Author: bugman
Date: Tue Nov 11 16:31:33 2014
New Revision: 26530
URL: http://svn.gna.org/viewcvs/relax?rev=26530&view=rev
Log:
Merged revisions 26516-26528 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r26516 | bugman | 2014-11-11 12:13:52 +0100 (Tue, 11 Nov 2014) | 5 lines
The ImportErrors in unit tests are now correctly handled by the relax test
suite.
If an ImportError occurred, this was previously killing the entire test
suite.
........
r26517 | bugman | 2014-11-11 13:39:57 +0100 (Tue, 11 Nov 2014) | 3 lines
The target_function.relax_fit module unit tests are now skipped if the C
module is not compiled.
........
r26518 | bugman | 2014-11-11 14:10:47 +0100 (Tue, 11 Nov 2014) | 3 lines
Expanded the Python 2 to 3 conversion document.
........
r26519 | bugman | 2014-11-11 14:26:23 +0100 (Tue, 11 Nov 2014) | 10 lines
Manual Python 3 fixes for the dict.key() function which returns a list or
iterator in Python 2 or 3.
This involves a number of changes. The biggest is the conversion of the "x
in y.keys()" statements
to "x in y". For code which requires a list of keys, the function calls
"list(y.keys())" or
preferably "sorted(y.keys())" are used throughout (sorted() ensures that
the list will be of the
same order on all operating systems and Python implementations). A number
of "x in list(y.keys())"
statements were simplified to "x in y", some list() calls changed to
sorted(), and some unnecessary
list() calls were removed.
........
r26520 | bugman | 2014-11-11 14:34:12 +0100 (Tue, 11 Nov 2014) | 9 lines
Python 3 fixes via 2to3 - elimination of all apply() calls.
This only affects the GUI which cannot run in Python 3 yet as wxPython is
not Python 3 compatible
yet.
The command used was:
2to3 -j 4 -w -f apply .
........
r26521 | bugman | 2014-11-11 14:34:56 +0100 (Tue, 11 Nov 2014) | 3 lines
Small update to the 2to3_checklist document - the print statement
conversion has been added.
........
r26522 | bugman | 2014-11-11 14:43:25 +0100 (Tue, 11 Nov 2014) | 9 lines
Python 3 fixes via 2to3 - proper handling of the dict.items() and
dict.values() functions.
These are now all wrapped in list() function calls to ensure that the
Python 3 iterators are
converted to list objects before they are accessed.
The command used was:
2to3 -j 4 -w -f dict .
........
r26523 | bugman | 2014-11-11 14:55:38 +0100 (Tue, 11 Nov 2014) | 6 lines
Python 3 fixes via 2to3 - the execfile() function does not exist in Python
3.
The command used was:
2to3 -j 4 -w -f execfile .
........
r26524 | bugman | 2014-11-11 15:52:43 +0100 (Tue, 11 Nov 2014) | 6 lines
The lib.errors module is now importing lib.compat.pickle for better Python
2 and 3 support.
This shifts the compatibility code from lib.errors into lib.compat so that
the 2to3 program will not
touch the lib.errors module.
........
r26525 | bugman | 2014-11-11 15:58:45 +0100 (Tue, 11 Nov 2014) | 7 lines
Better Python 3 compatibility in some test suite shared data profiling
scripts.
These changes invert the logic, importing the Python 3 builtins module and
aliasing xrange() to
range(), and passing if an ImporError occurs. The code will now no longer
be modified by the 2to3
program.
........
r26526 | bugman | 2014-11-11 16:06:36 +0100 (Tue, 11 Nov 2014) | 5 lines
Unicode fixes for the "\u" string in "\usepackage" in the module docstring.
This requires escaping as "\\usepackage" to avoid the unicode character
'\u'.
........
r26527 | bugman | 2014-11-11 16:13:25 +0100 (Tue, 11 Nov 2014) | 5 lines
The lib.check_types now imports io.IOBase from the lib.compat module.
This is to shift more Python 2 vs. 3 compatibility into lib.compat and out
of all other modules.
........
r26528 | bugman | 2014-11-11 16:21:12 +0100 (Tue, 11 Nov 2014) | 7 lines
Python 3 improvements - changed how the Python 3 absent builtins.unicode()
function is handled.
The aliased builtins.str() function is now referenced as
lib.compat.unicode(). The Python 2
__builtin__.unicode() function is also aliased to lib.compat.unicode().
The GUI using this function
now import it from lib.compat.
........
