relax SVN archive

Converted align_tensor.init to the Desc_container object design to test itemised lists.

The Desc_container object now supports itemised lists.

Lists are now formatted for the prompt uf help strings from the Desc_container objects.

Converted the align_tensor.display user function to the new Desc_container design.

This is to test out the list generation.

The Desc_container.add_list_element() method now groups list elements together.

Converted the prompt user function objects to use the new Desc_container objects for the help strings.

Started to redesign the user function definition descriptions.

The desc object has been converted into a list which will contain instances of the new
Desc_container class. This class will hold the description information as blocks of text, including
unformatted paragraphs, verbatim text, lists, tables, and relax prompt examples. The object has a
number of methods used for inputting all of the information, as well as extracting it.

The information in the Desc_container object is not formatted, for example tables will be stored as
lists of lists. This will remove the need for parsing list, tables, verbatim text, etc. by the
docs.latex.fetch_docstrings module. But these will need to be recreated for the prompt help
strings, for the GUI user function descriptions, and for the user manual.

Converted the align_tensor.copy user function description to the new design.

This is a test for the implementation of the description abstraction through the Desc_container
objects. The 'desc', 'additional', and 'prompt examples' will all be merged into one 'desc'
structure.

Broke a circular import trigged by the user manual compilation.

The error from running 'scons user_manual_pdf' was:

scons: *** [fetch_docstrings] ImportError : cannot import name fill_object_contents
Traceback (most recent call last):
File "/usr/lib/python2.7/site-packages/SCons/Action.py", line 1046, in execute
result = self.execfunction(target=target, source=rsources, env=env)
File "/data/relax/branches/uf_redesign/scons/manuals.py", line 471, in fetch_docstrings
from docs.latex.fetch_docstrings import Fetch_docstrings
File "/data/relax/branches/uf_redesign/docs/latex/fetch_docstrings.py", line 34, in <module>
from user_functions.data import Uf_info; uf_info = Uf_info()
File "/data/relax/branches/uf_redesign/user_functions/__init__.py", line 85, in <module>
import user_functions.align_tensor
File "/data/relax/branches/uf_redesign/user_functions/align_tensor.py", line 28, in <module>
from generic_fns import align_tensor, pipes
File "/data/relax/branches/uf_redesign/generic_fns/align_tensor.py", line 35, in <module>
from angles import wrap_angles
File "/data/relax/branches/uf_redesign/generic_fns/angles.py", line 32, in <module>
from generic_fns import pipes
File "/data/relax/branches/uf_redesign/generic_fns/pipes.py", line 32, in <module>
from data import Relax_data_store; ds = Relax_data_store()
File "/data/relax/branches/uf_redesign/data/__init__.py", line 36, in <module>
from pipe_container import PipeContainer
File "/data/relax/branches/uf_redesign/data/pipe_container.py", line 28, in <module>
from align_tensor import AlignTensorList
File "/data/relax/branches/uf_redesign/data/align_tensor.py", line 31, in <module>
from data_classes import Element
File "/data/relax/branches/uf_redesign/data/data_classes.py", line 32, in <module>
from relax_xml import fill_object_contents, xml_to_object
File "/data/relax/branches/uf_redesign/data/relax_xml.py", line 44, in <module>
import arg_check
File "/data/relax/branches/uf_redesign/arg_check.py", line 39, in <module>
from relax_io import DummyFileObject
File "/data/relax/branches/uf_redesign/relax_io.py", line 50, in <module>
from generic_fns.mol_res_spin import generate_spin_id_data_array, spin_id_to_data_list
File "/data/relax/branches/uf_redesign/generic_fns/mol_res_spin.py", line 47, in <module>
from data.mol_res_spin import MoleculeContainer, ResidueContainer, SpinContainer
File "/data/relax/branches/uf_redesign/data/mol_res_spin.py", line 36, in <module>
from relax_xml import fill_object_contents, object_to_xml, xml_to_object
ImportError: cannot import name fill_object_contents
scons: building terminated because of errors.

The structure.load_spins spin_id arg no longer defaults to '@N'.

This was introduced at r16545, but causes many test suite failures!