move order of args in testing

src/pynxtools/testing/nexus_conversion.py

@@ -40,7 +40,7 @@ class ReaderTest:
     """Generic test for reader plugins."""
 
     def __init__(
-        self, nxdl, reader_name, files_or_dir, ref_log_file, tmp_path, caplog
+        self, nxdl, reader_name, files_or_dir, tmp_path, caplog, ref_log_file=None
     ) -> None:
         """Initialize the test object.
 
@@ -53,22 +53,24 @@ def __init__(
         files_or_dir : str
             List of input files or full path string to the example data directory that contains all the files
             required for running the data conversion through the reader.
-        ref_log_file : str
-            Full path string to the reference log file generated from the same
-            set of input files.
         tmp_path : pathlib.PosixPath
             Pytest fixture variable, used to clean up the files generated during the test.
         caplog : _pytest.logging.LogCaptureFixture
             Pytest fixture variable, used to capture the log messages during the test.
+        ref_log_file : str
+            Full path string to the reference log file generated from the same
+            set of input files in files_or_dir. This can also be parsed automatically if files_or_dir
+            is the full path string to the example data directory and there is only one reference
+            log file.
         """
 
         self.nxdl = nxdl
         self.reader_name = reader_name
         self.reader = get_reader(self.reader_name)
         self.files_or_dir = files_or_dir
-        self.ref_log_file = ref_log_file
         self.tmp_path = tmp_path
         self.caplog = caplog
+        self.ref_log_file = ref_log_file
         self.created_nexus = f"{tmp_path}/{os.sep}/output.nxs"
 
     def convert_to_nexus(
@@ -95,7 +97,9 @@ def convert_to_nexus(
             ][0]
         assert self.ref_log_file, "Reference nexus .log file not found"
 
-        input_files = [file for file in example_files if not file.endswith(".nxs")]
+        input_files = [
+            file for file in example_files if not file.endswith((".nxs", ".log"))
+        ]
 
         assert (
             self.nxdl in self.reader.supported_nxdls
@@ -140,8 +144,8 @@ def check_reproducibility_of_nexus(self):
             "DEBUG - value: v",
             "DEBUG - value: https://github.com/FAIRmat-NFDI/nexus_definitions/blob/",
         ]
-        gen_log = get_log_file(self.created_nexus, "gen_nexus.log", self.tmp_path)
-        with open(gen_log, "r", encoding="utf-8") as gen, open(
+        gen_log_file = get_log_file(self.created_nexus, "gen_nexus.log", self.tmp_path)
+        with open(gen_log_file, "r", encoding="utf-8") as gen, open(
             self.ref_log_file, "r", encoding="utf-8"
         ) as ref:
             gen_lines = gen.readlines()