[Savannah-register-public] [task #14528] Submission of relax

URL: Summary: Submission of relax Project: Savannah Administration Submitted by: bugman Submitted on: Mon 29 May 2017 07:28:33 PM AEST Should Start On: Mon 29 May 2017 12:00:00 AM AEST

[Savannah-register-public] [task #14528] Submission of relax

Follow-up Comment #2, task #14528 (project administration): We are in the process of looking at a svn to git migration, or uploading the last good backup of the svn backend before the unfortunate Gna! shutdown. We will probably post an archive of the SVN repository to https://sourceforge.net/proj

[Savannah-register-public] [task #14528] Submission of relax

Follow-up Comment #4, task #14528 (project administration): No problem. I'm in the process of trying to convert the old svn repository to git, preserving history, and if successful I'll make the changes in the new git repository (which will hopefully be hosted here).

[Savannah-register-public] [task #14528] Submission of relax

Follow-up Comment #6, task #14528 (project administration): After a lot of work - the svn to git migration while preserving all branch and non-standard trunk history , as well as the process of adding valid lice

[Savannah-register-public] [task #14528] Submission of relax

Follow-up Comment #8, task #14528 (project administration): > Thank you, great work! > > Unfortunately, some issues still need resolving. > > Licensing of some files in extern/ is not very clear, > for example, extern/sobol/sobol_lib.py has no copyright notices, > and it could have more unambigu

[Savannah-register-public] [task #14528] Submission of relax

Follow-up Comment #10, task #14528 (project administration): >> ... a numdifftools README added. > This is not sufficient, all files should have notices (and the license isn't clear itself: what is ?) README files have now been placed in all directories listing the copyrights. Note this is a di

[Savannah-register-public] [task #14528] Submission of relax

Follow-up Comment #11, task #14528 (project administration): Note the latest relax code is mirrored - for backup purposes - in three different locations: https://sourceforge.net/p/nmr-relax/code/ci/master/tree/ https://github.com/nmr-relax/relax https://gitlab.com/nmr-relax/relax The main branch

[Savannah-register-public] [task #14528] Submission of relax

Follow-up Comment #13, task #14528 (project administration): I have submitted an issue for numdifftools for licence clarity: https://github.com/pbrod/numdifftools/issues/34 And for downloads, another automatically created archive is: https://github.com/nmr-relax/relax/archive/master.zip This i

[Savannah-register-public] [task #14528] Submission of relax

Follow-up Comment #14, task #14528 (project administration): As numdifftools is now quite easy to install on Python using pip, I have simply removed the extern/numdifftools package from relax: https://sourceforge.net/p/nmr-relax/code/ci/174fd5a42b54c08202eb8306be828f9125f86a95/ This was only bun

[Savannah-register-public] [task #14528] Submission of relax

Follow-up Comment #16, task #14528 (project administration): I have added the LGPLv3 licence text to the extern/sobol package: https://sourceforge.net/p/nmr-relax/code/ci/master/tree/extern/sobol/COPYING.LESSER For the copyrights in the README, I s

[Savannah-register-public] [task #14528] Submission of relax

Follow-up Comment #18, task #14528 (project administration): >> The files already contain notices, but these are actually placed as comments >> after every single function, e.g.: >> https://sourceforge.net/p/nmr-relax/code/ci/master/tree/extern/sobol/sobol_lib.py > > > There are no copyright noti

[Savannah-register-public] [task #14528] Submission of relax

Follow-up Comment #19, task #14528 (project administration): Hi, I was wondering if you had had a chance to look at the manually reconstructed copyright notices in the extern/sobol Python package? This reconstruction by code comparison was a relatively easy task. Cheers! ___

[Savannah-register-public] [task #14528] Submission of relax

Follow-up Comment #22, task #14528 (project administration): Sorry, I've been quite busy lately with RL and haven't had a chance to respond. But the relax users are still waiting for me to set up mailing lists, bug trackers, and the rest of the infrastructure. I have checked all files and, to me

[Savannah-register-public] [task #14528] Submission of relax

Follow-up Comment #23, task #14528 (project administration): Hi Pavel! Have you had a chance to look at our project again? We are really looking forward to hosting our project on Savannah non-GNU, and finally finding a new home after a year of uncertainty. Cheers, Edward __

