align with main, groupings in manual (#411)

* bring in changes from nexusformat/1428

* typo fix

* fix links in manual

* CI/CD: install tools for SVG vector graphics support

* use sphinx.ext.imgconverter

* bring in changes from main

* bring in groupings in manual

* nyaml-nxdl conversion

* found unintentional nameType in NXstm

* cleanup for groupings in manual

* adjust custom dict for spellcheck

* nyaml-nxdl consistency

* formatting

* review comments

* fix start date in NXelectron_detector

---------

Co-authored-by: Lukas Pielsticker <you@example.com>

Author: lukaspie

.cspell/custom-dictionary.txt

@@ -61,7 +61,8 @@ DCOM
 DFM
 DXRD
 Defocus
-Delocalization,
+Delocalization
+EASI
 EBSD
 EBSP
 ECCI
@@ -109,6 +110,7 @@ ISSN
 IVAS
 Idev
 Inconel
+INDU
 Inplane
 Iontype
 Iontypes
@@ -144,6 +146,7 @@ Raman
 Ronchigram
 SAS
 SAXS
+SENB
 SERS
 SNSnxtranslate
 SPIE
@@ -173,6 +176,7 @@ WWPDB
 XDMF
 XFEL
 XPCS
+Xtranslation
 Zincblende
 Zirconate
 aabb
@@ -254,6 +258,7 @@ detectorn
 deuterated
 diagionalized
 diffractogram
+diffractograms
 disclination
 disorientations
 dispersoids
@@ -313,7 +318,6 @@ hydroxonium
 hyperslab
 hyperspectral
 ibeam
-illuminatable
 infty
 inplane
 interconvert
@@ -491,6 +495,7 @@ underconstrained
 underload
 undulator
 unvalidated
+varepsilon
 vibropolishing
 voxelated
 voxelization
@@ -633,6 +638,7 @@ Ophus
 PANalytical
 Patala
 Pauly
+Pawley
 Pedersen
 Peltier
 Pennycock
@@ -646,6 +652,7 @@ Reichmann
 Reimer
 Remmele
 Rielli
+Rietveld
 Rochon
 Rollett
 Romaner
@@ -723,6 +730,21 @@ paraprobe-parmsetup-nanochem
 pynxtools
 pyxem
 
+# Data plotting
+azim
+DAXIS
+edgecolors
+facecolors
+figsize
+fontsize
+mplot
+toolkits
+verts
+XAXIS
+xlim
+ylim
+zlim
+
 # other languages
 Institut
 
@@ -767,6 +789,16 @@ recreatable
 speciality
 timeslot
 timestamping
+tracability
 unlooped
 unranged
-weared
+weared
+
+# to fix in future releases (all in NXstress)
+acquistion
+acquistions
+asscociated
+dimensioness
+folowing
+reproducability
+Uncentrainties

.github/workflows/ci.yaml

@@ -81,6 +81,13 @@ jobs:
             texlive-fonts-recommended
           tex --version
 
+      - name: Install tools for SVG vector graphics support
+        run: |
+          sudo apt-get update -y && \
+          sudo apt-get install -y \
+            inkscape \
+            imagemagick
+
       - name: Generate build files
         env:
           GH_TOKEN: ${{ (env.python_version == env.python_deploy_version && (github.event.inputs.deploy || github.event.inputs.upload)) && secrets.GITHUB_TOKEN  || 'NONE' }}

README.md

@@ -7,6 +7,12 @@
 
 ## NeXus definition developers
 
+After making a change to the NeXus class definitions there are two important checks
+to be made before commiting the change:
+
+1. check whether the change does not violate any syntax rules
+2. verify whether the change looks as intended in the HTML documentation
+
 First install the test and build requirements with this command (only run once)
 
     make install

applications/NXapm.nxdl.xml

@@ -84,7 +84,7 @@
         is considered as a narrow synonym for crystal defects.
 
         The aim of the NXapm application definition is to provide a general yet specific enough
-        solution to serialize artifacts for virtually all atom probe and field-ion microcopy experiments.
+        solution to serialize artifacts for virtually all atom probe and field-ion microscopy experiments.
 
