Merge remote-tracking branch 'upstream/RELEASE_next_patch' into RELEA…

…SE_next_minor

.github/workflows/docs.yml

@@ -0,0 +1,52 @@
+name: Docs
+
+on: [push, pull_request]
+
+jobs:
+  build_doc:
+    name: Docs (PR comments)
+    runs-on: ubuntu-latest
+    env:
+      BUILD_DEPS: python3-dev build-essential graphviz
+      LATEX_DEPS: dvipng latexmk texlive-latex-recommended texlive-latex-extra texlive-fonts-recommended
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: ericpre/sphinx-action@latest_sphinx
+        with:
+          pre-build-command: "apt-get update -y && apt-get install -y ${{ env.BUILD_DEPS }} ${{ env.LATEX_DEPS }} && pip install .[all,build-doc]"
+          build-command: make html
+          docs-folder: doc/
+
+      - uses: actions/upload-artifact@v3
+        with:
+          path: ./doc/_build/html/
+          name: doc_build
+
+  check_links:
+    # This build is to check external links
+    name: Check external links
+    runs-on: ubuntu-latest
+    env:
+      DOCS_PATH: ./doc/_build/html/
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - uses: actions/setup-python@v3
+        name: Install Python
+        with:
+          python-version: '3.10'
+
+      - name: Install build docs
+        shell: bash -l {0}
+        run: |
+          pip install .[build-doc]
+
+      - name: Check links
+        shell: bash -l {0}
+        run: |
+          cd doc
+          make linkcheck

.github/workflows/tests.yml

@@ -84,26 +84,3 @@ jobs:
       - name: Upload coverage to Codecov
         if: ${{ always() }} && ${{ matrix.PYTEST_ARGS_COVERAGE }}
         uses: codecov/codecov-action@v2
-
-  build_doc:
-    name: Build doc
-    runs-on: ubuntu-latest
-    env:
-      BUILD_DEPS: python3-dev build-essential graphviz
-      LATEX_DEPS: dvipng latexmk texlive-latex-recommended texlive-latex-extra texlive-fonts-recommended
-
-    steps:
-      - uses: actions/checkout@v3
-
-      - uses: ericpre/sphinx-action@latest_sphinx
-        with:
-          # once numba 0.55 is release, remove "--pre" option to "pip install"
-          pre-build-command: "apt-get update -y && apt-get install -y ${{ env.BUILD_DEPS }} ${{ env.LATEX_DEPS }} && pip install --pre .[all,build-doc]"
-          build-command: make html
-          docs-folder: doc/
-
-      - uses: actions/upload-artifact@v3
-        with:
-          path: ./doc/_build/html/
-          name: doc_build
-

doc/conf.py

@@ -40,6 +40,16 @@
     'sphinxcontrib.towncrier',
 ]
 
+linkcheck_ignore = [
+    'https://www.jstor.org/stable/24307705',  # 403 Client Error: Forbidden for url
+    'https://anaconda.org',  # 403 Client Error: Forbidden for url
+]
+
+linkcheck_exclude_documents = [
+    'user_guide/io/*',
+    'api/hyperspy.io_plugins*',
+    ]
+
 try:
     import sphinxcontrib.spelling
     extensions.append('sphinxcontrib.spelling')

doc/user_guide/axes.rst

@@ -501,7 +501,7 @@ can be set and retrieved as quantity.
          <undefined> |     10 |        |     2.5 | 2.5e+03 |     nm
 
 
-Internally, HyperSpy uses the `pint <http://pint.readthedocs.io>`_ library to
+Internally, HyperSpy uses the `pint <https://pint.readthedocs.io>`_ library to
 manage the scale and offset quantities. The ``scale_as_quantity`` and
 ``offset_as_quantity`` attributes return pint object:
 
@@ -685,4 +685,3 @@ and a manually specified length as inputs:
     >>> from hyperspy.axes import GeneratorLen
     >>> gen = GeneratorLen(reverse_flyback_generator(), 6)
     >>> s.axes_manager.iterpath = gen
-

doc/user_guide/bibliography.rst

@@ -28,7 +28,7 @@ Bibliography
    of Atomic Form Factors, Photoelectric Absorption and Scattering Cross
    Section, and Mass Attenuation Coefficients for Z = 1-92 from E = 1-10 eV
    to E = 0.4-1.0 MeV" *NIST Standard Reference Data*
-   [`<http://physics.nist.gov/ffast>`_].
+   [`<https://physics.nist.gov/ffast>`_].
 
