Author: bugman
Date: Wed May 30 17:04:53 2012
New Revision: 16530
URL: http://svn.gna.org/viewcvs/relax?rev=16530&view=rev
Log:
Complete redesign and creation of the 2nd version of the relax XML format for
save and results files.
This is a BIG set of changes! It includes the following:
- The XML files now have the new 'file_version' attribute within the 'relax'
XML element. This is
now set to '2', and if unset it is assumed that the file version should be 1.
- The file_version integer value is now propagated through all of the
from_xml() methods so it can
be passed into the data.relax_xml.xml_to_object() function. This prevents a
mixture of v1 and v2
being assumed for different parts of the XML.
- An XML namespace fix - the xmlns="http://www.nmr-relax.com"; attribute is
now finally visible.
- The data.relax_xml.object_to_xml() function has been added for creating the
new relax XML syntax.
This will handle and convert many more basic Python object types into
IEEE-754 byte arrays, for
example lists and dictionaries of floats, or numpy vectors and matrices.
This function is now used
throughout the code base for converting Python objects to XML.
- The data.relax_xml.xml_to_object() function has been expanded to match the
functionality of
data.relax_xml.object_to_xml().
- The Python object XML elements now have the 'type' attribute indicating the
Python object type.
This is important for the processing of the file, especially for handling all
types of numpy
structures.
- The Python object value is now stored in a sub XML element called
'<value>'. If it is a float, or
is a simple type which contains floats, then the sub XML element
<ieee_754_byte_array> is created
for storing a full precision version of the floats. The
<ieee_754_byte_array> value will always
trump the <value> value!
- The v1 and v2 of the format together with the pre- and post-Python 2.7.3
XML toprettyxml() changes
are now represented as
test_suite/shared_data/model_free/OMP/final_results_trunc_1.3*.bz2 files. A
5th file is added to test the IEEE-754 conversions by corrupting many of the
floats. Each results
file is tested with 5 new model-free system tests.
Added:
branches/uf_redesign/test_suite/shared_data/model_free/OMP/final_results_trunc_1.3_pre_py2.7.3_v1.bz2
- copied unchanged from r16529,
branches/uf_redesign/test_suite/shared_data/model_free/OMP/final_results_trunc_1.3.bz2
branches/uf_redesign/test_suite/shared_data/model_free/OMP/final_results_trunc_1.3_pre_py2.7.3_v2.bz2
(with props)
branches/uf_redesign/test_suite/shared_data/model_free/OMP/final_results_trunc_1.3_v1.bz2
- copied, changed from r16529,
branches/uf_redesign/test_suite/shared_data/model_free/OMP/final_results_trunc_1.3_new.bz2
branches/uf_redesign/test_suite/shared_data/model_free/OMP/final_results_trunc_1.3_v2.bz2
(with props)
branches/uf_redesign/test_suite/shared_data/model_free/OMP/final_results_trunc_1.3_v2_broken.bz2
(with props)
Removed:
branches/uf_redesign/test_suite/shared_data/model_free/OMP/final_results_trunc_1.3.bz2
branches/uf_redesign/test_suite/shared_data/model_free/OMP/final_results_trunc_1.3_new.bz2
Modified:
branches/uf_redesign/data/__init__.py
branches/uf_redesign/data/align_tensor.py
branches/uf_redesign/data/data_classes.py
branches/uf_redesign/data/diff_tensor.py
branches/uf_redesign/data/gui.py
branches/uf_redesign/data/mol_res_spin.py
branches/uf_redesign/data/pipe_container.py
branches/uf_redesign/data/relax_xml.py
branches/uf_redesign/generic_fns/structure/api_base.py
branches/uf_redesign/generic_fns/structure/internal.py
branches/uf_redesign/generic_fns/structure/scientific.py
branches/uf_redesign/test_suite/system_tests/model_elimination.py
branches/uf_redesign/test_suite/system_tests/model_free.py
branches/uf_redesign/test_suite/system_tests/scripts/bmrb_rw.py
branches/uf_redesign/test_suite/system_tests/scripts/model_free/latex_mf_table.py
branches/uf_redesign/test_suite/system_tests/scripts/model_free/omp_model_free.py
branches/uf_redesign/test_suite/system_tests/scripts/palmer_omp.py
branches/uf_redesign/test_suite/unit_tests/_specific_fns/_model_free/test_main.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/uf_redesign/data/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/uf_redesign/data/__init__.py?rev=16530&r1=16529&r2=16530&view=diff
Modified: branches/uf_redesign/data/align_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/uf_redesign/data/align_tensor.py?rev=16530&r1=16529&r2=16530&view=diff
Modified: branches/uf_redesign/data/data_classes.py
URL:
http://svn.gna.org/viewcvs/relax/branches/uf_redesign/data/data_classes.py?rev=16530&r1=16529&r2=16530&view=diff
Modified: branches/uf_redesign/data/diff_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/uf_redesign/data/diff_tensor.py?rev=16530&r1=16529&r2=16530&view=diff
