nxtomomill 2.1.1__tar.gz → 2.2.0.dev0__tar.gz

{nxtomomill-2.1.1/nxtomomill.egg-info → nxtomomill-2.2.0.dev0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nxtomomill
-Version: 2.1.1
+Version: 2.2.0.dev0
 Summary: applications and library to convert raw format to NXtomo format
 Author-email: Henri Payno <henri.payno@esrf.fr>, Pierre Paleo <pierre.paleo@esrf.fr>, Pierre-Olivier Autran <pierre-olivier.autran@esrf.fr>, Jérôme Lesaint <jerome.lesaint@esrf.fr>, Alessandro Mirone <mirone@esrf.fr>
 License: 
@@ -58,7 +58,8 @@ Requires-Dist: silx>=2.0
 Requires-Dist: nxtomo>=3.1.0dev1
 Requires-Dist: pint
 Requires-Dist: packaging
-Requires-Dist: tomoscan[full]>=2.2.0a4
+Requires-Dist: tomoscan[full]>=3.0.0dev0
+Requires-Dist: tomobase>=0.0.0dev0
 Requires-Dist: tqdm
 Requires-Dist: pydantic
 Requires-Dist: eval_type_backport; python_version < "3.10"

{nxtomomill-2.1.1 → nxtomomill-2.2.0.dev0}/doc/conf.py

@@ -9,7 +9,7 @@
 from importlib.metadata import version as get_version
 
 project = "nxtomomill"
-copyright = "2020-2025, ESRF"
+copyright = "2020-2026, ESRF"
 author = "P.-O. Autran, J. Lesaint, A. Mirone, C. Nemoz, P. Paleo, H. Payno, A. Sole, N. Vigano"
 
 release = get_version("nxtomomill")

nxtomomill-2.2.0.dev0/nxtomomill/__init__.py

@@ -0,0 +1,31 @@
+"""a set of applications and tools around the `NXtomo <https://manual.nexusformat.org/classes/applications/NXtomo.html>`_ format defined by the `NeXus community <https://manual.nexusformat.org/index.html>`_"""
+
+import atexit
+
+import logging
+
+from importlib.metadata import version as _get_version, PackageNotFoundError
+
+try:
+    __version__ = _get_version("nxtomomill")
+except PackageNotFoundError:
+    __version__ = "unknown"
+
+_logger = logging.getLogger(__name__)
+
+
+@atexit.register
+def _close_leftover_tqdm_instances():
+    import tqdm
+
+    # tqdm progress bars can end up only reachable through a reference cycle,
+    # so they are not closed by simple refcounting and survive until the
+    # interpreter's final garbage-collection pass. Closing a bar twice is a
+    # no-op, so closing them here proactively (while stdout/stderr are still
+    # usable) prevents their `__del__` from running during interpreter
+    # shutdown, where it can segfault (observed with Python 3.14).
+    for bar in list(tqdm.tqdm._instances):
+        try:
+            bar.close()
+        except Exception as e:
+            _logger.error("Error when closing the progress bar: %s", e)

{nxtomomill-2.1.1 → nxtomomill-2.2.0.dev0}/nxtomomill/__main__.py

@@ -12,7 +12,7 @@ from collections import namedtuple
 
 from silx.utils.launcher import Launcher as _Launcher
 
-import nxtomomill.version
+import nxtomomill
 from nxtomomill.utils.io import deprecated_warning
 
 logging.basicConfig()
@@ -118,7 +118,7 @@ def main():
 
     :returns: The execution status
     """
-    _version = nxtomomill.version.version
+    _version = nxtomomill.__version__
     launcher = Launcher(prog="nxtomomill", version=_version)
     launcher.add_command(
         "nx-copy",

{nxtomomill-2.1.1 → nxtomomill-2.2.0.dev0}/nxtomomill/app/blissfluo2nx.py

@@ -90,7 +90,8 @@ def main(argv):
     config.general_section.dimension = options.dimension
     config.general_section.overwrite = options.overwrite
 
-    converter.from_blissfluo_to_nx(
-        configuration=config,
-        progress=tqdm("blissfluo2nx"),
-    )
+    with tqdm("blissfluo2nx") as progress:
+        converter.from_blissfluo_to_nx(
+            configuration=config,
+            progress=progress,
+        )

