Hi Edward. I keep a "to do" email folder, with stuff I should fix in relax. There were 3 items, now there is 2.
I ran the test inside the relax folder. Could that have an influence on the possibility to import files? Best Troels 2014-09-19 9:25 GMT+02:00 Edward d'Auvergne <[email protected]>: > Hi Troels, > > I have fixed this myself. It was rather basic: > http://thread.gmane.org/gmane.science.nmr.relax.scm/23657. Next time > there is a change in trunk which causes the test suite to fail, and no > fixes are forthcoming, I will just have to revert the change that > broke the trunk. I try to keep the trunk in a 100% functional state > so that I can fix bugs reported by users and can release a new relax > version within a day (if the bug is urgent enough). If there are > disruptive changes planned, just create a quick branch. Working on > your auto-analysis is ok, as the auto-analyses are quite isolated from > the rest of relax. But please don't break the trunk again. > > If the software verification test did not fail, the relax library > independence can be tested by checking out the library by itself: > > $ svn co http://svn.gna.org/svn/relax/trunk/lib@r25904 ~/tmp/lib_test > $ cd ~/tmp > $ python >>>> import lib_test >>>> from lib_test.spectrum import nmrpipe > > That is the revision before the fix. These command should work, but I > see an ImportError. I cannot work out why the test did not fail for > you. On which operating system was this? Maybe I need to check how > well the software verification tests are set up for different > operating systems. > > Cheers, > > Edward > > > > On 18 September 2014 18:28, Edward d'Auvergne <[email protected]> wrote: >> Hmmm, that's very strange! I see the messages below. These tests >> should not pass as lib.spectrum.nmrpipe imports dep_check, but this is >> not in lib, breaking the independence of lib and hence the test should >> fail. The dep_check module, or any non-relax library module can never >> be imported into the lib package. >> >> Regards, >> >> Edward >> >> >> [edward@localhost relax-trunk]$ ./relax --verification-tests >> >> >> =============================== >> = Software verification tests = >> =============================== >> >> F. >> ====================================================================== >> FAIL: test_library_independence >> (test_suite.verification_tests.library.Library) >> Throughly check the independence of the relax library by importing it >> from a non-relax directory. >> ---------------------------------------------------------------------- >> Package 'lib.alignment'. >> Module 'lib.alignment.alignment_tensor'. >> Module 'lib.alignment.paramag_centre'. >> Module 'lib.alignment.pcs'. >> Module 'lib.alignment.rdc'. >> Module 'lib.ansi'. >> Module 'lib.arg_check'. >> Package 'lib.auto_relaxation'. >> Module 'lib.auto_relaxation.ri'. >> Module 'lib.auto_relaxation.ri_comps'. >> Module 'lib.auto_relaxation.ri_prime'. >> Module 'lib.check_types'. >> Package 'lib.chemical_shift'. >> Module 'lib.compat'. >> Package 'lib.curve_fit'. >> Module 'lib.curve_fit.exponential'. >> Package 'lib.diffusion'. >> Module 'lib.diffusion.correlation_time'. >> Module 'lib.diffusion.direction_cosine'. >> Module 'lib.diffusion.main'. >> Module 'lib.diffusion.weights'. >> Package 'lib.dispersion'. >> Module 'lib.dispersion.b14'. >> Module 'lib.dispersion.cr72'. >> Module 'lib.dispersion.dpl94'. >> Module 'lib.dispersion.it99'. >> Module 'lib.dispersion.lm63'. >> Module 'lib.dispersion.lm63_3site'. >> Module 'lib.dispersion.m61'. >> Module 'lib.dispersion.m61b'. >> Module 'lib.dispersion.matrix_exponential'. >> Module 'lib.dispersion.matrix_power'. >> Module 'lib.dispersion.mmq_cr72'. >> Module 'lib.dispersion.mp05'. >> Module 'lib.dispersion.ns_cpmg_2site_3d'. >> Module 'lib.dispersion.ns_cpmg_2site_expanded'. >> Module 'lib.dispersion.ns_cpmg_2site_star'. >> Module 'lib.dispersion.ns_matrices'. >> Module 'lib.dispersion.ns_mmq_2site'. >> Module 'lib.dispersion.ns_mmq_3site'. >> Module 'lib.dispersion.ns_r1rho_2site'. >> Module 'lib.dispersion.ns_r1rho_3site'. >> Module 'lib.dispersion.tap03'. >> Module 'lib.dispersion.tp02'. >> Module 'lib.dispersion.tsmfk01'. >> Module 'lib.dispersion.two_point'. >> Module 'lib.errors'. >> Module 'lib.float'. >> Package 'lib.frame_order'. >> Module 'lib.frame_order.double_rotor'. >> Module 'lib.frame_order.format'. >> Module 'lib.frame_order.free_rotor'. >> Module 'lib.frame_order.iso_cone'. >> Module 'lib.frame_order.iso_cone_free_rotor'. >> Module 'lib.frame_order.iso_cone_torsionless'. >> Module 'lib.frame_order.matrix_ops'. >> Module 'lib.frame_order.pseudo_ellipse'. >> Module 