Modified:
branches/space_mapping_refactor/ (props changed)
branches/space_mapping_refactor/data_store/__init__.py
branches/space_mapping_refactor/data_store/align_tensor.py
branches/space_mapping_refactor/data_store/data_classes.py
branches/space_mapping_refactor/data_store/diff_tensor.py
branches/space_mapping_refactor/data_store/pipe_container.py
branches/space_mapping_refactor/data_store/prototype.py
branches/space_mapping_refactor/docs/devel/2to3_checklist
branches/space_mapping_refactor/extern/sobol/sobol_lib.py
branches/space_mapping_refactor/graphics/wizards/dipole_pair/VectorFieldPlot.py
branches/space_mapping_refactor/gui/analyses/__init__.py
branches/space_mapping_refactor/gui/components/relax_data.py
branches/space_mapping_refactor/gui/components/relax_data_meta.py
branches/space_mapping_refactor/gui/components/spectrum.py
branches/space_mapping_refactor/gui/export_bmrb.py
branches/space_mapping_refactor/gui/interpreter.py
branches/space_mapping_refactor/gui/misc.py
branches/space_mapping_refactor/gui/spin_viewer/containers.py
branches/space_mapping_refactor/gui/spin_viewer/tree.py
branches/space_mapping_refactor/gui/string_conv.py
branches/space_mapping_refactor/gui/uf_objects.py
branches/space_mapping_refactor/lib/check_types.py
branches/space_mapping_refactor/lib/compat.py
branches/space_mapping_refactor/lib/errors.py
branches/space_mapping_refactor/lib/structure/internal/molecules.py
branches/space_mapping_refactor/lib/xml.py
branches/space_mapping_refactor/pipe_control/align_tensor.py
branches/space_mapping_refactor/pipe_control/bmrb.py
branches/space_mapping_refactor/pipe_control/error_analysis.py
branches/space_mapping_refactor/pipe_control/interatomic.py
branches/space_mapping_refactor/pipe_control/pcs.py
branches/space_mapping_refactor/pipe_control/pipes.py
branches/space_mapping_refactor/pipe_control/plotting.py
branches/space_mapping_refactor/pipe_control/rdc.py
branches/space_mapping_refactor/pipe_control/relax_data.py
branches/space_mapping_refactor/pipe_control/sequence.py
branches/space_mapping_refactor/pipe_control/spectrometer.py
branches/space_mapping_refactor/pipe_control/spectrum.py
branches/space_mapping_refactor/pipe_control/state.py
branches/space_mapping_refactor/prompt/interpreter.py
branches/space_mapping_refactor/prompt/tab_completion.py
branches/space_mapping_refactor/prompt/uf_objects.py
branches/space_mapping_refactor/sample_scripts/model_free/table_latex.py
branches/space_mapping_refactor/specific_analyses/consistency_tests/api.py
branches/space_mapping_refactor/specific_analyses/frame_order/data.py
branches/space_mapping_refactor/specific_analyses/frame_order/optimisation.py
branches/space_mapping_refactor/specific_analyses/frame_order/uf.py
branches/space_mapping_refactor/specific_analyses/jw_mapping/api.py
branches/space_mapping_refactor/specific_analyses/model_free/api.py
branches/space_mapping_refactor/specific_analyses/model_free/bmrb.py
branches/space_mapping_refactor/specific_analyses/model_free/data.py
branches/space_mapping_refactor/specific_analyses/noe/api.py
branches/space_mapping_refactor/specific_analyses/parameter_object.py
branches/space_mapping_refactor/specific_analyses/relax_disp/api.py
branches/space_mapping_refactor/specific_analyses/relax_disp/checks.py
branches/space_mapping_refactor/specific_analyses/relax_disp/data.py
branches/space_mapping_refactor/specific_analyses/relax_disp/parameters.py
branches/space_mapping_refactor/specific_analyses/relax_disp/uf.py
branches/space_mapping_refactor/specific_analyses/relax_fit/api.py
branches/space_mapping_refactor/specific_analyses/relax_fit/parameter_object.py
branches/space_mapping_refactor/status.py
branches/space_mapping_refactor/test_suite/gui_tests/rx.py
branches/space_mapping_refactor/test_suite/relax_test_runner.py
branches/space_mapping_refactor/test_suite/shared_data/curve_fitting/profiling/profiling_relax_fit.py
branches/space_mapping_refactor/test_suite/shared_data/dispersion/Hansen/generate_r2eff_files.py
branches/space_mapping_refactor/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/exp_error_analysis/correlation.py
branches/space_mapping_refactor/test_suite/shared_data/dispersion/bug_22146_unpacking_r2a_r2b_cluster/cpmg_synthetic.py
branches/space_mapping_refactor/test_suite/shared_data/dispersion/profiling/base.py
branches/space_mapping_refactor/test_suite/shared_data/frame_order/cam/iso_cone_torsionless/frame_order_matrix.py
branches/space_mapping_refactor/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_matrix.py
branches/space_mapping_refactor/test_suite/shared_data/frame_order/cam/rotor2/pcs_only/ave_pos_back_calc.py
branches/space_mapping_refactor/test_suite/system_tests/bmrb.py
branches/space_mapping_refactor/test_suite/system_tests/dasha.py
branches/space_mapping_refactor/test_suite/system_tests/model_free.py
