0.9.62

bugfixes:

• XAS_Viewer: Feff-fitting paths (and so also parameters) are refreshed for each fit (#377, #374)
• XAS_Viewer: most main windows are now resizable (#372)
• better checking and auto-pip-installing of wxutls and wxmplot (#376)

0.9.61

[0.9.61 - 2022-05-26]

Added

• XAS Viewer: Entries for the fit histories of pre-edge peak fitting and Feff fitting can now be erased.

Fixed

• XAS Viewer: the merging of groups now works ;).
• XAS Viewer: setting and energy shift for a group will copy that shift to other groups with the same energy reference. There is a preference setting to turn off this automated copying of energy shifts.
• XAS Viewer: fixed very slow plotting -- now just back to normal "not fast".
• XAS Viewer: dialogs have generally better sizes.
• XAS Viewer: fixes for plotting of Pre-edge peak fits.
• XAS Viewer: improvements in Journal entries for some processed groups.
• XAS Viewer: fixes for combining default and per-group configuration.

0.9.60

[0.9.60 - 2022-05-23]

Release announcement

Added

• each Group of XAFS data will have a Journal - a list of entries with (label, value, timestamp) that will be used to record processing steps. The XAFS processing functions will write the parameters they were called with to this Journal. Users can add notes as Journal entries too.

• XAS Viewer allows editing of program-wide Preferences, that set the default values and settings for the various analysis steps and program behavior.

• In many windows showing analysis results, XAS Viewer supports setting the plot window number (1 through 9) so that more than one or two plot windows can be shown at a time.

• Session-wide Project files (.larix extension) can now be saved and reloaded. These files contain essentially all the arrays for each Group of data, including Journals, processing results, and fit histories. The "processing workspaces" for pre-edge peak fitting, PCA, Linear Combinations, Regressions, and Feff fitting. These Session files can be saved/loaded by plain Python commands. When loading these into XAS Viewer, the fit histories and workspaces will be available. To allow better debugging and tracking of provenance, these Session Files include "configuration" data about the Session (python, larch version, etc) and a complete set of Larch commands for the session, though session commands are not "restored". The files are compressed and use a customized JSON encoding.

• These Session files are now auto-saved by XAS Viewer periodically (every 15 minutes of activity, by default, and rotated so that a small number (3, by default) of the most recent auto-saved files are kept. On startup, "restore the last session" is available (Ctrl-I).

Fixed

• XAS Viewer PCA fixed.
• XAS Viewer now displays how each Group was created, for example "-log(i1/i0)".
• XAS Viewer panels have more uniform energy range settings, relative to E0, per group.
• XAS Viewer has more consistent coloring and font sizes.
• XAS Viewer Quit dialog now lists the last saved Session file.
• XAS Viewer now works even harder to keep _xasgroups correct.
• pycifrw added as a dependency from conda-forge
• copying parameters from one group to another is much improved.
• rebinning of EXAFS data better avoids duplicate energies.
• a few bugs with the handling of some CIFs were improved
• Feff calculations now default to L3 edge for Z>= 60.
• Python 3.10 is better supported, Python 3.7 seems to still work.

0.9.59

[0.9.59 - 2022-04-01]

Release announcement

Added

• Reading files from FDMNES.
• XAS Viewer allows reading in a reference spectrum from the same file as a spectrum.
• XAS_Viewer better supports each spectrum having an "energy reference spectrum". This
  can be set on reading spectra, or afterward. Recalibrating energies can propagate
  calibrations to spectra that share a reference.
• XAS Viewer better supports an "energy shift" for each spectrum -- this can be copied
  to other spectra or "undone" to go back to the original (as read-in) data.
• XAS Viewer: data can be deglitched while plotting in "k" space"
• XAS Viewer: "flattened" spectra can be used for linear analysis in more places.
• Example using Jupyter and Fe pre-edge peaks.

Changed

• XAS Viewer: the action of the "pin icon" for selecting points from a plot has now changed.
  Previously hitting the pin icon meant "use most recently clicked point on plot". Now,
  hitting the pin icon starts a timer which will look for mouse clicks after hitting
  the pin icon:
  a) if there are new mouse clicks on the plot, wait at least 3 seconds, and return
  the most recent position.
  b) if there are no mouse clicks after 15 seconds, return the most recent position
  (even before clicking on the pin)

Fixed

• Reading columns names from one-line header, and for files that announce as XDI but
  break XDI specs (say, by having >128 columns).
• Better handling of CIFs with partial occupancy when generating feff.inp.
• NLEG is set to 6 by default when generating feff.inp.
• By default, hydrogen atoms are removed when generating feff.inp (XAS Viewer and cif2feff)
• Athena project files with very long journals are better supported.
• Some permission problems for the installation of Applications on MacOS have been avoided.
• "get current working directory" is now tested uniformly for permission errors.
• MapViewer: more robust and flexible search for tomographic rotation axis.
• Fix for spec/HDF5 files with broken "scan" link.
• XRF Display spectral fitting: faster, better guesses for parameter scales, and show
  filled eigenvectors (wxmplot 0.9.49)
• MapViewer / XRF Display: much improved ADD ROIs, including pushing XRF ROIs added in
  XRF Display back to the list in Mapviewer.
• MapViewer: The order of ROIs added is now preserved, including for work arrays and
  Abundances from XRF analysis.

Removed

• Plugins are now completely removed
• 32-bit Windows is no longer supported: libraries and executables have been removed.
• Cromer-Libermann is more deprecated and hidden (but not completely gone, yet)

0.958

This release is mostly a set of bug fixes related to installation issues.

0.9.57

[0.9.57 - 2021-12-02]

Added

• Read RIXS files from BM16 at ESRF.
• Option --devel in GetLarch.sh to install from source.
• xas_viewer
  • File->Save as

Changed

• Module rixsdata moved from larch.qtrixs to larch.io
• Force UTF8 encoding in read_ascii
• xas_viewer
  • File->Save overwrites by default.
  • Better deglitching dialog, including viewing data as chi(E).
  • Loading a Peak Model is now allowed at any time.
  • Default Project filenames are taken from timestamp.

Fixed

• Problem with yaml load in GetLarch.sh
• Problem in interpolation with nearly repeated x values
• Messages reporting progress when processing XRF Maps
• Reading Athena Project files with non-ASCII characters

0.9.56

many small fixes, especially to be compatible with lmfit version 1.0.3

0.9.55

update action badges

0.9.53

[0.9.53 - 2021-07-02]

Fixed

• XAS viewer
  • fixed various bugs in Spec/BLISS files importer -- silx version 0.15.2 is now required.
  • "GetLarch.sh" and "GetLarch.bat" scripts now use "miniforge", should provide faster downloads and installs.
  • fixed (hopefully) random Text controls events on startup on Windows.
  • several small improvement feffpath and feffit functions for better managing Path Parameters with lmfit

Added

• XAS viewer
  • Add GUI Browser for CIF Files from American Mineralogist Crystal Structure Database
  • Code for converting CIF files to feff6/8 input files, GUI form to run Feff, organize results in users .larch/feff folder
  • Feff Path Browser for import Feff.dat files from .larch/feff
  • Feffit Tab added to XAS Viewer for (1 data set) Feff Fitting, with history of fits, saving of fit script.
  • EXAFS Panel can show chi(q) data.

0.9.53rc1

test of 0.9.53