Author: bugman
Date: Tue Nov 11 12:02:16 2014
New Revision: 26515
URL: http://svn.gna.org/viewcvs/relax?rev=26515&view=rev
Log:
Merged revisions 26498-26513 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r26498 | bugman | 2014-11-10 19:56:07 +0100 (Mon, 10 Nov 2014) | 7 lines
Removed debugging code from the N_state_model.test_CaM_IQ_tensor_fit system
test.
This was an accidentally introduced state.save user function used to catch
the system test state.
It would results in the 'x.bz2' file being dumped in the current directory.
It was introduced in
r26359 (http://article.gmane.org/gmane.science.nmr.relax.scm/24110).
........
r26499 | bugman | 2014-11-10 23:24:54 +0100 (Mon, 10 Nov 2014) | 5 lines
Loosened the checks in the Relax_disp.test_baldwin_synthetic_full system
test.
This is to allow the test to pass on Python 2.5 and 3.1 on a 32-bit
GNU/Linux system.
........
r26500 | bugman | 2014-11-10 23:32:07 +0100 (Mon, 10 Nov 2014) | 6 lines
Fix for the Relax_disp.test_cpmg_synthetic_dx_map_points system test for
certain systems.
This change is to allow the test to pass on Python 2.5 and 3.1 on a 32-bit
GNU/Linux system. This
may be related to 32-bit numpy 1.6.2 verses later numpy versions causing
precision differences.
........
r26501 | bugman | 2014-11-10 23:43:15 +0100 (Mon, 10 Nov 2014) | 6 lines
Python 3 fixes for the relax codebase.
These changes were made using the command:
2to3 -j 4 -w -f buffer -f idioms -f set_literal -f ws_comma -x except -x
import -x imports -x long -x numliterals -x xrange .
........
r26502 | bugman | 2014-11-11 09:19:53 +0100 (Tue, 11 Nov 2014) | 6 lines
Python 3 fixes throughout relax, as identified by the 2to3 script.
The command used was:
2to3 -j 4 -w -f except -f import -f imports -f long -f numliterals -f
xrange .
........
r26503 | bugman | 2014-11-11 09:45:48 +0100 (Tue, 11 Nov 2014) | 3 lines
Python 3 fixes - eliminated all usage of the dictionary iteritems() calls
as this no longer exists.
........
r26504 | bugman | 2014-11-11 09:53:01 +0100 (Tue, 11 Nov 2014) | 7 lines
Fixes for the Relax_disp.test_hansen_cpmg_data_missing_auto_analysis system
test for certain systems.
The optimisation precision has been increased, and the value checking
precision has been decreased.
This change is to allow the test to pass on Python 2.5 and 3.1 on a 32-bit
GNU/Linux system. This
may be related to 32-bit numpy 1.6.2 verses later numpy versions causing
precision differences.
........
r26505 | bugman | 2014-11-11 10:03:19 +0100 (Tue, 11 Nov 2014) | 6 lines
Python 3 fixes using 2to3 for the extern.numdifftools package (mainly
spacing fixes).
The command used was:
2to3 -j 4 -w -f buffer -f idioms -f set_literal -f ws_comma -x except -x
import -x imports -x long -x numliterals -x xrange .
........
r26506 | bugman | 2014-11-11 10:04:21 +0100 (Tue, 11 Nov 2014) | 6 lines
Python 3 fixes using 2to3 for the extern.numdifftools package.
The command used was:
2to3 -j 4 -w -f except -f import -f imports -f long -f numliterals -f
xrange .
........
r26507 | bugman | 2014-11-11 10:09:43 +0100 (Tue, 11 Nov 2014) | 3 lines
Converted all the extern.numdifftools modules using the dos2unix program.
........
r26508 | bugman | 2014-11-11 10:12:48 +0100 (Tue, 11 Nov 2014) | 5 lines
Python 3 fixes for all print statements in the extern.numdifftools package.
The print statements have been manually converted into print() functions.
........
r26509 | bugman | 2014-11-11 10:20:30 +0100 (Tue, 11 Nov 2014) | 3 lines
Updated the Python 2 to Python 3 migration document to be more current.
........
r26510 | bugman | 2014-11-11 10:20:56 +0100 (Tue, 11 Nov 2014) | 3 lines
Small edit of the docs/devel/2to3_checklist document.
........
r26511 | bugman | 2014-11-11 10:26:07 +0100 (Tue, 11 Nov 2014) | 6 lines
Python 3 fixes via 2to3 - elimination of all map and lambda usage in relax.
The command used was:
2to3 -j 4 -w -f map .
........
r26512 | bugman | 2014-11-11 10:43:30 +0100 (Tue, 11 Nov 2014) | 6 lines
Python 3 fixes via 2to3 - replacement of all `x` with repr(x).
The command used was:
2to3 -j 4 -w -f repr .