 .. _Egerton2011:
 
@@ -199,9 +199,9 @@ Bibliography
 .. _Lerotic2004:
 
 :ref:`[Lerotic2004] <Lerotic2004>`
-   M Lerotic, C Jacobsen, T Schafer, S Vogt 
+   M Lerotic, C Jacobsen, T Schafer, S Vogt
    "Cluster analysis of soft X-ray spectromicroscopy data".
-   Ultramicroscopy 100 (2004) 35–57 
+   Ultramicroscopy 100 (2004) 35–57
    [`<https://doi.org/10.1016/j.ultramic.2004.01.008>`_]
 
 .. _Iakoubovskii2008:

doc/user_guide/eds.rst

@@ -519,7 +519,7 @@ EDS curve fitting
 
 The intensity of X-ray lines can be extracted using curve-fitting in HyperSpy.
 This example uses an EDS-SEM spectrum of a test material (EDS-TM001) provided
-by `BAM <http://www.webshop.bam.de>`_.
+by `BAM <https://www.webshop.bam.de>`_.
 
 First, we load the spectrum, define the chemical composition of the sample and
 set the beam energy:

doc/user_guide/getting_started.rst

@@ -22,7 +22,7 @@ Starting Python in Linux and MacOS
 You can start IPython by opening a system terminal and executing ``ipython``,
 (optionally followed by the "frontend": "qtconsole" for example). However, in
 most cases, **the most agreeable way** to work with HyperSpy interactively
-is using the `Jupyter Notebook <http://jupyter.org>`_ (previously known as
+is using the `Jupyter Notebook <https://jupyter.org>`_ (previously known as
 the IPython Notebook), which can be started as follows:
 
 .. code-block:: bash
@@ -38,7 +38,7 @@ Starting HyperSpy in the notebook (or terminal)
 -----------------------------------------------
 Typically you will need to `set up IPython for interactive plotting with
 matplotlib
-<http://ipython.readthedocs.org/en/stable/interactive/plotting.html>`_ using
+<https://ipython.readthedocs.org/en/stable/interactive/plotting.html>`_ using
 ``%matplotlib`` (which is known as a 'Jupyter magic')
 *before executing any plotting command*. So, typically, after starting
 IPython, you can import HyperSpy and set up interactive matplotlib plotting by
@@ -70,9 +70,9 @@ and the
 Possible warnings when importing HyperSpy?
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-HyperSpy supports different GUIs and 
-`matplotlib backends <https://matplotlib.org/tutorials/introductory/usage.html#backends>`_ 
-which in specific cases can lead to warnings when importing HyperSpy. Most of the time 
+HyperSpy supports different GUIs and
+`matplotlib backends <https://matplotlib.org/stable/users/explain/backends.html>`_
+which in specific cases can lead to warnings when importing HyperSpy. Most of the time
 there is nothing to worry about — the warnings simply inform you of several choices you have.
 There may be several causes for a warning, for example:
 
@@ -102,8 +102,8 @@ These warnings can be turned off using the
 
 
 .. versionchanged:: v1.3
-    HyperSpy works with all matplotlib backends, including the ``notebook`` 
-    (also called ``nbAgg``) backend that enables interactive plotting embedded 
+    HyperSpy works with all matplotlib backends, including the ``notebook``
+    (also called ``nbAgg``) backend that enables interactive plotting embedded
     in the jupyter notebook.
 
 
@@ -134,26 +134,24 @@ accessed by adding a question mark to the name of a function. e.g.:
 
 This syntax is a shortcut to the standard way one of displaying the help
 associated to a given functions (docstring in Python jargon) and it is one of
-the many features of `IPython <http://ipython.scipy.org/moin/>`_, which is the
+the many features of `IPython <https://ipython.readthedocs.io/>`_, which is the
 interactive python shell that HyperSpy uses under the hood.
 
 Please note that the documentation of the code is a work in progress, so not
 all the objects are documented yet.
 
 Up-to-date documentation is always available in `the HyperSpy website.
-<http://hyperspy.org/documentation.html>`_
+<https://hyperspy.org/documentation.html>`_
 
 
 Autocompletion
 --------------
 
-Another useful `IPython <http://ipython.scipy.org/moin/>`_ feature is the
-autocompletion of commands and filenames using the tab and arrow keys. It is
-highly recommended to read the `Ipython documentation
-<http://ipython.scipy.org/moin/Documentation>`_ (specially their `Getting
-started <http://ipython.org/ipython-doc/stable/interactive/tutorial.html>`_
-section) for many more useful features that will boost your efficiency when
-working with HyperSpy/Python interactively.
+Another useful IPython feature is the
+`autocompletion <https://ipython.readthedocs.io/en/stable/interactive/tutorial.html#tab-completion>`_
+of commands and filenames using the tab and arrow keys. It is highly recommended
+to read the `Ipython introduction <https://ipython.readthedocs.io/en/stable/interactive/tutorial.html>`_ for many more useful features that will
+boost your efficiency when working with HyperSpy/Python interactively.
 
 
 Loading data
@@ -176,7 +174,7 @@ the use of a specific IO-plugin, you can provide the ``reader`` attribute:
 .. note::
 
    When the file contains several datasets, the :py:func:`~.io.load` function
-   will return a list of HyperSpy signals, instead of a single HyperSpy signal. 
+   will return a list of HyperSpy signals, instead of a single HyperSpy signal.
    Each signal can then be accessed using list indexation.
 
    .. code-block:: python
@@ -188,7 +186,7 @@ the use of a specific IO-plugin, you can provide the ``reader`` attribute:
        <Signal1D, title: ham, dimensions: (32,32|1024)>]
 
    Using indexation to access the first signal (index 0):
-   
+
    .. code-block:: python
 
       >>> s[0]
@@ -261,7 +259,7 @@ experimental data.
 .. _eelsdb-label:
 
 The :py:func:`~.misc.eels.eelsdb.eelsdb` function in `hs.datasets` can
-directly load spectra from `The EELS Database <http://eelsdb.eu>`_. For
+directly load spectra from `The EELS Database <https://eelsdb.eu>`_. For
 example, the following loads all the boron trioxide spectra currently
 available in the database:
 

doc/user_guide/install.rst

@@ -149,8 +149,8 @@ Installation using pip
 ----------------------
 
 HyperSpy is listed in the `Python Package Index
-<http://pypi.python.org/pypi>`_. Therefore, it can be automatically downloaded
-and installed  `pip <http://pypi.python.org/pypi/pip>`__. You may need to
+<https://pypi.python.org/pypi>`_. Therefore, it can be automatically downloaded
+and installed  `pip <https://pypi.python.org/pypi/pip>`__. You may need to
 install pip for the following commands to run.
 
 To install all of HyperSpy's functionalities, run:
@@ -170,9 +170,9 @@ See the following list of selectors to select the installation of optional
 dependencies required by specific functionalities:
 
 * ``learning`` for some machine learning features,
-* ``gui-jupyter`` to use the `Jupyter widgets <http://ipywidgets.readthedocs.io/en/stable/>`_
+* ``gui-jupyter`` to use the `Jupyter widgets <https://ipywidgets.readthedocs.io/en/stable/>`_
   GUI elements,
-* ``gui-traitsui`` to use the GUI elements based on `traitsui <http://docs.enthought.com/traitsui/>`_,
+* ``gui-traitsui`` to use the GUI elements based on `traitsui <https://docs.enthought.com/traitsui/>`_,
 * ``mrcz`` to read mrcz file,
 * ``speed`` to speed up some functionalities,
 * ``usid`` to read usid file,
@@ -271,7 +271,7 @@ Clone the hyperspy repository
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 To get the development version from our git repository you need to install `git
-<http://git-scm.com//>`_. Then just do:
+<https://git-scm.com//>`_. Then just do:
 
 .. code-block:: bash
 
@@ -287,8 +287,8 @@ To get the development version from our git repository you need to install `git
 
 Installation in a Anaconda/Miniconda distribution
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-Optionally, create an environment to separate your hyperspy installation from 
-other anaconda environments (`read more about environments here 
+Optionally, create an environment to separate your hyperspy installation from
+other anaconda environments (`read more about environments here
 <https://conda.io/projects/conda/en/latest/user-guide/concepts/environments.html>`_):
 
 .. code-block:: bash
@@ -307,7 +307,7 @@ The package ``hyperspy-dev`` will install the development dependencies required
 for testing and building the documentation.
 
 From the root folder of your hyperspy repository (folder containing the
-``setup.py`` file) run `pip <http://www.pip-installer.org>`_ in development mode:
+``setup.py`` file) run `pip <https://pip.pypa.io/>`_ in development mode:
 
 .. code-block:: bash
 
@@ -317,7 +317,7 @@ Installation in other (non-system) Python distribution
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 From the root folder of your hyperspy repository (folder containing the
-``setup.py`` file) run `pip <http://www.pip-installer.org>`_ in development mode:
+``setup.py`` file) run `pip <https://pip.pypa.io/>`_ in development mode:
 
 .. code-block:: bash
 
@@ -341,7 +341,7 @@ When using a system Python distribution, it is recommended to install the
 dependencies using your system package manager.
 
 From the root folder of your hyperspy repository (folder containing the
-``setup.py`` file) run `pip <http://www.pip-installer.org>`_ in development mode.
+``setup.py`` file) run `pip <https://pip.pypa.io/>`_ in development mode.
 
 .. code-block:: bash
 
@@ -361,4 +361,3 @@ You can create binaries for Debian/Ubuntu from the source by running the
 
     For this to work, the following packages must be installed in your system
     python-stdeb, debhelper, dpkg-dev and python-argparser are required.
-

doc/user_guide/intro.rst

@@ -61,5 +61,5 @@ that sets its character:
   and
   `hyperspy-gui-traitsui <https://github.com/hyperspy/hyperspy_gui_traitsui>`_
   packages for details. Not enough? If you
-  need a full, standalone GUI, `HyperSpyUI <http://hyperspy.org/hyperspyUI/>`_
+  need a full, standalone GUI, `HyperSpyUI <https://hyperspy.org/hyperspyUI/>`_
   is for you.

doc/user_guide/io.rst

@@ -134,7 +134,7 @@ functions, e.g.:
 
     >>> s = hs.load(["file1.hspy", "file2.hspy"])
 
-or by using `shell-style wildcards <http://docs.python.org/library/glob.html>`_:
+or by using `shell-style wildcards <https://docs.python.org/library/glob.html>`_:
 
 .. code-block:: python
 
@@ -1905,7 +1905,7 @@ Extra loading arguments
   acquired last frame, which typically occurs when the acquisition was
   interrupted. When loading incomplete data (``only_valid_data=False``),
   the missing data are filled with zeros. If ``sum_frames=True``, this argument
-  will be ignored to enforce consistent sum over the mapped area. 
+  will be ignored to enforce consistent sum over the mapped area.
 - ``read_em_image`` : bool, default False.
   for ``pts`` file only, If ``read_em_image=True``,
   read SEM/STEM image from pts file if available. In this case, both
@@ -1953,8 +1953,8 @@ TVIPS format
 
 The TVIPS format is the default format for image series collected by pixelated
 cameras from the TVIPS company. Typically individual images captured by these
-cameras are stored in the :ref:`TIFF format<tiff-format>` which can also be 
-loaded by Hyperspy. This format instead serves to store image streams from 
+cameras are stored in the :ref:`TIFF format<tiff-format>` which can also be
+loaded by Hyperspy. This format instead serves to store image streams from
 in-situ and 4D-STEM experiments. During collection, the maximum file size is
 typically capped meaning the dataset is typically split over multiple files
 ending in `_xyz.tvips`. The `_000.tvips` will contain the main header and
@@ -1969,7 +1969,7 @@ will not work if no such file is found.
    interoperability with the official software can neither be guaranteed.
 
 .. warning::
-    
+
    The TVIPS format currently stores very limited amount of metadata about
    scanning experiments. To reconstruct scan data, e.g. 4D-STEM datasets,
    parameters like the shape and scales of the scan dimensions should be
@@ -1982,7 +1982,7 @@ Extra loading arguments
   in the x direction. If this argument is not provided, the data will be loaded
   as a 1D stack of images. `auto` is also an option which aims to reconstruct
   the scan based on the `rotidx` indices in frame headers. Since this only
-  works for square scan grids and is prone to failure, this option is not 
+  works for square scan grids and is prone to failure, this option is not
   recommended.
 - ``scan_start_frame``: index of the first frame of the dataset to consider,
   mainly relevant for 4D-STEM datasets. If `scan_shape="auto"` this parameter
@@ -2002,11 +2002,11 @@ Extra loading arguments
   default setting of `auto` rechunking is performed such that the navigation axes
   are optimally chunked and the signal axes are not chunked. If set to anything else, the
   value will be passed to the `chunks` argument in `dask.array.rechunk`.
-  
+
 Extra saving arguments
 ^^^^^^^^^^^^^^^^^^^^^^
 
-- ``max_file_size``: approximate maximum size of individual files in bytes. 
+- ``max_file_size``: approximate maximum size of individual files in bytes.
   In this way a dataset can be split into multiple files. A file needs to be
   at least the size of the main header in the first file plus one frame and its
   frame header. By default there is no maximum and the entire dataset is saved