nxtomomill 2.1.5__tar.gz → 2.2.0.dev1__tar.gz

{nxtomomill-2.1.5/nxtomomill.egg-info → nxtomomill-2.2.0.dev1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nxtomomill
-Version: 2.1.5
+Version: 2.2.0.dev1
 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]<3.0,>=2.2.0a4
+Requires-Dist: tomoscan>=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-2.1.5 → nxtomomill-2.2.0.dev1}/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-2.1.5 → nxtomomill-2.2.0.dev1}/nxtomomill/__init__.py

@@ -4,9 +4,12 @@ import atexit
 
 import logging
 
-from .version import version as __version
+from importlib.metadata import version as _get_version, PackageNotFoundError
 
-__version__ = __version
+try:
+    __version__ = _get_version("nxtomomill")
+except PackageNotFoundError:
+    __version__ = "unknown"
 
 _logger = logging.getLogger(__name__)
 

{nxtomomill-2.1.5 → nxtomomill-2.2.0.dev1}/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-2.1.5 → nxtomomill-2.2.0.dev1}/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-2.1.5 → nxtomomill-2.2.0.dev1}/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-2.1.5 → nxtomomill-2.2.0.dev1}/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-2.1.5 → nxtomomill-2.2.0.dev1}/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-2.1.5 → nxtomomill-2.2.0.dev1}/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-2.1.5 → nxtomomill-2.2.0.dev1}/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-2.1.5 → nxtomomill-2.2.0.dev1}/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-2.1.5 → nxtomomill-2.2.0.dev1}/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-2.1.5 → nxtomomill-2.2.0.dev1}/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-2.1.5 → nxtomomill-2.2.0.dev1}/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-2.1.5 → nxtomomill-2.2.0.dev1}/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-2.1.5 → nxtomomill-2.2.0.dev1}/nxtomomill/converter/edf/tests/test_edf2nx.py

@@ -10,13 +10,13 @@ import numpy
 import pytest
 
 from tqdm import tqdm
+from h5py import File as HDF5File
 
-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
 
@@ -83,7 +83,7 @@ def test_edf_to_nx_converter(
     # 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-2.1.5 → nxtomomill-2.2.0.dev1}/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-2.1.5 → nxtomomill-2.2.0.dev1}/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-2.1.5 → nxtomomill-2.2.0.dev1}/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-2.1.5 → nxtomomill-2.2.0.dev1}/nxtomomill/converter/hdf5/acquisition/tests/test_acquisition.py

@@ -7,7 +7,7 @@ import h5py
 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,
@@ -93,7 +93,8 @@ 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-2.1.5 → nxtomomill-2.2.0.dev1}/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-2.1.5 → nxtomomill-2.2.0.dev1}/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-2.1.5 → nxtomomill-2.2.0.dev1}/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-2.1.5 → nxtomomill-2.2.0.dev1}/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-2.1.5 → nxtomomill-2.2.0.dev1}/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-2.1.5 → nxtomomill-2.2.0.dev1}/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-2.1.5 → nxtomomill-2.2.0.dev1}/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(

{nxtomomill-2.1.5 → nxtomomill-2.2.0.dev1}/nxtomomill/converter/hdf5/hdf5converter.py

@@ -14,8 +14,8 @@ import h5py
 from tqdm import tqdm
 
 from silx.io.url import DataUrl
-from tomoscan.io import HDF5File
-from tomoscan.utils.io import filter_esrf_mounting_points
+from nxtomo.io import HDF5File
+from tomobase.utils.io import filter_esrf_mounting_points
 
 from nxtomomill.converter.hdf5.acquisition.utils import group_series
 from nxtomomill.converter.baseconverter import BaseConverter

{nxtomomill-2.1.5 → nxtomomill-2.2.0.dev1}/nxtomomill/converter/hdf5/post_processing/dark_flat_copy.py

