Re: r7049 - in /1.3: generic_fns/grace.py generic_fns/value.py specific_fns/noe.py -- August 01, 2008 - 10:59

Hi,

Thanks for these cleanups.  I have one small functionally unimportant
suggestion though, and it relates to this change:

> -        self.file_path = self.relax.IO.file_path(file, dir)
> +        self.get_file_path = get_file_path(file, dir)

For the future, it would be less confusing to leave the file path
variable with the name 'self.file_path'.  There was one other place
where this variable is later referenced which changed as well.

Cheers,

Edward


On Thu, Jul 31, 2008 at 4:05 PM,  <sebastien.morin.1@xxxxxxxxx> wrote:
> Author: semor
> Date: Thu Jul 31 16:05:37 2008
> New Revision: 7049
>
> URL: http://svn.gna.org/viewcvs/relax?rev=7049&view=rev
> Log:
> More conversions of 'relax.IO' to 'relax_io'.
>
> Old instances are now completely converted.
>
>
> Modified:
>    1.3/generic_fns/grace.py
>    1.3/generic_fns/value.py
>    1.3/specific_fns/noe.py
>
> Modified: 1.3/generic_fns/grace.py
> URL: 
> http://svn.gna.org/viewcvs/relax/1.3/generic_fns/grace.py?rev=7049&r1=7048&r2=7049&view=diff
> ==============================================================================
> --- 1.3/generic_fns/grace.py (original)
> +++ 1.3/generic_fns/grace.py Thu Jul 31 16:05:37 2008
> @@ -32,6 +32,7 @@
>  from data import Relax_data_store; ds = Relax_data_store()
>  from generic_fns.mol_res_spin import exists_mol_res_spin_data, spin_loop
>  from relax_errors import RelaxError, RelaxNoPipeError, 
> RelaxNoSequenceError, RelaxNoSimError, RelaxRegExpError
> +from relax_io import get_file_path, open_write_file, test_binary
>
>
>
> @@ -177,13 +178,13 @@
>         """Function for running Grace."""
>
>         # Test the binary file string corresponds to a valid executable.
> -        self.relax.IO.test_binary(grace_exe)
> +        test_binary(grace_exe)
>
>         # File path.
> -        self.file_path = self.relax.IO.file_path(file, dir)
> +        self.get_file_path = get_file_path(file, dir)
>
>         # Run Grace.
> -        system(grace_exe + " " + self.file_path + " &")
> +        system(grace_exe + " " + self.get_file_path + " &")
>
>
>     def write(self, x_data_type='res', y_data_type=None, res_num=None, 
> res_name=None, plot_data='value', norm=1, file=None, dir=None, force=False):
> @@ -228,7 +229,7 @@
>             raise RelaxNoSimError, self.run
>
>         # Open the file for writing.
> -        self.file = self.relax.IO.open_write_file(file, dir, force)
> +        self.file = open_write_file(file, dir, force)
>
>         # Function type.
>         function_type = ds.run_types[ds.run_names.index(run)]
>
> Modified: 1.3/generic_fns/value.py
> URL: 
> http://svn.gna.org/viewcvs/relax/1.3/generic_fns/value.py?rev=7049&r1=7048&r2=7049&view=diff
> ==============================================================================
> --- 1.3/generic_fns/value.py (original)
> +++ 1.3/generic_fns/value.py Thu Jul 31 16:05:37 2008
> @@ -34,6 +34,7 @@
>  from generic_fns.minimise import reset_min_stats
>  from generic_fns.mol_res_spin import exists_mol_res_spin_data, spin_loop
>  from relax_errors import RelaxError, RelaxFileEmptyError, RelaxNoResError, 
> RelaxNoPipeError, RelaxNoSequenceError, RelaxParamSetError, 
> RelaxRegExpError, RelaxUnknownParamError, RelaxValueError
> +from relax_io import extract_data, open_write_file, strip
>  from specific_fns.setup import get_specific_fn
>
>
> @@ -459,7 +460,7 @@
>                 raise RelaxValueError, (self.param, self.run)
>
>         # Extract the data from the file.
> -        file_data = self.relax.IO.extract_data(file)
> +        file_data = extract_data(file)
>
>         # Count the number of header lines.
>         header_lines = 0
> @@ -475,7 +476,7 @@
>         file_data = file_data[header_lines:]
>
>         # Strip the data.
> -        file_data = self.relax.IO.strip(file_data)
> +        file_data = strip(file_data)
>
>         # Do nothing if the file does not exist.
>         if not file_data:
> @@ -574,7 +575,7 @@
>             raise RelaxNoSequenceError
>
>         # Open the file for writing.
> -        file = self.relax.IO.open_write_file(file, dir, force)
> +        file = open_write_file(file, dir, force)
>
>         # Write the data.
>         self.write_data(file, return_value)
>
> Modified: 1.3/specific_fns/noe.py
> URL: 
> http://svn.gna.org/viewcvs/relax/1.3/specific_fns/noe.py?rev=7049&r1=7048&r2=7049&view=diff
> ==============================================================================
> --- 1.3/specific_fns/noe.py (original)
> +++ 1.3/specific_fns/noe.py Thu Jul 31 16:05:37 2008
> @@ -27,6 +27,7 @@
>  # relax module imports.
>  from data import Relax_data_store; ds = Relax_data_store()
>  from relax_errors import RelaxArgNotInListError, RelaxError, 
> RelaxInvalidDataError, RelaxNoPipeError, RelaxNoSequenceError, 
> RelaxRegExpError
> +from relax_io import open_write_file
>
>
>  class Noe:
> @@ -392,7 +393,7 @@
>             raise RelaxNoSequenceError
>
>         # Open the file for writing.
> -        noe_file = self.relax.IO.open_write_file(file, dir, force)
> +        noe_file = open_write_file(file, dir, force)
>
>         # Write the data.
>         self.relax.generic.value.write_data(self.run, None, noe_file, 
> return_value=self.return_value)
>
>
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