Pace-neutrons

* New features
- Add support for Horace parallel framework. Use `m.hpc('on')` to activate and then set the cluster type `m.hpc_config().parallel_cluster = <x>` where `<x> = 'parpool'`, `'herbert'` or `'mpiexec_mpi'`.

* Bugfixes
- Fix bug where Matlab `+namespaces` were not accessible in Python
- Several small bugs when using with Spyder.

[v0.1.4](https://github.com/pace-neutrons/pace-python/compare/v0.1.3...v0.1.4)

* New features
- New `pace_neutrons` wrapper script to launch PACE, setting all needed paths
- Can also launch jupyter or spyder with `pace_neutrons --spyder` or `pace_neutrons --jupyter`
- Facility to download and install MCR automatically or on first use

* Bugfixes
- If neither spyder or jupyter installed will use IPython (now a dependency)
- Fix logic error in searching for MCR runtime DLL. Will use registry on Windows.

[v0.1.3](https://github.com/pace-neutrons/pace-python/compare/v0.1.1...v0.1.3)

Updated to Horace 3.6.1.

* Bugfixes
- Fix MatlabProxyObject `__setattr__` - can now do e.g. `h = m.herbert_config(); h.use_mex = True`
- Fix `worker_v2 not found in initialisation` error
- Fix DataTypes.py encoding list recursion.

[v0.1.1](https://github.com/pace-neutrons/pace-python/compare/v0.1.0...v0.1.1)

Initial public beta version of pace_python.

Please download the `pace_python_matlab_installer` file for your OS and run it. This will install the Matlab Runtime and a GUI installer app. Run the installer app (`pace_python_installer`) which will install miniconda and the `pace_python` module (if you have an existing Python installation you wish to use, select `Custom Installation` in the app).

If you select `Jupyter` and/or `Spyder` (both recommended) in the `Default Installation` option, then after the installation finishes, you will see links to Jupyter and Spyder in your start menu (on Windows) which you can use to start Jupyter/Spyder with pace-python. Then run:


import pace_python
m = pace_python.Matlab()
m.horace()


To start the Horace GUI.

If you have any problems, please create an issue on this repository.


`Unreleased <https://github.com/pace-neutrons/Euphonic/compare/v0.6.4...HEAD>`_
----------

- Bug fixes:

- Allow read of ``phonopy.yaml`` quantities in ``'au'`` (bohr) units.
Previously this was interpreted as an astronomical unit by Pint.

------

- Improvements:

- The ``euphonic-dos``, ``euphonic-dispersion`` and
``euphonic-intensity-map`` command-line tools can now read
files that don't contain eigenvectors, if eigenvectors are
not required for the chosen options.
- A new ``--save-json`` option is available for command-line tools
which produce plots, this will output the produced spectrum to
a Euphonic .json file.
- There is now the option to use a fast, approximate variable-width broadening method when
adaptively broadening dos:

- Added new ``adaptive_method`` and ``adaptive_error`` arguments for ``calculate_dos``
which specify which adaptive broadening method to use (``reference`` or ``fast``) and an
acceptable error level when using the ``fast`` method.
- Fast adaptive broadening can be used in the ``euphonic-dos`` tool with the
``--adaptive-method`` and ``--adaptive-error`` arguments.

- Changes:

- ``euphonic.cli.force_constants_from_file`` and ``modes_from_file``
have been deprecated in favour of ``euphonic.cli.load_data_from_file``.
- Using ``Spectrum1D/1DCollection/2D.broaden`` on an axis with unequal
bin widths is now deprecated, as broadening is performed via convolution,
which is incorrect in this case. In the future, this will raise a
``ValueError``. To broaden anyway, ``method='convolve'`` can be supplied,
which will just emit a warning.

------

- New Features:

- New ``Spectrum1D.to_text_file`` and ``Spectrum1DCollection.to_text_file``
methods to write to column text files

- An expanded and consistent set of styling options is made
available for command-line tools that produce plots.

- Consistent styling and advanced changes can be made using
Matplotlib stylesheet files, either as a CLI argument or
using ``matplotlib.style.context()`` in a Python script.

- Improvements:

- Internally, plot theming has been adjusted to rely on Matplotlib
style contexts. This means user changes and style context are more
likely to be respected.
- Additional aliases for plot arguments in the command-line tools have
been added, for example either ``--x-label`` or ``--xlabel`` can be used.

