Merge pull request #228 from FAIRmat-NFDI/222-c-flag-not-working-in-r…

…ead-nexus

Read_nexus README: warn windows users to set MSYS_NO_PATHCONV through bash

pynxtools/nexus/README.md

@@ -1,28 +1,35 @@
+# NeXus file reader and debugger
+
 This utility outputs a debug log for a given NeXus file by annotating the data and
 metadata entries with the schema definitions from the respective NeXus base classes
 and application definitions to which the file refers to.
 
-```
-Options:
-    -f, --nexus-file : Name of nexus output file (.nxs) to enquiry.
-    -d, --documentation : Definition path in nexus output (.nxs) file. Returns debug
-                          log relavent with that definition path.
-                          Example: /entry/data/delays
-    -c, --concept : Concept path from application definition file (.nxdl,xml). Finds out
-                    all the available concept definition (IS-A realation) for rendered
-                    concept path.
-                    Example: /NXarpes/ENTRY/INSTRUMENT/analyser
-    --help : To get the documentaion above
-    NOTE: Only one option from (-d and -c) is acceptable.
-
-In console:
-
-read_nexus [Options] <path_to_nexus_file>
-
+```console
+user@box:~$ read_nexus --help
+Usage: read_nexus [OPTIONS]
 
+  The main function to call when used as a script.
 
+Options:
+  -f, --nexus-file TEXT     NeXus file with extension .nxs to learn NeXus
+                            different concept documentation and concept.
+  -d, --documentation TEXT  Definition path in nexus output (.nxs) file.
+                            Returns debuglog relavent with that definition
+                            path. Example: /entry/data/delays
+  -c, --concept TEXT        Concept path from application definition file
+                            (.nxdl,xml). Finds outall the available concept
+                            definition (IS-A realation) for renderedconcept
+                            path. Example: /NXarpes/ENTRY/INSTRUMENT/analyser
+  --help                    Show this message and exit.
+
+NOTE: Only one option from (-d and -c) is acceptable.
 ```
 
+The following example dataset can be used to test the `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).
+
+## Using a different set of NeXus definitions
 _The environmental variable called "NEXUS_DEF_PATH" can be set to
 a directory, which contains the NeXus definitions as XML files. If this environmental
 variable is not defined, the module will use the definitions in its bundle._
@@ -33,6 +40,11 @@ An environmental variable can be set as follows:
 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).
+## A note to Windows users
+If you run `read_nexus` from `git bash`, you need to set the environmental variable
+`MSYS_NO_PATHCONV` to avoid the [path translation in Windows Git MSys](https://stackoverflow.com/questions/7250130/how-to-stop-mingw-and-msys-from-mangling-path-names-given-at-the-command-line#34386471).
+The easiest way is to prefix the `read_nexus` call with `MSYS_NO_PATHCONV=1`:
+
+```
+MSYS_NO_PATHCONV=1 read_nexus -c /NXarpes/ENTRY/INSTRUMENT/analyser
+```