Bump hyperspy from 1.7.6 to 2.0

[dependabot]

Bumps hyperspy from 1.7.6 to 2.0.

Changelog

Sourced from hyperspy's changelog.

2.0 (2023-12-20)

Release Highlights

• Hyperspy has split off some of the file reading/writing and domain specific functionalities into separate libraries!

  • RosettaSciIO <https://hyperspy.org/rosettasciio>: A library for reading and writing scientific data files. See RosettaSciIO release notes <https://hyperspy.org/rosettasciio/changes.html> for new features and supported formats.
  • exSpy <https://exspy.readthedocs.io>: A library for EELS and EDS analysis. See exSpy release notes <https://hyperspy.org/exspy/changes.html> for new features.
  • HoloSpy <https://holospy.readthedocs.io>: A library for analysis of (off-axis) electron holography data. See HoloSpy release notes <https://holospy.readthedocs.io/en/latest/changes.html> for new features.

• The :py:mod:~.api.plot.markers API has been refactored

  • Lazy markers are now supported
  • Plotting many markers is now much faster
  • Added :py:class:~.api.plot.markers.Polygons marker

• The documentation has been restructured and improved!

  • Short example scripts are now included in the documentation
  • Improved guides for lazy computing as well as an improved developer guide

• Plotting is easier and more consistent:

  • Added horizontal figure layout choice when using the ipympl backend
  • Changing navigation coordinates using the keyboard arrow-keys has been removed. Use Crtl + Arrow instead.
  • Jump to navigation position using shift + click in the navigator figure.

• HyperSpy now works with Pyodide/Jupyterlite, checkout hyperspy.org/jupyterlite-hyperspy <https://hyperspy.org/jupyterlite-hyperspy>_!

• The deprecated API has removed: see the list of API changes and removal in the :ref:sections below <hyperspy_2.0_api_changes>.

New features

• :py:meth:~._signals.lazy.LazySignal.compute will now pass keyword arguments to the dask :meth:dask.array.Array.compute method. This enables setting the scheduler and the number of computational workers. ([#2971](https://github.com/hyperspy/hyperspy/issues/2971) <https://github.com/hyperspy/hyperspy/issues/2971>_)

• Changes to :meth:~.api.signals.BaseSignal.plot:

  • Added horizontal figure layout choice when using the ipympl backend. The default layour can be set in the plot section of the preferences GUI. ([#3140](https://github.com/hyperspy/hyperspy/issues/3140) <https://github.com/hyperspy/hyperspy/issues/3140>_)

• Changes to :meth:~.api.signals.Signal2D.find_peaks:

  • Lazy signals return lazy peak signals
  • get_intensity argument added to get the intensity of the peaks
  • The signal axes are now stored in the metadata.Peaks.signal_axes attribute of the peaks' signal. ([#3142](https://github.com/hyperspy/hyperspy/issues/3142) <https://github.com/hyperspy/hyperspy/issues/3142>_)

• Change the logging output so that logging messages are not displayed in red, to avoid confusion with errors. ([#3173](https://github.com/hyperspy/hyperspy/issues/3173) <https://github.com/hyperspy/hyperspy/issues/3173>_)

... (truncated)

Commits

• ab853c3 Update hyperspy 2.0 announcement banner
• 9268066 Update release notes for 2.0
• 1d5d35f Update actions/download-artifact to v4
• 731251a Use fallback version for setuptools_scm
• 02e7e6a Merge pull request #3282 from ericpre/remove_beta_lazy
• ecaccf0 Merge pull request #3281 from ericpre/doctest
• 3e7bf70 Tweak example code in user guide and docstrings
• e848200 Add changelog entry
• 3f87a45 Make warning of "beta" state of lazy signals more specific
• 6585a97 Tweak user guide
• Additional commits viewable in compare view

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[dependabot]

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[jan-janssen]

======================================================================
ERROR: setUpClass (test_hs_line_profiles.TestHSLineProfiles)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/runner/work/pyiron_experimental/pyiron_experimental/tests/test_hs_line_profiles.py", line 15, in setUpClass
    data = hs.load(os.path.join(cls.project.path, '../../notebooks/experiment.emd'))
  File "/usr/share/miniconda3/envs/test/lib/python3.10/site-packages/hyperspy/io.py", line 517, in load
    objects = [load_single_file(filename, lazy=lazy, **kwds)
  File "/usr/share/miniconda3/envs/test/lib/python3.10/site-packages/hyperspy/io.py", line 517, in <listcomp>
    objects = [load_single_file(filename, lazy=lazy, **kwds)
  File "/usr/share/miniconda3/envs/test/lib/python3.10/site-packages/hyperspy/io.py", line 576, in load_single_file
    return load_with_reader(filename=filename, reader=reader, **kwds)
  File "/usr/share/miniconda3/envs/test/lib/python3.10/site-packages/hyperspy/io.py", line 597, in load_with_reader
    file_data_list = importlib.import_module(reader["api"]).file_reader(filename,
  File "/usr/share/miniconda3/envs/test/lib/python3.10/site-packages/rsciio/emd/_api.py", line 201, in file_reader
    raise e
  File "/usr/share/miniconda3/envs/test/lib/python3.10/site-packages/rsciio/emd/_api.py", line 189, in file_reader
    emd_reader.read_file(file)
  File "/usr/share/miniconda3/envs/test/lib/python3.10/site-packages/rsciio/emd/_emd_velox.py", line 112, in read_file
    self._read_data(self.select_type)
  File "/usr/share/miniconda3/envs/test/lib/python3.10/site-packages/rsciio/emd/_emd_velox.py", line 142, in _read_data
    self._read_spectrum_stream()
  File "/usr/share/miniconda3/envs/test/lib/python3.10/site-packages/rsciio/emd/_emd_velox.py", line 541, in _read_spectrum_stream
    s0 = _read_stream(subgroup_keys[0])
  File "/usr/share/miniconda3/envs/test/lib/python3.10/site-packages/rsciio/emd/_emd_velox.py", line 533, in _read_stream
    stream = FeiSpectrumStream(spectrum_stream_group[key], self)
  File "/usr/share/miniconda3/envs/test/lib/python3.10/site-packages/rsciio/emd/_emd_velox.py", line 892, in __init__
    self.spectrum_image = self.stream_to_array(stream_data=stream_data)
  File "/usr/share/miniconda3/envs/test/lib/python3.10/site-packages/rsciio/emd/_emd_velox.py", line 937, in stream_to_array
    import rsciio.utils.fei_stream_readers as stream_readers
  File "/usr/share/miniconda3/envs/test/lib/python3.10/site-packages/rsciio/utils/fei_stream_readers.py", line 21, in <module>
    import sparse
ModuleNotFoundError: No module named 'sparse'

----------------------------------------------------------------------
Ran 0 tests in 1.210s

[jan-janssen]

Input Notebook:  matchseries.ipynb
Output Notebook: matchseries-out.ipynb

Executing:   0%|          | 0/10 [00:00<?, ?cell/s]Kernelspec name python3 cannot be found!
No such kernel named python3
Traceback (most recent call last):
  File "/usr/share/miniconda3/envs/test/lib/python3.11/site-packages/jupyter_client/manager.py", line 87, in wrapper
    out = await method(self, *args, **kwargs)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/share/miniconda3/envs/test/lib/python3.11/site-packages/jupyter_client/manager.py", line 435, in _async_start_kernel
    kernel_cmd, kw = await self._async_pre_start_kernel(**kw)
                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/share/miniconda3/envs/test/lib/python3.11/site-packages/jupyter_client/manager.py", line 397, in _async_pre_start_kernel
    self.kernel_spec,
    ^^^^^^^^^^^^^^^^
  File "/usr/share/miniconda3/envs/test/lib/python3.11/site-packages/jupyter_client/manager.py", line 195, in kernel_spec
    self._kernel_spec = self.kernel_spec_manager.get_kernel_spec(self.kernel_name)
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/share/miniconda3/envs/test/lib/python3.11/site-packages/jupyter_client/kernelspec.py", line 285, in get_kernel_spec
    raise NoSuchKernel(kernel_name)
jupyter_client.kernelspec.NoSuchKernel: No such kernel named python3

