Merge pull request #226 from FAIRmat-NFDI/readme-updates

Update main, nexus, generate_eln READMEs

README.md

@@ -43,6 +43,10 @@ data into the NeXus standard and visualising the files content.
 
 - [**dataconverter**](https://github.com/FAIRmat-NFDI/pynxtools/blob/master/pynxtools/dataconverter/README.md): Creates compliant instances of NeXus/HDF5 files to [NeXus schemas](https://nexusformat.org).
 - [**read_nexus**](https://github.com/FAIRmat-NFDI/pynxtools/blob/master/pynxtools/nexus/README.md): Outputs a debug log for a given NeXus file.
+- [**generate_eln**](https://github.com/FAIRmat-NFDI/pynxtools/blob/master/pynxtools/eln_mapper/README.md): Outputs ELN files that can be used to add metadata to the dataconverter routine.
+
+# Documentation
+Documentation for the different tools can be found [here](https://fairmat-nfdi.github.io/pynxtools/).
 
 # Contributing
 

pynxtools/eln_mapper/README.md

@@ -1,19 +1,24 @@
 # ELN generator
-This is a helper tool for generating eln
-- The simple eln generator that can be used in a console or jupyter-notebook
-- Scheme based eln generator that can be used in NOMAD and the eln can be used as a custom scheme in NOMAD.
+This is a helper tool for generating ELN files that can be used to add metadata to the dataconverter routine.
+Two types of ELN are supported (by passing the flag `eln-type`):
+- **eln**: The simple ELN generator that can be used in a console or jupyter-notebook.
+- **scheme_eln**: Scheme based ELN generator that can be used in NOMAD and the ELN can be used as a custom scheme in NOMAD.
 
 ```
-$ eln_generator --options <value>
+user@box:~$ generate_eln --help
+Usage: generate_eln [OPTIONS]
+
+  Helper tool for generating ELN files in YAML format.
 
 Options:
   --nxdl TEXT                  Name of NeXus definition without extension
                                (.nxdl.xml).  [required]
-  --skip-top-levels INTEGER    To skip upto a level of parent hierarchical structure.
+  --skip-top-levels INTEGER    To skip the level of parent hierarchy level.
                                E.g. for default 1 the part Entry[ENTRY] from
                                /Entry[ENTRY]/Instrument[INSTRUMENT]/... will
                                be skiped.  [default: 1]
-  --output-file TEXT           Name of  output file.
-  --eln-type [eln|scheme_eln]  Choose a type from the eln or scheme_eln.  [required]
+  --output-file TEXT           Name of file that is neede to generated output
+                               file.
+  --eln-type [eln|scheme_eln]  Choose a type of ELN output (eln or
+                               scheme_eln).  [required]
   --help                       Show this message and exit.
-```

pynxtools/eln_mapper/eln_mapper.py

@@ -34,7 +34,7 @@
     type=int,
     show_default=True,
     help=(
-        "To skip the level of parent hierarchy level. E.g. for default 1 the part"
+        "To skip the level of parent hierarchy level. E.g. for default 1 the part "
         "Entry[ENTRY] from /Entry[ENTRY]/Instrument[INSTRUMENT]/... will be skiped."
     ),
 )
@@ -49,20 +49,10 @@
     required=True,
     type=click.Choice(["eln", "scheme_eln"], case_sensitive=False),
     default="eln",
+    help=("Choose a type of ELN output (eln or scheme_eln)."),
 )
 def get_eln(nxdl: str, skip_top_levels: int, output_file: str, eln_type: str):
-    """To generate ELN in yaml file format.
-
-    Parameters
-    ----------
-
-        nxdl : str
-            Name of NeXus definition e.g. NXmpes
-        skip_top_levels : int
-            To skip hierarchical levels
-        output_file : str
-            Name of the output file.
-    """
+    """Helper tool for generating ELN files in YAML format."""
     eln_type = eln_type.lower()
     if eln_type == "eln":
         generate_eln(nxdl, output_file, skip_top_levels)

pynxtools/nexus/README.md

@@ -35,4 +35,4 @@ export 'NEXUS_DEF_PATH'=<folder_path_that_contains_nexus_defs>
 
 Following example dataset can be used to test `read_nexus` module `tests/data/nexus/201805_WSe2_arpes.nxs`.
 This is an angular-resolved photoelectron spectroscopy (ARPES) dataset and it is formatted according to
-the [NXarpes application definition of NEXUS](https://manual.nexusformat.org/classes/applications/NXarpes.html#nxarpes).
+the [NXarpes application definition of NeXus](https://manual.nexusformat.org/classes/applications/NXarpes.html#nxarpes).