[JOSS REVIEW] Unit tests have missing dependency

[finsberg]

When trying to install the test as outlined here I get the following failures

python3 -m pytest --json-report -v tests/ | tee unit_tests.txt
============================= test session starts ==============================
platform darwin -- Python 3.12.9, pytest-9.0.2, pluggy-1.6.0 -- /Users/finsberg/local/src/pySEMTools/venv/bin/python3
cachedir: .pytest_cache
metadata: {'Python': '3.12.9', 'Platform': 'macOS-26.3-arm64-arm-64bit', 'Packages': {'pytest': '9.0.2', 'pluggy': '1.6.0'}, 'Plugins': {'anyio': '4.12.1', 'json-report': '1.5.0', 'metadata': '3.1.1'}}
rootdir: /Users/finsberg/local/src/pySEMTools
configfile: pyproject.toml
plugins: anyio-4.12.1, json-report-1.5.0, metadata-3.1.1
collecting ... collected 39 items

tests/test_autograd.py::test_autograd PASSED                             [  2%]
tests/test_coef.py::test_coef_2d PASSED                                  [  5%]
tests/test_coef.py::test_coef_3d PASSED                                  [  7%]
tests/test_dssum.py::test_dssum PASSED                                   [ 10%]
tests/test_examples.py::test_data_types FAILED                           [ 12%]
tests/test_examples.py::test_calculus FAILED                             [ 15%]
tests/test_examples.py::test_interpolation FAILED                        [ 17%]
tests/test_examples.py::test_reduced_order_modelling FAILED              [ 20%]
tests/test_examples.py::test_statistics FAILED                           [ 23%]
tests/test_interpolator.py::test_single_point_interpolator PASSED        [ 25%]
tests/test_interpolator.py::test_multiple_point_interpolator_numpy PASSED [ 28%]
tests/test_interpolator.py::test_multiple_point_interpolator_torch PASSED [ 30%]
tests/test_interpolator.py::test_multiple_point_interpolator_torch_autograd SKIPPED [ 33%]
tests/test_io_data_types.py::test_read_data_single PASSED                [ 35%]
tests/test_io_data_types.py::test_wrapper PASSED                         [ 38%]
tests/test_io_data_types.py::test_read_data_double PASSED                [ 41%]
tests/test_io_data_types.py::test_write_data_single PASSED               [ 43%]
tests/test_io_data_types.py::test_write_data_double PASSED               [ 46%]
tests/test_io_data_types.py::test_write_data_single_no_mesh PASSED       [ 48%]
tests/test_io_data_types.py::test_write_data_double_no_mesh PASSED       [ 51%]
tests/test_io_data_types_2D.py::test_read_data_single PASSED             [ 53%]
tests/test_io_data_types_2D.py::test_read_data_double PASSED             [ 56%]
tests/test_io_data_types_2D.py::test_write_data_single PASSED            [ 58%]
tests/test_io_data_types_2D.py::test_write_data_double PASSED            [ 61%]
tests/test_io_data_types_2D.py::test_write_data_single_no_mesh PASSED    [ 64%]
tests/test_io_data_types_2D.py::test_write_data_double_no_mesh PASSED    [ 66%]
tests/test_io_hdf5.py::test_io_hdf5 PASSED                               [ 69%]
tests/test_ppymech.py::test_read_double PASSED                           [ 71%]
tests/test_ppymech.py::test_read_single PASSED                           [ 74%]
tests/test_ppymech.py::test_write_double PASSED                          [ 76%]
tests/test_ppymech.py::test_write_single PASSED                          [ 79%]
tests/test_probes.py::test_probes_msh_single PASSED                      [ 82%]
tests/test_probes.py::test_probes_msh_double PASSED                      [ 84%]
tests/test_rom.py::test_POD PASSED                                       [ 87%]
tests/test_rotations.py::test_cartesian_to_cylindrical PASSED            [ 89%]
tests/test_statistics.py::test_time_averaging_1_batches PASSED           [ 92%]
tests/test_statistics.py::test_time_averaging_2_batches PASSED           [ 94%]
tests/test_statistics.py::test_space_averaging PASSED                    [ 97%]
tests/test_uq.py::test_NOBM PASSED                                       [100%]

