Re: repository line 1.3 -- July 09, 2007 - 11:34

Hi,

I'm really sorry for the late response.  Work has been intense lately
and this crappy Deutsche Telekom has taken 1 and a half months to get
my phone working (which it still isn't, my number goes to someone
else's phone), let alone set up my internet (which isn't anywhere in
sight).  Hence I haven't had any free time combined with access to the
internet.  So much for Germany efficiency.

You are most welcome to play with anything you like.  Writing unit or
system tests is useful to learn the internal structure of relax.  The
unit tests check that individual functions in relax operate as they
should.  The system tests check the complete operation of a specific
functionality in relax.  Formatting problems, docstring documentation,
gradual conversion of 1.3 line code to the new data structure system -
the list is large.  Even adding new features useful to yourself
(including differently formatted data input and output) to the 1.3
line would be useful.  But if you would like to play with this, I
suggest having a read of chapters 3 and 9 of the user manual (for
relax 1.2) which describe the open source infrastructure in detail, as
well as the posts on the redesign process.  The best way to make
changes is in small patches which can be sent to the relax-devel
mailing list.  These can then be applied to the 1.3 code and
committed.  After demonstrating your ability (the merging of your
consistency testing code will be very useful here) we, the relax
developers, can vote to add you to the development team.  This is the
standard open source way of doing things.  You'll need a Gna! account
first though.  All of the fine details are described in the user
manual.  Oh, it's useful to discuss the changes you plan on this
mailing list first.  With open source, all development is transparent
and publicly visible (well it should be anyway).

Cheers,

Edward



On 6/27/07, Sebastien Morin <sebastien.morin.1@xxxxxxxxx> wrote:
> Hi Ed,
>
> That's fine. I perfectly understand how one can miss time..!
>
> If there is anything I can do (simple things for a beginner, maybe
> fixing format problems as those found with the 'code validator', or
> maybe adding some tests in the test suite, anything), let me know. It
> would be a pleasure for me to participate.
>
> Cheers
>
>
> Sébastien  :)
>
>
> Edward d'Auvergne wrote:
> > Hi,
> >
> > The 1.3 development line is currently experiencing a massive work
> > over.  See the thread starting at
> > https://mail.gna.org/public/relax-devel/2006-10/msg00053.html for a
> > full description.  The last few months the development of this branch
> > has considerably slowed down mainly due to me moving from a PhD in
> > Melbourne, Australia to a postdoc in Germany (as well as Chris
> > MacRaild moving from Leeds, England to Australia).  But I will be
> > getting back to completing this redesign of relax soon.
> >
> > At the moment almost everything is broken.  The reason is because a
> > lot of new core infrastructure has been put into place, replacing many
> > old methods, but that the old code does not yet use this
> > infrastructure and is hence broken.  There is also the writing of unit
> > tests which will significantly help to decrease the bug count in relax
> > and also allow much more flexibility for code redesign in the future.
> > And there are general improvements as well including a better
> > organisation of the code in classes vs. modules, breaking of large
> > files, etc. and the updating of function and method docstrings into
> > the Epydoc format (for the relax API documentation).  All of this
> > however takes time.
> >
> > Even though everything is broken a new type of analysis can be added
> > to this line, utilising the new infrastructure (there is no choice
> > there anyway), but which will function perfectly independent of the
> > rest of the program.
> >
> > Regards,
> >
> > Edward
> >
> >
> >
> > On 6/27/07, Sebastien Morin <sebastien.morin.1@xxxxxxxxx> wrote:
> >> Hi,
> >>
> >> I just checked out the repository line 1.3 and tried the test suite
> >> without success.
> >>
> >> Should the 1.3 line work or is it supposed to crash on almost every
> >> single test..?
