Hi,
Some of these patch will require a number of fixes before being
applied. I will outline the issues below.
On 12 April 2010 05:13, Michael Bieri <NO-REPLY.INVALID-ADDRESS@xxxxxxx>
wrote:
Follow-up Comment #45, task #6847 (project relax):
Patches for relax_fit.py in the 1.3 line:
definition and pipename:
relax_fit.py accepts additional keywords for beter cooperation with the GUI.
In addition, the pipe names are supplemented with the date and time to allow
multiple calculations of the same kind in the same session.
This patch is not yet applied. Firstly some formatting - the epydoc
type text should be 'str' rather than 'str (directory)', etc. An
empty line has been added at line 76 which should not be there. And
the last one is that function argument default values should not have
spaces around the = sign, i.e. 'directory = None' should be
'directory=None'.
For appending the time info being appended to the pipe name, this
removes flexibility from the code and is a bit counter intuitive for
the API. There are 2 better solutions for this. The first is that
the default is set to None, and if no argument is given then the
automatic pipe name with time is created. The second is that the
calling code generates the data pipe with time stamp. I see either
way as being acceptable. The reasoning here is simple - if someone
uses this code and asks for a the data to be located in a defined data
pipe, changing the name of their special pipe (which might already
contain data) would be bad. They will struggle to work out why their
data pipe is empty or not modified. We should never clobber the
names, data, etc. of the calling code.
--------------------------------
correct repetitions spectra (again...)
Repeated spectra are set correctly and unresolved file is read correctly.
Applied! The 'again...' text suggests that a link would be useful in
the commit message ;)
---------------------------
output files:
Output files can get set by different interfaces.
Default name is 'rx', but the GUI will set them as for example r1.600.out
and
r1.600.save. In addition, saved plots are only automatically displayed if
chosen.
This has not yet been applied. Firstly the new view_plots flag should
be in a separate patch, and it should be introduced as a method arg
simultaneously so that the code will function without a second fixing
patch.
Secondly for the relax coding style, the dir arg should not have space
around the = sign, i.e. 'dir = self.grace_dir' should be
'dir=self.grace_dir'.
-----------------------
load sequence:
relax_fit.py reads sequence from either a sequence file or a pdb file.
There is also a better way to perform this operation. If no PDB file
is selected by the user, i.e. a sequence file is given, then the GUI
should set the PDB file name to None rather than '!!! Sequence file
selected !!!'. This string is not needed. The GUI can check that the
user has specified one or the other. Even better would be to check if
self.seq_args is None.
Cheers,
Edward
Re: [task #6847] The Bieri graphical user interface.