Hi Troels, I can identify this commit as the reason why the software verification tests fail. The dep_check module is not part of the relax library so you cannot use it here. Instead just import the subprocess module in a try statement (like in the dep_check module). You can then create your own subprocess_module flag for this lib module and avoid the dep_check module.
Cheers, Edward On 3 September 2014 22:50, <[email protected]> wrote: > Author: tlinnet > Date: Wed Sep 3 22:50:33 2014 > New Revision: 25603 > > URL: http://svn.gna.org/viewcvs/relax?rev=25603&view=rev > Log: > To the lib function of spectrum.nmrpipe, added function to call the NMRPipe > program showApod, to get the output from the program. > > Modified: > trunk/lib/spectrum/nmrpipe.py > > Modified: trunk/lib/spectrum/nmrpipe.py > URL: > http://svn.gna.org/viewcvs/relax/trunk/lib/spectrum/nmrpipe.py?rev=25603&r1=25602&r2=25603&view=diff > ============================================================================== > --- trunk/lib/spectrum/nmrpipe.py (original) > +++ trunk/lib/spectrum/nmrpipe.py Wed Sep 3 22:50:33 2014 > @@ -28,8 +28,14 @@ > from warnings import warn > > # relax module imports. > +import dep_check > from lib.errors import RelaxError > +from lib.io import get_file_path > from lib.warnings import RelaxWarning > + > +# Check subprocess is available. > +if dep_check.subprocess_module: > + import subprocess > > > def read_seriestab(peak_list=None, file_data=None, int_col=None): > @@ -185,3 +191,35 @@ > > # Add the assignment to the peak list object. > peak_list.add(res_nums=[res_num1, res_num2], res_names=[res_name1, > res_name2], spin_names=[name1, name2], shifts=[w1, w2], > intensity=intensities, intensity_name=spectra) > + > + > +def show_apod_extract(file_name=None, dir=None, path_to_command='showApod'): > + """Extract showApod information for spectrum fourier transformed with > NMRPipe. > + > + @keyword file: The filename of the NMRPipe fourier > transformed file. > + @type file: str > + @keyword dir: The directory where the file is located. > + @type dir: str > + @keyword path_to_command: If showApod not in PATH, then specify > absolute path as: /path/to/showApod > + @type dir: str > + @return: The output from showApod as list of lines. > + @rtype: list of lines > + """ > + > + # Get the file path. > + file_path = get_file_path(file_name=file_name, dir=dir) > + > + if dep_check.subprocess_module: > + # Call function. > + Temp=subprocess.Popen([path_to_command, file_path], > stdout=subprocess.PIPE) > + > + # Communicate with program, and get outout and exitcode. > + (output, errput) = Temp.communicate() > + > + # Wait for finish and get return code. > + return_value = Temp.wait() > + > + return output.splitlines() > + > + else: > + raise RelaxError("python module 'subprocess' not found. Cannot call > showApod.") > > > _______________________________________________ > relax (http://www.nmr-relax.com) > > This is the relax-commits mailing list > [email protected] > > 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-commits _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-devel mailing list [email protected] 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
