add logo

doc/conf.py

@@ -53,6 +53,7 @@
 
 intersphinx_mapping = {
     "dask": ("https://docs.dask.org/en/latest", None),
+    "exspy": ("https://hyperspy.org/exspy", None),
     "hyperspy": ("https://hyperspy.org/hyperspy-doc/current/", None),
     "kikuchipy": ("https://kikuchipy.org/en/latest/", None),
     "matplotlib": ("https://matplotlib.org/stable", None),
@@ -91,15 +92,17 @@
         },
     ],
     "logo": {
-        "image_light": "_static/hyperspy_logo.png",
-        "image_dark": "_static/hyperspy_logo.png",
+        "image_light": "_static/holospy-banner-light.svg",
+        "image_dark": "_static/holospy-banner-dark.svg",
     },
     "header_links_before_dropdown": 6,
 }
 
 # -- Options for sphinx_favicon extension -----------------------------------
 
-favicons = {"rel": "icon", "href": "logo_sq.svg", "type": "image/svg+xml"}
+favicons = [
+    "holospy.ico",
+]
 
 # Check links to API when building documentation
 nitpicky = False

doc/user_guide/electron_holography.rst

@@ -79,7 +79,7 @@ hologram should be provided to the method either as Hyperspy's
 Using the reconstructed wave, one can access its amplitude and phase (also
 unwrapped phase) using
 ``amplitude`` and ``phase`` properties
-(also the :external+hyperspy:py:meth:`hyperspy._signals.complex_signal.ComplexSignal.unwrapped_phase`
+(also the :external+hyperspy:meth:`hyperspy.api.signals.ComplexSignal.unwrapped_phase`
 method):
 
 .. code-block:: python

doc/user_guide/metadata_structure.rst

@@ -6,7 +6,7 @@ HoloSpy metadata structure
 HoloSpy extends the :external+hyperspy:ref:`HyperSpy metadata structure
 <metadata_structure>`
 with conventions for metadata specific to its signal types. Refer to the
-:external+hyperspy:doc:`HyperSpy metadata documentation <user_guide/metadata_structure>`
+:external+hyperspy:ref:`HyperSpy metadata documentation <metadata_structure>`
 for general metadata fields.
 
 The metadata of any **signal objects** is stored in the `metadata` attribute,
@@ -49,14 +49,14 @@ all types of leaves will apply to every type of measurement.
 General
 =======
 
-See `HyperSpy-Metadata-General
-<https://hyperspy.org/hyperspy-doc/current/user_guide/metadata_structure.html#general>`_.
+See :external+hyperspy:ref:`HyperSpy-Metadata-General
+<general-metadata>`.
 
 Sample
 ======
 
-See `HyperSpy-Metadata-Sample
-<https://hyperspy.org/hyperspy-doc/current/user_guide/metadata_structure.html#sample>`_.
+See :external+hyperspy:ref:`HyperSpy-Metadata-Sample
+<sample-metadata>`.
 
 Signal
 ======
@@ -67,9 +67,8 @@ signal_type
     String that describes the type of signal. Currently, the only HoloSpy
     specific signal class is ``hologram``.
 
-See `HyperSpy-Metadata-Signal
-<https://hyperspy.org/hyperspy-doc/current/user_guide/metadata_structure.html#signal>`__
-for additional fields.
+See :external+hyperspy:ref:`HyperSpy-Metadata-Signal <signal-metadata>` for
+additional fields.
 
 Acquisition Instrument
 ======================
@@ -98,5 +97,4 @@ voltage
 
     Voltage of electrostatic biprism in volts
 
-See `HyperSpy-Metadata-TEM <https://hyperspy.org/hyperspy-doc/current/user_guide/metadata_structure.html#tem>`_
-	for additional fields.
+See :external+exspy:ref:`eXSpy TEM metadata <source-metadata>` for additional fields.

holospy/signals/hologram_image.py

@@ -150,7 +150,6 @@ def _estimate_fringe_contrast_statistical(holo):
 
 
 class HologramImage(Signal2D):
-
     """Signal class for holograms acquired via off-axis electron holography."""
 
     _signal_type = "hologram"
@@ -937,7 +936,6 @@ def statistics(
 
 
 class LazyHologramImage(LazySignal, HologramImage):
-
     """
     Lazy signal class for holograms acquired via off-axis electron
     holography.

upcoming_changes/26.doc.rst

@@ -0,0 +1 @@
+Add holoSpy logo

upcoming_changes/README.rst

@@ -0,0 +1,36 @@
+This directory contains "news fragments" which are short files that contain a small **ReST**-formatted
+text that will be added to the next ``CHANGELOG``.
+
+The ``CHANGELOG`` will be read by **users**, so this description should be aimed to holoSpy users
+instead of describing internal changes which are only relevant to the developers.
+
+Each file should be named like ``<ISSUE>.<TYPE>.rst``, where
+``<ISSUE>`` is an issue number, and ``<TYPE>`` is one of:
+
+* ``new``: new user facing features, like new command-line options and new behavior.
+* ``bugfix``: fixes a bug.
+* ``doc``: documentation improvement, like rewording an entire session or adding missing docs.
+* ``deprecation``: feature deprecation.
+* ``enhancements``: improvement of existing functionality, usually without requiring user intervention.
+* ``api``: a change which may break an existing script, such as feature removal or behavior change.
+* ``maintenance``: a change related to the test suite, packaging, etc.
+
+So for example ``1412.new.rst`` or ``2773.bugfix.rst``.
+
+If your PR fixes an issue, use the number of the issue here. If there is no issue,
+then after you submit the PR and get the PR number you can add a
+changelog using that instead.
+
+If you are not sure what issue type to use, don't hesitate to ask in your PR.
+
+``towncrier`` preserves multiple paragraphs and formatting (code blocks, lists, and so on), but for entries
+other than ``new`` it is usually better to stick to a single paragraph to keep it concise. For ``new``,
+it is recommended to add a hyperlink to the user guide.
+
+To make a draft of the changelog, run from the command line:
+
+   .. code-block:: bash
+
+       $ towncrier build --draft
+
+See https://github.com/twisted/towncrier for more details.