> >>
> >> Please find below the error output (first 120 lines) from the test
> >> suite. You'll see that the error is always something like :
> >>
> >>          self.relax.generic.runs.create(self.run, 'mf')
> >>      AttributeError: Generic instance has no attribute 'runs'
> >>
> >> Thanks !
> >>
> >>
> >> Sébastien
> >>
> >>
> >> relax --test-suite >& error_output.log
> >>
> >> =========================
> >>
> >> Traceback (most recent call last):
> >>   File "/home/semor/packages/relax-1.3/test_suite/system_tests/main.py",
> >> line 265, in exec_tests
> >>     test_array[i].passed = test_array[i].test(self.run)
> >>   File
> >> "/home/semor/packages/relax-1.3/test_suite/system_tests/sequence.py",
> >> line 66, in read
> >>     self.relax.generic.runs.create(run, 'mf')
> >> AttributeError: Generic instance has no attribute 'runs'
> >> Traceback (most recent call last):
> >>   File "/home/semor/packages/relax-1.3/test_suite/system_tests/main.py",
> >> line 265, in exec_tests
> >>     test_array[i].passed = test_array[i].test(self.run)
> >>   File
> >> "/home/semor/packages/relax-1.3/test_suite/system_tests/sequence.py",
> >> line 53, in pdb
> >>     self.relax.generic.runs.create(run, 'mf')
> >> AttributeError: Generic instance has no attribute 'runs'
> >> Traceback (most recent call last):
> >>   File "/home/semor/packages/relax-1.3/test_suite/system_tests/main.py",
> >> line 265, in exec_tests
> >>     test_array[i].passed = test_array[i].test(self.run)
> >>   File
> >> 
> "/home/semor/packages/relax-1.3/test_suite/system_tests/diffusion_tensor.py",
> >>
> >> line 107, in init
> >>     self.initialise_tensors()
> >>   File
> >> 
> "/home/semor/packages/relax-1.3/test_suite/system_tests/diffusion_tensor.py",
> >>
> >> line 117, in initialise_tensors
> >>     self.relax.generic.runs.create('sphere', 'mf')
> >> AttributeError: Generic instance has no attribute 'runs'
> >> Traceback (most recent call last):
> >>   File "/home/semor/packages/relax-1.3/test_suite/system_tests/main.py",
> >> line 265, in exec_tests
> >>     test_array[i].passed = test_array[i].test(self.run)
> >>   File
> >> 
> "/home/semor/packages/relax-1.3/test_suite/system_tests/diffusion_tensor.py",
> >>
> >> line 77, in delete
> >>     self.initialise_tensors()
> >>   File
> >> 
> "/home/semor/packages/relax-1.3/test_suite/system_tests/diffusion_tensor.py",
> >>
> >> line 117, in initialise_tensors
> >>     self.relax.generic.runs.create('sphere', 'mf')
> >> AttributeError: Generic instance has no attribute 'runs'
> >> Traceback (most recent call last):
> >>   File "/home/semor/packages/relax-1.3/test_suite/system_tests/main.py",
> >> line 265, in exec_tests
> >>     test_array[i].passed = test_array[i].test(self.run)
> >>   File
> >> 
> "/home/semor/packages/relax-1.3/test_suite/system_tests/diffusion_tensor.py",
> >>
> >> line 92, in display
> >>     self.initialise_tensors()
> >>   File
> >> 
> "/home/semor/packages/relax-1.3/test_suite/system_tests/diffusion_tensor.py",
> >>
> >> line 117, in initialise_tensors
> >>     self.relax.generic.runs.create('sphere', 'mf')
> >> AttributeError: Generic instance has no attribute 'runs'
> >> Traceback (most recent call last):
> >>   File "/home/semor/packages/relax-1.3/test_suite/system_tests/main.py",
> >> line 265, in exec_tests
> >>     test_array[i].passed = test_array[i].test(self.run)
> >>   File
> >> 
> "/home/semor/packages/relax-1.3/test_suite/system_tests/diffusion_tensor.py",
> >>
> >> line 57, in copy
