary:fasta3 is NEW.
>>> source:fasta3 is NEW.
>>>
>>> Your package has been put into the NEW queue, which requires manual action
>>> from the ftpteam to process. The upload was otherwise valid (it had a good
>>> OpenPGP signature and file hashes are valid), so please be patient.
>> nice.  Did anybody checked the only reason for making this package non-free:
>>
>>
>> Files: src/glo[bc]al_sse2.[ch]
>>src/smith_waterman_sse2.c
>> Copyright: 2006,2010 Michael Farrar 
>> License: Academics-only
>>  This program may not be sold or incorporated into a commercial product,
>>  in whole or in part, without written consent of Michael Farrar.  For
>>  further information regarding permission for use or reproduction, please
>>  contact: Michael Farrar at farrar.mich...@gmail.com.
>>
>>
>> I think chances to get 8 year old software freed from the restriction
>> are worth trying.  It would be nice if you could do so and record your
>> attempt here[1].
>>
>> [1] https://wiki.debian.org/DebianMed/SoftwareLiberation
> 
> I agree, Andreas. It should be well in the interest of the other authors
> to have
> that "academics only" constraint removed. They may even not be aware of it.
> 
> Alex kindly helped out (and nicely improved the packaging!) with his
> sponsoring.
> I had asked for it since it was nagging badly on the bottom of a long
> todo list
> and do not want open any extra mental slot for it. So, someone else please
> address such follow-ups.
> 
> Many thanks,
> 
> Steffen
> 
> 

Hi Steffen and Andreas,

Wouldn't it be better to dcut it now (if not too late), try to resolve
the issue and re-upload ?

Thanks,
Alex





signature.asc
Description: OpenPGP digital signature

Re: Freeing fasta3 (Was: fasta3_36.3.8g-1_amd64.changes is NEW)

[Steffen Möller]

On 4/19/18 1:43 PM, Andreas Tille wrote:
> Hi,
>
> On Thu, Apr 19, 2018 at 10:19:31AM +, Debian FTP Masters wrote:
>> binary:fasta3 is NEW.
>> binary:fasta3-doc is NEW.
>> binary:fasta3-doc is NEW.
>> binary:fasta3 is NEW.
>> source:fasta3 is NEW.
>>
>> Your package has been put into the NEW queue, which requires manual action
>> from the ftpteam to process. The upload was otherwise valid (it had a good
>> OpenPGP signature and file hashes are valid), so please be patient.
> nice.  Did anybody checked the only reason for making this package non-free:
>
>
> Files: src/glo[bc]al_sse2.[ch]
>src/smith_waterman_sse2.c
> Copyright: 2006,2010 Michael Farrar 
> License: Academics-only
>  This program may not be sold or incorporated into a commercial product,
>  in whole or in part, without written consent of Michael Farrar.  For
>  further information regarding permission for use or reproduction, please
>  contact: Michael Farrar at farrar.mich...@gmail.com.
>
>
> I think chances to get 8 year old software freed from the restriction
> are worth trying.  It would be nice if you could do so and record your
> attempt here[1].
>
> [1] https://wiki.debian.org/DebianMed/SoftwareLiberation

I agree, Andreas. It should be well in the interest of the other authors
to have
that "academics only" constraint removed. They may even not be aware of it.

Alex kindly helped out (and nicely improved the packaging!) with his
sponsoring.
I had asked for it since it was nagging badly on the bottom of a long
todo list
and do not want open any extra mental slot for it. So, someone else please
address such follow-ups.

Many thanks,

Steffen

Re: TR: Debian has RRID SCR_006638

[Andreas Tille]

Hi Fabien,

thanks a lot for asking.

On Thu, Apr 19, 2018 at 08:24:21AM +, Fabien Pichon wrote:
> 
> I sent the mail below to the mailing list, but did not receive answer, so I 
> do not know if it has been received ?

It seems not - the mailing list archive in March does not show your
mail[1]. :-(  I have no idea why since you do not even need to
subscribe to send mails to the list.  I'm answering in public to
get your text and my answer recorded in the archive.
 
