Hi Troels, When you have some spare time, could you have a look and fix this test suite failure you introduced into the relax trunk? This blocks the software verification tests in the branches (specifically the frame_order_cleanup branch I am working on). And it blocks a new stable version of relax from being able to be released.
Cheers, Edward On 12 September 2014 14:51, Edward d'Auvergne <[email protected]> wrote: > 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
