Quick fixes (due to different SciPy version?). Allow empty or unknown data.

atkparser/atkio.py

@@ -30,7 +30,9 @@ class Reader:
         self.conf_names = None
         self.calc_names = None
         self.f = netcdf_file(fname, 'r', mmap=True)
-        self.atk_version = self.f.version[:].decode('utf-8').split()[-1]
+        self.atk_version = 'unavailable'
+        # TODO this implementation causes an error, in current SciPy netcdf_file has no .version
+        # self.atk_version = self.f.version[:].decode('utf-8').split()[-1]
         self.read_names()
         for gid in self.calc_names.keys():
             conf_name = self.conf_names[gid]
@@ -118,7 +120,9 @@ class Reader:
            the finger print table which maps between calculated
            quantities and configurations.
         """
-        self._names = self.f._names[:].decode('utf-8').split(';')
+        # TODO there are no ._names in this SciPy version
+        # self._names = self.f._names[:].decode('utf-8').split(';')
+        self._names = self.f.variables.keys()  # [:].decode('utf-8').split(';')
         self.conf_names = self._read_configuration_names()
         self.calc_names = self._read_calculator_names()
         self.finger_print_table = self._read_finger_print_table()

atkparser/parser_atk.py

@@ -51,29 +51,29 @@ metaInfoEnv, warnings = loadJsonFile(
     extraArgsHandling = InfoKindEl.ADD_EXTRA_ARGS, uri = None)
 
 class ATKParserWrapper():
-    """ A proper class envolop for running this parser using Noamd-FAIRD infra. """
+    """ A proper class envolop for running this parser using nomad-FAIRDI infra. """
     def __init__(self, backend, **kwargs):
         self.backend_factory = backend
 
     def parse(self, mainfile):
-        from unittest.mock import patch
         logging.info('ATK parser started')
         logging.getLogger('nomadcore').setLevel(logging.WARNING)
         backend = self.backend_factory(metaInfoEnv)
-        backend = parse_without_class(mainfile, backend)
+        parse_without_class(mainfile, backend)
         return backend
 
 def parse_without_class(filename, backend):
+    p = backend  # JsonParseEventsWriterBackend(metaInfoEnv)
+    o = open_section
+
     r = Reader(filename)
     indices = range(r.get_number_of_calculators())
     for index in indices:
         r.c = r.get_calculator(index)
         if r.c is None:
-            return
+            return backend
         r.atoms = r.get_atoms(index)
 
-        p = backend  # JsonParseEventsWriterBackend(metaInfoEnv)
-        o = open_section
         p.startedParsingSession(filename, parser_info)
         with o(p, 'section_run'):
             p.addValue('program_name', 'ATK')
@@ -186,6 +186,13 @@ def parse_without_class(filename, backend):
         p.finishedParsingSession("ParseSuccess", None)
         return p
 
+    logging.getLogger('nomadcore').warn('no known calculator found, maybe not a ATK file?')
+    with o(p, 'section_run'):
+        p.addValue('program_name', 'ATK')
+        p.addValue('program_version', r.atk_version)
+    return p
+
+
 if __name__ == '__main__':
     import sys
     filename = sys.argv[1]