Viperleed

See betatest repository for executable.

**Note:** This release is mainly for archival purposes and can be considered a "Golden Master" version before the soon to be released v1.0.0.

What's Changed
* The Installable viperleed branch by amimre has been merged (see https://github.com/viperleed/viperleed/pull/94). This makes viperleed pip installable and brings a major refactoring of the project structure.
* Improve utilities by michele-riva in https://github.com/viperleed/viperleed/pull/196
* Compatibility with new TensErLEED organization, version numbers and TensErLEED v2.0.0 by amimre in https://github.com/viperleed/viperleed/pull/207
* Major updates to the docs with the installable branch.
* TensErLEED is no longer contained in the main viperleed repository. Instead it is hosted on https://github.com/viperleed/viperleed-tensorleed

**Full Changelog**: https://github.com/viperleed/viperleed/compare/v0.11.0...v0.12.0

- Refactor and improve POSCAR read/write (91)
- Refactor and improve Slab (114)
- Update license (93)
- warn for ambiguous PHI (71)
- utility to write file for VASP (98, expanded on in the installable branch)
- More general PoscarReader/Writer and some refactor (100)
- Fix beamgen (106)
- Refactor tests (102)
- Add some more structure to classes.layer (110)
- Partial cleanup of Atom (112)
- Ensure compatibility with python v3.7 (126, 173)
- Fix search segfault by (128)
- Faster tests by (127)
- Refactor parameters file (130)
- Fe2O3 Example (177)
- Fix 187

- fixed slab transformation (76)
- input files saved to history are now unmodified version from work/original_inputs
- fixed race condition in structure optimization when control.chem is read during write
- implemented more consistency/syntax checks for PARAMETERS
- unrecognized parameters raise error instead of being silently ignored
- implement a style sheet with font type 42 by default (85, 77)
- better unit tests for ASE interface
- unit tests for parameters
- replaced the Fortran beamgen script by a Python version (60)
- updated viperleed conda environments

- reworked the output of the error calculation and added estimates of statistical errors of parameters.
- added parameter "ZIP_COMPRESSION_LEVEL".
- various clarifications in the documentation.
- catch IEEE errors in superpos output.
- changed SD.TL output interval to fit parameter dgen.
- improved PHASESHIFTS consistency checks.
- suppress warning for non-available f2py package.
- various bug fixes.

- completely overhauled the documentation. Added missing pages, sections and example systems.
- updates to the ASE interface.
- various fixes related to plotting.
- fix level R+var(R) in Errors.pdf.
- fixed issue with gfortran compiler options.
- add option for checksum computation of TensErLEED code (and parameter TL_IGNORE_CHECKSUM).
- fix issue with LMAX > 16 in delta-amplitudes and search.
- fix various issues for importing tleedm.
- better handling of compile logs.
- fix mix ups in symmetry reduction.
- improved log messages.
- removed case-sensitivity in element names for consistency.

See betatest repository for executable.

- job.py can accept ViPErLEED source code and working directories via command line arguments.
- Include .yml files with recommended conda environments for running ViPErLEED calculation.
- New version of R-factor calculation with a compiled python module. This is in testing stage and can be enabled with the option R_FACTOR_LEGACY = False.
- Added a Makefile for beamgen and EASiSSS.
- Added an API to call ViPErLEED refcalc from ASE atoms objects and calculate R-factor between two THEOBEAMS.csv files. (not part of tleedm)
- Enabled more general unit cell operations on slab objects.
- Fixes backwards compatibility issue with TensErLEED v1.72.
- Fixes issue in Tensor output of TensErLEED v1.73.
- Fixes issue in symmetry reduction for hexagonal to cm.

ImageJ plugin:
- Added macro scripting capabilities.
- Enabled reading I_00 from dark frames.
- More help buttons.
- Ability to set parameters from log file of previos Spot Tracker output.
- Various bug fixes.