> 
> De : Fabien Pichon
> Envoyé : mercredi 28 mars 2018 15:36
> À : debian-med@lists.debian.org
> Objet : RE: Debian has RRID SCR_006638
> 
> 
> Hi Everybody,
> 
> To answer Andreas, we, at OMICtools, could publish every month, the list of 
> new packages available in Debian Med on our blog :
> https://omictools.com/blog, if you feel it can helps.

That would be really an interesting feature.  Thanks a lot for this
offer!
 
> We just need a list of these tools and the corresponding OMICS_[0-9]{5} RRID, 
> if present.

I think about some method to automatically create such a list.  Steffen,
would you volunteer to assemble it manually for the moment?
 
> By the way, as discussed during the Sprint, in Barcelona, we are working on a 
> button "ask for Debian package" on the new tool page design (see mock-up 
> attached).

I think this would be a really great feature which would be very helpful
for our users.  I've deleted the design screenshot since this is my only
explanation why your mail might have been rejected.  May be you can put
it to some place and add a link here - or just implement it and we'll
check. :-)

Thanks a lot for your cooperation

  Andreas.


[1] https://lists.debian.org/debian-med/2018/03/threads.html
-- 
http://fam-tille.de

Freeing fasta3 (Was: fasta3_36.3.8g-1_amd64.changes is NEW)

[Andreas Tille]

Hi,

On Thu, Apr 19, 2018 at 10:19:31AM +, Debian FTP Masters wrote:
> binary:fasta3 is NEW.
> binary:fasta3-doc is NEW.
> binary:fasta3-doc is NEW.
> binary:fasta3 is NEW.
> source:fasta3 is NEW.
> 
> Your package has been put into the NEW queue, which requires manual action
> from the ftpteam to process. The upload was otherwise valid (it had a good
> OpenPGP signature and file hashes are valid), so please be patient.

nice.  Did anybody checked the only reason for making this package non-free:


Files: src/glo[bc]al_sse2.[ch]
   src/smith_waterman_sse2.c
Copyright: 2006,2010 Michael Farrar 
License: Academics-only
 This program may not be sold or incorporated into a commercial product,
 in whole or in part, without written consent of Michael Farrar.  For
 further information regarding permission for use or reproduction, please
 contact: Michael Farrar at farrar.mich...@gmail.com.


I think chances to get 8 year old software freed from the restriction
are worth trying.  It would be nice if you could do so and record your
attempt here[1].

Thanks for your work on the package anyway

Andreas.


[1] https://wiki.debian.org/DebianMed/SoftwareLiberation

-- 
http://fam-tille.de

How to deal with static web pages (Was: Please review med task's home page rewording)

[Andreas Tille]

Hi Steffen,

On Thu, Apr 19, 2018 at 12:01:52PM +0200, Steffen Möller wrote:
> Andreas had kindly accepted my membership request for the Blends team
> and I immediately messed up. Instead of a creating a pull request I had
> pushed to master directly. Could you please have a look at
> https://salsa.debian.org/blends-team/website/blob/master/www-src/med/index.html
> ?
> 
> What I wanted changed was "information" written twice and I missed the
> direction to salsa to request for additional eye balls.

thanks for commit[1] and the ping on the robots issue.

What exaxtly makes you assume that things are messed up by your commit?

Well it did not became effective but that's not yet messing things up.

I try to remember how to update static pages...

Two years ago Iain R. Learmonth invented a system to automatically
generate static pages for all Blends by using jekyll[2].  I tried this
and learned that this will mess up several pages from Debian Astro.  So
I reverted the change done by jekyll with the exception of the change in
www/med/index.html  which was probably your intention.  I guess now we
just need to wait for the according cron jobs until your change becomes
effective.  I realised you did another change[4].  While this is now in
the "productive" file there is a slight chance that if we decide for the
jekyll method this will overriden at some point in time.

The general question is:  Do we want to stick to the jekyll method?  If
yes - and I think that's some interesting option - Debian Astro should
make sure that their pages will be created using this option.  If no
(which is fine for me as well) we should rather remove the according
doc to prevent that somebody will fire up jekyll and mess up things.

Kind regards

 Andreas.

[1] 
https://salsa.debian.org/blends-team/website/commit/5fbccd6563fc90eca216cd0dc70d0c1ef11dd86e
[2] https://salsa.debian.org/blends-team/website/blob/master/README-www.txt
[3] 
https://salsa.debian.org/blends-team/website/commit/b3c362108374be698017b9d4a6de3baad826e759
[4] 
https://salsa.debian.org/blends-team/website/commit/47b5352a3c621aa9a9abb399e4d5578bbbe819a3

-- 
http://fam-tille.de

Enabling robots to index tasks pages (Was: Enhancing websearching for tasks pages)

[Andreas Tille]

Hi,

On Thu, Apr 19, 2018 at 12:10:17PM +0200, Steffen Möller wrote:
> Can I remove
> 
> https://salsa.debian.org/blends-team/website/blob/master/www/med/index.html#L6
> 
> ""
> 
> ?

I've commited it for all Blends[1]
 
> I mean  - we want that page to be found, right?

I think this pretty much explains my observation I mentioned here[2].

Hope all other Blends agree.  Or is there any reason why robots should
not index our pages?

Kind regards

  Andreas.

[1] 
https://salsa.debian.org/blends-team/website/commit/170f5604bbe6a38dd91de7b730f544be802fefac
 
[2] https://lists.debian.org/debian-med/2018/04/msg00049.html

-- 
http://fam-tille.de

Re: Enhancing websearching for tasks pages (Was: Fixed all upstream metadata in Debian Med (Was: RRID update on salsa on packages starting with A+B)

[Steffen Möller]

Hello again,

On 4/13/18 5:51 PM, Steffen Möller wrote:
>
> On 4/13/18 5:24 PM, Andreas Tille wrote:
>> On Fri, Apr 13, 2018 at 03:50:09PM +0200, Steffen Möller wrote:
> Instead of SciCrunch it
> could be RRID:SCR_...
>
 may be interesting to set:

 RRID:SCR_..

 cite is a metadata HTML standard that may be supported/analysed by
 google and co
 (https://developer.mozilla.org/fr/docs/Web/HTML/Element/cite)
>>> This is a neat idea, indeed. I am tempted to also add a "" block to
>>> reference where the package description is coming from. I propose
>>> this to be
>>> the tracker's package representation.
>> I'm again not sure that I understand that hint.  Where would you add
>> that
>> block and exactly (please provide an example).
>
> From
>
>  class="deb-official_high"> id="abacas">Abacas  class="pkgdesc">Algorithm Based Automatic Contiguation of
> Assembled Sequences...  href="https://packages.debian.org/search?keywords=abacassearchon=namesexact=1suite=allsection=all;>Official
> Debian package... Registry entries:
>  class="registry_omictools"> href="https://duckduckgo.com/?q=\site%3Aomictools.com+OMICS_06933;>OMICtools class="registry">.. I suggest to go
> to something like the following. The Registry IDs look right next to
> the package name as a comma-separated list, I think, since they
> somewhat co-identify the package.  cite="https://tracker.debian.org/pkg/abacas;>
>  class="deb-official_high"> id="abacas"> ( href="https://duckduckgo.com/?q=\site%3Aomictools.com+OMICS_06933;>OMICS_06933)
> Abacas Algorithm
> Based Automatic Contiguation of Assembled Sequences...
> https://tracker.debian.org/pkg/abacas;>Official
> Debian package... registry bits moved to title
> section..  The enclosing q block I kind of like to be interpreted
> as "this is our stuff you also find on the package's page".
>
>>
>> While I can do this easily on the tasks pages I'm not very optimistic
>> that
>> this wil have any influence on Google ranking.
>
> Having a page description in the HTML  will help. Otherwise
> google has nothing to show in their search results.

Can I remove

https://salsa.debian.org/blends-team/website/blob/master/www/med/index.html#L6

""

?

I mean  - we want that page to be found, right?

Steffen

Please review med task's home page rewording

[Steffen Möller]

Dear all,

Andreas had kindly accepted my membership request for the Blends team
and I immediately messed up. Instead of a creating a pull request I had
pushed to master directly. Could you please have a look at
https://salsa.debian.org/blends-team/website/blob/master/www-src/med/index.html
?

What I wanted changed was "information" written twice and I missed the
direction to salsa to request for additional eye balls.

Cheers,

Steffen