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
Re: Hi again