=================================== FAILURES ===================================
_______________________________ test_data_types ________________________________

    def test_data_types():
    
    
        examples_path = "examples/1-datatypes_and_io/"
        notebook_files = ["1-datatypes_io.ipynb",
                          "2-sem_subdomains.ipynb"]
    
        passed = []
        for notebook in notebook_files:
            notebook_path = os.path.join(examples_path, notebook)
    
            print(f"Executing notebook: {notebook_path}")
            _path=os.path.abspath(notebook_path)
            _name=os.path.basename(notebook_path)
            command = f"jupyter nbconvert --to notebook --execute {notebook_path} --output ./executed_{_name}"
            process = subprocess.run(command, capture_output=True, shell=True)
            if process.returncode != 0:
                print("Error executing notebook:")
                print(process.stdout.decode())
                print(process.stderr.decode())
                _passed = False
            else:
                print("Notebook executed successfully.")
                _passed = True
    
            passed.append(_passed)
    
>       assert all(passed)
E       assert False
E        +  where False = all([False, False])

tests/test_examples.py:54: AssertionError
----------------------------- Captured stdout call -----------------------------
Executing notebook: examples/1-datatypes_and_io/1-datatypes_io.ipynb
Error executing notebook:

[NbConvertApp] WARNING | Config option `template_path` not recognized by `NotebookExporter`.
Traceback (most recent call last):
  File "/Users/finsberg/local/src/pySEMTools/venv/bin/jupyter-nbconvert", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/jupyter_core/application.py", line 284, in launch_instance
    super().launch_instance(argv=argv, **kwargs)
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/traitlets/config/application.py", line 1075, in launch_instance
    app.start()
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/nbconvertapp.py", line 420, in start
    self.convert_notebooks()
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/nbconvertapp.py", line 585, in convert_notebooks
    cls = get_exporter(self.export_format)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/base.py", line 110, in get_exporter
    if getattr(exporter(config=config), "enabled", True):
               ^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/exporter.py", line 123, in __init__
    self._init_preprocessors()
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/exporter.py", line 294, in _init_preprocessors
    self.register_preprocessor(preprocessor, enabled=True)
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/exporter.py", line 253, in register_preprocessor
    preprocessor_cls = import_item(preprocessor)
                       ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/traitlets/utils/importstring.py", line 33, in import_item
    module = __import__(package, fromlist=[obj])
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ModuleNotFoundError: No module named 'jupyter_contrib_nbextensions'

Executing notebook: examples/1-datatypes_and_io/2-sem_subdomains.ipynb
Error executing notebook:

[NbConvertApp] WARNING | Config option `template_path` not recognized by `NotebookExporter`.
Traceback (most recent call last):
  File "/Users/finsberg/local/src/pySEMTools/venv/bin/jupyter-nbconvert", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/jupyter_core/application.py", line 284, in launch_instance
    super().launch_instance(argv=argv, **kwargs)
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/traitlets/config/application.py", line 1075, in launch_instance
    app.start()
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/nbconvertapp.py", line 420, in start
    self.convert_notebooks()
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/nbconvertapp.py", line 585, in convert_notebooks
    cls = get_exporter(self.export_format)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/base.py", line 110, in get_exporter
    if getattr(exporter(config=config), "enabled", True):
               ^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/exporter.py", line 123, in __init__
    self._init_preprocessors()
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/exporter.py", line 294, in _init_preprocessors
    self.register_preprocessor(preprocessor, enabled=True)
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/exporter.py", line 253, in register_preprocessor
    preprocessor_cls = import_item(preprocessor)
                       ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/traitlets/utils/importstring.py", line 33, in import_item
    module = __import__(package, fromlist=[obj])
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ModuleNotFoundError: No module named 'jupyter_contrib_nbextensions'

________________________________ test_calculus _________________________________

    def test_calculus():
    
    
        examples_path = "examples/3-calculus_in_sem_mesh/"
        if have_torch:
            notebook_files = ["1-differentiation.ipynb",
                              "1.5-differentiation_torch.ipynb",
                              "2-integration.ipynb"]
        else:
            notebook_files = ["1-differentiation.ipynb",
                              "2-integration.ipynb"]
    
        passed = []
        for notebook in notebook_files:
            notebook_path = os.path.join(examples_path, notebook)
    
            print(f"Executing notebook: {notebook_path}")
            _path=os.path.abspath(notebook_path)
            _name=os.path.basename(notebook_path)
            command = f"jupyter nbconvert --to notebook --execute {notebook_path} --output ./executed_{_name}"
            process = subprocess.run(command, capture_output=True, shell=True)
            if process.returncode != 0:
                print("Error executing notebook:")
                print(process.stdout.decode())
                print(process.stderr.decode())
                _passed = False
            else:
                print("Notebook executed successfully.")
                _passed = True
    
            passed.append(_passed)
    
>       assert all(passed)
E       assert False
E        +  where False = all([False, False, False])

tests/test_examples.py:88: AssertionError
----------------------------- Captured stdout call -----------------------------
Executing notebook: examples/3-calculus_in_sem_mesh/1-differentiation.ipynb
Error executing notebook:

[NbConvertApp] WARNING | Config option `template_path` not recognized by `NotebookExporter`.
Traceback (most recent call last):
  File "/Users/finsberg/local/src/pySEMTools/venv/bin/jupyter-nbconvert", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/jupyter_core/application.py", line 284, in launch_instance
    super().launch_instance(argv=argv, **kwargs)
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/traitlets/config/application.py", line 1075, in launch_instance
    app.start()
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/nbconvertapp.py", line 420, in start
    self.convert_notebooks()
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/nbconvertapp.py", line 585, in convert_notebooks
    cls = get_exporter(self.export_format)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/base.py", line 110, in get_exporter
    if getattr(exporter(config=config), "enabled", True):
               ^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/exporter.py", line 123, in __init__
    self._init_preprocessors()
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/exporter.py", line 294, in _init_preprocessors
    self.register_preprocessor(preprocessor, enabled=True)
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/exporter.py", line 253, in register_preprocessor
    preprocessor_cls = import_item(preprocessor)
                       ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/traitlets/utils/importstring.py", line 33, in import_item
    module = __import__(package, fromlist=[obj])
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ModuleNotFoundError: No module named 'jupyter_contrib_nbextensions'

Executing notebook: examples/3-calculus_in_sem_mesh/1.5-differentiation_torch.ipynb
Error executing notebook:

[NbConvertApp] WARNING | Config option `template_path` not recognized by `NotebookExporter`.
Traceback (most recent call last):
  File "/Users/finsberg/local/src/pySEMTools/venv/bin/jupyter-nbconvert", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/jupyter_core/application.py", line 284, in launch_instance
    super().launch_instance(argv=argv, **kwargs)
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/traitlets/config/application.py", line 1075, in launch_instance
    app.start()
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/nbconvertapp.py", line 420, in start
    self.convert_notebooks()
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/nbconvertapp.py", line 585, in convert_notebooks
    cls = get_exporter(self.export_format)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/base.py", line 110, in get_exporter
    if getattr(exporter(config=config), "enabled", True):
               ^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/exporter.py", line 123, in __init__
    self._init_preprocessors()
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/exporter.py", line 294, in _init_preprocessors
    self.register_preprocessor(preprocessor, enabled=True)
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/exporter.py", line 253, in register_preprocessor
    preprocessor_cls = import_item(preprocessor)
                       ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/traitlets/utils/importstring.py", line 33, in import_item
    module = __import__(package, fromlist=[obj])
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ModuleNotFoundError: No module named 'jupyter_contrib_nbextensions'

Executing notebook: examples/3-calculus_in_sem_mesh/2-integration.ipynb
Error executing notebook:

[NbConvertApp] WARNING | Config option `template_path` not recognized by `NotebookExporter`.
Traceback (most recent call last):
  File "/Users/finsberg/local/src/pySEMTools/venv/bin/jupyter-nbconvert", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/jupyter_core/application.py", line 284, in launch_instance
    super().launch_instance(argv=argv, **kwargs)
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/traitlets/config/application.py", line 1075, in launch_instance
    app.start()
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/nbconvertapp.py", line 420, in start
    self.convert_notebooks()
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/nbconvertapp.py", line 585, in convert_notebooks
    cls = get_exporter(self.export_format)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/base.py", line 110, in get_exporter
    if getattr(exporter(config=config), "enabled", True):
               ^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/exporter.py", line 123, in __init__
    self._init_preprocessors()
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/exporter.py", line 294, in _init_preprocessors
    self.register_preprocessor(preprocessor, enabled=True)
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/exporter.py", line 253, in register_preprocessor
    preprocessor_cls = import_item(preprocessor)
                       ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/traitlets/utils/importstring.py", line 33, in import_item
    module = __import__(package, fromlist=[obj])
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ModuleNotFoundError: No module named 'jupyter_contrib_nbextensions'

______________________________ test_interpolation ______________________________

sem_data_path = 'examples/data/sem_data'

    def test_interpolation(sem_data_path):
    
    
        examples_path = "examples/4-interpolation/"
        notebook_files = ["1-interpolation_to_query_points.ipynb",
                          "2-element_interpolation.ipynb",
                          "3-interpolation_from_2d_sem_mesh.ipynb",
                          "5-structured_mesh.ipynb",
                          "6-interpolating_file_sequences.ipynb",
                          "8-mirroring_fields.ipynb"]
    
        passed = []
        for notebook in notebook_files:
            notebook_path = os.path.join(examples_path, notebook)
    
            print(f"Executing notebook: {notebook_path}")
            _path=os.path.abspath(notebook_path)
            _name=os.path.basename(notebook_path)
            command = f"jupyter nbconvert --to notebook --execute {notebook_path} --output ./executed_{_name}"
            process = subprocess.run(command, capture_output=True, shell=True)
            if process.returncode != 0:
                print("Error executing notebook:")
                print(process.stdout.decode())
                print(process.stderr.decode())
                _passed = False
            else:
                print("Notebook executed successfully.")
                _passed = True
    
            passed.append(_passed)
    
>       assert all(passed)
E       assert False
E        +  where False = all([False, False, False, False, False, False])

tests/test_examples.py:121: AssertionError
---------------------------- Captured stdout setup -----------------------------
Sem data found.
----------------------------- Captured stdout call -----------------------------
Executing notebook: examples/4-interpolation/1-interpolation_to_query_points.ipynb
Error executing notebook:

[NbConvertApp] WARNING | Config option `template_path` not recognized by `NotebookExporter`.
Traceback (most recent call last):
  File "/Users/finsberg/local/src/pySEMTools/venv/bin/jupyter-nbconvert", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/jupyter_core/application.py", line 284, in launch_instance
    super().launch_instance(argv=argv, **kwargs)
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/traitlets/config/application.py", line 1075, in launch_instance
    app.start()
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/nbconvertapp.py", line 420, in start
    self.convert_notebooks()
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/nbconvertapp.py", line 585, in convert_notebooks
    cls = get_exporter(self.export_format)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/base.py", line 110, in get_exporter
    if getattr(exporter(config=config), "enabled", True):
               ^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/exporter.py", line 123, in __init__
    self._init_preprocessors()
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/exporter.py", line 294, in _init_preprocessors
    self.register_preprocessor(preprocessor, enabled=True)
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/exporter.py", line 253, in register_preprocessor
    preprocessor_cls = import_item(preprocessor)
                       ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/traitlets/utils/importstring.py", line 33, in import_item
    module = __import__(package, fromlist=[obj])
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ModuleNotFoundError: No module named 'jupyter_contrib_nbextensions'

Executing notebook: examples/4-interpolation/2-element_interpolation.ipynb
Error executing notebook:

[NbConvertApp] WARNING | Config option `template_path` not recognized by `NotebookExporter`.
Traceback (most recent call last):
  File "/Users/finsberg/local/src/pySEMTools/venv/bin/jupyter-nbconvert", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/jupyter_core/application.py", line 284, in launch_instance
    super().launch_instance(argv=argv, **kwargs)
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/traitlets/config/application.py", line 1075, in launch_instance
    app.start()
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/nbconvertapp.py", line 420, in start
    self.convert_notebooks()
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/nbconvertapp.py", line 585, in convert_notebooks
    cls = get_exporter(self.export_format)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/base.py", line 110, in get_exporter
    if getattr(exporter(config=config), "enabled", True):
               ^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/exporter.py", line 123, in __init__
    self._init_preprocessors()
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/exporter.py", line 294, in _init_preprocessors
    self.register_preprocessor(preprocessor, enabled=True)
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/exporter.py", line 253, in register_preprocessor
    preprocessor_cls = import_item(preprocessor)
                       ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/traitlets/utils/importstring.py", line 33, in import_item
    module = __import__(package, fromlist=[obj])
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ModuleNotFoundError: No module named 'jupyter_contrib_nbextensions'

Executing notebook: examples/4-interpolation/3-interpolation_from_2d_sem_mesh.ipynb
Error executing notebook:

[NbConvertApp] WARNING | Config option `template_path` not recognized by `NotebookExporter`.
Traceback (most recent call last):
  File "/Users/finsberg/local/src/pySEMTools/venv/bin/jupyter-nbconvert", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/jupyter_core/application.py", line 284, in launch_instance
    super().launch_instance(argv=argv, **kwargs)
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/traitlets/config/application.py", line 1075, in launch_instance
    app.start()
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/nbconvertapp.py", line 420, in start
    self.convert_notebooks()
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/nbconvertapp.py", line 585, in convert_notebooks
    cls = get_exporter(self.export_format)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/base.py", line 110, in get_exporter
    if getattr(exporter(config=config), "enabled", True):
               ^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/exporter.py", line 123, in __init__
    self._init_preprocessors()
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/exporter.py", line 294, in _init_preprocessors
    self.register_preprocessor(preprocessor, enabled=True)
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/exporter.py", line 253, in register_preprocessor
    preprocessor_cls = import_item(preprocessor)
                       ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/traitlets/utils/importstring.py", line 33, in import_item
    module = __import__(package, fromlist=[obj])
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ModuleNotFoundError: No module named 'jupyter_contrib_nbextensions'

Executing notebook: examples/4-interpolation/5-structured_mesh.ipynb
Error executing notebook:

[NbConvertApp] WARNING | Config option `template_path` not recognized by `NotebookExporter`.
Traceback (most recent call last):
  File "/Users/finsberg/local/src/pySEMTools/venv/bin/jupyter-nbconvert", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/jupyter_core/application.py", line 284, in launch_instance
    super().launch_instance(argv=argv, **kwargs)
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/traitlets/config/application.py", line 1075, in launch_instance
    app.start()
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/nbconvertapp.py", line 420, in start
    self.convert_notebooks()
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/nbconvertapp.py", line 585, in convert_notebooks
    cls = get_exporter(self.export_format)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/base.py", line 110, in get_exporter
    if getattr(exporter(config=config), "enabled", True):
               ^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/exporter.py", line 123, in __init__
    self._init_preprocessors()
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/exporter.py", line 294, in _init_preprocessors
    self.register_preprocessor(preprocessor, enabled=True)
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/exporter.py", line 253, in register_preprocessor
    preprocessor_cls = import_item(preprocessor)
                       ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/traitlets/utils/importstring.py", line 33, in import_item
    module = __import__(package, fromlist=[obj])
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ModuleNotFoundError: No module named 'jupyter_contrib_nbextensions'

Executing notebook: examples/4-interpolation/6-interpolating_file_sequences.ipynb
Error executing notebook:

[NbConvertApp] WARNING | Config option `template_path` not recognized by `NotebookExporter`.
Traceback (most recent call last):
  File "/Users/finsberg/local/src/pySEMTools/venv/bin/jupyter-nbconvert", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/jupyter_core/application.py", line 284, in launch_instance
    super().launch_instance(argv=argv, **kwargs)
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/traitlets/config/application.py", line 1075, in launch_instance
    app.start()
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/nbconvertapp.py", line 420, in start
    self.convert_notebooks()
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/nbconvertapp.py", line 585, in convert_notebooks
    cls = get_exporter(self.export_format)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/base.py", line 110, in get_exporter
    if getattr(exporter(config=config), "enabled", True):
               ^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/exporter.py", line 123, in __init__
    self._init_preprocessors()
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/exporter.py", line 294, in _init_preprocessors
    self.register_preprocessor(preprocessor, enabled=True)
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/exporter.py", line 253, in register_preprocessor
    preprocessor_cls = import_item(preprocessor)
                       ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/traitlets/utils/importstring.py", line 33, in import_item
    module = __import__(package, fromlist=[obj])
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ModuleNotFoundError: No module named 'jupyter_contrib_nbextensions'

Executing notebook: examples/4-interpolation/8-mirroring_fields.ipynb
Error executing notebook:

[NbConvertApp] WARNING | Config option `template_path` not recognized by `NotebookExporter`.
Traceback (most recent call last):
  File "/Users/finsberg/local/src/pySEMTools/venv/bin/jupyter-nbconvert", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/jupyter_core/application.py", line 284, in launch_instance
    super().launch_instance(argv=argv, **kwargs)
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/traitlets/config/application.py", line 1075, in launch_instance
    app.start()
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/nbconvertapp.py", line 420, in start
    self.convert_notebooks()
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/nbconvertapp.py", line 585, in convert_notebooks
    cls = get_exporter(self.export_format)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/base.py", line 110, in get_exporter
    if getattr(exporter(config=config), "enabled", True):
               ^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/exporter.py", line 123, in __init__
    self._init_preprocessors()
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/exporter.py", line 294, in _init_preprocessors
    self.register_preprocessor(preprocessor, enabled=True)
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/exporter.py", line 253, in register_preprocessor
    preprocessor_cls = import_item(preprocessor)
                       ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/traitlets/utils/importstring.py", line 33, in import_item
    module = __import__(package, fromlist=[obj])
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ModuleNotFoundError: No module named 'jupyter_contrib_nbextensions'