> >>     self.initialise_tensors()
> >>   File
> >> 
> "/home/semor/packages/relax-1.3/test_suite/system_tests/diffusion_tensor.py",
> >>
> >> line 117, in initialise_tensors
> >>     self.relax.generic.runs.create('sphere', 'mf')
> >> AttributeError: Generic instance has no attribute 'runs'
> >> Traceback (most recent call last):
> >>   File "/home/semor/packages/relax-1.3/test_suite/system_tests/main.py",
> >> line 265, in exec_tests
> >>     test_array[i].passed = test_array[i].test(self.run)
> >>   File
> >> "/home/semor/packages/relax-1.3/test_suite/system_tests/angles.py", line
> >> 40, in test
> >>     self.relax.interpreter._Run.create(run, 'mf')
> >> AttributeError: Interpreter instance has no attribute '_Run'
> >> Traceback (most recent call last):
> >>   File "/home/semor/packages/relax-1.3/test_suite/system_tests/main.py",
> >> line 265, in exec_tests
> >>     test_array[i].passed = test_array[i].test(self.run)
> >>   File
> >> "/home/semor/packages/relax-1.3/test_suite/system_tests/relax_fit.py",
> >> line 56, in read_sparky
> >>     self.relax.interpreter._State.load(file='rx.save', dir=sys.path[-1]
> >> + '/test_suite/system_tests/data/curve_fitting')
> >>   File "/home/semor/packages/relax-1.3/prompt/state.py", line 95, in
> >> load
> >>     self.__relax__.generic.state.load(file=file, dir=dir)
> >>   File "/home/semor/packages/relax-1.3/generic_fns/state.py", line 48,
> >> in load
> >>     relax_data_store = load(file)
> >> ImportError: No module named main
> >> Traceback (most recent call last):
> >>   File "/home/semor/packages/relax-1.3/test_suite/system_tests/main.py",
> >> line 265, in exec_tests
> >>     test_array[i].passed = test_array[i].test(self.run)
> >>   File
> >> "/home/semor/packages/relax-1.3/test_suite/system_tests/model_free.py",
> >> line 947, in read_relax_data
> >>     self.relax.generic.runs.create(self.run, 'mf')
> >> AttributeError: Generic instance has no attribute 'runs'
> >> Traceback (most recent call last):
> >>   File "/home/semor/packages/relax-1.3/test_suite/system_tests/main.py",
> >> line 265, in exec_tests
> >>     test_array[i].passed = test_array[i].test(self.run)
> >>   File
> >> "/home/semor/packages/relax-1.3/test_suite/system_tests/model_free.py",
> >> line 1218, in set_csa
> >>     self.relax.generic.runs.create(self.run, 'mf')
> >> AttributeError: Generic instance has no attribute 'runs'
> >> Traceback (most recent call last):
> >>   File "/home/semor/packages/relax-1.3/test_suite/system_tests/main.py",
> >> line 265, in exec_tests
> >>     test_array[i].passed = test_array[i].test(self.run)
> >>   File
> >> "/home/semor/packages/relax-1.3/test_suite/system_tests/model_free.py",
> >> line 1218, in set_csa
> >>     self.relax.generic.runs.create(self.run, 'mf')
> >> AttributeError: Generic instance has no attribute 'runs'
> >> Traceback (most recent call last):
> >>   File "/home/semor/packages/relax-1.3/test_suite/system_tests/main.py",
> >> line 265, in exec_tests
> >>     test_array[i].passed = test_array[i].test(self.run)
> >>   File
> >> "/home/semor/packages/relax-1.3/test_suite/system_tests/model_free.py",
> >> line 1244, in set_csa_bond_length
> >>     self.relax.generic.runs.create(self.run, 'mf')
> >> AttributeError: Generic instance has no attribute 'runs'
> >> Traceback (most recent call last):
> >>   File "/home/semor/packages/relax-1.3/test_suite/system_tests/main.py",
> >> line 265, in exec_tests
> >>     test_array[i].passed = test_array[i].test(self.run)
