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Additional methods for FormatISISSXD to extract data more efficiently. #743

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merged 10 commits into from
Aug 12, 2024

Merge branch 'additional_formatisissxd_methods' of github.com:toastis…

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Merged

Additional methods for FormatISISSXD to extract data more efficiently. #743

Merge branch 'additional_formatisissxd_methods' of github.com:toastis…
fb590ae
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Azure Pipelines / cctbx.dxtbx failed Jul 31, 2024 in 10m 19s

Build #20240731.5 had test failures

Details

Tests

  • Failed: 82 (2.66%)
  • Passed: 1,506 (48.90%)
  • Other: 1,492 (48.44%)
  • Total: 3,080
Code coverage

  • 1777 of 5731 branches covered (31.01%)
  • 6929 of 16890 lines covered (41.02%)

Annotations

Check failure on line 385 in Build log

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@azure-pipelines azure-pipelines / cctbx.dxtbx

Build log #L385

Bash exited with code '2'.

Check failure on line 380 in Build log

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@azure-pipelines azure-pipelines / cctbx.dxtbx

Build log #L380

Bash exited with code '2'.

Check failure on line 793 in Build log

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@azure-pipelines azure-pipelines / cctbx.dxtbx

Build log #L793

21 test(s) failed, 770 test(s) collected.

Check failure on line 3084 in Build log

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@azure-pipelines azure-pipelines / cctbx.dxtbx

Build log #L3084

Cmd.exe exited with code '1'.

Check failure on line 1 in tests/model/test_detector.py::test_get_panel_projection_2d_from_axes

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@azure-pipelines azure-pipelines / cctbx.dxtbx

tests/model/test_detector.py::test_get_panel_projection_2d_from_axes

dials_data = <DataFetcher: D:\a\1\data>

    def test_get_panel_projection_2d_from_axes(dials_data):
        # Get test data
        pytest.importorskip("h5py")
        filename = dials_data("image_examples", pathlib=True) / "dectris_eiger_master.h5"
>       experiment = ExperimentListFactory.from_filenames([filename])[0]

modules\dxtbx\tests\model\test_detector.py:331: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
conda_base\Lib\site-packages\dxtbx\model\experiment_list.py:662: in from_filenames
    format_class = find_format.find_format(filename)
conda_base\Lib\site-packages\dxtbx\model\experiment_list.py:92: in find_format
    self._format_class = get_format_class_for_file(filename)
conda_base\Lib\site-packages\dxtbx\format\Registry.py:130: in get_format_class_for_file
    return recurse(format, image_file_str)
conda_base\Lib\site-packages\dxtbx\format\Registry.py:120: in recurse
    if scheme in format_class.schemes and format_class.understand(image_file):
conda_base\Lib\site-packages\dxtbx\format\FormatHDF5EigerNearlyNexus.py:316: in understand
    return is_eiger_nearly_nexus_file(image_file)
conda_base\Lib\site-packages\dxtbx\format\FormatHDF5EigerNearlyNexus.py:48: in is_eiger_nearly_nexus_file
    entry = find_entries(handle)
conda_base\Lib\site-packages\dxtbx\format\FormatHDF5EigerNearlyNexus.py:35: in find_entries
    if entry.attrs["NX_class"] == np.string_("NXentry"):
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

attr = 'string_'

    def __getattr__(attr):
        # Warn for expired attributes
        import warnings
    
        if attr == "linalg":
            import numpy.linalg as linalg
            return linalg
        elif attr == "fft":
            import numpy.fft as fft
            return fft
        elif attr == "dtypes":
            import numpy.dtypes as dtypes
            return dtypes
        elif attr == "random":
            import numpy.random as random
            return random
        elif attr == "polynomial":
            import numpy.polynomial as polynomial
            return polynomial
        elif attr == "ma":
            import numpy.ma as ma
            return ma
        elif attr == "ctypeslib":
            import numpy.ctypeslib as ctypeslib
            return ctypeslib
        elif attr == "exceptions":
            import numpy.exceptions as exceptions
            return exceptions
        elif attr == "testing":
            import numpy.testing as testing
            return testing
        elif attr == "matlib":
            import numpy.matlib as matlib
            return matlib
        elif attr == "f2py":
            import numpy.f2py as f2py
            return f2py
        elif attr == "typing":
            import numpy.typing as typing
            return typing
        elif attr == "rec":
            import numpy.rec as rec
            return rec
        elif attr == "char":
            import numpy.char as char
            return char
        elif attr == "array_api":
            raise AttributeError("`numpy.array_api` is not available from "
                                 "numpy 2.0 onwards")
        elif attr == "core":
            import numpy.core as core
            return core
        elif attr == "strings":
            import numpy.strings as strings
            return strings
        elif attr == "distutils":
            if 'distutils' in __numpy_submodules__:
                import numpy.distutils as distutils
                return distutils
            else:
                raise AttributeError("`numpy.distutils` is not available from "
                                     "Python 3.12 onwards")
    
        if attr in __future_scalars__:
            # And future warnings for those that will change, but also give
            # the AttributeError
            warnings.warn(
                f"In the future `np.{attr}` will be defined as the "
                "corresponding NumPy scalar.", 
Raw output
D:\a\1\conda_base\Lib\site-packages\numpy\__init__.py:397: AttributeError: `np.string_` was removed in the NumPy 2.0 release. Use `np.bytes_` instead.. Did you mean: 'strings'?

Check failure on line 1 in tests/nexus/test_build_dxtbx_models.py::test_get_dxtbx_goniometer_multi_axis

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@azure-pipelines azure-pipelines / cctbx.dxtbx

tests/nexus/test_build_dxtbx_models.py::test_get_dxtbx_goniometer_multi_axis

Test failed

Check failure on line 1 in tests/nexus/test_build_dxtbx_models.py::test_get_dxtbx_beam

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@azure-pipelines azure-pipelines / cctbx.dxtbx

tests/nexus/test_build_dxtbx_models.py::test_get_dxtbx_beam

Test failed

Check failure on line 1 in tests/nexus/test_build_dxtbx_models.py::test_get_dxtbx_scan

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@azure-pipelines azure-pipelines / cctbx.dxtbx

tests/nexus/test_build_dxtbx_models.py::test_get_dxtbx_scan

Test failed