Hyperspy

===================

Bug Fixes
---------

- Allows for loading of ``.hspy`` files saved with version 2.0.0 and greater and no unit or name set
for some axis. (`3241 <https://github.com/hyperspy/hyperspy/issues/3241>`_)


Maintenance
-----------

- Backport of 3189: fix Numpy1.25 deprecation: implicite array to scalar conversion in :py:meth:`~.api.signals.Signal2D.align2D` (`3243 <https://github.com/hyperspy/hyperspy/issues/3243>`_)
- Pin pillow to <10.1 to avoid imageio error. (`3251 <https://github.com/hyperspy/hyperspy/issues/3251>`_)


.. _changes_1.7.5:

===================

Bug Fixes
---------

- Fix plotting boolean array with :py:func:`~.api.plot.plot_images` (`3118 <https://github.com/hyperspy/hyperspy/issues/3118>`_)
- Fix test with scipy1.11 and update deprecated ``scipy.interpolate.interp2d`` in the test suite (`3124 <https://github.com/hyperspy/hyperspy/issues/3124>`_)
- Use intersphinx links to fix links to scikit-image documentation (`3125 <https://github.com/hyperspy/hyperspy/issues/3125>`_)


Enhancements
------------

- Improve performance of `model.multifit` by avoiding `axes.is_binned` repeated evaluation (`3126 <https://github.com/hyperspy/hyperspy/issues/3126>`_)


Maintenance
-----------

- Simplify release workflow and replace deprecated ``actions/create-release`` action with ``softprops/action-gh-release``. (`3117 <https://github.com/hyperspy/hyperspy/issues/3117>`_)
- Add support for python 3.11 (`3134 <https://github.com/hyperspy/hyperspy/issues/3134>`_)
- Pin ``imageio`` to <2.28 (`3138 <https://github.com/hyperspy/hyperspy/issues/3138>`_)


.. _changes_1.7.4:

===================

Bug Fixes
---------

- Fixes an array indexing bug when loading a .sur file format spectra series. (`3060 <https://github.com/hyperspy/hyperspy/issues/3060>`_)
- Speed up ``to_numpy`` function to avoid slow down when used repeatedly, typically during fitting (`3109 <https://github.com/hyperspy/hyperspy/issues/3109>`_)


Improved Documentation
----------------------

- Replace ``sphinx.ext.imgmath`` by ``sphinx.ext.mathjax`` to fix the math rendering in the *ReadTheDocs* build (`3084 <https://github.com/hyperspy/hyperspy/issues/3084>`_)


Enhancements
------------

- Add support for Phenom .elid revision 3 and 4 formats (`3073 <https://github.com/hyperspy/hyperspy/issues/3073>`_)


Maintenance
-----------

- Add pooch as test dependency, as it is required to use scipy.dataset in latest scipy (1.10) and update plotting test. Fix warning when plotting non-uniform axis (`3079 <https://github.com/hyperspy/hyperspy/issues/3079>`_)
- Fix matplotlib 3.7 and scikit-learn 1.4 deprecations (`3102 <https://github.com/hyperspy/hyperspy/issues/3102>`_)
- Add support for new pattern to generate random numbers introduced in dask 2023.2.1. Deprecate usage of :py:class:`numpy.random.RandomState` in favour of :py:func:`numpy.random.default_rng`. Bump scipy minimum requirement to 1.4.0. (`3103 <https://github.com/hyperspy/hyperspy/issues/3103>`_)
- Fix checking links in documentation for domain, which aren't compatible with sphinx linkcheck (`3108 <https://github.com/hyperspy/hyperspy/issues/3108>`_)


.. _changes_1.7.3:

===================

Bug Fixes
---------

- Fix error when reading Velox containing FFT with odd number of pixels (`3040 <https://github.com/hyperspy/hyperspy/issues/3040>`_)
- Fix pint Unit for pint>=0.20 (`3052 <https://github.com/hyperspy/hyperspy/issues/3052>`_)


Maintenance
-----------

- Fix deprecated import of scipy ``ascent`` in docstrings and the test suite (`3032 <https://github.com/hyperspy/hyperspy/issues/3032>`_)
- Fix error handling when trying to convert a ragged signal to non-ragged for numpy >=1.24 (`3033 <https://github.com/hyperspy/hyperspy/issues/3033>`_)
- Fix getting random state dask for dask>=2022.10.0 (`3049 <https://github.com/hyperspy/hyperspy/issues/3049>`_)


.. _changes_1.7.2:

===================

Bug Fixes
---------

- Fix some errors and remove unnecessary code identified by `LGTM
<https://lgtm.com/projects/g/hyperspy/hyperspy/>`_. (`#2977 <https://github.com/hyperspy/hyperspy/issues/2977>`_)
- Fix error which occurs when guessing output size in the :py:meth:`~.api.signals.BaseSignal.map` function and using dask newer than 2022.7.1 (`2981 <https://github.com/hyperspy/hyperspy/issues/2981>`_)
- Fix display of x-ray lines when using log norm and the intensity at the line is 0 (`2995 <https://github.com/hyperspy/hyperspy/issues/2995>`_)
- Fix handling constant derivative in :py:meth:`~.api.signals.Signal1D.spikes_removal_tool` (`3005 <https://github.com/hyperspy/hyperspy/issues/3005>`_)
- Fix removing horizontal or vertical line widget; regression introduced in hyperspy 1.7.0 (`3008 <https://github.com/hyperspy/hyperspy/issues/3008>`_)


Improved Documentation
----------------------

- Add a note in the user guide to explain that when a file contains several datasets, :py:func:`~.api.load` returns a list of signals instead of a single signal and that list indexation can be used to access a single signal. (`2975 <https://github.com/hyperspy/hyperspy/issues/2975>`_)


Maintenance
-----------

- Fix extension test suite CI workflow. Enable workflow manual trigger (`2982 <https://github.com/hyperspy/hyperspy/issues/2982>`_)
- Fix deprecation warning and time zone test failing on windows (locale dependent) (`2984 <https://github.com/hyperspy/hyperspy/issues/2984>`_)
- Fix external links in the documentation and add CI build to check external links (`3001 <https://github.com/hyperspy/hyperspy/issues/3001>`_)
- Fix hyperlink in bibliography (`3015 <https://github.com/hyperspy/hyperspy/issues/3015>`_)
- Fix matplotlib ``SpanSelector`` import for matplotlib 3.6 (`3016 <https://github.com/hyperspy/hyperspy/issues/3016>`_)


.. _changes_1.7.1:

===================

Bug Fixes
---------

- Fixes invalid file chunks when saving some signals to hspy/zspy formats. (`2940 <https://github.com/hyperspy/hyperspy/issues/2940>`_)
- Fix issue where a TIFF image from an FEI FIB/SEM navigation camera image would not be read due to missing metadata (`2941 <https://github.com/hyperspy/hyperspy/issues/2941>`_)
- Respect ``show_progressbar`` parameter in :py:meth:`~.api.signals.BaseSignal.map` (`2946 <https://github.com/hyperspy/hyperspy/issues/2946>`_)
- Fix regression in :py:meth:`~hyperspy.models.model1d.Model1D.set_signal_range` which was raising an error when used interactively (`2948 <https://github.com/hyperspy/hyperspy/issues/2948>`_)
- Fix :py:class:`~.api.roi.SpanROI` regression: the output of :py:meth:`~.roi.BaseInteractiveROI.interactive` was not updated when the ROI was changed. Fix errors with updating limits when plotting empty slice of data. Improve docstrings and test coverage. (`2952 <https://github.com/hyperspy/hyperspy/issues/2952>`_)
- Fix stacking signals that contain their variance in metadata. Previously it was raising an error when specifying the stacking axis. (`2954 <https://github.com/hyperspy/hyperspy/issues/2954>`_)
- Fix missing API documentation of several signal classes. (`2957 <https://github.com/hyperspy/hyperspy/issues/2957>`_)
- Fix two bugs in :py:meth:`~.api.signals.BaseSignal.decomposition`:

* The poisson noise normalization was not applied when giving a `signal_mask`
* An error was raised when applying a ``signal_mask`` on a signal with signal dimension larger than 1. (`2964 <https://github.com/hyperspy/hyperspy/issues/2964>`_)


Improved Documentation
----------------------

- Fix and complete docstrings of :py:meth:`~.api.signals.Signal2D.align2D` and :py:meth:`~.api.signals.Signal2D.estimate_shift2D`. (`2961 <https://github.com/hyperspy/hyperspy/issues/2961>`_)


Maintenance
-----------

- Minor refactor of the EELS subshells in the ``elements`` dictionary. (`2868 <https://github.com/hyperspy/hyperspy/issues/2868>`_)
- Fix packaging of test suite and tweak tests to pass on different platform of blas implementation (`2933 <https://github.com/hyperspy/hyperspy/issues/2933>`_)


.. _changes_1.7.0: