taskSavannah Administration - Tasks: task #10626, Submission of ESPResSo

 
 

task #10626: Submission of ESPResSo

Submitter:  Olaf Lenz <olenz>
Submitted:  Wed 22 Sep 2010 01:16:38 PM UTC
   
 
Should Start On:  Wed 22 Sep 2010 12:00:00 AM UTC Should be Finished on:  Sat 02 Oct 2010 12:00:00 AM UTC
Category:  Project Approval Priority:  * 5 - Normal
Status:  Done Privacy:  Public
Assigned to:  alexfernandez Open/Closed:  Closed
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Sat 13 Nov 2010 05:31:32 PM UTC, comment #24: 

Archives imported, closing.  (I wrote Olaf separately too.)

Karl Berry <karl>
Site Administrator
Wed 10 Nov 2010 11:00:27 PM UTC, comment #23: 

It is possible.  If you send me (off-list) the flat-file mbox archives for your lists (or url's to them), I can import them easily enough.

Of course it would be best to import them before the new lists are used at all.

best,
-email is unavailable-

Karl Berry <karl>
Site Administrator
Wed 10 Nov 2010 10:10:14 AM UTC, comment #22: 

Hi again,

we have archives of our old mailing lists. Is it possible to upload these archives to the new mailing list archives?

Cheers
  Olaf

Olaf Lenz <olenz>
Tue 09 Nov 2010 12:21:56 PM UTC, comment #21: 

Hi Alex,

Excellent! Now everything works as intended.

Olaf

Olaf Lenz <olenz>
Tue 09 Nov 2010 11:55:29 AM UTC, comment #20: 

Hi Olaf,

Done, your espressomd.git was moved out of the way. Could you try again? Thanks!

Alex.

Alex Fernandez <alexfernandez>
Sun 07 Nov 2010 08:43:02 AM UTC, comment #19: 

Hi Karl, Alex,

  • I will care for underscore.sty, probably by asking Don Arsenau to relicense it under GPL, if possible. Thanks for the idea. Somehow, one always tends to think of technical solutions first...


  • I will not make a release before all of the issues are resolved. In fact, we have some more issues on our mind that we want to do before doing the next release.


  • The first thing I tried was to upload our git repo. Unfortunately, I used a messed-up version of the repo. I tried to clean up what I did by removing the repo and reuploading it, but that seems to be impossible due to restrictions (namely that I cannot delete the current branch of the repo). Therefore, I suppose that I need the help of a Savannah Admin. Could you please remove the botched espressomd.git? I have already deactivated git support, so that there is no danger of a user accidentally downloading the damaged repo, so there should be no problem...


Best regards
  Olaf

Olaf Lenz <olenz>
Wed 03 Nov 2010 10:46:43 PM UTC, comment #18: 

Hi Karl,

OK, I did not understand correctly the implications of including underscore.sty. Thanks for the correction!

Alex Fernandez <alexfernandez>
Wed 03 Nov 2010 10:30:55 PM UTC, comment #17: 

Alex -- the problem with underscore.sty occurs because it is loaded by TeX at the same time as their original documentation, which I assume is under GPL or GFDL.  Technically speaking, this is an incompatibility according to our interpretation of the GPL/GFDL.  For instance, there is an exception at the top of texinfo.tex to address the same basic issue.

Other interpretations weaken the GPL/GFDL, hence the desire not to go that way.

Karl Berry <karl>
Site Administrator
Wed 03 Nov 2010 10:27:50 PM UTC, comment #16: 

Hi Olaf,

Thanks for your careful attention to these things.

Regarding history: as long as nothing you will put on savannah is actually proprietary or nonfree, I don't see a problem with including the historical files without notices, etc.  After all, "copyright bugs" happen all the time, even with long-standing projects.

underscore.sty is more problematic. Whether you modify it or not doesn't matter.  One approach would be to ask Don Arseneau to allow use under the GPL/FDL as well as the LPPL. 

Strictly speaking, the alternative is to (1) add an additional permission to your doc license that says "Permission is also granted to use packages covered by the LPPL" (we could work on the exact wording), and (2) not include underscore.sty in your dev repo on savannah.  Most TeX users will have it already, and those who don't could download it from CTAN, or your web page if you provide it there, or wherever.

Sorry for the extra trouble caused by the incompatibility of these two free software licenses, but the goal for savannah is that everything should be GPL/GFDL-compatible.