........
r26513 | bugman | 2014-11-11 11:04:45 +0100 (Tue, 11 Nov 2014) | 3 lines
Expanded the Python 2 to 3 conversion document to list the 2to3 command
individually.
........
Modified:
branches/space_mapping_refactor/ (props changed)
branches/space_mapping_refactor/auto_analyses/relax_disp_repeat_cpmg.py
branches/space_mapping_refactor/auto_analyses/relax_fit.py
branches/space_mapping_refactor/devel_scripts/log_converter.py
branches/space_mapping_refactor/docs/devel/2to3_checklist
branches/space_mapping_refactor/extern/numdifftools/__init__.py
branches/space_mapping_refactor/extern/numdifftools/core.py
branches/space_mapping_refactor/extern/numdifftools/html/epydoc.css
branches/space_mapping_refactor/extern/numdifftools/html/index.html
branches/space_mapping_refactor/extern/numdifftools/info.py
branches/space_mapping_refactor/extern/numdifftools/license.py
branches/space_mapping_refactor/extern/numdifftools/nd_algopy.py
branches/space_mapping_refactor/extern/numdifftools/nd_scientific.py
branches/space_mapping_refactor/extern/numdifftools/numdifftools.prj
branches/space_mapping_refactor/extern/numdifftools/speed_comparison/benchmark1.py
branches/space_mapping_refactor/extern/numdifftools/speed_comparison/prettyplotting.py
branches/space_mapping_refactor/extern/numdifftools/speed_comparison/run_benchmarks.py
branches/space_mapping_refactor/extern/numdifftools/speed_comparison/use_adolc.py
branches/space_mapping_refactor/extern/numdifftools/speed_comparison/use_algopy.py
branches/space_mapping_refactor/extern/numdifftools/speed_comparison/use_funcdesigner.py
branches/space_mapping_refactor/extern/numdifftools/speed_comparison/use_theano.py
branches/space_mapping_refactor/extern/numdifftools/test/test_hessian.py
branches/space_mapping_refactor/extern/numdifftools/test/testnumdifftools.py
branches/space_mapping_refactor/lib/structure/internal/object.py
branches/space_mapping_refactor/pipe_control/structure/main.py
branches/space_mapping_refactor/sample_scripts/n_state_model/conformation_analysis_rdc+pcs.py
branches/space_mapping_refactor/scons/install.py
branches/space_mapping_refactor/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/5_clustered_analyses.py
branches/space_mapping_refactor/test_suite/shared_data/dispersion/profiling/base.py
branches/space_mapping_refactor/test_suite/shared_data/dispersion/profiling/profiling_matrix_power.py
branches/space_mapping_refactor/test_suite/shared_data/user_functions/uf_list_1_2.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/relax_fit.py
branches/space_mapping_refactor/test_suite/system_tests/scripts/relax_disp/hansen_data_missing.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified:
branches/space_mapping_refactor/auto_analyses/relax_disp_repeat_cpmg.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/auto_analyses/relax_disp_repeat_cpmg.py?rev=26515&r1=26514&r2=26515&view=diff
Modified: branches/space_mapping_refactor/auto_analyses/relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/auto_analyses/relax_fit.py?rev=26515&r1=26514&r2=26515&view=diff
Modified: branches/space_mapping_refactor/devel_scripts/log_converter.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/devel_scripts/log_converter.py?rev=26515&r1=26514&r2=26515&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=26515&r1=26514&r2=26515&view=diff
Modified: branches/space_mapping_refactor/extern/numdifftools/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/extern/numdifftools/__init__.py?rev=26515&r1=26514&r2=26515&view=diff
Modified: branches/space_mapping_refactor/extern/numdifftools/core.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/extern/numdifftools/core.py?rev=26515&r1=26514&r2=26515&view=diff
Modified: branches/space_mapping_refactor/extern/numdifftools/html/epydoc.css
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/extern/numdifftools/html/epydoc.css?rev=26515&r1=26514&r2=26515&view=diff
Modified: branches/space_mapping_refactor/extern/numdifftools/html/index.html
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/extern/numdifftools/html/index.html?rev=26515&r1=26514&r2=26515&view=diff
Modified: branches/space_mapping_refactor/extern/numdifftools/info.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/extern/numdifftools/info.py?rev=26515&r1=26514&r2=26515&view=diff
Modified: branches/space_mapping_refactor/extern/numdifftools/license.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/extern/numdifftools/license.py?rev=26515&r1=26514&r2=26515&view=diff
Modified: branches/space_mapping_refactor/extern/numdifftools/nd_algopy.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/extern/numdifftools/nd_algopy.py?rev=26515&r1=26514&r2=26515&view=diff
Modified: branches/space_mapping_refactor/extern/numdifftools/nd_scientific.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/extern/numdifftools/nd_scientific.py?rev=26515&r1=26514&r2=26515&view=diff
Modified: branches/space_mapping_refactor/extern/numdifftools/numdifftools.prj
