Hi, Ok, all the changes that happened to pystarlib in both relax (http://nmr-relax.com) and in bmrblib (http://gna.org/projects/bmrblib/) have been pushed upstream into pystarlib (http://code.google.com/p/pystarlib/). Feel free to revert anything you don't like.
Regards, Edward On 22 June 2011 16:22, Edward d'Auvergne <[email protected]> wrote: > Hi, > > Sorry for not getting back to you earlier. I'm been playing around to > see what is necessary. I have integrated pystarlib into the bmrblib > project (http://gna.org/projects/bmrblib/), which is a higher level > abstraction of the BMRB. Pystarlib is used to parse the basic STAR > format, and bmrblib handles saveframes, tag categories, etc. > > There are a number of changes to pystarlib I have made. This is hard > to follow as bmrblib used to be part of the project relax > (http://www.nmr-relax.com/). And originally, pystarlib was in the > base relax directory. I have already made the python-3k changes and > tested it, and it seems to work fine. I would suggest the following > modifications can be integrated upstream. Working back in time, > starting with bmrblib (see > https://mail.gna.org/public/bmrblib-commits/2011-03/msg00001.html): > > ------------------------------------------------------------------------ > r182 | bugman | 2011-03-22 16:58:01 +0100 (Tue, 22 Mar 2011) | 6 lines > Changed paths: > M /trunk/bmrblib/pystarlib/Text.py > > Fix for the semicolon multiline STAR format parsing. > > This was failing if there was text after the terminating ';', but this > is allowed in the STAR format > and is present in many BMRB entries! > > ------------------------------------------------------------------------ > > > > Back when bmrblib was part of relax (see > https://mail.gna.org/public/relax-commits/2009-10/msg00297.html): > > ------------------------------------------------------------------------ > r9861 | bugman | 2009-10-29 19:12:15 +0100 (Thu, 29 Oct 2009) | 3 lines > Changed paths: > M /branches/bmrb/bmrblib/pystarlib/Text.py > > Suppressed a retarded warning message in pystarlib. > > ------------------------------------------------------------------------ > > > > And back when pystarlib was in the base relax directory (see > https://mail.gna.org/public/relax-commits/2009-09/msg00017.html, > https://mail.gna.org/public/relax-commits/2009-09/msg00016.html, > https://mail.gna.org/public/relax-commits/2009-09/msg00006.html, > https://mail.gna.org/public/relax-commits/2009-01/msg00155.html) > > ------------------------------------------------------------------------ > r9455 | bugman | 2009-09-03 15:24:48 +0200 (Thu, 03 Sep 2009) | 19 lines > Changed paths: > M /branches/bmrb/bmrblib/base_classes.py > M /branches/bmrb/bmrblib/misc.py > M /branches/bmrb/prompt/bmrb.py > M /branches/bmrb/pystarlib/File.py > M /branches/bmrb/pystarlib/FileTest.py > M /branches/bmrb/pystarlib/TagTable.py > M /branches/bmrb/pystarlib/TagTableTest.py > M /branches/bmrb/pystarlib/Text.py > M /branches/bmrb/pystarlib/TextTest.py > M /branches/bmrb/pystarlib/Utils.py > M /branches/bmrb/pystarlib/UtilsTest.py > > More updates for Python3k. > > The command used was: > 2to3 -w \ > -f buffer \ > -f idioms \ > -f set_literal \ > -f ws_comma \ > -x except \ > -x import \ > -x imports \ > -x long \ > -x numliterals \ > -x xrange \ > relax . > > This is from the docs/2to3_checklist document. > > ------------------------------------------------------------------------ > r9442 | bugman | 2009-09-03 14:29:19 +0200 (Thu, 03 Sep 2009) | 17 lines > Changed paths: > M /branches/bmrb/bmrblib/NMR_parameters/chem_shift_anisotropy.py > M /branches/bmrb/bmrblib/base_classes.py > M /branches/bmrb/bmrblib/kinetics/general_relaxation.py > M /branches/bmrb/bmrblib/kinetics/heteronucl_NOEs.py > M /branches/bmrb/bmrblib/kinetics/heteronucl_T1_relaxation.py > M /branches/bmrb/bmrblib/kinetics/heteronucl_T2_relaxation.py > M /branches/bmrb/bmrblib/misc.py > M /branches/bmrb/bmrblib/thermodynamics/order_parameters.py > M /branches/bmrb/generic_fns/bmrb.py > M /branches/bmrb/generic_fns/mol_res_spin.py > M /branches/bmrb/generic_fns/relax_data.py > M /branches/bmrb/prompt/bmrb.py > M /branches/bmrb/pystarlib/File.py > M /branches/bmrb/pystarlib/FileTest.py > M /branches/bmrb/pystarlib/SaveFrame.py > M /branches/bmrb/pystarlib/TagTable.py > M /branches/bmrb/pystarlib/Text.py > M /branches/bmrb/pystarlib/Utils.py > M /branches/bmrb/pystarlib/testAll.py > M /branches/bmrb/specific_fns/model_free/bmrb.py > > Updates for Python3k. > > The command used was: > 2to3 -w \ > -x except \ > -x import \ > -x imports \ > -x long \ > -x numliterals \ > -x xrange \ > relax . > > This is from the docs/2to3_checklist document. One print statement > change in pystarlib/TagTable.py > had to be manually fixed afterwards, as the end arg to the print > statement does not exist in all > python 2.x versions. > > ------------------------------------------------------------------------ > r8380 | bugman | 2009-01-11 15:46:03 +0100 (Sun, 11 Jan 2009) | 5 lines > Changed paths: > M /branches/bmrb/pystarlib/File.py > M /branches/bmrb/pystarlib/FileTest.py > M /branches/bmrb/pystarlib/SaveFrame.py > M /branches/bmrb/pystarlib/SaveFrameTest.py > M /branches/bmrb/pystarlib/TagTable.py > M /branches/bmrb/pystarlib/TagTableTest.py > M /branches/bmrb/pystarlib/Text.py > M /branches/bmrb/pystarlib/TextTest.py > M /branches/bmrb/pystarlib/testAll.py > > Import fixes for pystarlib, as they were all screwed up. > > This allows the unit test framework to function and allows importing > of the code into relax. > > ------------------------------------------------------------------------ > r8370 | bugman | 2009-01-11 10:55:33 +0100 (Sun, 11 Jan 2009) | 6 lines > Changed paths: > A /branches/bmrb/pystarlib/File.py > A /branches/bmrb/pystarlib/FileTest.py > A /branches/bmrb/pystarlib/SaveFrame.py > A /branches/bmrb/pystarlib/SaveFrameTest.py > A /branches/bmrb/pystarlib/TagTable.py > A /branches/bmrb/pystarlib/TagTableTest.py > A /branches/bmrb/pystarlib/Text.py > A /branches/bmrb/pystarlib/TextTest.py > A /branches/bmrb/pystarlib/Utils.py > A /branches/bmrb/pystarlib/UtilsTest.py > A /branches/bmrb/pystarlib/__init__.py > A /branches/bmrb/pystarlib/testAll.py > > Added all the pystarlib code. > > The original SVN repository path for this code is > http://pystarlib.googlecode.com/svn/trunk/src/STAR > and the code was copied at r15. > > ------------------------------------------------------------------------ > r8369 | bugman | 2009-01-11 10:52:13 +0100 (Sun, 11 Jan 2009) | 11 lines > Changed paths: > A /branches/bmrb/pystarlib > > Added a directory for packaging the pystarlib STAR format > reader/writer library with relax. > > The pystarlib project by Jurgen F. Doreleijers (jurgenfd att gmail dot > com) is located at > http://code.google.com/p/pystarlib/. > > This packaging with relax is temporary until relax can fully use the > library to read and write STAR > files containing relaxation analysis results (model-free for now) for > submission to the BMRB. The > pystarlib library also needs to be packaged with distutils for easy > installation, prior to > reseparation. > > ------------------------------------------------------------------------ > > > > I can apply all of these changes, one by one, to the pystarlib > repository. These can of course be reverted if deemed unnecessary. > > Regards, > > > P. S. What is Jenkins CI? > > > > On 18 June 2011 21:45, Jurgen F. Doreleijers <[email protected]> wrote: >> Hi Edward, >> All going well for you? I missed your comment back in 2009 on issue list. >> Sorry. >> Since we got the python pystarlib up on Google Code we might as well do it >> right. Could you please commit the changes you made to get the unit tests >> working again? See: http://code.google.com/p/pystarlib/issues/detail?id=3. I >> see you are a owner there so there should be no limits for you to do so. >> There are a couple of reasons to do this. >> - Hunter Mosley asked about this lib. >> - It's a nice little lib to test my Jenkins CI with. >> - Could be nice to test python 3 compatibility with. >> Interested? >> Cheers, >> Jurgen >> >> -- >> Jurgen F. Doreleijers >> Centre for Molecular & Biomolecular Informatics (CMBI) >> Radboud University Nijmegen Medical Centre (RUNMC) >> Visitors: NCMLS Research building, room 0.25, Geert-Grooteplein 26-28 >> Mail: CMBI 260, PO Box 9101, 6500 HB Nijmegen, The Netherlands >> Direct line: jurgenfd or +31 24 3619674 >> > _______________________________________________ relax (http://nmr-relax.com) This is the relax-devel mailing list [email protected] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel
