hyperspy 2.2.0__tar.gz → 2.3.0__tar.gz

{hyperspy-2.2.0 → hyperspy-2.3.0}/.github/workflows/release.yml

@@ -52,4 +52,4 @@ jobs:
         uses: actions/checkout@v4
       - name: Create Release
         if: ${{ startsWith(github.ref, 'refs/tags/') && github.repository_owner == 'hyperspy' }}
-        uses: softprops/action-gh-release@c062e08bd532815e2082a85e87e3ef29c3e6d191
+        uses: softprops/action-gh-release@c95fe1489396fe8a9eb87c0abf8aa5b2ef267fda

{hyperspy-2.2.0 → hyperspy-2.3.0}/.github/workflows/tests.yml

@@ -16,28 +16,28 @@ jobs:
       matrix:
         os: [ubuntu, windows, macos]
         os_version: [latest]
-        PYTHON_VERSION: ['3.9', '3.10', ]
+        PYTHON_VERSION: ['3.10', '3.12']
         PIP_SELECTOR: ['[all, tests, coverage]']
         include:
           # test oldest supported version of main dependencies on python 3.8
           - os: ubuntu
             os_version: latest
-            PYTHON_VERSION: '3.8'
+            PYTHON_VERSION: '3.9'
             PIP_SELECTOR: '[all, tests, coverage]'
             OLDEST_SUPPORTED_VERSION: true
             # Don't install pillow 10.4.0 because of its incompatibility with numpy 1.20.x
             # https://github.com/python-pillow/Pillow/pull/8187
-            DEPENDENCIES: dask[array]==2021.5.1 matplotlib==3.6.0 numba==0.52 numpy==1.20.0 scipy==1.6 scikit-image==0.18 scikit-learn==1.0.1 pillow!=10.4.0
+            DEPENDENCIES: dask[array]==2022.9.2 matplotlib==3.6.0 numba==0.53 numpy==1.20.0 scipy==1.6 sympy==1.10 scikit-image==0.18 scikit-learn==1.0.1 pillow!=10.4.0 numexpr==2.8
             LABEL: -oldest
           # test minimum requirement
           - os: ubuntu
             os_version: latest
-            PYTHON_VERSION: '3.12'
+            PYTHON_VERSION: '3.13'
             PIP_SELECTOR: '[tests, coverage]'
             LABEL: -minimum
           - os: ubuntu
             os_version: latest
-            PYTHON_VERSION: '3.8'
+            PYTHON_VERSION: '3.9'
             PIP_SELECTOR: '[all, tests, coverage]'
           - os: ubuntu
             os_version: latest
@@ -84,16 +84,16 @@ jobs:
           python --version
           pip --version
 
-      - name: Install oldest supported version
-        if: ${{ matrix.OLDEST_SUPPORTED_VERSION }}
-        run: |
-          pip install ${{ matrix.DEPENDENCIES }} -v
-
       - name: Install
         shell: bash
         run: |
           pip install ${{ env.PIP_ARGS }} .'${{ matrix.PIP_SELECTOR }}'
 
+      - name: Install oldest supported version
+        if: ${{ matrix.OLDEST_SUPPORTED_VERSION }}
+        run: |
+          pip install ${{ matrix.DEPENDENCIES }} -v
+
       - name: Pip list
         run: |
           pip list
@@ -109,6 +109,6 @@ jobs:
 
       - name: Upload coverage to Codecov
         if: ${{ github.repository_owner == 'hyperspy' }}
-        uses: codecov/codecov-action@v4
+        uses: codecov/codecov-action@v5
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

{hyperspy-2.2.0 → hyperspy-2.3.0}/.github/workflows/tests_extension.yml

@@ -16,13 +16,13 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        #EXTENSION_VERSION: ['release', 'dev']
-        EXTENSION_VERSION: ['dev']
+        EXTENSION_VERSION: ['release', 'dev']
 
     env:
       MPLBACKEND: agg
-      EXTENSION: kikuchipy lumispy pyxem atomap
+      EXTENSION: atomap etspy exspy holospy kikuchipy lumispy pyxem
       TEST_DEPS: pytest pytest-xdist pytest-rerunfailures pytest-instafail
+      PYTHON_VERSION: '3.12'
     defaults:
       run:
         shell: bash -l {0}
@@ -32,21 +32,25 @@ jobs:
 
       - uses: conda-incubator/setup-miniconda@v3
         with:
-          miniforge-variant: Mambaforge
           miniforge-version: latest
-          # use base environment, so that when using pip, this is from the
-          # mambaforge distribution
-          auto-activate-base: true
-          activate-environment: ""
+          python-version: ${{ env.PYTHON_VERSION }}
+          activate-environment: "test"
+          conda-remove-defaults: "true"
 
+      - name: Install pip, astra-toolbox, ffmpeg and test dependencies
+        run: |
+          # astra-toolbox and ffmpeg are etspy dependencies
+          mamba install pip astra-toolbox ffmpeg ${{ env.TEST_DEPS }} 
+          
       - name: Conda info
         run: |
           conda info
           conda list
 
-      - name: Install extensions and Test dependencies
+      - name: Install extensions (release)
+        if: contains(matrix.EXTENSION_VERSION, 'release')
         run: |
-          mamba install hyperspy-base ${{ env.EXTENSION }} ${{ env.TEST_DEPS }}
+          mamba install hyperspy-base ${{ env.EXTENSION }}
 
       - name: Conda list
         run: |
@@ -56,15 +60,16 @@ jobs:
         run: |
           pip install .
 
-      - name: Install Extension Dev
+      - name: Install Extension (dev)
         if: contains(matrix.EXTENSION_VERSION, 'dev')
         run: |
-          pip install https://github.com/lumispy/lumispy/archive/main.zip
+          pip install https://github.com/atomap-dev/atomap/archive/main.zip
+          pip install https://github.com/usnistgov/etspy/archive/master.zip
+          pip install https://github.com/hyperspy/exspy/archive/main.zip
+          pip install https://github.com/hyperspy/holospy/archive/main.zip
           pip install https://github.com/pyxem/kikuchipy/archive/develop.zip
+          pip install https://github.com/lumispy/lumispy/archive/main.zip
           pip install https://github.com/pyxem/pyxem/archive/main.zip
-          pip install https://gitlab.com/atomap/atomap/-/archive/master/atomap-master.zip
-          pip install https://github.com/hyperspy/holospy/archive/main.zip
-          pip install https://github.com/hyperspy/exspy/archive/main.zip
 
       - name: Install xvfb
         run: |
@@ -75,7 +80,6 @@ jobs:
         if: ${{ always() }}
         run: |
           # Virtual buffer (xvfb) required for tests using PyVista
-          sudo apt-get install xvfb
           xvfb-run python -m pytest --pyargs kikuchipy
 
       - name: Run LumiSpy Test Suite
@@ -98,10 +102,12 @@ jobs:
         run: |
           python -m pytest --pyargs exspy
   
-      #  The currently released version of Atomap (0.3.1) does not work with this test
-      #  environment. Thus, only the dev version is currently tested. If a newer version
-      #  of Atomap is released, the "if" can be changed to always().
       - name: Run atomap Test Suite
-        if: contains(matrix.EXTENSION_VERSION, 'dev')
+        if: ${{ always() }}
         run: |
           python -m pytest --pyargs atomap
+
+      - name: Run ETSpy Test Suite
+        if: ${{ always() }}
+        run: |
+          python -m pytest --pyargs etspy

{hyperspy-2.2.0 → hyperspy-2.3.0}/.gitignore

@@ -29,28 +29,16 @@ desktop.ini
 dist
 /MANIFEST
 build/*
-bin/*.bat
-PortableInstall/*
 hyperspy.egg-info/*
 data/octave-core
 deb_dist/*
-doc/_build/*
-doc/.build/*
-doc/api/*
 doc/auto_examples
-doc/gh-pages
+doc/backreferences
+doc/_build
 doc/log.txt
-doc/user_guide/_build/*
-doc/user_guide/.build/*
 examples/io/*.msa
 examples/io/rgb*.jpg
 examples/region_of_interest/*.msa
-hyperspy/io_plugins/unbcf_fast.c
-hyperspy/misc/etc/test_compilers.obj
-hyperspy/tests/io/edax_files.zip
-hyperspy/tests/misc/cython/test_cython_integration.c
-setup/windows/requires/*
-setup/windows/reccomends/*
 