{nxtomomill-2.1.1 → nxtomomill-2.2.0.dev0}/nxtomomill/app/edf2nx.py

@@ -108,7 +108,8 @@ def main(argv):
     assert isinstance(
         config.output_checks, tuple
     ), f"config.output_checks is expected to be a tuple. Gets {type(config.output_checks)}"
-    converter.from_edf_to_nx(
-        configuration=config,
-        progress=tqdm(desc="edf2nx", bar_format="{l_bar}{bar}{postfix}"),
-    )
+    with tqdm(desc="edf2nx", bar_format="{l_bar}{bar}{postfix}") as progress:
+        converter.from_edf_to_nx(
+            configuration=config,
+            progress=progress,
+        )

{nxtomomill-2.1.1 → nxtomomill-2.2.0.dev0}/nxtomomill/app/fluo2nx.py

@@ -125,7 +125,8 @@ def main(argv):
                 f"The value entered for --mode is not valid. Should be either 'newfile' or 'overwrite'. {options.mode} was given."
             )
 
-    converter.from_fluo_to_nx(
-        configuration=config,
-        progress=tqdm("fluo2nx"),
-    )
+    with tqdm("fluo2nx") as progress:
+        converter.from_fluo_to_nx(
+            configuration=config,
+            progress=progress,
+        )

{nxtomomill-2.1.1 → nxtomomill-2.2.0.dev0}/nxtomomill/app/h52nx.py

@@ -334,9 +334,10 @@ def main(argv):
         logging.getLogger("nxtomomill").setLevel(
             configuration_handler.configuration.log_level
         )
-        from_h5_to_nx(
-            configuration=configuration_handler.configuration,
-            progress=tqdm(desc="h52nx", delay=1, bar_format="{l_bar}{bar}"),
-            input_callback=None,
-            detector_sel_callback=callback_det_sel,
-        )
+        with tqdm(desc="h52nx", delay=1, bar_format="{l_bar}{bar}") as progress:
+            from_h5_to_nx(
+                configuration=configuration_handler.configuration,
+                progress=progress,
+                input_callback=None,
+                detector_sel_callback=callback_det_sel,
+            )

{nxtomomill-2.1.1 → nxtomomill-2.2.0.dev0}/nxtomomill/app/patch_nx.py

@@ -13,7 +13,7 @@ import os
 
 from silx.io.url import DataUrl
 from silx.utils.enum import Enum as _Enum
-from tomoscan.esrf.scan.nxtomoscan import NXtomoScan
+from tomoscan.scans.nxtomoscan import NXtomoScan
 
 from nxtomomill import utils
 from nxtomo.nxobject.nxdetector import ImageKey

{nxtomomill-2.1.1 → nxtomomill-2.2.0.dev0}/nxtomomill/app/split_nxfile.py

@@ -11,7 +11,7 @@ import logging
 import string
 
 from nxtomo.application.nxtomo import NXtomo
-from tomoscan.esrf.scan.nxtomoscan import NXtomoScan
+from tomoscan.scans.nxtomoscan import NXtomoScan
 from silx.io.utils import open as open_hdf5
 from nxtomomill.utils._os import abspath
 

{nxtomomill-2.1.1 → nxtomomill-2.2.0.dev0}/nxtomomill/app/tests/test_edf2nx_app.py

@@ -2,7 +2,7 @@
 
 import os
 
-from tomoscan.esrf.mock import MockEDF
+from tomoscan.tests.mock import MockEDF
 
 from nxtomomill.app.edf2nx import main
 

{nxtomomill-2.1.1 → nxtomomill-2.2.0.dev0}/nxtomomill/app/tests/test_patch_nx_app.py

@@ -3,7 +3,7 @@
 import os
 import tempfile
 
-from tomoscan.esrf.mock import MockNXtomo
+from tomoscan.tests.mock import MockNXtomo
 
 from nxtomomill.app.patch_nx import main
 

{nxtomomill-2.1.1 → nxtomomill-2.2.0.dev0}/nxtomomill/app/tests/test_split_nxfile_app.py

