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 <jurgenfd@xxxxxxxxx> 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