 ### Code ###
 # Visual Studio Code - https://code.visualstudio.com/

{hyperspy-2.2.0 → hyperspy-2.3.0}/.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.6.8
+    rev: v0.9.4
     hooks:
       # Run the linter.
       - id: ruff
@@ -13,3 +13,4 @@ ci:
     # "pre-commit.ci autofix" on a pull request to manually trigger auto-fixing 
     autofix_prs: false
     autoupdate_branch: 'RELEASE_next_patch'
+    autoupdate_schedule: monthly

{hyperspy-2.2.0 → hyperspy-2.3.0}/CHANGES.rst

@@ -1,3 +1,7 @@
+.. _RosettaSciIO: https://hyperspy.org/rosettasciio
+.. _eXSpy: https://hyperspy.org/exspy
+.. _holoSpy: https://hyperspy.org/holospy
+
 .. _changelog:
 
 Changelog
@@ -10,6 +14,49 @@ https://hyperspy.readthedocs.io/en/latest/changes.html
 
 .. towncrier release notes start
 
+2.3.0 (2025-03-02)
+==================
+
+New features
+------------
+
+- Add :meth:`~.api.signals.BaseSignal.remove_spikes` method to remove spikes on :class:`~.api.signals.Signal1D` and :class:`~.api.signals.Signal2D` using local median. (`#3436 <https://github.com/hyperspy/hyperspy/issues/3436>`_)
+- Add :meth:`~.api.signals.Signal1D.remove_baseline` to remove baseline using `pybaselines <https://pybaselines.readthedocs.io>`_; see the :ref:`baseline removal <signal1D.remove_baseline>` section in the user guide. (`#3441 <https://github.com/hyperspy/hyperspy/issues/3441>`_)
+
+
+Enhancements
+------------
+
+- Fix and improve :meth:`~.model.BaseModel.as_signal`:
+
+  -  Fix lazy support which stops working from dask version 2024.12.0.
+  -  Add vectorised implementation using ``function_nd`` method of Components. For components not implementing ``function_nd`` (for example, in HyperSpy extensions, old or custom components), the old slow implementation is used. All :class:`~.api.model.components1D.Expression` based-components have the ``function_nd`` created automatically. (`#3476 <https://github.com/hyperspy/hyperspy/issues/3476>`_)
+- Improve setting chunking:
+
+  - add automatic chunking in :meth:`~.api.signals.BaseSignal.map` for non-lazy signal to optimize chunking for multiple core processing,
+  - :meth:`~.api.signals.BaseSignal.as_lazy` can now take the ``chunks`` argument,
+  - improve documentation of the ``rechunk`` argument. (`#3489 <https://github.com/hyperspy/hyperspy/issues/3489>`_)
+
+
+Bug Fixes
+---------
+
+- Fix plotting single spectra in :func:`~.api.plot.plot_spectra` with ``style="mosaic"``. (`#3483 <https://github.com/hyperspy/hyperspy/issues/3483>`_)
+
+
+Improved Documentation
+----------------------
+
+- Document implementation of model convolution for subclassing :class:`~hyperspy.models.model1d.Model1D` in the :ref:`extension guide <extension_components_label>`. (`#3494 <https://github.com/hyperspy/hyperspy/issues/3494>`_)
+
+
+Maintenance
+-----------
+
+- Add support for python 3.13. (`#3468 <https://github.com/hyperspy/hyperspy/issues/3468>`_)
+- Clean up dependencies, which are now used in eXSpy_ and RosettaSciIO_. (`#3482 <https://github.com/hyperspy/hyperspy/issues/3482>`_)
+
+
 2.2.0 (2024-11-08)
 ==================
 
@@ -211,11 +258,11 @@ 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.
+  - 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.
+  - eXSpy_: A library for EELS and EDS analysis.
+    See `eXSpy release notes <https://hyperspy.org/exspy/changes.html>`_ for new features.
+  - holoSpy_: 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
@@ -576,7 +623,7 @@ Maintenance
 - Drop support for python 3.7, update oldest supported dependencies and simplify code accordingly (`#3144 <https://github.com/hyperspy/hyperspy/issues/3144>`_)
 - IPython and IParallel are now optional dependencies (`#3145 <https://github.com/hyperspy/hyperspy/issues/3145>`_)
 - Fix Numpy 1.25 deprecation: implicit array to scalar conversion in :py:meth:`~.signals.Signal2D.align2D` (`#3189 <https://github.com/hyperspy/hyperspy/issues/3189>`_)
-- Replace deprecated :mod:`scipy.misc` by :mod:`scipy.datasets` in documentation (`#3225 <https://github.com/hyperspy/hyperspy/issues/3225>`_)
+- Replace deprecated ``scipy.misc`` by :mod:`scipy.datasets` in documentation (`#3225 <https://github.com/hyperspy/hyperspy/issues/3225>`_)
 - Fix documentation version switcher (`#3228 <https://github.com/hyperspy/hyperspy/issues/3228>`_)
 - Replace deprecated :py:class:`scipy.interpolate.interp1d` with :py:func:`scipy.interpolate.make_interp_spline` (`#3233 <https://github.com/hyperspy/hyperspy/issues/3233>`_)
 - Add support for python 3.12 (`#3256 <https://github.com/hyperspy/hyperspy/issues/3256>`_)
@@ -998,7 +1045,7 @@ Enhancements
 * Improve error message when file not found (`#2597 <https://github.com/hyperspy/hyperspy/pull/2597>`_)
 * Add update instructions to user guide (`#2621 <https://github.com/hyperspy/hyperspy/pull/2621>`_)
 * Improve plotting navigator of lazy signals, add ``navigator`` setter to lazy signals (`#2631 <https://github.com/hyperspy/hyperspy/pull/2631>`_)
-* Use ``'dask_auto'`` when rechunk=True in :py:meth:`~._signals.lazy.LazySignal.change_dtype` for lazy signal (`#2645 <https://github.com/hyperspy/hyperspy/pull/2645>`_)
+* Use ``'dask_auto'`` when rechunk=True in :py:meth:`~.api.signals.BaseSignal.change_dtype` for lazy signal (`#2645 <https://github.com/hyperspy/hyperspy/pull/2645>`_)
 * Use dask chunking when saving lazy signal instead of rechunking and leave the user to decide what is the suitable chunking (`#2629 <https://github.com/hyperspy/hyperspy/pull/2629>`_)
 * Added lazy reading support for FFT and DPC datasets in FEI emd datasets (`#2651 <https://github.com/hyperspy/hyperspy/pull/2651>`_).
 * Improve error message when initialising SpanROI with left >= right (`#2604 <https://github.com/hyperspy/hyperspy/pull/2604>`_)

{hyperspy-2.2.0 → hyperspy-2.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: hyperspy
-Version: 2.2.0
+Version: 2.3.0
 Summary: Multidimensional data analysis toolbox
 Author: The HyperSpy Community
 License:                     GNU GENERAL PUBLIC LICENSE
@@ -691,20 +691,20 @@ Classifier: Intended Audience :: Developers
 Classifier: Intended Audience :: Science/Research
 Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
 Classifier: Operating System :: OS Independent
-Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 Classifier: Topic :: Scientific/Engineering
 Classifier: Topic :: Scientific/Engineering :: Physics
 Classifier: Topic :: Software Development :: Libraries
-Requires-Python: >=3.8
+Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: COPYING.txt
 License-File: AUTHORS.txt
 Requires-Dist: cloudpickle
-Requires-Dist: dask[array]>=2021.5.1
+Requires-Dist: dask[array]>=2022.9.2
 Requires-Dist: importlib-metadata>=3.6
 Requires-Dist: jinja2
 Requires-Dist: matplotlib>=3.6
@@ -712,25 +712,28 @@ Requires-Dist: natsort
 Requires-Dist: numpy>=1.20.0
 Requires-Dist: packaging
 Requires-Dist: pint>=0.10
-Requires-Dist: pooch
 Requires-Dist: prettytable>=2.3
-Requires-Dist: python-dateutil>=2.5.0
 Requires-Dist: pyyaml
-Requires-Dist: requests
 Requires-Dist: rosettasciio[hdf5]
 Requires-Dist: scikit-image>=0.18
 Requires-Dist: scipy>=1.6.0
-Requires-Dist: sympy>=1.6
-Requires-Dist: tqdm>=4.9.0
+Requires-Dist: sympy>=1.10
+Requires-Dist: tqdm>=4.59.0
 Requires-Dist: traits>=4.5.0
 Provides-Extra: all
+Requires-Dist: hyperspy[dask-image]; extra == "all"
+Requires-Dist: hyperspy[baseline]; extra == "all"
 Requires-Dist: hyperspy[gui-jupyter]; extra == "all"
 Requires-Dist: hyperspy[gui-traitsui]; extra == "all"
 Requires-Dist: hyperspy[ipython]; extra == "all"
 Requires-Dist: hyperspy[learning]; extra == "all"
 Requires-Dist: hyperspy[speed]; extra == "all"
+Provides-Extra: baseline
+Requires-Dist: pybaselines; extra == "baseline"
 Provides-Extra: coverage
 Requires-Dist: pytest-cov; extra == "coverage"
+Provides-Extra: dask-image
+Requires-Dist: dask-image; extra == "dask-image"
 Provides-Extra: dev
 Requires-Dist: black; extra == "dev"
 Requires-Dist: hyperspy[all]; extra == "dev"
@@ -742,6 +745,7 @@ Requires-Dist: holospy; extra == "doc"
 Requires-Dist: IPython; extra == "doc"
 Requires-Dist: pickleshare; extra == "doc"
 Requires-Dist: numpydoc; extra == "doc"
+Requires-Dist: pybaselines; extra == "doc"
 Requires-Dist: pydata_sphinx_theme; extra == "doc"
 Requires-Dist: setuptools_scm; extra == "doc"
 Requires-Dist: sphinx-copybutton; extra == "doc"
@@ -750,8 +754,8 @@ Requires-Dist: sphinx-favicon; extra == "doc"
 Requires-Dist: sphinx-gallery; extra == "doc"
 Requires-Dist: sphinx>=1.7; extra == "doc"
 Requires-Dist: sphinxcontrib-mermaid; extra == "doc"
-Requires-Dist: sphinxcontrib-towncrier>=0.3.0a0; extra == "doc"
-Requires-Dist: towncrier<24; extra == "doc"
+Requires-Dist: sphinxcontrib-towncrier>=0.5.0a0; extra == "doc"
+Requires-Dist: towncrier; extra == "doc"
 Provides-Extra: gui-jupyter
 Requires-Dist: hyperspy_gui_ipywidgets>=2.0; extra == "gui-jupyter"
 Requires-Dist: ipympl; extra == "gui-jupyter"
@@ -763,9 +767,10 @@ Requires-Dist: ipyparallel; extra == "ipython"
 Provides-Extra: learning
 Requires-Dist: scikit-learn>=1.0.1; extra == "learning"
 Provides-Extra: speed
-Requires-Dist: numba; extra == "speed"
-Requires-Dist: numexpr; extra == "speed"
+Requires-Dist: numba>=0.53; extra == "speed"
+Requires-Dist: numexpr>=2.8; extra == "speed"
 Provides-Extra: tests
+Requires-Dist: pooch; extra == "tests"
 Requires-Dist: pytest-instafail; extra == "tests"
 Requires-Dist: pytest-mpl; extra == "tests"
 Requires-Dist: pytest-rerunfailures; extra == "tests"

{hyperspy-2.2.0 → hyperspy-2.3.0}/azure-pipelines.yml

@@ -27,27 +27,27 @@ strategy:
   matrix:
     Linux_Python39:
       vmImage: 'ubuntu-latest'
-      PYTHON_VERSION: '3.9'
+      PYTHON_VERSION: '3.10'
       MINIFORGE_PATH: $(Agent.BuildDirectory)/miniforge3
     Linux_Python310:
       vmImage: 'ubuntu-latest'
-      PYTHON_VERSION: '3.10'
+      PYTHON_VERSION: '3.11'
       MINIFORGE_PATH: $(Agent.BuildDirectory)/miniforge3
     MacOS_Python39:
       vmImage: 'macOS-latest'
-      PYTHON_VERSION: '3.9'
+      PYTHON_VERSION: '3.10'
       MINIFORGE_PATH: $(Agent.BuildDirectory)/miniforge3
     MacOS_Python310:
       vmImage: 'macOS-latest'
-      PYTHON_VERSION: '3.10'
+      PYTHON_VERSION: '3.11'
       MINIFORGE_PATH: $(Agent.BuildDirectory)/miniforge3
     Windows_Python39:
       vmImage: 'windows-latest'
-      PYTHON_VERSION: '3.9'
+      PYTHON_VERSION: '3.10'
       MINIFORGE_PATH: $(Agent.BuildDirectory)\miniforge3
     Windows_Python310:
       vmImage: 'windows-latest'
-      PYTHON_VERSION: '3.10'
+      PYTHON_VERSION: '3.11'
       MINIFORGE_PATH: $(Agent.BuildDirectory)\miniforge3
 
 pool:

{hyperspy-2.2.0 → hyperspy-2.3.0}/conda_environment.yml

@@ -2,26 +2,24 @@ name: test_env
 channels:
 - conda-forge
 dependencies:
-- dask-core >=2021.3.1
+- dask-core >=2022.9.2
 - dill
 - importlib-metadata
 - h5py
 - jinja2
 - matplotlib-base >=3.6
 - natsort
-- numba >=0.52
-- numexpr
+- numba >=0.53
+- numexpr >=2.8
 - numpy >=1.20
 - packaging
 - pint >=0.10
 - prettytable >=2.3
-- python-dateutil >=2.5.0
 - pyyaml
-- requests
 - rosettasciio-base
 - scikit-image >=0.18
 - scikit-learn >=1.0.1
 - scipy >=1.6.0
-- sympy >=1.6.0
-- tqdm >=4.9.0
+- sympy >=1.10
+- tqdm >=4.59.0
 - traits >=4.5.0

{hyperspy-2.2.0 → hyperspy-2.3.0}/doc/Makefile

@@ -36,6 +36,7 @@ help:
 clean:
 	rm -rf $(BUILDDIR)/*
 	rm -rf auto_examples/
+	rm -rf backreferences/
 
 html:
 	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html

{hyperspy-2.2.0 → hyperspy-2.3.0}/doc/_static/switcher.json

@@ -12,7 +12,7 @@
     },
     {
         "version": "2.1",
-        "url": "https://hyperspy.org/hyperspy-doc/v2.1/",
+        "url": "https://hyperspy.org/hyperspy-doc/v2.1/"
     },
     {
         "version": "2.0",

