GenX Files

This package contains GenX 3.6 a program to refine x-ray and neutron reflectivity as well as surface x-ray diffraction using differential evolution. It can also serve as a general fitting program.

Support
=======
Tutorials can be found at: http://genx.sourceforge.net/doc/
Examples can be found in the Menu Help->Examples.
If you need more support send an e-mail to artur.glavic@psi.ch.

References
==========
If you use the program please give reference to the following publication:
A. Glavic and M. Björck J. Appl. Cryst. 55, 1063-1071 (2022).

Changes 3.6.27
==============
 * Fix bug when using log function within column calulation that prohibited use of D17 dataloader.

Changes 3.6.26
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 * Add documentation tutorial about ORSO file integration.
 * Update of SNAP builde system, should allow use with Waylend and fix some other minor issues.
 * Update of Windows build libraries for additional functionality.
 * Add debian build for newer Ubuntu versions (22.04 / 24.04). See documentation for installation details.
 * Add a GUI dialog when critical python errors occure that required console/logging to be noticed before.
 * Fix incompatibility with numpy 2.x due to bool/numpy.bool confusion.

Changes 3.6.25
==============
 * Fix bug in MagSLD where magnetization was reported 10x too high in graph (see Ticket #205).
 * Fix inconsistent behavor for x-values <=0 (see Ticket #201).

Changes 3.6.24
==============
 * Add compatibility to ORSO binary format.
 * Export ORSO simple model language description of GenX simulation in ORT export.
 * Accept ORSO datasets for new models using drag-n-drop.
 * Fix ORSO export for current orsopy version.

Changes 3.6.23
==============
 * Fix plot style dialog not working on newer version of WX.
 * Fix handling of some chemical formulae.
 * Fix issue when closing the GUI through the menu.

Changes 3.6.22
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 * Fix a bug with the update code for newer urllib3 versions (see PR #5, thanks to azelcer)
 * Upgrade windows build to python 3.11 and recent libraries.

Changes 3.6.21
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 * Add data loader for nja XRR file format.
 * Add pint and latest orsopy to binary distributions to allow for better parsing of .ort metadata.
 * Fix the Bumps error dialog filling the wrong error ranges into the parameter grid.
 * Fix a multiprocessing logger related bug that crashes the program under certain circumstances.

Changes 3.6.20
==============
 * Fix Rigaku data loader to include attenuation factors.

Changes 3.6.19
==============
 * Introduce crop_sigma sample option to spec_adaptive model that allows to limit the
   influence of the interface transition function within the adjacent layers.
   Thanks to Rico Ehrler for the suggestion.

Changes 3.6.18
==============
 * Update gsecars_ctr data loader to detect additional columns by first header line
 * Some minor fixes for wxPython 4.2.0 and newer numba

Changes 3.6.17
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 * Use single numba cache directory for any GenX executable, speeding up program start 
 * Fix multiprocessing fit stuck in Windows binary
 * Better logging and error reporting in multiprocessing fit

Changes 3.6.16
==============
 * Improve error handling and allow forcefull termination of multiprocessing fits
 * Add full logging support when running fit with multiprocessing
 * Add caching of GPU kernels for newver versions of numba
 * Correctly count the number of functions to be compiled with numba
 * Fix error when trying to use multiprocessing fit without numba installed

Changes 3.6.15
==============
 * Add new LayerGraphics plugin that creates a simple sketch drawing for reflectometry models
   to use in presentations etc.
 * Update the Mac build system to Mac OS 12 and system python 3.10 using new wxPython 4.2 PyPI package

Changes 3.6.14
==============
 * Fix re-compilation of numba code when opening project filed directly on Windows
 * Add some NeXus file attributes to the .hgx file format to allow plotting of the data e.g. with nexpy
 * Small change to the MacOS configuration that should support file type filtering in open dialog

Changes 3.6.13
==============
 * Fix a bug where exporting the script with special characters raised an error under windows (ticket #197)
 * Fix some bugs in export and parsing of .ort files
 * Some refactoring

Changes 3.6.12
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 * Fix a bug where fitting from console with autosave and --error options stopped the fit after first autosave
 * Improve the meta data editing capability

Changes 3.6.11
==============
 * Update the ORSO file definition to version 1.0.0 released recently
 * Modify the metadata dialog to allow adding and editing values
 * Add a new data loader for the Rigaku .ras format
 * Fix default and resolution loader to ignore non utf-8 encoded values

Changes 3.6.10
==============
 * Implement a tech-preview using alternative plotting backend with improved performance
   (selected in Settings -> Startup Profile... menu.)
 * Automatically restart the window when switching from legacy to widescreen layout.

