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