branches/space_mapping_refactor/test_suite/system_tests/n_state_model.py
branches/space_mapping_refactor/test_suite/system_tests/relax_disp.py
branches/space_mapping_refactor/test_suite/system_tests/scripts/n_state_model/phthalic_acid_noes.py
branches/space_mapping_refactor/test_suite/system_tests/scripts/relax_disp/cpmg_synthetic.py
branches/space_mapping_refactor/test_suite/unit_tests/_specific_analyses/_relax_disp/test_data.py
branches/space_mapping_refactor/test_suite/unit_tests/_target_functions/test_relax_fit.py
branches/space_mapping_refactor/test_suite/unit_tests/state_testing_base.py
branches/space_mapping_refactor/user_functions/data.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/space_mapping_refactor/data_store/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/data_store/__init__.py?rev=26530&r1=26529&r2=26530&view=diff
Modified: branches/space_mapping_refactor/data_store/align_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/data_store/align_tensor.py?rev=26530&r1=26529&r2=26530&view=diff
Modified: branches/space_mapping_refactor/data_store/data_classes.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/data_store/data_classes.py?rev=26530&r1=26529&r2=26530&view=diff
Modified: branches/space_mapping_refactor/data_store/diff_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/data_store/diff_tensor.py?rev=26530&r1=26529&r2=26530&view=diff
Modified: branches/space_mapping_refactor/data_store/pipe_container.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/data_store/pipe_container.py?rev=26530&r1=26529&r2=26530&view=diff
Modified: branches/space_mapping_refactor/data_store/prototype.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/data_store/prototype.py?rev=26530&r1=26529&r2=26530&view=diff
Modified: branches/space_mapping_refactor/docs/devel/2to3_checklist
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/docs/devel/2to3_checklist?rev=26530&r1=26529&r2=26530&view=diff
Modified: branches/space_mapping_refactor/extern/sobol/sobol_lib.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/extern/sobol/sobol_lib.py?rev=26530&r1=26529&r2=26530&view=diff
Modified:
branches/space_mapping_refactor/graphics/wizards/dipole_pair/VectorFieldPlot.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/graphics/wizards/dipole_pair/VectorFieldPlot.py?rev=26530&r1=26529&r2=26530&view=diff
Modified: branches/space_mapping_refactor/gui/analyses/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/gui/analyses/__init__.py?rev=26530&r1=26529&r2=26530&view=diff
Modified: branches/space_mapping_refactor/gui/components/relax_data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/gui/components/relax_data.py?rev=26530&r1=26529&r2=26530&view=diff
Modified: branches/space_mapping_refactor/gui/components/relax_data_meta.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/gui/components/relax_data_meta.py?rev=26530&r1=26529&r2=26530&view=diff
Modified: branches/space_mapping_refactor/gui/components/spectrum.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/gui/components/spectrum.py?rev=26530&r1=26529&r2=26530&view=diff
Modified: branches/space_mapping_refactor/gui/export_bmrb.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/gui/export_bmrb.py?rev=26530&r1=26529&r2=26530&view=diff
Modified: branches/space_mapping_refactor/gui/interpreter.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/gui/interpreter.py?rev=26530&r1=26529&r2=26530&view=diff
Modified: branches/space_mapping_refactor/gui/misc.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/gui/misc.py?rev=26530&r1=26529&r2=26530&view=diff
Modified: branches/space_mapping_refactor/gui/spin_viewer/containers.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/gui/spin_viewer/containers.py?rev=26530&r1=26529&r2=26530&view=diff
Modified: branches/space_mapping_refactor/gui/spin_viewer/tree.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/gui/spin_viewer/tree.py?rev=26530&r1=26529&r2=26530&view=diff
Modified: branches/space_mapping_refactor/gui/string_conv.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/gui/string_conv.py?rev=26530&r1=26529&r2=26530&view=diff
Modified: branches/space_mapping_refactor/gui/uf_objects.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/gui/uf_objects.py?rev=26530&r1=26529&r2=26530&view=diff
Modified: branches/space_mapping_refactor/lib/check_types.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/lib/check_types.py?rev=26530&r1=26529&r2=26530&view=diff
Modified: branches/space_mapping_refactor/lib/compat.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/lib/compat.py?rev=26530&r1=26529&r2=26530&view=diff
Modified: branches/space_mapping_refactor/lib/errors.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/lib/errors.py?rev=26530&r1=26529&r2=26530&view=diff