If I'm missing some other solution, I'm sure someone else will chime in.

Best,
Karl

Karl Berry <karl>
Site Administrator
Wed 03 Nov 2010 10:22:56 PM UTC, comment #15: 

If underscore.sty is used by the project but not integrated with it (i.e. not linked or compiled into), then I would say it is just joint distribution -- valid under the GPL. It doesn't matter whether you modify the file or not.

It is also fine to upload the whole repository history for the source code -- after all you are not distributing a binary, so most of the GPL requirements do not apply. Distributing source code as long as you have the right to do it is OK. Just be sure to correct everything before you do the first release from within Savannah, and notify us afterwards so we can close this task.

Alex Fernandez <alexfernandez>
Wed 03 Nov 2010 01:39:45 PM UTC, comment #14: 

I just found out that there seems to be a more recent version of underscore.sty available at CTAN:
  http://ftp.gwdg.de/pub/ctan/macros/latex/contrib/underscore/

This one seems to be published under the LPPL. LPPL is not compatible with GPL, but it is still free software. As far as I understand, as long as I do not modify the file, I can simply keep it within our package, right?

Olaf Lenz <olenz>
Wed 03 Nov 2010 01:23:47 PM UTC, comment #13: 

Thank you very much for approving the project!

  • I will care about the README file, i.e. the license as well as the listing of all binary files in one README.


  • We are using underscore.sty for our documentation. All it does is to make "_" a regular character within TeX so that we do not have to use "\_" all the time. I hope that I can find a replacement, as it makes writing the docs much simpler.


  • So far I planned to simply put our whole repository including the development history onto Savannah. Now I notice that in this way I will indirectly put up material that might not be all GNNU-compliant, for example as the licenses are not correct yet, etc. Is this a problem? Or does the repository have to start with the exact code from the tarball?
Olaf Lenz <olenz>
Mon 01 Nov 2010 09:49:17 PM UTC, comment #12: 

Hi again,

Everything seems fine.

  • I believe we can live with a README file per directory, although it would be best if all binary files were listed.
  • However, the license for underscore.sty is undoubtedly not compatible with the GPL. It remains to see if you are "linking" it or it is just mere aggregation. I will ask: how are you using this file, but I will leave it to others on the list to answer.
  • Also, the README file does not contain the GPL header.


I am approving the submission so we can move along, but I am leaving this task open so you can work on these issues and you can notify us when you are ready. Welcome, and have fun!



I've approved your project--welcome on board! :-)

You'll receive a mail notification with further instructions shortly.

--
Happy hacking!

Alex Fernandez <alexfernandez>
Fri 29 Oct 2010 04:18:42 PM UTC, comment #11: 

Finally we can continue. I believe I have managed to make ESPResSo GNU-compliant.

You can find a new tarball here:

  http://www.icp.uni-stuttgart.de/~icp/espresso-2.9.0.tar.gz

What have I done:

  • I have changed the license to pure GPLv3. Even though this was not formally necessary, I have asked for the contributors for consent, and all that could be reached agreed.


  • I have added the corresponding license notice into all files.


  • I have added the files AUTHORS, NEWS etc. as recommended by the GNU Autotools.


  • I have added README files to all directories that contain binary files.


Two questions remain open:

  • In the subdir doc/ug/figures I have added a README file that states: "All files within this directory are copyrighted and licensed as indicated below:"

...and then the classical header. Is this OK, or do I have to state all files explicitly?

  • I noticed that doc/ug/underscore.sty contains the copyright notice

  % Copyright 1998,2001 Donald Arseneau;  Distribute freely if unchanged.
  % Instructions follow after the definitions.

  Is this compatible with the GPL, or do we have to look for an alternative? My TeX competence is not enough to rewrite that stuff...

Cheers from Germany!

Olaf Lenz <olenz>
Thu 14 Oct 2010 07:51:50 PM UTC, comment #10: 

Ah, OK, I thought you wanted to resubmit the project (not just the tarball). There is no real problem on our side to keep it open. I will just mark it as "postponed" so we don't have to feed it :D

Alex Fernandez <alexfernandez>
Thu 14 Oct 2010 07:26:53 AM UTC, comment #9: 

I thought this task would stay open until I'm finished. But it it's easier for you, close the task.

If I resubmit, does that mean I simply add a new comment to the closed task, or should I really use "Register New Project" again?