[Savannah-register-public] [task #14528] Submission of relax

Follow-up Comment #24, task #14528 (project administration): For the record, here was our previous Gna! homepage, archived on the Internet Archive Wayback Machine: https://web.archive.org/web/20170301004608/https://gna.org/projects/relax __

[Savannah-register-public] [task #14528] Submission of relax

Follow-up Comment #26, task #14528 (project administration): Sorry, that was a single mistake in my automated FSF Copyright Validation script , specifically: DIR_SKIP = [ '.git', '.svn', 'graphics/oxygen_ico

[Savannah-register-public] [task #14528] Submission of relax

Follow-up Comment #27, task #14528 (project administration): Actually, the error was rather in the FSF Copright Validation script configuration file for relax . __

[Savannah-register-public] [task #14528] Submission of relax

Follow-up Comment #28, task #14528 (project administration): > See you in June. Does this mean that we have to wait ~4 months for any progress on this task? ___ Reply to this item at: _

[Savannah-register-public] [task #14528] Submission of relax

Follow-up Comment #30, task #14528 (project administration): >> Does this mean that we have to wait ~4 months for any progress on this task? > > Strictly speaking, you don't have: you could make sure that Savannah hosting requirements (for example, the documentation should be released in a FDL1.3+

[Savannah-register-public] [task #14528] Submission of relax

Follow-up Comment #32, task #14528 (project administration): > While mathematical equations may not be copyrigtable, their expressions are. The text around the equations are copyrightable, but the expression of the formula itself is not. The formulae expressed in the relax manual are standard fo

[Savannah-register-public] [task #14528] Submission of relax

Follow-up Comment #34, task #14528 (project administration): Sorry for the delay, I have just returned from holidays. > These are text files (as well as AUTHORS), they should include the notices. README is only a fallback for binary files. The PDB text file format is very rigid, it is a strict

[Savannah-register-public] [task #14528] Submission of relax

Follow-up Comment #36, task #14528 (project administration): >> ...the REMARK section numbering and format can be important... in many cases intricate, automated, software-specific formatting is used that simple hand edits could easily break > >It's up to you to make sure that the license notices

[Savannah-register-public] [task #14528] Submission of relax

Follow-up Comment #38, task #14528 (project administration): No problems. I have pushed the improved documentation: https://sourceforge.net/p/nmr-relax/code/ci/92fa48c65f970a9f81daa53be16347166a5aa573/ ___ Reply to this item at:

[Savannah-register-public] [task #14528] Submission of relax

Follow-up Comment #39, task #14528 (project administration): I was wondering if the improved documentation for the 3D structure files is sufficient? ___

[Savannah-register-public] [task #14528] Submission of relax

Follow-up Comment #41, task #14528 (project administration): The statement says: "Data files contained in the PDB archive (ftp://ftp.wwpdb.org) are free of all copyright restrictions..." There are no re

[Savannah-register-public] [task #14528] Submission of relax

Follow-up Comment #44, task #14528 (project administration): Well, none of the 3D structures (PDB files) in relax contain any patent, copyright or other claims. That we are 100% certain of. Almost all structures are the natural form of the molecule. I'll quote from: Rochelle K Seide & Alic

[Savannah-register-public] [task #14528] Submission of relax

Follow-up Comment #46, task #14528 (project administration): [comment #45 comment #45:] > I suggest putting the patent issue aside and discussing copyright of the files. > > > Well, none of the 3D structures (PDB files) in relax contain any patent, copyright or other claims. That we are 100% cer

[Savannah-register-public] [task #14528] Submission of relax

Follow-up Comment #49, task #14528 (project administration): Of course! But note that the advisory notice you quoted earlier specifically covers patent issues: "The user assumes all responsibility for insuring that intellectual property claims associated with any data set deposited in the PDB ar

[Savannah-register-public] [task #14528] Submission of relax

Follow-up Comment #51, task #14528 (project administration): Yes, as all copyrights have been waived by the authors upon submission. So copyright law does not come into it. The other "intellectual property" categories - trade secrets, trademarks, design patents, etc. - are not applicable. The o

[Savannah-register-public] [task #14528] Submission of relax

Follow-up Comment #53, task #14528 (project administration): Since the very start, the copyright has been waived for all data sets deposited in the PDB database upon submission. How could that "advisory notice" text also cover copyright when all copyright has been waived - i.e. all contents of th