{hyperspy-2.2.0 → hyperspy-2.3.0}/doc/conf.py

@@ -331,6 +331,7 @@ towncrier_draft_working_directory = ".."
 intersphinx_mapping = {
     "cupy": ("https://docs.cupy.dev/en/stable", None),
     "dask": ("https://docs.dask.org/en/latest", None),
+    "dask_image": ("https://image.dask.org/en/latest", None),
     "exspy": ("https://exspy.readthedocs.io/en/latest", None),
     "h5py": ("https://docs.h5py.org/en/stable", None),
     "holospy": ("https://holospy.readthedocs.io/en/latest", None),
@@ -340,6 +341,7 @@ intersphinx_mapping = {
     "matplotlib": ("https://matplotlib.org/stable", None),
     "numpy": ("https://numpy.org/doc/stable", None),
     "pint": ("https://pint.readthedocs.io/en/stable", None),
+    "pybaselines": ("https://pybaselines.readthedocs.io/en/stable", None),
     "python": ("https://docs.python.org/3", None),
     "rsciio": ("https://hyperspy.org/rosettasciio/", None),
     "scipy": ("https://docs.scipy.org/doc/scipy", None),
@@ -425,6 +427,11 @@ numpydoc_class_members_toctree = False
 sphinx_gallery_conf = {
     "examples_dirs": "../examples",  # path to your example scripts
     "gallery_dirs": "auto_examples",  # path to where to save gallery generated output
+    # directory where function/class granular galleries are stored
+    "backreferences_dir": "backreferences",
+    # Modules for which function/class level galleries are created. In
+    # this case hyperspy in a tuple of strings.
+    "doc_module": ("hyperspy",),
     "filename_pattern": ".py",  # pattern to define which will be executed
     "ignore_pattern": "_sgskip.py",  # pattern to define which will not be executed
     "compress_images": (

{hyperspy-2.2.0 → hyperspy-2.3.0}/doc/dev_guide/writing_extensions.rst

@@ -193,6 +193,8 @@ This option can be used if a signal subclass is needed for certain functionaliti
 such as casting to a different signal subclass, but should usually not be set
 directly by the user.
 
+.. _extension_components_label:
+
 Creating new HyperSpy model components
 --------------------------------------
 
@@ -320,6 +322,13 @@ Equivalently, to add a new component 2D:
   the component online if e.g. the package is renamed or the component
   relocated.
 
+Convoluting model components
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The implementation of the convolution of components in subclasses of :class:`~hyperspy.models.model1d.Model1D`
+is explained in the :ref:`extension gallery <extension_gallery-label>`:
+
+.. minigallery:: ../examples/extensions/model_convolution*
 
 Creating and registering new widgets and toolkeys
 -------------------------------------------------

{hyperspy-2.2.0 → hyperspy-2.3.0}/doc/make.bat

@@ -38,6 +38,7 @@ if "%1" == "clean" (
 	for /d %%i in (%BUILDDIR%\*) do rmdir /q /s %%i
 	del /q /s %BUILDDIR%\*
 	rmdir /q /s auto_examples
+	rmdir /q /s backreferences
 	goto end
 )
 

{hyperspy-2.2.0 → hyperspy-2.3.0}/doc/user_guide/model/model_components.rst

@@ -148,6 +148,39 @@ following template to suit your needs:
             p2 = self.parameter_2.value
             return p1 + x * p2
 
+        # Optional vectorised implementation of function to optimize
+        # performance for specific features such as linear fitting and
+        # `BaseModel.as_signal`
+        def function_nd(self, x, parameters_values=None):
+            """
+            Parameters
+            ----------
+            x : numpy.ndarray
+                The axis used to calculate the 
+            parameters_values : list of numpy.ndarray or None
+                The list of parameters values.
+                If None, the parameters values will obtained
+                from ``Parameter.map["values"]``.
+            
+            Returns
+            -------
+            numpy.ndarray
+                Results of the component calculated over the axis ``x``.
+            """
+            if parameters_values is None:
+                parameters_values = [
+                    self.parameter_1.map["values"],
+                    self.parameter_2.map["values"],
+                    ]
+            if self._is_navigation_multidimensional:
+                x = x[np.newaxis, :]
+                p1 = parameters_values[0][..., np.newaxis]
+                p2 = parameters_values[1][..., np.newaxis]
+            else:
+                p1 = self.parameter_1.value
+                p2 = self.parameter_2.value
+            return np.ones_like(x) * p1 + x * p2
+
         # Optionally define the gradients of each parameter
         def grad_parameter_1(self, x):
             """
@@ -161,6 +194,7 @@ following template to suit your needs:
             """
             return x
 
+
 Define components from a fixed-pattern
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^