FAIRmat-NFDI · lukaspie · Apr 28, 2025 · Apr 28, 2025 · Apr 28, 2025 · Apr 28, 2025
diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
@@ -32,18 +32,17 @@ jobs:
       - name: Install nomad
         if: "${{ matrix.python-version != '3.8' && matrix.python-version != '3.9'}}"
         run: |
-          uv pip install nomad-lab[infrastructure]
-        # @git+https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR.git
+          uv pip install nomad-lab[infrastructure]@git+https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR.git
       - name: Install pynx
         run: |
           uv pip install -e ".[dev]"
       - name: Test with pytest
         run: |
-          coverage run -m pytest -sv --show-capture=no tests -n auto --dist loadgroup
+          pytest --cov --cov-report xml:cobertura.xml --full-trace --show-capture=no -sv -n auto --dist loadgroup tests/
       - name: Submit to coveralls
         continue-on-error: true
-        if: "${{ matrix.python-version == '3.12'}}"
-        env:
-            GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        run: |
-            coveralls --service=github
+        if: ${{ matrix.python-version == '3.12' }}
+        uses: coverallsapp/github-action@v2
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          file: ./cobertura.xml
diff --git a/scripts/generate_ref_nexus_log.py b/scripts/generate_ref_nexus_log.py
@@ -0,0 +1,57 @@
+import os
+import logging
+import numpy as np
+
+from pynxtools.nexus.nexus import HandleNexus
+
+# Set up the logger for the test output
+logger = logging.getLogger("pynxtools")
+
+
+def generate_ref_log():
+    """
+    Function to run the nexus test and generate the Ref_nexus_test.log file.
+    """
+    dirpath = os.path.join(
+        os.path.dirname(os.path.abspath(__file__)), "../tests/data/nexus"
+    )
+    dirpath = os.path.abspath(dirpath)
+    example_data = os.path.join(
+        os.path.dirname(os.path.abspath(__file__)),
+        "../src/pynxtools/data/201805_WSe2_arpes.nxs",
+    )
+    example_data = os.path.abspath(example_data)
+
+    # Ensure the directory exists for the log file
+    if not os.path.exists(dirpath):
+        os.makedirs(dirpath)
+
+    # Set up logger to write directly to the reference log
+    logger.handlers.clear()
+    logger.setLevel(logging.DEBUG)
+    ref_log_path = os.path.join(dirpath, "Ref_nexus_test.log")
+    handler = logging.FileHandler(ref_log_path, "w", encoding="utf-8")
+    formatter = logging.Formatter("%(levelname)s - %(message)s")
+    handler.setLevel(logging.DEBUG)
+    handler.setFormatter(formatter)
+    logger.addHandler(handler)
+
+    # Set default print options for numpy (if needed)
+    default_print_options = {
+        "edgeitems": 3,
+        "threshold": 1000,
+        "precision": 8,
+        "linewidth": 75,
+    }
+
+    np.set_printoptions(**default_print_options)
+
+    # Run the actual processing with the nexus_helper
+    nexus_helper = HandleNexus(logger, example_data, None, None)
+    nexus_helper.process_nexus_master_file(None)
+
+    print(f"Reference log generated at {ref_log_path}")
+
+
+if __name__ == "__main__":
+    generate_ref_log()
diff --git a/tests/nexus/test_nexus.py b/tests/nexus/test_nexus.py
@@ -23,6 +23,7 @@
 import lxml.etree as ET
 import numpy as np
 import pytest
+import difflib
 
 from pynxtools.definitions.dev_tools.utils.nxdl_utils import (
     get_inherited_nodes,
@@ -159,7 +160,6 @@ def test_get_nexus_classes_units_attributes():
     assert "NX_FLOAT" in nexus_attribute_list
 
 
-@pytest.mark.xdist_group(name="shared_file_201805_WSe2_arpes")
 def test_nexus(tmp_path):
     """
     The nexus test function
@@ -177,6 +177,15 @@ def test_nexus(tmp_path):
     handler.setFormatter(formatter)
     logger.addHandler(handler)
     nexus_helper = HandleNexus(logger, example_data, None, None)
+
+    default_print_options = {
+        "edgeitems": 3,
+        "threshold": 1000,
+        "precision": 8,
+        "linewidth": 75,
+    }
+
+    np.set_printoptions(**default_print_options)
     nexus_helper.process_nexus_master_file(None)
 
     with open(
@@ -203,11 +212,6 @@ def test_nexus(tmp_path):
             f"Log output does not match reference even though each individual line matches."
         )
 
-    # import filecmp
-    # # didn't work with filecmp library
-    # log = os.path.join(local_dir, '../data/nexus_test_data/nexus_test.log')
-    # ref = os.path.join(local_dir, '../data/nexus_test_data/Ref_nexus_test.log')
-
 
 def test_get_node_at_nxdl_path():
     """Test to verify if we receive the right XML element for a given NXDL path"""

diff --git a/tests/nomad/test_parsing.py b/tests/nomad/test_parsing.py
@@ -36,7 +36,6 @@
 from pynxtools.nomad.utils import _rename_nx_for_nomad as rename_nx_for_nomad
 
 
-@pytest.mark.xdist_group(name="shared_file_201805_WSe2_arpes")
 def test_nexus_example():
     archive = EntryArchive()