Modified: branches/uf_redesign/data/gui.py
URL:
http://svn.gna.org/viewcvs/relax/branches/uf_redesign/data/gui.py?rev=16530&r1=16529&r2=16530&view=diff
Modified: branches/uf_redesign/data/mol_res_spin.py
URL:
http://svn.gna.org/viewcvs/relax/branches/uf_redesign/data/mol_res_spin.py?rev=16530&r1=16529&r2=16530&view=diff
Modified: branches/uf_redesign/data/pipe_container.py
URL:
http://svn.gna.org/viewcvs/relax/branches/uf_redesign/data/pipe_container.py?rev=16530&r1=16529&r2=16530&view=diff
Modified: branches/uf_redesign/data/relax_xml.py
URL:
http://svn.gna.org/viewcvs/relax/branches/uf_redesign/data/relax_xml.py?rev=16530&r1=16529&r2=16530&view=diff
Modified: branches/uf_redesign/generic_fns/structure/api_base.py
URL:
http://svn.gna.org/viewcvs/relax/branches/uf_redesign/generic_fns/structure/api_base.py?rev=16530&r1=16529&r2=16530&view=diff
Modified: branches/uf_redesign/generic_fns/structure/internal.py
URL:
http://svn.gna.org/viewcvs/relax/branches/uf_redesign/generic_fns/structure/internal.py?rev=16530&r1=16529&r2=16530&view=diff
Modified: branches/uf_redesign/generic_fns/structure/scientific.py
URL:
http://svn.gna.org/viewcvs/relax/branches/uf_redesign/generic_fns/structure/scientific.py?rev=16530&r1=16529&r2=16530&view=diff
Removed:
branches/uf_redesign/test_suite/shared_data/model_free/OMP/final_results_trunc_1.3.bz2
URL:
http://svn.gna.org/viewcvs/relax/branches/uf_redesign/test_suite/shared_data/model_free/OMP/final_results_trunc_1.3.bz2?rev=16529&view=auto
Removed:
branches/uf_redesign/test_suite/shared_data/model_free/OMP/final_results_trunc_1.3_new.bz2
URL:
http://svn.gna.org/viewcvs/relax/branches/uf_redesign/test_suite/shared_data/model_free/OMP/final_results_trunc_1.3_new.bz2?rev=16529&view=auto
Added:
branches/uf_redesign/test_suite/shared_data/model_free/OMP/final_results_trunc_1.3_pre_py2.7.3_v2.bz2
URL:
http://svn.gna.org/viewcvs/relax/branches/uf_redesign/test_suite/shared_data/model_free/OMP/final_results_trunc_1.3_pre_py2.7.3_v2.bz2?rev=16530&view=auto
Copied:
branches/uf_redesign/test_suite/shared_data/model_free/OMP/final_results_trunc_1.3_v1.bz2
(from r16529,
branches/uf_redesign/test_suite/shared_data/model_free/OMP/final_results_trunc_1.3_new.bz2)
URL:
http://svn.gna.org/viewcvs/relax/branches/uf_redesign/test_suite/shared_data/model_free/OMP/final_results_trunc_1.3_v1.bz2?p2=branches/uf_redesign/test_suite/shared_data/model_free/OMP/final_results_trunc_1.3_v1.bz2&p1=branches/uf_redesign/test_suite/shared_data/model_free/OMP/final_results_trunc_1.3_new.bz2&r1=16529&r2=16530&rev=16530&view=diff
Added:
branches/uf_redesign/test_suite/shared_data/model_free/OMP/final_results_trunc_1.3_v2.bz2
URL:
http://svn.gna.org/viewcvs/relax/branches/uf_redesign/test_suite/shared_data/model_free/OMP/final_results_trunc_1.3_v2.bz2?rev=16530&view=auto
Added:
branches/uf_redesign/test_suite/shared_data/model_free/OMP/final_results_trunc_1.3_v2_broken.bz2
URL:
http://svn.gna.org/viewcvs/relax/branches/uf_redesign/test_suite/shared_data/model_free/OMP/final_results_trunc_1.3_v2_broken.bz2?rev=16530&view=auto
Modified: branches/uf_redesign/test_suite/system_tests/model_elimination.py
URL:
http://svn.gna.org/viewcvs/relax/branches/uf_redesign/test_suite/system_tests/model_elimination.py?rev=16530&r1=16529&r2=16530&view=diff
Modified: branches/uf_redesign/test_suite/system_tests/model_free.py
URL:
http://svn.gna.org/viewcvs/relax/branches/uf_redesign/test_suite/system_tests/model_free.py?rev=16530&r1=16529&r2=16530&view=diff
Modified: branches/uf_redesign/test_suite/system_tests/scripts/bmrb_rw.py
URL:
http://svn.gna.org/viewcvs/relax/branches/uf_redesign/test_suite/system_tests/scripts/bmrb_rw.py?rev=16530&r1=16529&r2=16530&view=diff
Modified:
branches/uf_redesign/test_suite/system_tests/scripts/model_free/latex_mf_table.py
URL:
http://svn.gna.org/viewcvs/relax/branches/uf_redesign/test_suite/system_tests/scripts/model_free/latex_mf_table.py?rev=16530&r1=16529&r2=16530&view=diff
Modified:
branches/uf_redesign/test_suite/system_tests/scripts/model_free/omp_model_free.py
URL:
http://svn.gna.org/viewcvs/relax/branches/uf_redesign/test_suite/system_tests/scripts/model_free/omp_model_free.py?rev=16530&r1=16529&r2=16530&view=diff
Modified: branches/uf_redesign/test_suite/system_tests/scripts/palmer_omp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/uf_redesign/test_suite/system_tests/scripts/palmer_omp.py?rev=16530&r1=16529&r2=16530&view=diff
Modified:
branches/uf_redesign/test_suite/unit_tests/_specific_fns/_model_free/test_main.py
URL:
http://svn.gna.org/viewcvs/relax/branches/uf_redesign/test_suite/unit_tests/_specific_fns/_model_free/test_main.py?rev=16530&r1=16529&r2=16530&view=diff
r16530 - in /branches/uf_redesign: data/ generic_fns/structure/ test_suite/shared_data/model_free/OMP/ test_suite/system_tes...