Changes

| next = 4.1.3| keywords = Frame order, GUI, manual

* System tests: Added two tests to catch bug #12 ([https://sourceforge.net/p/nmr-relax/tickets/12/). This is bug #12, the failure to catch the '#' character when setting the molecule name]. The tests are [http://www.nmr-relax.com/api/4.1/test_suite.system_tests.structure.Structure-class.html#test_bug_12_hash_in_mol_name_via_arg Structure.test_bug_12_hash_in_mol_name_via_arg] and [http://www.nmr-relax.com/api/4.1/test_suite.system_tests.structure.Structure-class.html#test_bug_12_hash_in_mol_name_via_fileStructure.test_bug_12_hash_in_mol_name_via_file]. These cover the two ways a '<code>#' </code> character can enter a molecule name - via the file name or via the set_mol_name argument. Both the [http://www.nmr-relax.com/manual/structure_read_pdb.html structure.read_pdb ] and [http://www.nmr-relax.com/manual/structure_read_xyz.html structure.read_xyz ] user functions are checked.* Test suite: 2 new system tests to catch the failure of reading newer Bruker DC files. The system tests are [http://www.nmr-relax.com/api/4.1/test_suite.system_tests.bruker.Bruker-class.html#test_bug_13_T1_read_fail Bruker.test_bug_13_T1_read_fail] and [http://www.nmr-relax.com/api/4.1/test_suite.system_tests.bruker.Bruker-class.html#test_bug_13_T2_read_fail Bruker.test_bug_13_T2_read_fail] and these catch bug #13 ([https://sourceforge.net/p/nmr-relax/tickets/13/)bug #13].* User function definitions: Clarifications for the [http://www.nmr-relax.com/manual/bruker_read.html bruker.read ] text.* User manual: Clean up of the bibliography entry titles. Species names are properly italicised with genus names capitalised, nuclear isotopes are superscripted, {{:R1rho}}, {{:R2}}, etc. are properly subscripted, the Perrin articles are translated into English, symbols are now symbols, and unnecessary capitalisation has been removed from the bibtex.

* Travis CI config: Attempt at installing wxPython for Ubuntu and Python 2.7. This would allow for the whole test suite to be run on Travis CI on at least one OS. The instructions come from the stackoverflow response by dthor at [https://stackoverflow.com/questions/29290011/using-travis-ci-with-wxpython-testsstackoverflow response by dthor].

* FSF Copyright Validation script: Support for saving and reading the committer information. This allows the committer information (file name, committer name, and copyright years) from older repositories to be saved and later read into the script. In this case, the old Subversion history has been read and the committer information placed into the <code>fsfcv.svn_committer_info.bz2 </code> file (in the <code>devel_scripts/ </code> directory). This compressed file is now specified in the <code>fsfcv.conf.py </code> configuration file. The result is that the <code>fsfcv </code> script can be run on the relax git repository without requiring a checkout of the old SVN repository.

* API manual: Scons compilation via epydoc now fails if a warning or error is found. This manually parses the epydoc output to skip the unavoidable wxPython warnings. Any error or warning will now cause an error to be raised. This results in a non-zero return code from scons to allow the <code>api_manual_html </code> target to be checked in scripts.

* Travis CI config: Fix for the Mac OS X build. This job passes, but the test suite fails with the following traceback message when trying to import matplotlib: "ImportError: Python is not installed as a framework. The Mac OS X backend will not be able to function correctly if Python is not installed as a framework. See the Python documentation for more information on installing Python as a framework on Mac OS X. Please either reinstall Python as a framework, or try one of the other backends. If you are using (Ana)Conda please install python.app and replace the use of 'python' with 'pythonw'. See 'Working with Matplotlib on OSX' in the Matplotlib FAQ for more information.". The fix is simply to create <code>$HOME/.matplotlib/matplotlibrc </code> with the contents '<code>backend: TkAgg'</code>.* API manual: Greater filtering of the file list passed to epydoc. Now only relax modules ending in <code>*.py </code> are processed. That means that all base directory scripts, including '<code>sconstruct'</code>, are excluded from the API documentation.