Modified: branches/space_mapping_refactor/lib/structure/internal/molecules.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/lib/structure/internal/molecules.py?rev=26530&r1=26529&r2=26530&view=diff
Modified: branches/space_mapping_refactor/lib/xml.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/lib/xml.py?rev=26530&r1=26529&r2=26530&view=diff
Modified: branches/space_mapping_refactor/pipe_control/align_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/pipe_control/align_tensor.py?rev=26530&r1=26529&r2=26530&view=diff
Modified: branches/space_mapping_refactor/pipe_control/bmrb.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/pipe_control/bmrb.py?rev=26530&r1=26529&r2=26530&view=diff
Modified: branches/space_mapping_refactor/pipe_control/error_analysis.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/pipe_control/error_analysis.py?rev=26530&r1=26529&r2=26530&view=diff
Modified: branches/space_mapping_refactor/pipe_control/interatomic.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/pipe_control/interatomic.py?rev=26530&r1=26529&r2=26530&view=diff
Modified: branches/space_mapping_refactor/pipe_control/pcs.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/pipe_control/pcs.py?rev=26530&r1=26529&r2=26530&view=diff
Modified: branches/space_mapping_refactor/pipe_control/pipes.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/pipe_control/pipes.py?rev=26530&r1=26529&r2=26530&view=diff
Modified: branches/space_mapping_refactor/pipe_control/plotting.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/pipe_control/plotting.py?rev=26530&r1=26529&r2=26530&view=diff
Modified: branches/space_mapping_refactor/pipe_control/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/pipe_control/rdc.py?rev=26530&r1=26529&r2=26530&view=diff
Modified: branches/space_mapping_refactor/pipe_control/relax_data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/pipe_control/relax_data.py?rev=26530&r1=26529&r2=26530&view=diff
Modified: branches/space_mapping_refactor/pipe_control/sequence.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/pipe_control/sequence.py?rev=26530&r1=26529&r2=26530&view=diff
Modified: branches/space_mapping_refactor/pipe_control/spectrometer.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/pipe_control/spectrometer.py?rev=26530&r1=26529&r2=26530&view=diff
Modified: branches/space_mapping_refactor/pipe_control/spectrum.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/pipe_control/spectrum.py?rev=26530&r1=26529&r2=26530&view=diff
Modified: branches/space_mapping_refactor/pipe_control/state.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/pipe_control/state.py?rev=26530&r1=26529&r2=26530&view=diff
Modified: branches/space_mapping_refactor/prompt/interpreter.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/prompt/interpreter.py?rev=26530&r1=26529&r2=26530&view=diff
Modified: branches/space_mapping_refactor/prompt/tab_completion.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/prompt/tab_completion.py?rev=26530&r1=26529&r2=26530&view=diff
Modified: branches/space_mapping_refactor/prompt/uf_objects.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/prompt/uf_objects.py?rev=26530&r1=26529&r2=26530&view=diff
Modified:
branches/space_mapping_refactor/sample_scripts/model_free/table_latex.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/sample_scripts/model_free/table_latex.py?rev=26530&r1=26529&r2=26530&view=diff
Modified:
branches/space_mapping_refactor/specific_analyses/consistency_tests/api.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/specific_analyses/consistency_tests/api.py?rev=26530&r1=26529&r2=26530&view=diff
Modified:
branches/space_mapping_refactor/specific_analyses/frame_order/data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/specific_analyses/frame_order/data.py?rev=26530&r1=26529&r2=26530&view=diff
Modified:
branches/space_mapping_refactor/specific_analyses/frame_order/optimisation.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/specific_analyses/frame_order/optimisation.py?rev=26530&r1=26529&r2=26530&view=diff
Modified: branches/space_mapping_refactor/specific_analyses/frame_order/uf.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/specific_analyses/frame_order/uf.py?rev=26530&r1=26529&r2=26530&view=diff
Modified: branches/space_mapping_refactor/specific_analyses/jw_mapping/api.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/specific_analyses/jw_mapping/api.py?rev=26530&r1=26529&r2=26530&view=diff
Modified: branches/space_mapping_refactor/specific_analyses/model_free/api.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/specific_analyses/model_free/api.py?rev=26530&r1=26529&r2=26530&view=diff
[... 99 lines stripped ...]
r26530 - in /branches/space_mapping_refactor: ./ data_store/ docs/devel/ extern/sobol/ graphics/wizards/dipole_pair/ gui/ gu...