Merge pull request #579 from FAIRmat-NFDI/read-nexus-log-level

Do not log `read_nexus` to the console in tests

src/pynxtools/testing/nexus_conversion.py

@@ -208,6 +208,8 @@ def compare_logs(gen_lines: List[str], ref_lines: List[str]) -> None:
 
             section_ignore_lines = []
             section = None
+
+            diffs = []
             for ind, (gen_l, ref_l) in enumerate(zip(gen_lines, ref_lines)):
                 if gen_l.startswith(SECTION_SEPARATOR) and ref_l.startswith(
                     SECTION_SEPARATOR
@@ -219,10 +221,13 @@ def compare_logs(gen_lines: List[str], ref_lines: List[str]) -> None:
                 if gen_l != ref_l and not should_skip_line(
                     gen_l, ref_l, IGNORE_LINES + section_ignore_lines
                 ):
-                    raise AssertionError(
-                        f"Log files are different at line {ind}\n"
-                        f"generated: {gen_l}\nreferenced: {ref_l}"
-                    )
+                    diffs += [
+                        f"Log files are different at line {ind}\ngenerated: {gen_l}\nreferenced: {ref_l}"
+                    ]
+
+            if diffs:
+                diff_report = "\n".join(diffs)
+                raise AssertionError(diff_report)
 
         # Load log paths
         ref_log_path = get_log_file(self.ref_nexus_file, "ref_nexus.log", self.tmp_path)

tests/nexus/test_nexus.py

@@ -19,6 +19,7 @@
 
 import logging
 import os
+import difflib
 
 import lxml.etree as ET
 import numpy as np
@@ -167,6 +168,8 @@ def test_nexus(tmp_path):
     example_data = os.path.join(
         os.getcwd(), "src", "pynxtools", "data", "201805_WSe2_arpes.nxs"
     )
+
+    logger.handlers.clear()
     logger.setLevel(logging.DEBUG)
     handler = logging.FileHandler(os.path.join(tmp_path, "nexus_test.log"), "w")
     formatter = logging.Formatter("%(levelname)s - %(message)s")
@@ -186,7 +189,19 @@ def test_nexus(tmp_path):
         encoding="utf-8",
     ) as reffile:
         ref = reffile.readlines()
-    assert log == ref
+
+    if log != ref:
+        differences = list(
+            difflib.unified_diff(
+                ref, log, fromfile="reference", tofile="actual", lineterm=""
+            )
+        )
+        diff_report = "\n".join(differences)
+        if diff_report:
+            pytest.fail(f"Log output does not match reference:\n{diff_report}")
+        pytest.fail(
+            f"Log output does not match reference even though each individual line matches."
+        )
 
     # import filecmp
     # # didn't work with filecmp library