> >>   File
> >> "/home/semor/packages/relax-1.3/test_suite/system_tests/model_free.py",
> >> line 1161, in select_m4
> >>     self.relax.generic.runs.create(self.run, 'mf')
> >> AttributeError: Generic instance has no attribute 'runs'
> >> Traceback (most recent call last):
> >>   File "/home/semor/packages/relax-1.3/test_suite/system_tests/main.py",
> >> line 265, in exec_tests
> >>     test_array[i].passed = test_array[i].test(self.run)
> >>   File
> >> "/home/semor/packages/relax-1.3/test_suite/system_tests/model_free.py",
> >> line 1161, in select_m4
> >>     self.relax.generic.runs.create(self.run, 'mf')
> >> AttributeError: Generic instance has no attribute 'runs'
> >> Traceback (most recent call last):
> >>   File "/home/semor/packages/relax-1.3/test_suite/system_tests/main.py",
> >> line 265, in exec_tests
> >>     test_array[i].passed = test_array[i].test(self.run)
> >>   File
> >> "/home/semor/packages/relax-1.3/test_suite/system_tests/model_free.py",
> >> line 978, in read_results
> >>     self.relax.interpreter._State.load(file='orig_state',
> >> dir=sys.path[-1] + '/test_suite/system_tests/data/model_free')
> >>   File "/home/semor/packages/relax-1.3/prompt/state.py", line 95, in
> >> load
> >>     self.__relax__.generic.state.load(file=file, dir=dir)
> >>   File "/home/semor/packages/relax-1.3/generic_fns/state.py", line 48,
> >> in load
> >>     relax_data_store = load(file)
> >> ImportError: No module named main
> >> Traceback (most recent call last):
> >>   File "/home/semor/packages/relax-1.3/test_suite/system_tests/main.py",
> >> line 265, in exec_tests
> >>     test_array[i].passed = test_array[i].test(self.run)
> >>   File
> >> "/home/semor/packages/relax-1.3/test_suite/system_tests/model_free.py",
> >> line 242, in opendx_s2_te_rex
> >>     self.relax.generic.runs.create(self.run, 'mf')
> >> AttributeError: Generic instance has no attribute 'runs'
> >> Traceback (most recent call last):
> >>   File "/home/semor/packages/relax-1.3/test_suite/system_tests/main.py",
> >> line 265, in exec_tests
> >>     test_array[i].passed = test_array[i].test(self.run)
> >>   File
> >> "/home/semor/packages/relax-1.3/test_suite/system_tests/model_free.py",
> >> line 281, in opendx_theta_phi_da
> >>     self.relax.generic.runs.create(self.run, 'mf')
> >> AttributeError: Generic instance has no attribute 'runs'
> >> ^[[?1034hFunction intros have been enabled.
> >>
> >>
> >>
> >>
> >> _______________________________________________
> >> relax (http://nmr-relax.com)
> >>
> >> This is the relax-devel mailing list
> >> relax-devel@xxxxxxx
> >>
> >> To unsubscribe from this list, get a password
> >> reminder, or change your subscription options,
> >> visit the list information page at
> >> https://mail.gna.org/listinfo/relax-devel
> >>
> >
> >
>
> --
>          ______________________________________
>      _______________________________________________
>     |                                               |
>    || Sebastien Morin                               ||
>   ||| Etudiant au PhD en biochimie                  |||
>  |||| Laboratoire de resonance magnetique nucleaire ||||
> ||||| Dr Stephane Gagne                             |||||
>  |||| CREFSIP (Universite Laval, Quebec, CANADA)    ||||
>   ||| 1-418-656-2131 #4530                          |||
>    ||                                               ||
>     |_______________________________________________|
>          ______________________________________