Re: r25603 - /trunk/lib/spectrum/nmrpipe.pyRe: r25603 - /trunk/lib/spectrum/nmrpipe.pyHi, The trunk breakages are rather important. For example you reported a possible problem with the relax_disp.r20_from_min_R2eff user function. If that is true, I will instantly release a new relax version once a fix is in place. The breakage has been in trunk now for 16 days, so I was forced to eliminate it. It was also blocking my testing of the frame_order_cleanup branch. Another important point is that long time breakages in the test suite, even within a branch, block the important debugging process of bisecting (using 'svn up -r...' to find the commit before and after the breakage). Bisecting is extremely powerful for finding the exact commit which introduced a bug - that is how I found that r25603 was the breakage point here. But if a second change broke the library independence after the first one did, then it is impossible to find this second breakage using bisecting. For the test, it makes no difference where you run it from. The Library.test_library_independence verification test copies the entire lib directory into the system's temporary directory, then creates a Python script to import all modules of the lib package one-by-one, and executes the script with an external 2nd instance of Python (the same Python executable as relax is running). It was failing in all cases on my system. Regards, Edward On 19 September 2014 09:59, Troels Emtekær Linnet <tlinnet@xxxxxxxxxxxxx> wrote:
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 <edward@xxxxxxxxxxxxx>: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 $ pythonimport lib_test from lib_test.spectrum import nmrpipeThat 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 <edward@xxxxxxxxxxxxx> 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 <tlinnet@xxxxxxxxxxxxx> 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 <edward@xxxxxxxxxxxxx>: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 <edward@xxxxxxxxxxxxx> 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, <tlinnet@xxxxxxxxxxxxx> 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 relax-commits@xxxxxxx 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 relax-devel@xxxxxxx 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