Remove remaining --input-file arguments

FAIRmat-NFDI · Feb 21, 2024 · f982c0e · f982c0e
1 parent a664b8c
commit f982c0e
Show file tree

Hide file tree

Showing 4 changed files with 10 additions and 9 deletions.
diff --git a/examples/json_map/README.md b/examples/json_map/README.md
@@ -19,17 +19,17 @@ user@box:~$ dataconverter --nxdl NXmynxdl --generate-template > mynxdl.mapping.j
 
 ### Automatically merge partial NeXus files
 ```console
-user@box:~$ dataconverter --nxdl NXiv_temp --input-file voltage_and_temperature.nxs --input-file current.nxs --output auto_merged.nxs
+user@box:~$ dataconverter --nxdl NXiv_temp voltage_and_temperature.nxs current.nxs --output auto_merged.nxs
 ```
 
 ### Map and copy over data to new NeXus file
 ```console
-user@box:~$ dataconverter --nxdl NXiv_temp --mapping merge_copied.mapping.json --input-file voltage_and_temperature.nxs --input-file current.nxs --output merged_copied.nxs
+user@box:~$ dataconverter --nxdl NXiv_temp --mapping merge_copied.mapping.json voltage_and_temperature.nxs current.nxs --output merged_copied.nxs
 ```
 
 ### Map and link over data to new NeXus file
 ```console
-user@box:~$ dataconverter --nxdl NXiv_temp --mapping merge_linked.mapping.json --input-file voltage_and_temperature.nxs --input-file current.nxs --output merged_linked.nxs
+user@box:~$ dataconverter --nxdl NXiv_temp --mapping merge_linked.mapping.json voltage_and_temperature.nxs current.nxs --output merged_linked.nxs
 ```
 
 ## Contact person in FAIRmat for this reader

diff --git a/examples/mpes/README.md b/examples/mpes/README.md
@@ -23,8 +23,8 @@ For XPS data you may use the data in [`tests/data/dataconverter/readers/xps`](ht
 ```shell
 dataconverter --reader xps \\
     --nxdl NXmpes \\
-    --input-file eln_data.yaml \\
-    --input-file In-situ_PBTTT_XPS_SPECS.xml \\
+    eln_data.yaml \\
+    In-situ_PBTTT_XPS_SPECS.xml \\
     --output xps_example.nxs
 ```
 

diff --git a/pynxtools/dataconverter/readers/json_map/reader.py b/pynxtools/dataconverter/readers/json_map/reader.py
@@ -16,16 +16,17 @@
 # limitations under the License.
 #
 """An example reader implementation for the DataConverter."""
-from typing import Tuple, Any
 import json
 import pickle
+from typing import Any, Tuple
+
 import numpy as np
 import xarray
 from mergedeep import merge
 
+from pynxtools.dataconverter import hdfdict
 from pynxtools.dataconverter.readers.base.reader import BaseReader
 from pynxtools.dataconverter.template import Template
-from pynxtools.dataconverter import hdfdict
 
 
 def parse_slice(slice_string):
@@ -211,7 +212,7 @@ def read(
                     {x: "/hierarchical/path/in/your/datafile" for x in template}
                 )
                 raise IOError(
-                    "Please supply a JSON mapping file: --input-file"
+                    "Please supply a JSON mapping file: "
                     " my_nxdl_map.mapping.json\n\n You can use this "
                     "template for the required fields: \n" + str(template)
                 )
@@ -228,3 +229,4 @@ def read(
 
 # This has to be set to allow the convert script to use this reader. Set it to "MyDataReader".
 READER = JsonMapReader
+READER = JsonMapReader
diff --git a/tests/dataconverter/test_convert.py b/tests/dataconverter/test_convert.py
@@ -146,7 +146,6 @@ def test_links_and_virtual_datasets(tmp_path):
             "NXtest",
             "--reader",
             "example",
-            "--input-file",
             os.path.join(dirpath, "testdata.json"),
             "--output",
             os.path.join(tmp_path, "test_output.h5"),