'lib.frame_order.pseudo_ellipse_free_rotor'. >> Module 'lib.frame_order.pseudo_ellipse_torsionless'. >> Module 'lib.frame_order.rotor'. >> Module 'lib.frame_order.rotor_axis'. >> Package 'lib.geometry'. >> Module 'lib.geometry.angles'. >> Module 'lib.geometry.coord_transform'. >> Module 'lib.geometry.lines'. >> Module 'lib.geometry.pec'. >> Module 'lib.geometry.rotations'. >> Module 'lib.geometry.vectors'. >> Module 'lib.io'. >> Package 'lib.linear_algebra'. >> Module 'lib.linear_algebra.kronecker_product'. >> Module 'lib.linear_algebra.matrix_exponential'. >> Module 'lib.linear_algebra.matrix_power'. >> Module 'lib.list'. >> Module 'lib.mathematics'. >> Module 'lib.model_selection'. >> Module 'lib.nmr'. >> Package 'lib.order'. >> Module 'lib.order.order_parameters'. >> Module 'lib.periodic_table'. >> Module 'lib.physical_constants'. >> Module 'lib.regex'. >> Module 'lib.selection'. >> Module 'lib.sequence'. >> Package 'lib.software'. >> Module 'lib.software.bruker_dc'. >> Module 'lib.software.grace'. >> Package 'lib.software.opendx'. >> Module 'lib.software.opendx.execute'. >> Module 'lib.software.opendx.files'. >> Module 'lib.software.xplor'. >> Package 'lib.spectral_densities'. >> Module 'lib.spectral_densities.model_free'. >> Module 'lib.spectral_densities.model_free_components'. >> Package 'lib.spectrum'. >> Module 'lib.spectrum.nmrpipe'. >> Module 'lib.spectrum.nmrview'. >> Module 'lib.spectrum.objects'. >> Module 'lib.spectrum.peak_list'. >> Module 'lib.spectrum.sparky'. >> Module 'lib.spectrum.xeasy'. >> Module 'lib.statistics'. >> Package 'lib.structure'. >> Module 'lib.structure.angles'. >> Module 'lib.structure.cones'. >> Module 'lib.structure.conversion'. >> Module 'lib.structure.files'. >> Module 'lib.structure.geometric'. >> Package 'lib.structure.internal'. >> Module 'lib.structure.internal.displacements'. >> Module 'lib.structure.internal.models'. >> Module 'lib.structure.internal.molecules'. >> Module 'lib.structure.internal.object'. >> Module 'lib.structure.mass'. >> Module 'lib.structure.pdb_read'. >> Module 'lib.structure.pdb_write'. >> Package 'lib.structure.represent'. >> Module 'lib.structure.represent.cone'. >> Module 'lib.structure.represent.diffusion_tensor'. >> Module 'lib.structure.represent.rotor'. >> Module 'lib.structure.statistics'. >> Module 'lib.structure.superimpose'. >> Package 'lib.text'. >> Module 'lib.text.gui'. >> Module 'lib.text.sectioning'. >> Module 'lib.text.string'. >> Module 'lib.text.table'. >> Module 'lib.timing'. >> Module 'lib.warnings'. >> Module 'lib.xml'. >> >> >> Import failures: >> lib.spectrum.nmrpipe: No module named dep_check >> lib.spectrum.peak_list: No module named dep_check >> >> >> >> >> >> Import failures: >> >> lib.spectrum.nmrpipe: No module named dep_check >> >> lib.spectrum.peak_list: No module named dep_check >> >> >> >> Traceback (most recent call last): >> File "/data/relax/relax-trunk/test_suite/verification_tests/library.py", >> line 224, in test_library_independence >> self.fail() >> AssertionError: None >> >> ---------------------------------------------------------------------- >> Ran 2 tests in 0.246s >> >> FAILED (failures=1) >> >> >> =================================== >> = Summary of the relax test suite = >> =================================== >> >> >> >> Optional packages/modules >> ========================= >> >> No tests skipped due to missing modules. >> >> >> >> Synopsis >> ======== >> >> Software verification tests >> ............................................................. [ Failed >> ] >> >> >> >> [edward@localhost relax-trunk]$ >> >> On 18 September 2014 18:13, Troels Emtekær Linnet <[email protected]> >> wrote: >>> I get this? >>> >>> [tlinnet@tomat relax_trunk]$ relax_tomat --verification-te >>> >>> >>> =============================== >>> = Software verification tests = >>> =============================== >>> >>> .. >>> ---------------------------------------------------------------------- >>> Ran 2 tests in 0.755s >>> >>> OK >>> >>> >>> =================================== >>> = Summary of the relax test suite = >>> =================================== >>> >>> >>> >>> Optional packages/modules >>> ========================= >>> >>> No tests skipped due to missing modules. >>> >>> >>> >>> Synopsis >>> ======== >>> >>> Software verification tests >>> ................................................................. [ OK >>> ] >>> >>> 2014-09-18 17:44 GMT+02:00 Edward d'Auvergne <[email protected]>: >>>> 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 _______________________________________________ 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