@@ -2,7 +2,8 @@ import os
 import numpy
 import pytest
 import pint
-from tomoscan.io import HDF5File, get_swmr_mode
+from h5py import File as HDF5File
+
 from nxtomo.application.nxtomo import NXtomo
 from nxtomomill.app.split_nxfile import split
 
@@ -73,7 +74,6 @@ def test_split_nxfile(tmp_path, duplicate_data):
     with HDF5File(
         tmp_path / "test_split_nx_file/output_dir_2/entry0002.nx",
         mode="r",
-        swmr=get_swmr_mode(),
     ) as h5f:
         assert "entry0002" in h5f.keys()
         assert "entry0000" not in h5f.keys()

{nxtomomill-2.1.1 → nxtomomill-2.2.0.dev0}/nxtomomill/app/z_concatenate_scans.py

@@ -9,10 +9,10 @@ import json
 import pint
 
 import numpy as np
+from h5py import File as HDF5File
 from silx.io.url import DataUrl
-from tomoscan.esrf.scan.nxtomoscan import NXtomoScan
-from tomoscan.scanbase import ReducedFramesInfos
-from tomoscan.io import HDF5File, get_swmr_mode
+from tomoscan.scans.nxtomoscan import NXtomoScan
+from tomoscan.scans.scanbase import ReducedFramesInfos
 
 from nxtomo.application.nxtomo import NXtomo
 from nxtomo.nxobject.utils import concatenate as nx_concatenate
@@ -178,7 +178,7 @@ def get_arguments(argv):
         args.pixel_size_m = float(args.pixel_size_m)
     else:
         args.overwrite_pixel_size = False
-        with HDF5File(args.file_list[0], "r", swmr=get_swmr_mode()) as h5f:
+        with HDF5File(args.file_list[0], "r") as h5f:
             args.pixel_size_m = h5f[
                 os.path.join(args.entry_name, "instrument", "detector", "x_pixel_size")
             ][()]

{nxtomomill-2.1.1 → nxtomomill-2.2.0.dev0}/nxtomomill/converter/dxfile/dxfileconverter.py

@@ -14,7 +14,7 @@ import h5py
 import numpy
 from silx.io.url import DataUrl
 from silx.io.utils import get_data, h5py_read_dataset
-from tomoscan.io import HDF5File
+from nxtomo.io import HDF5File
 from nxtomo.nxobject.nxdetector import FieldOfView, ImageKey
 from nxtomo.utils.frameappender import FrameAppender
 

{nxtomomill-2.1.1 → nxtomomill-2.2.0.dev0}/nxtomomill/converter/dxfile/tests/test_dxfile.py

@@ -9,7 +9,7 @@ from nxtomomill.converter.dxfile.dxfileconverter import from_dx_config_to_nx
 from nxtomomill.models.dx2nx import DX2nxModel
 from nxtomomill.tests.utils.dxfile import MockDxFile
 
-from tomoscan.esrf.scan.nxtomoscan import NXtomoScan
+from tomoscan.scans.nxtomoscan import NXtomoScan
 from tomoscan.validator import is_valid_for_reconstruction
 
 from silx.io.utils import get_data, h5py_read_dataset

nxtomomill-2.2.0.dev0/nxtomomill/converter/edf/_Blosc2Jp2kWrapper.py

@@ -0,0 +1,63 @@
+from __future__ import annotations
+import numpy
+from h5py import Dataset
+
+try:
+    import blosc2
+    import blosc2_grok
+except ImportError:
+    _has_blosc2 = False
+else:
+    _has_blosc2 = True
+
+
+class Blosc2Jp2kWrapper:
+    """Wrapper to apply JP2K conversion to a dataset"""
+
+    def __init__(self, dataset: Dataset, compression_params: dict):
+        self.dataset: Dataset = dataset
+        self.compression_params: dict = self.get_default_compression_params()
+        self.compression_params.update(compression_params)
+
+        blosc2_grok.set_params_defaults(
+            # codec=blosc2.Codec.GROK,
+            cod_format=blosc2_grok.GrkFileFmt.GRK_FMT_JP2,
+            num_threads=self.compression_params["nthreads"],
+            quality_mode="rates",
+            quality_layers=numpy.array(
+                [self.compression_params["cratio"]],
+                dtype=numpy.float64,
+            ),
+            verbose=True,
+        )
+
+    def __setitem__(self, name, value):
+        z, _, _ = name
+        Z, Y, X = self.dataset.shape
+
+        # Verify data type compatibility
+        if value.dtype not in [numpy.float32, numpy.float64, numpy.uint16]:
+            raise ValueError(f"Unsupported dtype: {value.dtype}")
+
+        b2im = blosc2.asarray(
+            value.reshape(1, Y, X),
+            chunks=(1, Y, X),
+            blocks=(1, Y, X),
+            cparams=self.compression_params,
+        )
+        cframe = b2im.schunk.to_cframe()
+        self.dataset.id.write_direct_chunk((z, 0, 0), cframe, filter_mask=0)
+
+    @classmethod
+    def get_default_compression_params(cls) -> dict:
+        if _has_blosc2:
+            return {
+                "codec": blosc2.Codec.GROK,
+                "filters": [],
+                "splitmode": blosc2.SplitMode.NEVER_SPLIT,
+                "nthreads": 4,
+                "cratio": 10,
+                "verbose": True,
+            }
+        else:
+            return {}

{nxtomomill-2.1.1 → nxtomomill-2.2.0.dev0}/nxtomomill/converter/edf/checks.py

@@ -4,7 +4,7 @@ from silx.utils.enum import Enum as _Enum
 from silx.io.utils import open as open_hdf5
 from silx.io.utils import get_data
 
-from tomoscan.esrf.scan.nxtomoscan import NXtomoScan
+from tomoscan.scans.nxtomoscan import NXtomoScan
 from nxtomo.paths.nxtomo import get_paths as get_nexus_paths
 
 _logger = logging.getLogger(__name__)

{nxtomomill-2.1.1 → nxtomomill-2.2.0.dev0}/nxtomomill/converter/edf/edfconverter.py

@@ -19,10 +19,10 @@ from tqdm import tqdm
 from silx.io.dictdump import dicttoh5
 from silx.utils.deprecation import deprecated
 
-from tomoscan.esrf.scan.edfscan import EDFTomoScan
-from tomoscan.esrf.scan.nxtomoscan import NXtomoScan
-from tomoscan.esrf.scan.utils import get_parameters_frm_par_or_info
-from tomoscan.io import HDF5File
+from tomoscan.scans.edfscan import EDFTomoScan
+from tomoscan.scans.nxtomoscan import NXtomoScan
+from tomoscan.scan_utils import get_parameters_frm_par_or_info
+from nxtomo.io import HDF5File
 
 from nxtomo.paths.nxtomo import get_paths as get_nexus_paths
 from nxtomo.nxobject.nxdetector import FieldOfView, ImageKey

{nxtomomill-2.1.1 → nxtomomill-2.2.0.dev0}/nxtomomill/converter/edf/tests/test_checks.py

@@ -3,8 +3,8 @@ import numpy
 from fabio.edfimage import EdfImage
 from silx.io.url import DataUrl
 from nxtomomill.converter.edf.checks import compare_volumes
-from tomoscan.esrf.scan.nxtomoscan import NXtomoScan
-from tomoscan.io import HDF5File
+from tomoscan.scans.nxtomoscan import NXtomoScan
+from nxtomo.io import HDF5File
 
 
 def test_compare_volumes(tmp_path):

{nxtomomill-2.1.1 → nxtomomill-2.2.0.dev0}/nxtomomill/converter/edf/tests/test_edf2nx.py

@@ -1,5 +1,6 @@
 # coding: utf-8
 
+import contextlib
 import os
 import shutil
 import tempfile
@@ -9,14 +10,13 @@ import numpy
 import pytest
 
 from tqdm import tqdm
+from h5py import File as HDF5File
 
-from tomoscan import version
-from tomoscan.esrf.mock import MockEDF
-from tomoscan.esrf.scan.edfscan import EDFTomoScan
-from tomoscan.esrf.scan.nxtomoscan import NXtomoScan
-from tomoscan.esrf.scan.utils import dump_info_file
+from tomoscan.tests.mock import MockEDF
+from tomoscan.scans.edfscan import EDFTomoScan
+from tomoscan.scans.nxtomoscan import NXtomoScan
+from tomoscan.scan_utils import dump_info_file
 from tomoscan.validator import is_valid_for_reconstruction
-from tomoscan.io import HDF5File, get_swmr_mode
 
 from nxtomo.io import cwd_context
 
@@ -29,12 +29,10 @@ from nxtomomill.models.edf2nx import EDF2nxModel
     "duplicate_data, external_link_type",
     ((False, "absolute"), (False, "relative"), (True, "absolute")),
 )
-@pytest.mark.parametrize("progress", (None, tqdm(desc="conversion from edf")))
-@pytest.mark.skipif(
-    condition=(version.MINOR < 7 and version.MAJOR == 0),
-    reason="dark_n and ref_n from EDFTomoScan where not existing",
-)
-def test_edf_to_nx_converter(tmp_path, progress, duplicate_data, external_link_type):
+@pytest.mark.parametrize("with_progress", (False, True))
+def test_edf_to_nx_converter(
+    tmp_path, with_progress, duplicate_data, external_link_type
+):
     folder = tmp_path
 
     scan_path = os.path.join(folder, "myscan")
@@ -64,10 +62,14 @@ def test_edf_to_nx_converter(tmp_path, progress, duplicate_data, external_link_t
     config.y_translation_unit = "cm"
     config.z_translation_unit = "m"
     config.sample_detector_distance_unit = "cm"
-    nx_file, nx_entry = converter.from_edf_to_nx(
-        configuration=config,
-        progress=progress,
+    progress_cm = (
+        tqdm(desc="conversion from edf") if with_progress else contextlib.nullcontext()
     )
+    with progress_cm as progress:
+        nx_file, nx_entry = converter.from_edf_to_nx(
+            configuration=config,
+            progress=progress,
+        )
 
     hdf5_scan = NXtomoScan(scan=nx_file, entry=nx_entry)
     assert len(hdf5_scan.projections) == n_proj
@@ -81,7 +83,7 @@ def test_edf_to_nx_converter(tmp_path, progress, duplicate_data, external_link_t
     # this will work with the tomotools suite as tomoscan will automatically create a working dircetory context when reading the file.
     # but this can be an issue when sharing data or reading data outside the tomotools suite
     with cwd_context(output_file):
-        with HDF5File(output_file, mode="r", swmr=get_swmr_mode()) as h5f:
+        with HDF5File(output_file, mode="r") as h5f:
             detector_data_path = f"/{nx_entry}/instrument/detector/data"
             assert (
                 f"/{nx_entry}/instrument/detector/data" in h5f

{nxtomomill-2.1.1 → nxtomomill-2.2.0.dev0}/nxtomomill/converter/edf/tests/test_edf2nx_check.py

@@ -1,8 +1,8 @@
 import os
 import pytest
 from glob import glob
-from tomoscan.esrf.mock import MockEDF
-from tomoscan.esrf.scan.edfscan import EDFTomoScan
+from tomoscan.tests.mock import MockEDF
+from tomoscan.scans.edfscan import EDFTomoScan
 from nxtomomill.converter.edf.checks import OUPUT_CHECK
 from nxtomomill.models.edf2nx import EDF2nxModel
 from nxtomomill.converter.edf.edfconverter import from_edf_to_nx, post_processing_check

{nxtomomill-2.1.1 → nxtomomill-2.2.0.dev0}/nxtomomill/converter/fluo/fluoscan.py

@@ -9,9 +9,9 @@ import pint
 
 import numpy
 
-from tomoscan.identifier import ScanIdentifier
-from tomoscan.scanbase import TomoScanBase
-from tomoscan.utils import docstring
+from tomoscan.identifiers.base import ScanIdentifier
+from tomoscan.scans.scanbase import TomoScanBase
+from tomobase.utils import docstring
 
 
 from dataclasses import dataclass, field

{nxtomomill-2.1.1 → nxtomomill-2.2.0.dev0}/nxtomomill/converter/fscan/fscanconverter.py

@@ -2,10 +2,10 @@ import logging
 from posixpath import join
 import numpy as np
 import pint
-from tomoscan.esrf.scan.h5utils import get_h5_value
+from tomoscan.h5utils import get_h5_value
 from nxtomo.application.nxtomo import NXtomo
 from nxtomo.nxobject.nxdetector import ImageKey
-from tomoscan.esrf.scan.fscan import FscanDataset, list_datasets
+from tomoscan.fscan import FscanDataset, list_datasets
 from silx.utils.deprecation import deprecated
 
 _logger = logging.getLogger(__name__)

{nxtomomill-2.1.1 → nxtomomill-2.2.0.dev0}/nxtomomill/converter/hdf5/acquisition/tests/test_acquisition.py

@@ -6,7 +6,7 @@ import tempfile
 import pytest
 from silx.io.url import DataUrl
 
-from tomoscan.io import HDF5File
+from nxtomo.io import HDF5File
 from nxtomomill.converter.hdf5.acquisition.baseacquisition import (
     BaseAcquisition,
     get_dataset_name_from_motor,
@@ -60,7 +60,8 @@ def test_frame_flips(tmp_path, monkeypatch):
     )
 
     scan_dir = GitlabDataset.get_dataset("h5_datasets")
-    assert scan_dir is not None
+    if scan_dir is None:
+        raise FileNotFoundError("Unable to download h5_datasets not found")
 
     configuration = TomoHDF5Config()
     configuration.input_file = os.path.join(

{nxtomomill-2.1.1 → nxtomomill-2.2.0.dev0}/nxtomomill/converter/hdf5/acquisition/tests/test_acquisition_utils.py

@@ -6,7 +6,7 @@ import pytest
 import h5py
 
 from silx.io.url import DataUrl
-from tomoscan.io import HDF5File
+from nxtomo.io import HDF5File
 from nxtomo.nxobject.nxdetector import ImageKey
 
 from nxtomomill.io.config import TomoHDF5Config

{nxtomomill-2.1.1 → nxtomomill-2.2.0.dev0}/nxtomomill/converter/hdf5/acquisition/tests/test_back_and_forth.py

@@ -17,7 +17,8 @@ _ureg = pint.get_application_registry()
 def test_back_and_forth_conversion(tmp_path):
     """test nxtomomill fluo2nx CLI with default parameters (handle all detectors found)"""
     scan_dir = GitlabDataset.get_dataset("h5_datasets")
-    assert scan_dir is not None
+    if scan_dir is None:
+        raise FileNotFoundError("Unable to download h5_datasets not found")
     input_file = os.path.join(scan_dir, "back_and_forth/bliss_tomo_2025_06_17.h5")
 
     output_file = os.path.join(tmp_path, "nexus_file.nx")

{nxtomomill-2.1.1 → nxtomomill-2.2.0.dev0}/nxtomomill/converter/hdf5/acquisition/tests/test_bliss_tomo_config.py

@@ -1,7 +1,8 @@
 import pytest
 import os
 import numpy
-from tomoscan.io import HDF5File, get_swmr_mode
+from h5py import File as HDF5File
+
 from nxtomomill.converter.hdf5.acquisition.blisstomoconfig import TomoConfig
 
 
@@ -56,7 +57,7 @@ def test_tomo_config(tmp_path):
     with pytest.raises(KeyError):
         TomoConfig.from_technique_group(h5s)
 
-    with HDF5File(file_path, mode="r", swmr=get_swmr_mode()) as h5s:
+    with HDF5File(file_path, mode="r") as h5s:
         tomo_config = TomoConfig.from_technique_group(h5s["/0/test/instrument"])
 
     numpy.testing.assert_array_equal(

{nxtomomill-2.1.1 → nxtomomill-2.2.0.dev0}/nxtomomill/converter/hdf5/acquisition/tests/test_holotomo.py

@@ -42,7 +42,8 @@ def test_holotomo_conversion_id16a(tmp_path):
         "h5_datasets", "holotomo", "id16a", "SiemensStar_HT_025nm_0002.h5"
     )
     input_file = GitlabDataset.get_dataset(dataset_file)
-    assert os.path.exists(input_file)
+    if input_file is None:
+        raise FileNotFoundError(f"Unable to download {dataset_file} not found")
     output_file = os.path.join(tmp_path, "nexus_file.nx")
 
     assert not os.path.exists(output_file), "output_file exists already"

{nxtomomill-2.1.1 → nxtomomill-2.2.0.dev0}/nxtomomill/converter/hdf5/acquisition/tests/test_legacy.py

@@ -19,14 +19,16 @@ _ureg = pint.get_application_registry()
 @pytest.fixture(scope="class")
 def S59_68p41b_16mm_6p5mm_F8_0001_Dataset() -> Path:
     scan_dir = GitlabDataset.get_dataset("h5_datasets")
-    assert scan_dir is not None
+    if scan_dir is None:
+        raise FileNotFoundError("Unable to download h5_datasets not found")
     return Path(os.path.join(scan_dir, "legacy", "S59_68p41b_16mm_6p5mm_F8_0001.h5"))
 
 
 @pytest.fixture(scope="class")
 def WGN_01_0000_P_110_8128_D_129_Dataset():
     scan_dir = GitlabDataset.get_dataset("h5_datasets")
-    assert scan_dir is not None
+    if scan_dir is None:
+        raise FileNotFoundError("Unable to download h5_datasets not found")
     return Path(os.path.join(scan_dir, "legacy", "WGN_01_0000_P_110_8128_D_129.h5"))
 
 

{nxtomomill-2.1.1 → nxtomomill-2.2.0.dev0}/nxtomomill/converter/hdf5/acquisition/tests/test_multitomo_zseries.py

@@ -17,7 +17,8 @@ def test_multitomo_z_series(tmp_path):
     """test nxtomomill h52nx with a 'multitomo z-series' acquisition"""
 
     scan_dir = GitlabDataset.get_dataset("h5_datasets")
-    assert scan_dir is not None
+    if scan_dir is None:
+        raise FileNotFoundError("Unable to download h5_datasets not found")
     input_file = os.path.join(
         scan_dir, "multitomo/Zseries_Volcano_passedevis_-1.7-aka720-bis_0002.h5"
     )

{nxtomomill-2.1.1 → nxtomomill-2.2.0.dev0}/nxtomomill/converter/hdf5/acquisition/tests/test_multitomoacquisition.py

@@ -3,12 +3,12 @@
 import os
 import numpy
 import pytest
+from h5py import File as HDF5File
 
 from nxtomo.application.nxtomo import NXtomo
 from nxtomo.nxobject.nxdetector import ImageKey
 
-from tomoscan.io import HDF5File, get_swmr_mode
-from tomoscan.esrf.scan.nxtomoscan import NXtomoScan
+from tomoscan.scans.nxtomoscan import NXtomoScan
 
 from nxtomomill import converter
 from nxtomomill.converter.hdf5.acquisition.multitomo import MultiTomoAcquisition
@@ -61,7 +61,7 @@ def test_multitomo_conversion(tmp_path, config: dict, multitomo_version: int):
     assert len(result) == nb_loop * nb_tomo
     n_projs = 10 * nb_loop * nb_tomo
     # check saved datasets
-    with HDF5File(sample_file, mode="r", swmr=get_swmr_mode()) as h5f:
+    with HDF5File(sample_file, mode="r") as h5f:
         darks = h5f["2.1/instrument/pcolinux/data"][()]
         assert len(darks) == n_darks
         flats_1 = h5f["3.1/instrument/pcolinux/data"][()]
@@ -72,7 +72,7 @@ def test_multitomo_conversion(tmp_path, config: dict, multitomo_version: int):
         assert len(flats_2) == n_flats
 
     for i_nx_tomo, (file_path, data_path) in enumerate(result):
-        with HDF5File(file_path, mode="r", swmr=get_swmr_mode()) as h5f:
+        with HDF5File(file_path, mode="r") as h5f:
             detector_path = "/".join([data_path, "instrument", "detector", "data"])
             detector_data = h5f[detector_path][()]
             expected_data = numpy.concatenate(