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/extern/numdifftools/numdifftools.prj?rev=26515&r1=26514&r2=26515&view=diff
Modified:
branches/space_mapping_refactor/extern/numdifftools/speed_comparison/benchmark1.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/extern/numdifftools/speed_comparison/benchmark1.py?rev=26515&r1=26514&r2=26515&view=diff
Modified:
branches/space_mapping_refactor/extern/numdifftools/speed_comparison/prettyplotting.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/extern/numdifftools/speed_comparison/prettyplotting.py?rev=26515&r1=26514&r2=26515&view=diff
Modified:
branches/space_mapping_refactor/extern/numdifftools/speed_comparison/run_benchmarks.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/extern/numdifftools/speed_comparison/run_benchmarks.py?rev=26515&r1=26514&r2=26515&view=diff
Modified:
branches/space_mapping_refactor/extern/numdifftools/speed_comparison/use_adolc.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/extern/numdifftools/speed_comparison/use_adolc.py?rev=26515&r1=26514&r2=26515&view=diff
Modified:
branches/space_mapping_refactor/extern/numdifftools/speed_comparison/use_algopy.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/extern/numdifftools/speed_comparison/use_algopy.py?rev=26515&r1=26514&r2=26515&view=diff
Modified:
branches/space_mapping_refactor/extern/numdifftools/speed_comparison/use_funcdesigner.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/extern/numdifftools/speed_comparison/use_funcdesigner.py?rev=26515&r1=26514&r2=26515&view=diff
Modified:
branches/space_mapping_refactor/extern/numdifftools/speed_comparison/use_theano.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/extern/numdifftools/speed_comparison/use_theano.py?rev=26515&r1=26514&r2=26515&view=diff
Modified:
branches/space_mapping_refactor/extern/numdifftools/test/test_hessian.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/extern/numdifftools/test/test_hessian.py?rev=26515&r1=26514&r2=26515&view=diff
Modified:
branches/space_mapping_refactor/extern/numdifftools/test/testnumdifftools.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/extern/numdifftools/test/testnumdifftools.py?rev=26515&r1=26514&r2=26515&view=diff
Modified: branches/space_mapping_refactor/lib/structure/internal/object.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/lib/structure/internal/object.py?rev=26515&r1=26514&r2=26515&view=diff
Modified: branches/space_mapping_refactor/pipe_control/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/pipe_control/structure/main.py?rev=26515&r1=26514&r2=26515&view=diff
Modified:
branches/space_mapping_refactor/sample_scripts/n_state_model/conformation_analysis_rdc+pcs.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/sample_scripts/n_state_model/conformation_analysis_rdc%2Bpcs.py?rev=26515&r1=26514&r2=26515&view=diff
Modified: branches/space_mapping_refactor/scons/install.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/scons/install.py?rev=26515&r1=26514&r2=26515&view=diff
Modified:
branches/space_mapping_refactor/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/5_clustered_analyses.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/5_clustered_analyses.py?rev=26515&r1=26514&r2=26515&view=diff
Modified:
branches/space_mapping_refactor/test_suite/shared_data/dispersion/profiling/base.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/test_suite/shared_data/dispersion/profiling/base.py?rev=26515&r1=26514&r2=26515&view=diff
Modified:
branches/space_mapping_refactor/test_suite/shared_data/dispersion/profiling/profiling_matrix_power.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/test_suite/shared_data/dispersion/profiling/profiling_matrix_power.py?rev=26515&r1=26514&r2=26515&view=diff
Modified:
branches/space_mapping_refactor/test_suite/shared_data/user_functions/uf_list_1_2.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/test_suite/shared_data/user_functions/uf_list_1_2.py?rev=26515&r1=26514&r2=26515&view=diff
Modified:
branches/space_mapping_refactor/test_suite/system_tests/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/test_suite/system_tests/n_state_model.py?rev=26515&r1=26514&r2=26515&view=diff
Modified:
branches/space_mapping_refactor/test_suite/system_tests/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/test_suite/system_tests/relax_disp.py?rev=26515&r1=26514&r2=26515&view=diff
Modified: branches/space_mapping_refactor/test_suite/system_tests/relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/test_suite/system_tests/relax_fit.py?rev=26515&r1=26514&r2=26515&view=diff
Modified:
branches/space_mapping_refactor/test_suite/system_tests/scripts/relax_disp/hansen_data_missing.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/test_suite/system_tests/scripts/relax_disp/hansen_data_missing.py?rev=26515&r1=26514&r2=26515&view=diff
r26515 - in /branches/space_mapping_refactor: ./ auto_analyses/ devel_scripts/ docs/devel/ extern/numdifftools/ extern/numdi...