_________________________ test_reduced_order_modelling _________________________

    def test_reduced_order_modelling():
    
    
        examples_path = "examples/5-reduced_order_modelling/"
        notebook_files = ["1-POD_from_pointclouds.ipynb",
                          "2-POD_fft_from_pointclouds.ipynb"]
    
        passed = []
        for notebook in notebook_files:
            notebook_path = os.path.join(examples_path, notebook)
    
            print(f"Executing notebook: {notebook_path}")
            _path=os.path.abspath(notebook_path)
            _name=os.path.basename(notebook_path)
            command = f"jupyter nbconvert --to notebook --execute {notebook_path} --output ./executed_{_name}"
            process = subprocess.run(command, capture_output=True, shell=True)
            if process.returncode != 0:
                print("Error executing notebook:")
                print(process.stdout.decode())
                print(process.stderr.decode())
                _passed = False
            else:
                print("Notebook executed successfully.")
                _passed = True
    
            passed.append(_passed)
    
>       assert all(passed)
E       assert False
E        +  where False = all([False, False])

tests/test_examples.py:150: AssertionError
----------------------------- Captured stdout call -----------------------------
Executing notebook: examples/5-reduced_order_modelling/1-POD_from_pointclouds.ipynb
Error executing notebook:

[NbConvertApp] WARNING | Config option `template_path` not recognized by `NotebookExporter`.
Traceback (most recent call last):
  File "/Users/finsberg/local/src/pySEMTools/venv/bin/jupyter-nbconvert", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/jupyter_core/application.py", line 284, in launch_instance
    super().launch_instance(argv=argv, **kwargs)
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/traitlets/config/application.py", line 1075, in launch_instance
    app.start()
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/nbconvertapp.py", line 420, in start
    self.convert_notebooks()
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/nbconvertapp.py", line 585, in convert_notebooks
    cls = get_exporter(self.export_format)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/base.py", line 110, in get_exporter
    if getattr(exporter(config=config), "enabled", True):
               ^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/exporter.py", line 123, in __init__
    self._init_preprocessors()
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/exporter.py", line 294, in _init_preprocessors
    self.register_preprocessor(preprocessor, enabled=True)
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/exporter.py", line 253, in register_preprocessor
    preprocessor_cls = import_item(preprocessor)
                       ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/traitlets/utils/importstring.py", line 33, in import_item
    module = __import__(package, fromlist=[obj])
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ModuleNotFoundError: No module named 'jupyter_contrib_nbextensions'

Executing notebook: examples/5-reduced_order_modelling/2-POD_fft_from_pointclouds.ipynb
Error executing notebook:

[NbConvertApp] WARNING | Config option `template_path` not recognized by `NotebookExporter`.
Traceback (most recent call last):
  File "/Users/finsberg/local/src/pySEMTools/venv/bin/jupyter-nbconvert", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/jupyter_core/application.py", line 284, in launch_instance
    super().launch_instance(argv=argv, **kwargs)
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/traitlets/config/application.py", line 1075, in launch_instance
    app.start()
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/nbconvertapp.py", line 420, in start
    self.convert_notebooks()
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/nbconvertapp.py", line 585, in convert_notebooks
    cls = get_exporter(self.export_format)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/base.py", line 110, in get_exporter
    if getattr(exporter(config=config), "enabled", True):
               ^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/exporter.py", line 123, in __init__
    self._init_preprocessors()
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/exporter.py", line 294, in _init_preprocessors
    self.register_preprocessor(preprocessor, enabled=True)
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/exporter.py", line 253, in register_preprocessor
    preprocessor_cls = import_item(preprocessor)
                       ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/traitlets/utils/importstring.py", line 33, in import_item
    module = __import__(package, fromlist=[obj])
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ModuleNotFoundError: No module named 'jupyter_contrib_nbextensions'

_______________________________ test_statistics ________________________________

sem_data_path = 'examples/data/sem_data'

    def test_statistics(sem_data_path):
    
        examples_path = "examples/6-statistics/"
        if have_torch:
            notebook_files = ["1-post_processing_mean_fields.ipynb",
                          "4-Budgets.ipynb",
                          "5-homogeneous_direction_averaging.ipynb",
                          "6-Stats_from_fld.ipynb"]
        else:
            notebook_files = ["1-post_processing_mean_fields.ipynb",
                          "4-Budgets.ipynb",
                          "5-homogeneous_direction_averaging.ipynb",]
    
        passed = []
        for notebook in notebook_files:
            notebook_path = os.path.join(examples_path, notebook)
    
            print(f"Executing notebook: {notebook_path}")
            _path=os.path.abspath(notebook_path)
            _name=os.path.basename(notebook_path)
            command = f"jupyter nbconvert --to notebook --execute {notebook_path} --output ./executed_{_name}"
            process = subprocess.run(command, capture_output=True, shell=True)
            if process.returncode != 0:
                print("Error executing notebook:")
                print(process.stdout.decode())
                print(process.stderr.decode())
                _passed = False
            else:
                print("Notebook executed successfully.")
                _passed = True
    
            passed.append(_passed)
    
>       assert all(passed)
E       assert False
E        +  where False = all([False, False, False, False])

tests/test_examples.py:185: AssertionError
----------------------------- Captured stdout call -----------------------------
Executing notebook: examples/6-statistics/1-post_processing_mean_fields.ipynb
Error executing notebook:

[NbConvertApp] WARNING | Config option `template_path` not recognized by `NotebookExporter`.
Traceback (most recent call last):
  File "/Users/finsberg/local/src/pySEMTools/venv/bin/jupyter-nbconvert", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/jupyter_core/application.py", line 284, in launch_instance
    super().launch_instance(argv=argv, **kwargs)
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/traitlets/config/application.py", line 1075, in launch_instance
    app.start()
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/nbconvertapp.py", line 420, in start
    self.convert_notebooks()
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/nbconvertapp.py", line 585, in convert_notebooks
    cls = get_exporter(self.export_format)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/base.py", line 110, in get_exporter
    if getattr(exporter(config=config), "enabled", True):
               ^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/exporter.py", line 123, in __init__
    self._init_preprocessors()
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/exporter.py", line 294, in _init_preprocessors
    self.register_preprocessor(preprocessor, enabled=True)
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/exporter.py", line 253, in register_preprocessor
    preprocessor_cls = import_item(preprocessor)
                       ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/traitlets/utils/importstring.py", line 33, in import_item
    module = __import__(package, fromlist=[obj])
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ModuleNotFoundError: No module named 'jupyter_contrib_nbextensions'

Executing notebook: examples/6-statistics/4-Budgets.ipynb
Error executing notebook:

[NbConvertApp] WARNING | Config option `template_path` not recognized by `NotebookExporter`.
Traceback (most recent call last):
  File "/Users/finsberg/local/src/pySEMTools/venv/bin/jupyter-nbconvert", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/jupyter_core/application.py", line 284, in launch_instance
    super().launch_instance(argv=argv, **kwargs)
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/traitlets/config/application.py", line 1075, in launch_instance
    app.start()
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/nbconvertapp.py", line 420, in start
    self.convert_notebooks()
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/nbconvertapp.py", line 585, in convert_notebooks
    cls = get_exporter(self.export_format)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/base.py", line 110, in get_exporter
    if getattr(exporter(config=config), "enabled", True):
               ^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/exporter.py", line 123, in __init__
    self._init_preprocessors()
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/exporter.py", line 294, in _init_preprocessors
    self.register_preprocessor(preprocessor, enabled=True)
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/exporter.py", line 253, in register_preprocessor
    preprocessor_cls = import_item(preprocessor)
                       ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/traitlets/utils/importstring.py", line 33, in import_item
    module = __import__(package, fromlist=[obj])
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ModuleNotFoundError: No module named 'jupyter_contrib_nbextensions'

Executing notebook: examples/6-statistics/5-homogeneous_direction_averaging.ipynb
Error executing notebook:

[NbConvertApp] WARNING | Config option `template_path` not recognized by `NotebookExporter`.
Traceback (most recent call last):
  File "/Users/finsberg/local/src/pySEMTools/venv/bin/jupyter-nbconvert", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/jupyter_core/application.py", line 284, in launch_instance
    super().launch_instance(argv=argv, **kwargs)
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/traitlets/config/application.py", line 1075, in launch_instance
    app.start()
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/nbconvertapp.py", line 420, in start
    self.convert_notebooks()
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/nbconvertapp.py", line 585, in convert_notebooks
    cls = get_exporter(self.export_format)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/base.py", line 110, in get_exporter
    if getattr(exporter(config=config), "enabled", True):
               ^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/exporter.py", line 123, in __init__
    self._init_preprocessors()
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/exporter.py", line 294, in _init_preprocessors
    self.register_preprocessor(preprocessor, enabled=True)
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/exporter.py", line 253, in register_preprocessor
    preprocessor_cls = import_item(preprocessor)
                       ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/traitlets/utils/importstring.py", line 33, in import_item
    module = __import__(package, fromlist=[obj])
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ModuleNotFoundError: No module named 'jupyter_contrib_nbextensions'

Executing notebook: examples/6-statistics/6-Stats_from_fld.ipynb
Error executing notebook:

[NbConvertApp] WARNING | Config option `template_path` not recognized by `NotebookExporter`.
Traceback (most recent call last):
  File "/Users/finsberg/local/src/pySEMTools/venv/bin/jupyter-nbconvert", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/jupyter_core/application.py", line 284, in launch_instance
    super().launch_instance(argv=argv, **kwargs)
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/traitlets/config/application.py", line 1075, in launch_instance
    app.start()
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/nbconvertapp.py", line 420, in start
    self.convert_notebooks()
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/nbconvertapp.py", line 585, in convert_notebooks
    cls = get_exporter(self.export_format)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/base.py", line 110, in get_exporter
    if getattr(exporter(config=config), "enabled", True):
               ^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/exporter.py", line 123, in __init__
    self._init_preprocessors()
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/exporter.py", line 294, in _init_preprocessors
    self.register_preprocessor(preprocessor, enabled=True)
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/nbconvert/exporters/exporter.py", line 253, in register_preprocessor
    preprocessor_cls = import_item(preprocessor)
                       ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/finsberg/local/src/pySEMTools/venv/lib/python3.12/site-packages/traitlets/utils/importstring.py", line 33, in import_item
    module = __import__(package, fromlist=[obj])
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ModuleNotFoundError: No module named 'jupyter_contrib_nbextensions'

--------------------------------- JSON report ----------------------------------
report saved to: .report.json
=========================== short test summary info ============================
FAILED tests/test_examples.py::test_data_types - assert False
FAILED tests/test_examples.py::test_calculus - assert False
FAILED tests/test_examples.py::test_interpolation - assert False
FAILED tests/test_examples.py::test_reduced_order_modelling - assert False
FAILED tests/test_examples.py::test_statistics - assert False
============= 5 failed, 33 passed, 1 skipped in 457.59s (0:07:37) ==============

which indicates that jupyter_contrib_nbextensions is a missing test dependency.

This should have been caught by the unit tests workflow, but this has not been turned on, see https://github.com/ExtremeFLOW/pySEMTools/actions/workflows/check_unit_test.yml

I would recommend to turn on testing for both pushes and pull requests to the main branch.

This is related to the ongoing review at openjournals/joss-reviews#8767

[adperezm]

Hi @finsberg , thank you for checking. This one is a bit weird to me because I just tested again on a fresh environment and for me the instructions work:

(testing) adperezm@adalberto:~/pySEMTools$ python3 -m pytest --json-report -v tests/test_examples.py | tee unit_
tests.txt
============================= test session starts ==============================
platform linux -- Python 3.12.9, pytest-9.0.2, pluggy-1.6.0 -- /home/adperezm/miniconda3/.conda/envs/testing/bin/python3
cachedir: .pytest_cache
metadata: {'Python': '3.12.9', 'Platform': 'Linux-6.6.87.2-microsoft-standard-WSL2-x86_64-with-glibc2.35', 'Packages': {'pytest': '9.0.2', 'pluggy': '1.6.0'}, 'Plugins': {'metadata': '3.1.1', 'anyio': '4.12.1', 'json-report': '1.5.0'}}
rootdir: /home/adperezm/pySEMTools
configfile: pyproject.toml
plugins: metadata-3.1.1, anyio-4.12.1, json-report-1.5.0
collecting ... collected 5 items

tests/test_examples.py::test_data_types PASSED                           [ 20%]
tests/test_examples.py::test_calculus PASSED                             [ 40%]
tests/test_examples.py::test_interpolation PASSED                        [ 60%]
tests/test_examples.py::test_reduced_order_modelling PASSED              [ 80%]
tests/test_examples.py::test_statistics PASSED                           [100%]

--------------------------------- JSON report ----------------------------------
report saved to: .report.json
======================== 5 passed in 176.55s (0:02:56) =========================

Regarding the tests, they do run on every pull request to main. And the only way to update main is through PRs. They are just called by another workflow:
https://github.com/ExtremeFLOW/pySEMTools/blob/77c8837b1b2be9998ea64aa122d0a9e4a7a4a772/.github/workflows/main.yml#L4C1-L7C21

The tests have run and passed for newer PRs since we introduced this change, so this has me confused.

We do not use jupyter_contrib_nbextensions explicitly, so I will check a bit more. It seems jupyter-nbconvert needs it according to this log, but I can run it without it...

(testing) adperezm@adalberto:~/pySEMTools/examples/1-datatypes_and_io$  jupyter nbconvert --to notebook --execute 1-datatypes_io.ipynb --output executed.ipynb
[NbConvertApp] Converting notebook 1-datatypes_io.ipynb to notebook
[NbConvertApp] Writing 51444 bytes to executed.ipynb