@@ -6,7 +6,7 @@ from typing import Literal
 
 from silx.io.url import DataUrl
 
-from tomoscan.esrf.scan.utils import get_series_slice, get_n_series
+from tomoscan.scan_utils import get_series_slice, get_n_series
 
 from nxtomo.application.nxtomo import NXtomo
 from nxtomo.nxobject.nxdetector import ImageKey

{nxtomomill-2.1.5 → nxtomomill-2.2.0.dev1}/nxtomomill/converter/hdf5/tests/test_frame_flip.py

@@ -17,6 +17,10 @@ def dataset_id16a(tmp_path):
     source_file = GitlabDataset.get_dataset(
         "h5_datasets/holotomo/id16a/Atomium_S2_holo4_HT_010nm_0001.h5"
     )
+    if source_file is None:
+        raise FileNotFoundError(
+            "Unable to download h5_datasets/holotomo/id16a/Atomium_S2_holo4_HT_010nm_0001.h5 not found"
+        )
     return shutil.copyfile(
         source_file,
         os.path.join(tmp_path, "Atomium_S2_holo1_HT_010nm_500proj_0003.h5"),

{nxtomomill-2.1.5 → nxtomomill-2.2.0.dev1}/nxtomomill/converter/hdf5/tests/test_h52nx_utils.py

@@ -236,7 +236,7 @@ def test_read_key(read_key_datasets, caplog):
             expected_unit=_ureg.centimeter,
         )
         numpy.testing.assert_array_equal(
-            quantity.to_base_units(), numpy.array([0.02] * 10)
+            quantity.to_base_units().magnitude, numpy.array([0.02] * 10)
         )
 
         # test with dataset with coherent size but incoherent units
@@ -256,7 +256,7 @@ def test_read_key(read_key_datasets, caplog):
             expected_unit=_ureg.centimeter,
         )
         numpy.testing.assert_array_equal(
-            quantity.to_base_units(), numpy.array([1.01] * 10)
+            quantity.to_base_units().magnitude, numpy.array([1.01] * 10)
         )
 
         # test arrays with incoherent size
@@ -274,7 +274,7 @@ def test_read_key(read_key_datasets, caplog):
             expected_unit=_ureg.centimeter,
         )
         numpy.testing.assert_array_equal(
-            quantity.to_base_units(), numpy.array([1.02] * 6)
+            quantity.to_base_units().magnitude, numpy.array([1.02] * 6)
         )
         assert expected_warning in caplog.record_tuples
 
@@ -286,7 +286,7 @@ def test_read_key(read_key_datasets, caplog):
             expected_unit=_ureg.centimeter,
         )
         numpy.testing.assert_array_equal(
-            quantity.to_base_units(), numpy.array([1 + 0.014 - 2] * 10)
+            quantity.to_base_units().magnitude, numpy.array([1 + 0.014 - 2] * 10)
         )
         # test incoherent arrays with scalar
         quantity: pint.Quantity = read_key(
@@ -296,5 +296,5 @@ def test_read_key(read_key_datasets, caplog):
             expected_unit=_ureg.centimeter,
         )
         numpy.testing.assert_array_equal(
-            quantity.to_base_units(), numpy.array([1 - 0.014 + 1] * 9)
+            quantity.to_base_units().magnitude, numpy.array([1 - 0.014 + 1] * 9)
         )

{nxtomomill-2.1.5 → nxtomomill-2.2.0.dev1}/nxtomomill/converter/hdf5/tests/test_hdf5converter.py

@@ -5,6 +5,7 @@ import sys
 import tempfile
 
 import h5py
+from h5py import File as HDF5File
 import numpy
 import pint
 import shutil
@@ -27,12 +28,7 @@ from nxtomomill.converter.hdf5.utils import (
 )
 from nxtomomill.models.h52nx import H52nxModel
 
-from tomoscan.io import HDF5File, get_swmr_mode
-
-try:
-    from tomoscan.esrf.scan.hdf5scan import NXtomoScan
-except ImportError:
-    from tomoscan.esrf.hdf5scan import NXtomoScan
+from tomoscan.scans.nxtomoscan import NXtomoScan
 
 import subprocess  # nosec B404
 from glob import glob
@@ -107,7 +103,7 @@ def test_simple_converter_with_nx_detector_attr(tmp_path):
         # insure only one file is generated
         assert os.path.exists(config.output_file)
         # insure data is here
-        with HDF5File(config.output_file, mode="r", swmr=get_swmr_mode()) as h5s:
+        with HDF5File(config.output_file, mode="r") as h5s:
             for _, entry_node in h5s.items():
                 assert "instrument/detector/data" in entry_node
                 dataset = entry_node["instrument/detector/data"]
@@ -187,7 +183,7 @@ def test_simple_converter_without_nx_detector_attr(tmp_path, create_tomo_config:
     # insure only one file is generated
     assert os.path.exists(output_file)
     # insure data is here
-    with HDF5File(output_file, mode="r", swmr=get_swmr_mode()) as h5s:
+    with HDF5File(output_file, mode="r") as h5s:
         for _, entry_node in h5s.items():
             assert "instrument/detector/data" in entry_node
             dataset = entry_node["instrument/detector/data"]
@@ -242,7 +238,7 @@ def test_providing_existing_camera_name(tmp_path):
     # insure only one file is generated
     assert os.path.exists(config.output_file)
     # insure data is here
-    with HDF5File(config.output_file, mode="r", swmr=get_swmr_mode()) as h5s:
+    with HDF5File(config.output_file, mode="r") as h5s:
         for _, entry_node in h5s.items():
             assert "instrument/detector/data" in entry_node
             dataset = entry_node["instrument/detector/data"]
@@ -408,7 +404,7 @@ def test_ignore_sub_entries(tmp_path):
         # insure only one file is generated
         assert os.path.exists(config.output_file)
         # insure data is here
-        with HDF5File(config.output_file, mode="r", swmr=get_swmr_mode()) as h5s:
+        with HDF5File(config.output_file, mode="r") as h5s:
             for _, entry_node in h5s.items():
                 assert "instrument/detector/data" in entry_node
                 dataset = entry_node["instrument/detector/data"]
@@ -445,7 +441,7 @@ def test_get_nx_detectors(tmp_path):
     with HDF5File(h5file, mode="w") as h5s:
         create_nx_detector(node=h5s, name="det1", with_nx_class=True)
         create_nx_detector(node=h5s, name="det2", with_nx_class=False)
-    with HDF5File(h5file, mode="r", swmr=get_swmr_mode()) as h5s:
+    with HDF5File(h5file, mode="r") as h5s:
         dets = get_nx_detectors(h5s)
         assert len(dets) == 1
         assert dets[0].name == "/det1"
@@ -453,7 +449,7 @@ def test_get_nx_detectors(tmp_path):
     with HDF5File(h5file, mode="a") as h5s:
         create_nx_detector(node=h5s, name="det3", with_nx_class=True)
         create_nx_detector(node=h5s, name="det4", with_nx_class=True)
-    with HDF5File(h5file, mode="r", swmr=get_swmr_mode()) as h5s:
+    with HDF5File(h5file, mode="r") as h5s:
         dets = get_nx_detectors(h5s)
         assert len(dets) == 3
 
@@ -467,7 +463,7 @@ def test_guess_nx_detector(tmp_path):
 
     with HDF5File(h5file, mode="w") as h5s:
         create_nx_detector(node=h5s, name="det2", with_nx_class=False)
-    with HDF5File(h5file, mode="r", swmr=get_swmr_mode()) as h5s:
+    with HDF5File(h5file, mode="r") as h5s:
         dets = get_nx_detectors(h5s)
         assert len(dets) == 0
         dets = guess_nx_detector(h5s)
@@ -553,7 +549,7 @@ def test_dataset_1(tmp_path):
 
     assert os.path.exists(config.output_file), "output file does not exists"
 
-    with HDF5File(config.output_file, mode="r", swmr=get_swmr_mode()) as h5s:
+    with HDF5File(config.output_file, mode="r") as h5s:
         assert len(h5s.items()) == 1
         assert "entry0000" in h5s
 
@@ -564,7 +560,7 @@ def test_dataset_1(tmp_path):
     assert len(scan.projections) == 20
     assert len(scan.darks) == 10
     # check data is a virtual dataset
-    with HDF5File(config.output_file, mode="r", swmr=get_swmr_mode()) as h5f:
+    with HDF5File(config.output_file, mode="r") as h5f:
         dataset = h5f["entry0000/instrument/detector/data"]
         assert dataset.is_virtual
         assert dataset.dtype == frame_data_type
@@ -663,14 +659,13 @@ def test_dataset_2(tmp_path):
 
     assert os.path.exists(config.output_file)
 
-    with HDF5File(config.output_file, mode="r", swmr=get_swmr_mode()) as h5s:
+    with HDF5File(config.output_file, mode="r") as h5s:
         assert "entry0000" in h5s
         assert len(h5s.items()) == 1
 
     with HDF5File(
         config.output_file.replace(".nx", "_0000.nx"),
         mode="r",
-        swmr=get_swmr_mode(),
     ) as h5s:
         assert "entry0000" in h5s
         assert "duplicate_data" in h5s
@@ -714,7 +709,7 @@ def test_dataset_2(tmp_path):
     flat_data = get_data(url)
     assert flat_data.min() != flat_data.max()
 
-    with HDF5File(config.output_file, mode="r", swmr=get_swmr_mode()) as h5f:
+    with HDF5File(config.output_file, mode="r") as h5f:
         dataset = h5f["entry0000/instrument/detector/data"][()]
         assert dataset.shape[0] == 60
     with EntryReader(dark_url_1, open_mode_for_reading="safe") as dark_entry:
@@ -873,7 +868,7 @@ def test_z_series_conversion_with_external_urls(tmp_path, z_series_version: str)
     )
     assert len(new_scans) == 3
     assert os.path.exists(config.output_file)
-    with HDF5File(config.output_file, mode="r", swmr=get_swmr_mode()) as h5f:
+    with HDF5File(config.output_file, mode="r") as h5f:
         assert "entry0000" in h5f
         assert "entry0001" in h5f
         assert "entry0002" in h5f
@@ -894,7 +889,7 @@ def test_z_series_conversion_with_external_urls(tmp_path, z_series_version: str)
         assert not url_has_been_copied(file_path=config.output_file, url=url)
 
     # test a few slices
-    with HDF5File(config.output_file, mode="r", swmr=get_swmr_mode()) as h5f:
+    with HDF5File(config.output_file, mode="r") as h5f:
         dataset = h5f["entry0000/instrument/detector/data"]
         assert dataset.shape[0] == 30
 
@@ -1049,7 +1044,7 @@ def test_h52nx_from_command_line(tmp_path):
                 assert dataset.dtype == numpy.uint32
         # FIXME: avoid keeping some file open. not clear why this is needed
         dataset = None
-        with HDF5File(output_file, "r", swmr=get_swmr_mode()) as h5f:
+        with HDF5File(output_file, "r") as h5f:
             assert "/entry0000/instrument/diode" not in h5f
 
         # insure an nxtomo can be created from it
@@ -1121,7 +1116,7 @@ def test_simple_conversion(input_type, tmp_path, rotation_is_clockwise: bool):
     # insure only one file is generated
     assert os.path.exists(config.output_file)
     # insure data is here
-    with HDF5File(config.output_file, mode="r", swmr=get_swmr_mode()) as h5s:
+    with HDF5File(config.output_file, mode="r") as h5s:
         for _, entry_node in h5s.items():
             assert "instrument/detector/data" in entry_node
             dataset = entry_node["instrument/detector/data"]