change how-to docs for validation (#698)

* change how-to docs for validation

* change learn docs for validation

* further cleanup

* build docs from feature branch

* spellcheck

* review comments

* remove installation manual for cnxvalidate

* revert changes to docs workflow

* spelling

Author: lukaspie

.cspell/custom-dictionary.txt

@@ -11,21 +11,26 @@ NXDL
 # Words related to experimental techniques
 
 # Software
+BASECLASS
 caplog
 cnxvalidate
 dataconverter
 DECTRIS
 electronanalyzer
 ELECTRONANALYZER
 ellipsometry
+GROUPNAME
 infty
 libiconv
 loadgroup
 mainfile
+Metainfo
 MSYS
 nexpy
+nexusformat
 nxdls
 PATHCONV
+pathtovalidate
 posint
 punx
 pynxtools
@@ -34,6 +39,7 @@ xdist
 Zenodo
 
 # examples
+alphabetagamma
 appdefdir
 CSET
 ellips
@@ -61,30 +67,53 @@ xfbaa
 arpes
 ARPES
 Bluesky
+emittance
+flatfield
+fluence
 mbar
+monochromator
+monoclinic
 MPES
 Raman
+setpoint
+xraylens
 
 # Names
+Brockhauser
+Brückner
+Dobener
+Draxl
+Fekete
 Forschungsgemeinschaft
+Ginzburg
+Haraszti
 José
 Kühbach
 Lukas
 lukaspie
+Maier
 Markus
+Márquez
 mkuehbach
 Mozumder
 NFDI
 Pielsticker
+Rettig
+Scheidgen
 Shabih
 Sherjeel
 sherjeelshabih
+tommaso
 
 # other languages
 
-# en-UK which requires to many changes
+# en-UK
+analyser
+oxidising
 
 # misc
+appdef
 appdefs
 hypothes
-speciality
+plottable
+underload

.github/workflows/build_docs.yml

@@ -30,7 +30,9 @@ jobs:
       - name: Check spelling
         uses: streetsidesoftware/cspell-action@v7
         with:
-          files: "docs/**/*.md README.md"
+          files: |
+            docs/**/*.md
+            README.md
           strict: true
           incremental_files_only: false
 

docs/getting-started.md

@@ -59,7 +59,7 @@ No. With the available [plugins](./reference/plugins.md) or community-developed
 
 NeXus is supported by the research data management platform NOMAD (as a [NOMAD plugin](https://nomad-lab.eu/prod/v1/docs/howto/plugins/plugins.html)). Experimental data files that are compatible with a NeXus application definition can easily be uploaded to NOMAD and translated into the [NOMAD Metainfo](https://nomad-lab.eu/prod/v1/gui/analyze/metainfo/pynxtools) data model using `pynxtools`. Therefore, the data file can be recognized by NOMAD's search system. If you want to learn more about uploading NeXus data to NOMAD, please refer to the [NeXus to NOMAD tutorial](./tutorial/nexus-to-nomad.md) of this documentation.
 
-To use the `pynxtools` Python package with NOMAD, simply install it in the same Python environment as the `nomad-lab` package. NOMAD will recognize `pynxtools` as a plugin automatically and offer automatic parsing of `.nxs` files. In addition, NOMAD will automatically transform the NeXus definitions shipped with `pynxtools` into its own datamodel called `Metainfo`. By default, `pynxtools` is already included in the NOMAD [production]https://nomad-lab.eu/prod/v1/gui/ and [staging](https://nomad-lab.eu/prod/v1/staging/gui/) deployments..
+To use the `pynxtools` Python package with NOMAD, simply install it in the same Python environment as the `nomad-lab` package. NOMAD will recognize `pynxtools` as a plugin automatically and offer automatic parsing of `.nxs` files. In addition, NOMAD will automatically transform the NeXus definitions shipped with `pynxtools` into its own data model called `Metainfo`. By default, `pynxtools` is already included in the NOMAD [production]https://nomad-lab.eu/prod/v1/gui/ and [staging](https://nomad-lab.eu/prod/v1/staging/gui/) deployments..
 
 !!! info "A note on FAIR data"
 

docs/how-tos/pynxtools/create-nexus-files-by-python.md

@@ -212,5 +212,5 @@ Note that you can also add instances for recommended or optional concepts to the
 
 ## What's next?
 
-- Once you have a finished NeXus file, you may continue [by validating the NeXus file](validate-nexus-file.md).
+- Once you have a finished NeXus file, you may continue [by validating the NeXus file](../pynxtools/validate-nexus-files.md).
 - If you find yourself in the situation that you need to run such Python code routinely to convert your data, we strongly recommend creating your own reader or plugin in the `pynxtools` ecosystem. You can find a how-to guide to get you started [here](build-a-plugin.md).

docs/how-tos/pynxtools/installation_notes_nxvalidate.md

@@ -78,7 +78,7 @@ Afterwards, the `ReaderTest.convert_to_nexus` method uses the NeXus annotator to
 This test can also be configured:
 
 - You can pass a keyword argument `ignore_lines` to `check_reproducibility_of_nexus`. `ignore_lines` is expected to be a list of lines for which the comparison shall be skipped. Specifically, any line that starts with any of the strings in `ignore_lines` is ignored.
-- In adddition, you can disable the comparison for a given line for a NeXus concept in the `read_nexus` output using the `ignore_sections` keyword. As an example, a typical section for a NeXus field in the output looks like this:
+- In addition, you can disable the comparison for a given line for a NeXus concept in the `read_nexus` output using the `ignore_sections` keyword. As an example, a typical section for a NeXus field in the output looks like this:
 
     ```
     DEBUG: 
@@ -104,7 +104,7 @@ This test can also be configured:
 
 ## How to write an integration test for a NOMAD example in a reader plugin
 
-It is also possible to ship NOMAD Example Uploads directly with the reader plugin. As an example, `pynxtools-mpes` comes with its own [NOMAD examplehere](https://github.com/FAIRmat-NFDI/pynxtools-mpes/tree/bring-in-examples/src/pynxtools_mpes/nomad) using the [`ExampleUploadEntryPoint`](https://nomad-lab.eu/prod/v1/staging/docs/howto/plugins/example_uploads.html) of NOMAD.
+It is also possible to ship NOMAD Example Uploads directly with the reader plugin. As an example, `pynxtools-mpes` comes with its own [NOMAD example](https://github.com/FAIRmat-NFDI/pynxtools-mpes/tree/bring-in-examples/src/pynxtools_mpes/nomad) using the [`ExampleUploadEntryPoint`](https://nomad-lab.eu/prod/v1/staging/docs/howto/plugins/example_uploads.html) of NOMAD.
 
 The `testing` sub-package of `pynxtools` provides two functionalities for testing the `ExampleUploadEntryPoint` defined in a `pynxtools` plugin: