Re: r25603 - /trunk/lib/spectrum/nmrpipe.pyRe: r25603 - /trunk/lib/spectrum/nmrpipe.pyHmmm, 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