Olaf Lenz <olenz>
Wed 13 Oct 2010 07:58:50 PM UTC, comment #8: 

So, do you want us to close this task? You can resubmit whenever you are ready to.

Alex Fernandez <alexfernandez>
Wed 13 Oct 2010 06:58:11 AM UTC, comment #7: 

Hi Karl, Alex,

Thanks for the replies! Indeed, they help a great deal.

Clause 4 in the ESPResSo license ("ESPResSo is intended only to be used for academic research ensuring proper knowledge about simulation techniques. It is not suited for commercial or industrial purposes.") is definitely meant as a recommendation only. In fact, ESPResSo is already used by some people in industry, so I think removing this clause would do no harm.

I will try to get an agreement by all contributors that we can reach, just to be sure, and also of the MPI. It will be impossible to get it from all contributors, however, in particular of the one who died (but he will most probably not sue as, anyway).

So I think I see now more clearly on how to proceed. Thank you very much, and we will resubmit soon.

Best regards
  Olaf

Olaf Lenz <olenz>
Tue 12 Oct 2010 09:26:19 PM UTC, comment #6: 

Karl has already given his expert opinion, which by the way is authoritative. Let me offer my amateur reading of the situation, based on official GNU documents; maybe it can help with the practical aspects.

According to the GPLv2:
_You should also get your employer (if you work as a programmer) or your school, if any, to sign a "copyright disclaimer" for the program, if necessary. Here is a sample; alter the names: Yoyodyne, Inc., hereby disclaims all copyright interest in the program `Gnomovision' (which makes passes at compilers) written
by James Hacker._

In this case the MPI holds the copyright and publishes the software under the GPL (plus restrictions), up to now. If you want to change the copyright holder you should get the MPI to sign the disclaimer, and then change the notices to "The ESPResSo team".

Now for the license change. The usual way of handling license changes is to contact all developers if possible, and let the rest complain if they do not agree; their contributions can be rewritten in this case. But here I don't think it's even necessary, as the spirit of the LICENSE.TXT is quite clear. Let us analyze it point by point.

1. The GNU GENERAL PUBLIC LICENSE (GPL) applies with the following additions.
All contributors have already agreed to the GPL, so the only problem is in removing the additions.

2. Use of ESPResSo is properly acknowledged in publications and communications. At present ESPResSo is cited as: ESPResSo, http://www.espresso.mpg.de
This is a standard attribution clause, but referring to use of the program (not distribution or modification). The GPL explicitly says: Activities other than copying, distribution and modification are not covered by this License; they are outside its scope. The act of running the Program is not restricted [...]. It is not even clear that a copyright license can limit usage of the software: once the software has been copied to the target machine the license does not bind the users anymore. So I would say this clause is useless except as a "gentleman's agreement", which can be stated in the README.

3. Users are encouraged to send feedback about bugs, code extensions, script additions and third party usage to: espresso@mpip-mainz.mpg.de
This is just some information which can also be added to the README.

4. ESPResSo is intended only to be used for academic research ensuring  proper knowledge about simulation techniques. It is not suited for commercial or industrial purposes.
As Karl said, if this is meant as a warning then it can be added to the README. Otherwise, if you want to impose additional restrictions then all recipients will be bound by it and by the GPL, which states: You may not impose any further restrictions on the recipients' exercise of the rights granted herein. So further redistribution would be impossible, which is directly against the GPL. We may thus safely infer that only the warning is desired.

5. ESPResSo is delivered without any warranty, expressed or implied. The authors are not liable for any loss or damage arising from the use of ESPResSo.
Disclaimer of warranty, already in the GPL.

6. Severability Clause: The provisions, sections, subdivisions and articles of this license shall be considered to be severable, so that if any section, paragraph, sentence, clause, phrase or any part of this license is declared to be unconstitutional or void, or if for any reason is declared to be invalid or of no effect, or its application to any person or circumstance is altered amended, abrogated, repealed, superseded by state law or held invalid, the remaining sections, paragraphs, sentences, clauses, phrases or parts thereof shall be in no manner affected thereby but shall remain in full force and effect.
If everything that remains of the license is the GPL then there is no problem with this clause.

I would say: remove LICENSE.TXT and relicense under the GPL, and add everything else to the README file (but outside the license itself, i.e. not mandatory).