* relax GUI: wxPython-Phoenix 4.x fix to allow relax to start again. In the later wxPython versions, relax would not be able to start either the GUI or any of the test suite due to a new error "wx._core.PyNoAppError: The wx.App object must be created first!". This was not present in wxPython-Phoenix 3. The [http://www.nmr-relax.com/api/4.1/gui.icons.Relax_icons -class .html Relax_icons class] (a <code>wx.IconBundle </code> derived class) is no longer instantiated on import.* Structure loading: Fix for [https://sourceforge.net/p/nmr-relax/tickets/12/ bug #12, the acceptance of the invalid '#' character in molecule names]. See httpsA simple check has not been added to the [http://sourceforgewww.net/p/nmr-relax.com/ticketsapi/124.1/lib. A simple check has not been added to the structure.internal.object.Internal-class.html#load_pdb load_pdb() ] and [http://www.nmr-relax.com/api/4.1/lib.structure.internal.object.Internal-class.html#load_xyz load_xyz() ] functions of the [http://www.nmr-relax.com/api/4.1/lib.structure.internal.object-module.html internal structural object in lib.structure.internal.object]. This ensures that the '<code>#' </code> character can never be set as the molecule name, independently if it was taken from a file name or set via the <code>set_mol_name </code> arguments of the [http://www.nmr-relax.com/manual/structure_read_pdb.html structure.read_pdb ] or [http://www.nmr-relax.com/manual/structure_read_xyz.html structure.read_xyz ] user functions.* Bruker DC: Complete redesign of the backend to support reading newer (or older) file versions. This fixes bug #13 ([https://sourceforge.net/p/nmr-relax/tickets/13/)bug #13, the failure of reading newer Bruker DC files]. The backend has been resigned so that the relax library produces a [http://www.nmr-relax.com/api/4.1/lib.software.bruker_dc.DCObject-class.html complex Python object representation of the Bruker DC results file]. This object now stores all of the data present within the Bruker DC file. The design is more flexible as precise column ordering no longer matters.* Fix for bug #14, the freezing of user functions in the GUI. See [https://sourceforge.net/p/nmr-relax/tickets/14/bug #14, the freezing of user functions in the GUI]. The user functions freeze if an error occurs that is not a RelaxError, with the mouse pointer stuck on the busy cursor. These non-RelaxErrors are now caught and manually dealt with by the GUI interpreter. Like all GUI freezing bugs, this was introduced with the huge GUI speed up prior in [[relax 4.1.0]]. These also only to appear to be a freeze, but it is actually the failure to update and show the relax controller combined with not turning off the busy mouse cursor.* GUI bug fix: Avoidance of the numpy depreciation of '<code>== None'</code>. This deprecation causes the GUI to fail with recent numpy versions.* Relaxation dispersion: Protection of all of the <code>MODEL_PARAMS_* </code> variables from modification. These are now only used with <code>copy.deepcopy()</code>. This removes a number of bugs in which the lists, which should be read-only, are permanently modified by the addition of <code>'r1'</code>. The system tests add <code>'r1' </code> and then the unit tests subsequently fail. This would also be an issue if an experiment without the <code>'r1' </code> parameter is analysed after one with that parameter, without restarting relax.* Relaxation dispersion bug fix: The <code>'r1' </code> parameter was missing from the nested parameter algorithm. This is the [http://www.nmr-relax.com/api/4.1/specific_analyses.relax_disp.model-module.html#nesting_param nesting_param() function ] of the [http://www.nmr-relax.com/api/4.1/specific_analyses.relax_disp.model-module.html specific_analyses.relax_disp.model module]. The <code>'r1' </code> parameter must be treated differently from the other model parameters, just as the <code>'r2*' </code> parameters are.* Dispersion auto-analysis: Bug fix for the plotting of the {{:R1 }} parameter. The plotting relied on the insertion of the <code>'r1' </code> parameter into the read only <code>MODEL_PARAMS_* </code> variables of [http://www.nmr-relax.com/api/4.1/lib.dispersion.variables-module.html lib.dispersion.variables]. Now the [http://www.nmr-relax.com/api/4.1/specific_analyses.relax_disp.model.Model_class-class.html Model_class class ] from [http://www.nmr-relax.com/api/4.1/specific_analyses.relax_disp.model-module.html specific_analyses.relax_disp.models model] is being used to dynamically determine the parameters of the model.

* [https://sourceforge.net/p/nmr-relax/mailman/message/3660715736650583/ Mailing list message].