Changes 3.6.9
=============
 * First version of MacOS binary distribution
 * Add new script "genx_mac" to PyPI package to start with framework build (pythonw)
 * Allow file names with upper case endings (.GX/.HGX)
 * Try to fix some plot drawing issues on some Linux systems with Wayland backend.
 * Open GenX model files on drag&drop to the window (if not above data list)
 * Fix GUI not remembering a model is unchanged after loading from a file
 * Fix bug where the parametr grid could be wrong after loading a model while value editor was active

Changes 3.6.8
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 * Fix a bug where values for the instrument parameters where parsed by int type if the script used integer values
 * Fix a compatibility issue with older wxPython/wxWidgets that would prevent genx from starting on fedora 35
 * Fix issues when running numba together with multiprocessing on UNIX bases systems due to fork method

Changes 3.6.7
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 * Fix compatibility with python 3.6-3.7

Changes 3.6.6
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 * Fix wx dialog issue where instrument editor in advanced reflectivity would not work (thanks to Leon Lohse)

Changes 3.6.5
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 * Fix parameter grid value cell out of bounds coloring lost after loading a new model

Changes 3.6.4
=============
 * Add simple syntax completion, object help and undo/redo to script editor. To use
   try ctrl+enter, shift+ctrl+enter, ctrl+alt+Z or shift+ctrl+alt+Z.
 * Do not raise an error when starting a fit with parameters outside of min/max boundaries
   if the optimizer does not use them. (ticket #175)
 * Fix compatibility issue with python 3.10, tested with wxPython 3.1.1 and 3.1.2a

Changes 3.6.3
=============
 * Fix a bug that could lead to a strange error messages when editing items in the Simulations tab.
 * Fix a crash on Linux when running the bumps dialog depending on wx version
 * Fix an issue where genx would not start on macOS environments with python >=3.9 and anaconda

Changes 3.6.2
=============
 * Add finite polarization effects for neutron reflectivity to spec_nx, spec_adaptive and spec_inhom models.
   To use you have to select instrument probe as "neutron pol spin-flip" and change the simulation function
   from "Specular" to "PolSpecular". This function has 4 additional parameters; p1, p2, F1, F2 for 
   polarizer, analyzer and filpper efficiencies. For definition see https://doi.org/10.1063/1.1150060
 * Update UserFuncs pluging to work with type-annotated functions to generate user dialogs automatically.
   The SXRD.hgx example shows a usage for storing XYZ files.
 * Add entry to the **Help** menu to open example files, directly jumping to the right directory.
   About dialog now shows the path where configuration files are stored.
 * Fix a bug where editing the script in some circumstances would loose lines.

Changes 3.6.1
=============
 * Add a batch processing interface to the GUI. This can be accessed through the File dialog. See
   new **Batch Fitting** section of the documentation.
 * Add generic definition for plot x- and y-labels. Build-in models define the values depending on last simulated
   scans and user can always overwrite in script with **__xlabel__** and **__ylabel__** special variables.
 * Add detailed documentation about SLD plot configuration and batch processing
 * Add more unit tests for models and loading/saving
 * Fix remote fit crashing server when ending normally instead of being stopped by the user

Changes 3.6.0
=============
 * Add new genx_server (python -m genx.server) script that allows to run a remote service
   on a cluster that can be used to fit from a GUI on a different machine.
   See: https://aglavic.github.io/genx/doc/tutorials/mpi.html for more information.
 * Implement asymmetric errors from bumps statistics, fix some bugs and add option to normalize parameter
   uncertainties by sqrt(chi2) to eliminate scaling factors on error bars. (see ticket #190)
 * New command line parameters for better control of refinement and performance
 * Improve console and logging output on MPI runs, q+<enter> can now stop a fit started with MPI
 * Fix some command line options
 * Allow changing of plot scales with mouse scroll wheel and ctrl-/alt-/shift-modifier, 
   always reset zoom with middle mouse button
 * Improve SLD plot context menu, allowing to show only first dataset, 
   external legend or coloring associated with datasets
 * Option to generate a SLD uncertainty graph based on a user-defined reference interface
 * Do not show separate mag_x SLD for neutron magnetic reflectivity, if there is no mag_y component
 * Slight improvement or SXRD model performance
 * Add a genx3server PyPI package without GUI package requirements
 * Updates on documentation concerning use from command line
 * Startup script to automatically select pythonw when run on Mac OS (untested)
 * Fix some more minor bugs

Changes 3.5.11
==============
 * Fix export of Table
 * Fix bumps statistics setting the error column of the parameter table
 * Add documentation for Norm FOM