Liquiddiffract

Bug Fix

- Fixes a crashing bug when using Qt6 caused by not setting Qt.ItemFlag explicitly

Major Changes

- **Compute *χ²* Map Toolbox**
This new toolbox allows the user to compute a map of *χ²* from the data and two chosen parameters.
Options are:
- *ρ*
- *b* (background scaling factor)
- *r*_min
- No. iterations

Options for setting parameter, normalising *χ²*, and plotting the data are provided.
Computed data can be saved or the plot directly exported as an image.

- **Optional corrections for self-shielding attenuation factor**
Optional corrections for self-shielding presuming a slab-type geometry can be made in the *Background Subtraction* tab. More complex geometries (e.g. cylindrical, including a container, etc.) may be added if there is demand.

- **Support for Qt 6 via qtpy**
This gives support for all major Qt bindings (PyQt5, PyQt6, PySide2 and PySide6). PyQt6 preferred over PySide6.

Minor Changes

- Option to plot self-scattering/compton scattering to compare against _I(Q)_ in the data/optimisation UI
- Automatic plotting of _αI(Q)_ to compare with _f(Q)_
- Optional zero-shift corrections in background subtraction tab
- Rebinned _I(Q)_ data is now filled with _I(Q_min)_ at _0 <= Q < Q_min_
- Auto rebinning when data and background have different ranges or step sizes
- More robust peak search for finding integration limits in structural information tab
- Refactored form factor / average scattering functions for memory efficiency and speed.
Creation of large arrays for compositions with many components is now avoided.
- Support for user input of fractional chemical compositions added for Faber-Ziman method. This avoids users having to multiply their formulae to get integer number of atoms. Ashcroft-Langreth structure factors set to only support molecular compositions.
(fixes issue 1)
- Minor improvements to user interface, including logic, optimisations, and bugfixes
- Minor optimisations to core modules

Bug Fixes

- Removed non-implemented chemical species
- Fixed breaking bug in _2&theta;_ to _Q_ conversion toolbox
- Updated usage of code deprecated in dependencies
- Fixed small errors in LiquidDiffract/scripts/
- Fixed rebinning errors when raw data has nans
- Minor bugfixes in core modules

Development Changes

- This changelog!
- Unit tests / functional tests for core module.
run `python -m unittest discover ./tests - v`
- Unit tests run remotely on push to develop branch via github actions.
Test matrix of:
os: [ubuntu-latest, macos-latest, windows-latest]
python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
- Dropped support for python < 3.8
Python 3.8 support maintained via importlib_resources. Support will be dropped in next release.

Bug Fixes

- Fixed a breaking bug due to the deprecation of np.float/np.int/np.str etc. as of numpy v1.20.0 in favour of built-in types.
- Fixed some possible buggy behaviour in user inputs

Minor Changes

- An option has been added to plot log(_I(Q)_) in the background subtraction tab to make small differences between the measured and background _I(Q)_ more obvious.
- Added a prompt to select a file header when a file load error occurs.

Patch release to fix errors in tabulated Compton scattering data

* The data in LiquidDiffract/LiquidDiffract/resources/hubbel_compton/ was incorrect for several elements due to a filename issue. Some filenames dropped a character and overwrote data for elements with single-character symbols. The affected elements were C, F, N, P, and S, and data for Ac, Am, Cm, Fm, Np, Pm, Sc, Tc, and Tm were missing. Using Hg resulted in a (crashing) error due to a mislabeling as hg. Data has been corrected for all elements and now matches the human-readable tabulations in LiquidDiffract/LiquidDiffract/resources/human_readable/hubbel_compton/

Patch release to fix minor (but crashing) bug in v1.1.9 when using Python v>=3.10

* LiquidDiffract/gui/optim_ui.py line 705: setResizeMode --> setSectionResizeMode
The QHeaderView attribute setResizeMode is deprecated in PyQt5 and causes an AttributeError in some version combinations of PyQt5 and Python. setSectionResizeMode replaces it and is compatible with all versions.

Major Changes

- **Background refinement**
The background scaling factor (_b_) can now be refined alongside the density in the _Refinement Tab_
Background refinement is optional and can be done independently from or simultaneously with density refinement.
The background scaling factor set in the _Background Subtraction Tab_ is used as the initial estimate by the solver.
The figure of merit is redefined to take into account the background scaling - _&Chi;_^2(&rho;;b)

- **LiquidDiffract publication**
There is now a paper describing LiquidDiffract:
[Heinen, B. J., & Drewitt, J. W. (2022). LiquidDiffract: Software for liquid total scattering analysis. Physics and Chemistry of Minerals, 49:9. doi:10.1007/s00269-022-01186-6](https://link.springer.com/content/pdf/10.1007/s00269-022-01186-6.pdf)
Please cite this paper if you use LiquidDiffract in your work!

Minor Changes

- LiquidDiffract.core.core now uses a separate objective function for density and/or background refinement - core.refinement_objfun.
As a result, the arguments taken by core.calc_impr_interference_function have been redefined. The docs and example scripts have been updated to reflect this.
- Fixed some documentation issues and removed some dead code