         Before summarizing the design of the base classes and the parts of the NXapm application definition,
         it is worthwhile to recall and distinguish concepts that are related to atom extraction
@@ -187,7 +187,7 @@
         NXapm defines constraints on the existence and cardinality of concepts and its concept branches but seeks to
         offer a compromise. The key design pattern followed is that most branches are made optional or at most recommended
         but their child concepts are conditionally required. Thereby, NXapm can cover a variety of simple but also complex
-        use cases. An example of this parent-optional-but-childs-stronger-restricted design is the combination of the
+        use cases. An example of this parent-optional-but-children-stronger-restricted design is the combination of the
         optional group ``measurement`` with its required child ``measurement/instrument``:
         Users which report simulations are not forced to document the instrument but users which have characterized
         a specimen are motivated to report about the instrument. They are though not  necessarily required to report all
@@ -215,7 +215,7 @@
         considered best practice by AMETEK/Cameca, ``raw_data`` for delay-line timing data, ``hit_finding`` for details of the
         hit finding algorithm, ``hit_spatial_filtering`` a process that filters hits of too low quality and those laying outside the about
         to be computed reconstruction volume. Furthermore, group ``voltage_and_bowl`` offers a place for documenting calibrations
-        and processing non-linearities. Group ``mass_to_charge_conversion`` is used to document the mass calibration and the
+        and processing nonlinearities. Group ``mass_to_charge_conversion`` is used to document the mass calibration and the
         conversion from time-of-flight to mass-to-charge-state-ratio values.
 
         Finally, the groups ``reconstruction`` and ``ranging`` were designed to match and document the classical approaches how
@@ -984,7 +984,7 @@
 
                         In the case of an open-source instrument, like P. Felfer's Oxcart or G. Schmitz's
                         M-TAP instruments, also use program1, program2, ... with program1 representing
-                        the control software e.g. `M. Monajem and P. Felfer pyCCAPT <https://pyccapt.readthedocs.io/en/latest/>`_.
+                        the control software e.g. `M. Monajem and P. Felfer PYCCAPT <https://pyccapt.readthedocs.io/en/latest/>`_.
                         Further instances (program2, ...) can be used to list the dependencies, the
                         python virtual environment.
                     </doc>

applications/NXcanSAS.nxdl.xml

@@ -72,7 +72,7 @@
         * NXcanSAS is for reduced SAS data and metadata to be stored together in one file.
         * *Reduced* SAS data consists of :math:`I(\vec{Q})` or :math:`I(|\vec{Q}|)`
         * External file links are not to be used for the reduced data. 
-        * A good practice/practise is, at least, to include a reference to how the data was acquired and processed.  Yet this is not a requirement.
+        * A good practice is, at least, to include a reference to how the data was acquired and processed.  Yet this is not a requirement.
         * There is no need for NXcanSAS to refer to any raw data.
 
         The canSAS data format has a structure similar to NeXus, not identical.

applications/NXellipsometry.nxdl.xml

@@ -280,7 +280,7 @@
                 <doc>
                     Spectral values (e.g. wavelength or energy) used for the measurement.
                     An array of 1 or more elements. Length defines N_spectrum. Replace
-                    'SPECTRUM' by the physical quantity that is used, e.g. wavelength.
+                    'NAME' by the physical quantity that is used, e.g. wavelength.
                 </doc>
                 <dimensions rank="1">
                     <dim index="1" value="N_spectrum"/>

applications/NXem.nxdl.xml

@@ -89,7 +89,7 @@
         relevant. NXem defines constraints on the existence and cardinality of concepts and its concept branches
         but seeks to offer a compromise. The key design pattern followed is that most branches are made optional
         or at most recommended but their child concepts conditional required. Thereby, NXem can cover a variety
-        of simple but also complex use cases. An example of this parent-optional-but-childs-stronger-restricted design
+        of simple but also complex use cases. An example of this parent-optional-but-children-stronger-restricted design
         is the combination of the optional group ``measurement`` with its required child
         ``measurement/instrument``: Users which report simulations are not forced to document the instrument
         but users which have characterized a sample are motivated to report about the instrument. They are though not
@@ -414,8 +414,8 @@
 
                     The information is recorded to qualify if the beam used was likely
                     able to shine through the specimen. For scanning electron microscopy,
-                    in many cases the specimen is typically thicker than what is
-                    illuminatable by the electron beam.
+                    in many cases the specimen is typically thicker than what is illuminable
+                    by the electron beam.
 
                     In this case the value should be set to the actual thickness of the specimen
                     viewed for an illumination situation where the nominal surface normal of the