Alex Fernandez <alexfernandez>
Tue 12 Oct 2010 08:52:33 PM UTC, comment #5: 

Hi Olaf,

Well, I'd probably be the one to answer if you wrote mentors@gnu.org, so let me write here.

First, what was the original intent of the authors with that clause "4. ESPResSo is intended only to be used for academic research"?  Was the idea simply to warn potential users that the program was not aimed at an industrial process?  Or is that you actively wished to disallow someone in industry from using it in their work?  The former is ok, essentially just a request, not part of the license.  The latter is an additional legal restriction, not ok.

As for relicensing under pure GPL (definitely a good outcome), permission of all the copyright holders is what is needed.  If all the contributors were working for MPI and MPI really does hold the copyright, then only MPI has to agree.

Independent of that, getting some sort of paper from an official at MPI that they agree with the program being licensed under the GPL would be a good thing.  (Not that we need to see it -- it's just for your own and the software's protection.)

If MPI keeps the copyright, there's no need to add individual contributor names.  It's also ok to use stuff like "Copyright 2010 The Espresso Project".

You shouldn't put the FSF or FSFE as the copyright holder, since you haven't transferred the copyright to them (and they couldn't accept it in the present state, anyway).

Hope this helps a little.  Let us know ...

Thanks,
Karl




Karl Berry <karl>
Site Administrator
Tue 12 Oct 2010 07:27:31 PM UTC, comment #4: 

Hi Alex,

In no way I wanted to suggest that you have been too slow or anything with my comment, it was more that I had hoped that all contributors to ESPResSo (including me) had worked such that submitting it to Savannah would work "out of the box". Well, we didn't.

To be able to go on with adapting ESPResSo to meet Savannah's requirements, I would like to ask a few things. The problem is that we are scientists, and all that legal stuff is pretty alien to us. We are willing to do it right, but we might need some help. I have tried to find answers to my questions at different places (e.g. http://www.gnu.org/licenses/gpl-faq.html), but I got lost in the legal jungle and didn't find what I was looking for.

We still know all contributors, and we can reconstruct who has done what on each file, as we have been using a VCS from the very start. However, not all of the contributors can be easily contacted. One of them has actually died, others are also pretty much out of our scope.

We (i.e. the ESPResSo core team) now think that it would be nice to change the license of ESPResSo to pure GPL instead of the modified version from LICENSE.TXT. Is there a way to do this legally?
I gather that it would be no problem if all contributors agree, and I'm pretty sure that none of the contributors would disagree. However, we will not be able to ask all of them. Is this a problem?

So far, the various files do not have copyright notices that specify individual copyright owners. Instead, the copyright owner for that time seem to be the "Max-Planck-Institute for Polymer Research, Theory Group". Of course we have to retain this copyright notice in the future.
As far as I understand, as the program was developed under the GPL (or the slightly modified version) right from the start, this can not cause any problem, even if the MPI would start to claim its copyright at some stage, right? Or would it be better to get an explicit copyright disclaimer from the institute? The institute fully agrees, so it shouldn't be a problem.

Finally I wonder what is the best thing to put into the copyright header in the future. Does it really make sense that everybody who makes any modification to any of the files adds himself to the copyright claim in the top? Or can we put in the FSF or FSFE as copyright holder and like that transfer the copyright? Or should we use something like "The ESPResSo team"?

I hope that you can help to make these things clearer to me, or maybe pass my questions on. Or should I directly pose these questions to mentors@gnu.org?

Best regards
  Olaf

Olaf Lenz <olenz>
Tue 12 Oct 2010 08:20:41 AM UTC, comment #3: 

Hi Olaf,

Please reply always using the task tracker. This way discussions are always public and easy to follow by everyone.

On Tue, Oct 12, 2010 at 8:31 AM, Olaf Lenz <olenz@icp.uni-stuttgart.de> wrote:

> I'm very sorry that I didn't reply earlier. We are currently holding a
> one-week tutorial workshop about the software, and I'm the main
> organizer. Therefore I was pretty busy.


I hope it was a success!

> In the workshop, we are already telling people that we will soon move to
> Savannah, so we definitely still want to host the project there. In
> fact, I did try to submit the project two weeks before the workshop
> because I hoped (probably naively) that it could be already finished at
> the workshop.


Keep in mind that we are volunteers here at Savannah, so we get to tasks when we find the time. It helps if you follow the hosting requirements and the check list to the letter: we get the job done faster.

