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Improved link formatting.
* Fix for the diffusion_tensor.init user function reference in the intro chapter of the manual. This was using a very old and now non-functional syntax.
* Created the Diffusion_tensor.test_bug_21561_tensor_pdb_failure system test. This is to catch [https://gna.org/bugs/?21561 bug #21561], as reported by [https://gna.org/users/mab Martin Ballaschk]. This catches the failure of the structure.create_diff_tensor_pdb user function for non-spherical diffusion tensors when no Monte Carlo simulations are present.
* Added the truncated data for creating a system test to catch [https://gna.org/bugs/?21562 bug #21562, the failure of the NOE analysis when spectra are replicated]. This bug was reported by [https://gna.org/users/dhanas Dhanas Muthu] and is the failure of the NOE analysis when spectra are replicated. This consists of the Sparky peak lists attached to the bug report and the modified 2AT7 PDB file. The data has been truncated to only include residues :12, :13, and :14.
* Shifted the NOE system test script into the new 'noe' directory.
* Created the Noe.test_bug_21562_noe_replicate_fail system test. This is to catch [https://gna.org/bugs/?21562 bug #21562, the failure of the NOE analysis when spectra are replicated], reported by [https://gna.org/users/dhanas Dhanas Muthu]. This is the failure of the NOE analysis when spectra are replicated. This uses the truncated data taken from the files attached to the bug report. The NOE output file is checked to see if the contents are correct.
* Better support for replicated spectra in the NOE analysis. The saturated and reference peak intensity and error are now properly averaged. Previously averaging was not used as the number of replicates N are cancelled in the ratios used for the NOE and error calculation. However this fails when the number of replicates for the saturated spectrum does not match the number of replicates for the reference spectrum. Now any data combination is possible.
* Another fix for the NOE analysis for when replicated spectra have been collected. Variance averaging rather than error averaging is now used for the peak intensity errors. This is important if the errors for each replicated spectra are different - a case which is rarely encountered as the replicates are almost always used to determine one error for all the replicates.
