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* Updated profiling text for [[CR72]] model. Now it is tested for 3 fields. This is related to: [https://gna.org/task/index.php?7807 Task #7807: Speed-up of dispersion models for Clustered analysis].
* Added searching for environment variable PYTHON_INCLUDE_DIR if Python.h is not found in standard Python library. This can be very handsome, if one has a Python virtual environment for multiple users. This relates to the wiki page: http://wiki.nmr-relax.com/Epd_canopy.
* The [http://www.nmr-relax.com/api/3.2/lib.compat-module.html#norm lib.compat.norm() replacement function ] for numpy.linalg.norm() now handles no axis argument. This is to allow the function to be used in all cases where numpy.linalg.norm() is used, while providing compatibility with the axis argument and all numpy versions.* Fix for the scons target for compiling the relax manual when using a repository checkout copy. The method for compiling the relax manual was calling the version.revision() function, however this has been replaced a while ago by the [http://www.nmr-relax.com/api/3.2/version-module.html version.repo_revision variable].* Created two unit tests for the [http://www.nmr-relax.com/api/3.2/lib.io-module.html#file_root lib.io.file_root() function]. The second of the tests demonstrate a failure of the function if multiple file extensions are present.
* Lowered χ<sup>2</sup> value test in system test Relax_disp.test_bug_22146_unpacking_r2a_r2b_cluster_NS_STAR. This is due to the data produced on 32 bit machine, and tested on 64 bit machines. The error was: AssertionError: 2.4659455670347743e-05 != 0.0 within 7 places. The reason for this is due to truncation artifacts.
* Fix for wrong path testing of Python.h. Python.h would be in PYTHON_PREFIX/include/pythonX.Y/Python.h and not in PYTHON_PREFIX/include/Python.h.
* Fixes for all of the relaxation dispersion system tests which were failing with the new minfx code. Due to the tuning of the log barrier constraint algorithm in minfx in the commit at http://article.gmane.org/gmane.science.mathematics.minfx.scm/25, many system tests needed to be slightly adjusted. Two of the Relax_disp.test_tp02_data_to_* system tests were also failing as the optimisation can no longer move out of the minimum at p<sub>A</sub> = 0.5 for one spin (due to the low quality grid search in the auto-analysis).
* Updated the release checklist document for the new 1.0.7 release of minfx.
* Fixes for the [http://www.nmr-relax.com/api/3.2/test_suite.system_tests.relax_disp.Relax_disp-class.html#test_hansen_cpmg_data_missing_auto_analysis Relax_disp.test_hansen_cpmg_data_missing_auto_analysis system test]. The p<sub>A</sub> parameter is no longer tested for one spin as it moves to random values on different operating systems and 32 vs. 64-bit systems. This is because this spin experiences no exchange, both Δω and k<sub>ex</sub> are zero.
* Decreased the value checking precision in the Relax_disp.test_hansen_cpmg_data_to_lm63 system test. This is to allow the test to pass on certain operating systems and 32-bit systems.
* Modified the precision of the output from the [http://www.nmr-relax.com/manual/relax_disp_sherekhan_input.html relax_disp.sherekhan_input user function]. This is simply to allow the Relax_disp.test_sod1wt_t25_to_sherekhan_input system test to pass on certain 32-bit systems, as the float output to 15 decimal places is not always the same. This system test has been updated for the change.
* Updated the numpy minimal dependency in the installation chapter of the manual to version 1.6.
* Added better epydoc sectioning to the lib.dispersion.ns_cpmg_2site_expanded module docstring. This is to better separate the original scripts used to document the code evolution.
* Empty lines are now handled by the [http://www.nmr-relax.com/api/3.2/lib.structure.pdb_write-module.html#remark lib.structure.pdb_write.recordremark() function]. By supplying the remark as None, empty lines can now be created in the REMARK section of a PDB file. This can be used for nicer formatting.
* Fixes for the Diffusion_tensor system tests due to the recent PDB file changes. Prior to the comparison of the generated PDB files, all REMARK PDB lines are now stripped out.
* Fixes for all system tests failing due to the expanded and improved PDB REMARK section. The system tests now remove all REMARK records prior to comparing file contents. The special strip_remarks() system test method has been created to simplify the stripping process.
* Fix for the software verification tests. The recent expansion and improvements of the REMARK records created by the internal structural object PDB writing method imported the relax version to place this information into the PDB files. However this breaks the relax library design, as shown by the verification tests. Instead the relax version information is being taken from the [http://www.nmr-relax.com/api/3.2/lib.structure.internal.object-module.html lib.structure.internal.object.RELAX_VERSION variable]. This defaults to None, however the version module now sets this variable directly when it is imported so that it is always set to the current relax version when running relax.
* General Python 3 fixes via the 2to3 script.
* Removed the lib.compat.sorted() function which was providing Python2.3 compatibility. For a while now, relax has been unable to run on Python versions less than 2.5. Therefore there is no use for having this replacement function for Python ≤ 2.3 which was being placed into the builtins module.
* Python 3 fixes for the entire codebase using the 2to3 script. The command used was: 2to3 -j 4 -w -f xrange .
* The internal structural object add_molecule() and has_molecule() methods are now model specific. This allows for finer control of structural object.
* Created the new [http://www.nmr-relax.com/api/3.2/lib.structure.files-module.html lib.structure.files module]. This currently contains the single find_pdb_files() function which will be used to find all *.pdb, *.pdb.gz and *.pdb.bz2 versions of the PDB file in a given path.
* Fix for the breakage of the relax help system. This was reported at http://thread.gmane.org/gmane.science.nmr.relax.devel/6481. The problem was that the TERM environmental variable was turned off to avoid the GNU readline library on Linux systems emitting the ^[[?1034h escape code. See the message at http://thread.gmane.org/gmane.science.nmr.relax.devel/6481/focus=6489 for more details. However the Python help system obviously requires this environmental variable. Now only if the TERM variable is set to 'xterm' will it be reset, and to 'linux' instead of the blank string "". This does not affect any relax releases.
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