> So, we still want to host ESPResSo at Savannah, but I will find to care
> for the modifications only next week.
> I hope that this is not a problem.


Not a problem, but please do a thorough audit of your project with the check list in mind before resubmitting the tarball.

Thanks, Alex.

Alex Fernandez <alexfernandez>
Mon 11 Oct 2010 04:46:48 PM UTC, comment #2: 

Hi,

I am waiting for an answer from you.

If within two weeks I still do not get a reply, I will remove
your project.  You will still be able to register it again once
you have the time to deal with the registration issues.

Are you still willing to host your project at Savannah? If not,
please tell us--we don't bite, and it will make us gain time.

--
Regards.

Alex Fernandez <alexfernandez>
Sat 02 Oct 2010 10:28:51 AM UTC, comment #1: 

Hi Olaf,

I am reviewing your submission on behalf of Savannah. There are a few issues with the project:

  • ESPResSo is supposed to be licensed under the GPLv2, but the file LICENSE.TXT says:

  4. ESPResSo is intended only to be used for academic research ensuring proper knowledge about simulation techniques. It is not suited for commercial or industrial purposes.
  However, the GPL states in section 10:
  You may not impose any further restrictions on the exercise of the rights granted or affirmed under this License.
  Both are not incompatible as long as your point 4 is intended as a recommendation only, not as a restriction on use. It would be good to clear this point or even make it explicit.

  • A related issue: the GPL should be applied following these guidelines, not with your own license header. Your additional restrictions can live in the file LICENSE.TXT, but the GPL header should be on every file.
  • Text files (such as the README or doc/dg/pages/build.doc) should also have the license header somewhere in their body (we recommend at the bottom).
  • There is a ton of binary data that goes with the project, such as in the testsuite/ directory. Also, there are many binary files such as images in doc/dg/figs/. They should be listed in the README with author and license information.
  • Also a recommendation: source code should probably be in a folder called src/ so that it does not obscure the contents of the top level directory (and this would make our job as reviewers easier!). This is not of course mandatory.


Can you provide an updated tarball which solves these issues? Thanks!

Alex Fernandez <alexfernandez>
Wed 22 Sep 2010 01:16:38 PM UTC, original submission:  

A new project has been registered at Savannah
This project account will remain inactive until a site admin approves or discards the registration.


Registration Administration


While this item will be useful to track the registration process, approving or discarding the registration must be done using the specific Group Administration page, accessible only to site administrators, effectively logged as site administrators (superuser):



Registration Details


  • Name: ESPResSo
  • System Name:  espressomd
  • Type: non-GNU software & documentation
  • License: GNU General Public License v2 or later





Description:

ESPResSo ("Extensible Simulation Package for the Research on Soft Matter Systems") is a scientific simulation software for Molecular Dynamics simulations of coarse-grained systems as used for soft matter research.

The software consists of a parallelized simulation core that is implemented in C (using MPI for parallelization). The simulations are controlled via scripts in the Tcl scripting language.

The software runs on Desktop machines as well as on commodity clusters and high performance supercomputers (e.g. IBM BlueGene).


Other Software Required:

Tcl
License: Tcl/Tk license (http://www.tcl.tk/software/tcltk/license.html)
Homepage: http://www.tcl.tk/

optional dependencies:
FFTW
License: GPL
Homepage: http://www.fftw.org/

an MPI implementation, e.g. OpenMPI
License: New BSD license (http://www.open-mpi.org/community/license.php)
Homepage: http://www.open-mpi.org/



Other Comments:

The software is already being used since about 10 years in at least 25 research groups all over the world. So far, the source code was self-hosted on a machine of the Max-Planck-society in Mainz. Unfortunately, this machine does not provide the various features of a source code hosting platform (e.g. a modern VCS, mailing lists, bugtracker, ...)

Meanwhile we were able to convince the maintainer of the package to move the package to a hosting platform. We would prefer to host the code on this platform, as it provides the greatest possible freedom.



Tarball URL:

http://espressowiki.mpip-mainz.mpg.de/wiki/uploads/f/f3/Espresso-2.2.0b.tar.gz


Olaf Lenz <olenz>

 

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    2010-11-01 alexfernandez StatusPostponed Done
    2010-10-14 alexfernandez StatusIn Progress Postponed
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