Executing:   0%|          | 0/10 [00:00<?, ?cell/s]
Traceback (most recent call last):
  File "/usr/share/miniconda3/envs/test/bin/papermill", line 10, in <module>
    sys.exit(papermill())
             ^^^^^^^^^^^
  File "/usr/share/miniconda3/envs/test/lib/python3.11/site-packages/click/core.py", line 1157, in __call__
    return self.main(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/share/miniconda3/envs/test/lib/python3.11/site-packages/click/core.py", line 1078, in main
    rv = self.invoke(ctx)
         ^^^^^^^^^^^^^^^^
  File "/usr/share/miniconda3/envs/test/lib/python3.11/site-packages/click/core.py", line 1434, in invoke
    return ctx.invoke(self.callback, **ctx.params)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/share/miniconda3/envs/test/lib/python3.11/site-packages/click/core.py", line 783, in invoke
    return __callback(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/share/miniconda3/envs/test/lib/python3.11/site-packages/click/decorators.py", line 33, in new_func
    return f(get_current_context(), *args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/share/miniconda3/envs/test/lib/python3.11/site-packages/papermill/cli.py", line 250, in papermill
    execute_notebook(
  File "/usr/share/miniconda3/envs/test/lib/python3.11/site-packages/papermill/execute.py", line 113, in execute_notebook
    nb = papermill_engines.execute_notebook_with_engine(
         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/share/miniconda3/envs/test/lib/python3.11/site-packages/papermill/engines.py", line 49, in execute_notebook_with_engine
    return self.get_engine(engine_name).execute_notebook(nb, kernel_name, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/share/miniconda3/envs/test/lib/python3.11/site-packages/papermill/engines.py", line 367, in execute_notebook
    cls.execute_managed_notebook(nb_man, kernel_name, log_output=log_output, **kwargs)
  File "/usr/share/miniconda3/envs/test/lib/python3.11/site-packages/papermill/engines.py", line 436, in execute_managed_notebook
    return PapermillNotebookClient(nb_man, **final_kwargs).execute()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/share/miniconda3/envs/test/lib/python3.11/site-packages/papermill/clientwrap.py", line 43, in execute
    with self.setup_kernel(**kwargs):
  File "/usr/share/miniconda3/envs/test/lib/python3.11/contextlib.py", line 137, in __enter__
    return next(self.gen)
           ^^^^^^^^^^^^^^
  File "/usr/share/miniconda3/envs/test/lib/python3.11/site-packages/nbclient/client.py", line 596, in setup_kernel
    self.start_new_kernel(**kwargs)
  File "/usr/share/miniconda3/envs/test/lib/python3.11/site-packages/jupyter_core/utils/__init__.py", line 165, in wrapped
    return loop.run_until_complete(inner)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/share/miniconda3/envs/test/lib/python3.11/asyncio/base_events.py", line 653, in run_until_complete
    return future.result()
           ^^^^^^^^^^^^^^^
  File "/usr/share/miniconda3/envs/test/lib/python3.11/site-packages/nbclient/client.py", line 546, in async_start_new_kernel
    await ensure_async(self.km.start_kernel(extra_arguments=self.extra_arguments, **kwargs))
  File "/usr/share/miniconda3/envs/test/lib/python3.11/site-packages/jupyter_core/utils/__init__.py", line 198, in ensure_async
    result = await obj
             ^^^^^^^^^
  File "/usr/share/miniconda3/envs/test/lib/python3.11/site-packages/jupyter_client/manager.py", line 96, in wrapper
    raise e
  File "/usr/share/miniconda3/envs/test/lib/python3.11/site-packages/jupyter_client/manager.py", line 87, in wrapper
    out = await method(self, *args, **kwargs)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/share/miniconda3/envs/test/lib/python3.11/site-packages/jupyter_client/manager.py", line 435, in _async_start_kernel
    kernel_cmd, kw = await self._async_pre_start_kernel(**kw)
                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/share/miniconda3/envs/test/lib/python3.11/site-packages/jupyter_client/manager.py", line 397, in _async_pre_start_kernel
    self.kernel_spec,
    ^^^^^^^^^^^^^^^^
  File "/usr/share/miniconda3/envs/test/lib/python3.11/site-packages/jupyter_client/manager.py", line 195, in kernel_spec
    self._kernel_spec = self.kernel_spec_manager.get_kernel_spec(self.kernel_name)
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/share/miniconda3/envs/test/lib/python3.11/site-packages/jupyter_client/kernelspec.py", line 285, in get_kernel_spec
    raise NoSuchKernel(kernel_name)
jupyter_client.kernelspec.NoSuchKernel: No such kernel named python3