- Changes:

- ``x_label``, ``y_label``, ``y_min`` and ``y_max`` in ``euphonic.plot``
functions have been deprecated in favour of ``xlabel``, ``ylabel``,
``ymin`` and ``ymax`` respectively, to match the Matplotlib arguments
they refer to, and to match other arguments like ``vmin``, ``vmax``.

------

- Improvements:

- Wheels are now provided with PyPI releases
- Type hinting is now handled more consistently across different Euphonic
classes and functions

- Bug Fixes:

- Will no longer raise a KeyError reading from ``phonopy.yaml`` if
``physical_unit`` key is not present, instead will assume default units
- Can now read Phonopy BORN files where the (optional) NAC conversion
factor is not present

------

- Bug fixes:

- The scaling of S(Q,w) as produced by ``StructureFactor.calculate_sqw_map``
was incorrect, and did not correctly scale with energy bin size (given its
units are now ``length**2/energy``). This has been fixed, and S(Q,w) scale
has changed by a factor of (hartee to energy bin unit conversion)/(energy
bin width magnitude). e.g. if using an energy bin width of 0.1 meV, the new
S(Q,w) will be scaled by 2.72e4/0.1 = 2.72e5. The original structure factors
can now be correctly recovered by multiplying S(Q,w) by the energy bin width.

------

- Euphonic can now calculate neutron-weighted partial density of states, and
has new ``Spectra`` features to handle PDOS data:

- Added ``QpointPhononModes.calculate_pdos`` method
- Added ``QpointFrequencies.calculate_dos_map`` method
- New ``Spectrum1D.__add__`` method, which adds 2 spectra together
- New ``Spectrum1DCollection.__add__`` method, which concatenates 2 collections
- Enabled indexing of ``Spectrum1DCollection`` by a sequence
- Added ``Spectrum1DCollection.group_by`` method, which allows grouping and
summing spectra by metadata keys e.g. ``group_by('species')``
- Added ``Spectrum1DCollection.select`` method, which allows selection
of spectra by metadata keys e.g. ``select(species='Si')``
- Added ``Spectrum1DCollection.sum`` method, which sums all spectra in a
collection
- Added ``-w={'coherent-dos','incoherent-dos','coherent-plus-incoherent-dos'}``
neutron-weighted PDOS options to ``euphonic-dos`` and ``euphonic-powder-map``
- Added ``--pdos`` options for plotting specific species PDOS to
``euphonic-dos`` and ``euphonic-powder-map``
- Deprecated ``--weights`` command-line argument in favour of ``--weighting``
for consistency with ``calculate_pdos``

- Improvements:

- LICENSE and `CITATION.cff <https://citation-file-format.github.io/>`_
files are now included in Euphonic's installation
- Add ability to interactively change the colormap intensity limits
in ``euphonic-powder-map``
- ``euphonic-optimise-dipole-parameter`` can now read from Phonopy sources
- ``euphonic-optimise-dipole-parameter`` can now also be used for non-polar
materials to get general per-qpoint timings
- Dimensioned Euphonic properties (e.g. ``frequencies``, ``cell_vectors``)
now have setters so can be set, previously this would raise an
``AttributeError``

- Changes:

- The units of density of states as produced by ``calculate_dos`` have
changed from dimensionless to ``1/energy``
- The scaling of density of states has also changed. Previously the
integration would sum to 1 (if the ``x_data`` were converted to Hartree
units), now the integration will sum to 3N in the same units as ``x_data``
- ``StructureFactor.structure_factors`` have been changed to be in absolute
units per atom (rather than per unit cell) so will have changed by a
factor of `1/2*n_atoms`, this formulation change has been reflected in the
``calculate_structure_factor`` docstring
- The default unit of ``StructureFactor.structure_factors`` has been changed
from ``angstrom**2`` to ``millibarn``
- The unit of S(Q,w) as produced by ``StructureFactor.calculate_sqw_map``
has changed dimension from ``length**2`` to ``length**2/energy``. Also,
as its unit is derived from the input ``StructureFactor`` object, its
default units are now ``millibarn/meV``
- The ``eta_scale`` argument in ``calculate_qpoint_phonon_modes`` has been
deprecated, ``dipole_parameter`` should be used instead.
- This means the ``euphonic-optimise-eta`` script has been renamed to
``euphonic-optimise-dipole-parameter``.