nexus-ellips-reader-docker-stacktrace

nexus-ellips-reader-docker-stacktrace

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RuntimeError                              Traceback (most recent call last)
Input In [2], in <cell line: 1>()
----> 1 convert(input_file=["test.yaml"],
      2         reader='ellips',
      3         nxdl='NXellipsometry',
      4         output='ellips.test.nxs')

File ~/nomad-parser-nexus/nexusparser/tools/dataconverter/convert.py:108, in convert(input_file, reader, nxdl, output, generate_template, fair, objects)
    104     data = data_reader().read(template=Template(template),
    105                               file_paths=input_file,
    106                               objects=objects)  # type: ignore[operator]
    107 else:
--> 108     data = data_reader().read(template=Template(template),
    109                               file_paths=input_file)  # type: ignore[operator]
    111 helpers.validate_data_dict(template, data, nxdl_root)
    113 if fair and data.undocumented.keys():

File ~/nomad-parser-nexus/nexusparser/tools/dataconverter/readers/ellips/reader.py:227, in EllipsometryReader.read(self, template, file_paths)
    224     raise Exception("No input files were given to Ellipsometry Reader.")
    226 # The header dictionary is filled with entries.
--> 227 header, psilist, deltalist = self.populate_header_dict_with_datasets(file_paths)
    229 # The template dictionary is filled
    230 template = populate_template_dict(header, template)

File ~/nomad-parser-nexus/nexusparser/tools/dataconverter/readers/ellips/reader.py:153, in EllipsometryReader.populate_header_dict_with_datasets(self, file_paths)
    140 def populate_header_dict_with_datasets(self, file_paths):
    141     """This is an ellipsometry-specific processing of data.
    142 
    143 The procedure is the following:
   (...)
    151 
    152 """
--> 153     header, data_file = populate_header_dict(file_paths)
    155     if os.path.isfile(data_file):
    156         whole_data = load_as_pandas_array(data_file, header)

File ~/nomad-parser-nexus/nexusparser/tools/dataconverter/readers/ellips/reader.py:101, in populate_header_dict(file_paths)
     99 for file_path in file_paths:
    100     if os.path.splitext(file_path)[1].lower() in [".yaml", ".yml"]:
--> 101         header = load_header(file_path, header)
    102         if "filename" not in header:
    103             raise KeyError("filename is missing from", file_path)

File ~/nomad-parser-nexus/nexusparser/tools/dataconverter/readers/ellips/reader.py:44, in load_header(filename, default)
     41 with open(filename, 'rt', encoding='utf8') as file:
     42     header = yaml.yaml.safe_load(file)
---> 44 for attr in header:
     45     if "@" in attr:
     46         header[attr.replace("\\@", "@")] = header.pop(attr)

RuntimeError: dictionary keys changed during iteration