tomwer 1.5.1__tar.gz → 1.5.2__tar.gz

{tomwer-1.5.1 → tomwer-1.5.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: tomwer
-Version: 1.5.1
+Version: 1.5.2
 Summary: "tomography workflow tools"
 Home-page: https://gitlab.esrf.fr/tomotools/tomwer
 Author: Henri Payno, Pierre Paleo, Pierre-Olivier Autran, Jérôme Lesaint, Alessandro Mirone
@@ -25,12 +25,11 @@ Requires-Dist: numpy
 Requires-Dist: setuptools
 Requires-Dist: psutil
 Requires-Dist: silx[full]>=2.1.1
-Requires-Dist: tomoscan>=2.2.0a6
+Requires-Dist: tomoscan[full_no_compression_plugins]>=2.2.0a6
 Requires-Dist: nxtomo>=2.0.0dev2
 Requires-Dist: nxtomomill>=1.2.0dev1
 Requires-Dist: processview>=1.5.0
 Requires-Dist: ewoks>=0.1.1
-Requires-Dist: ewokscore<1.1.0
 Requires-Dist: sluurp>=0.4.1
 Requires-Dist: packaging
 Requires-Dist: pint
@@ -39,83 +38,63 @@ Provides-Extra: full-base
 Requires-Dist: orange-canvas-core; extra == "full-base"
 Requires-Dist: orange-widget-base; extra == "full-base"
 Requires-Dist: ewoks[orange]>=0.1.1; extra == "full-base"
-Requires-Dist: ewoksorange>=0.7.0rc0; extra == "full-base"
+Requires-Dist: ewoksorange==1.1; extra == "full-base"
 Requires-Dist: rsyncmanager; extra == "full-base"
 Requires-Dist: fabio; extra == "full-base"
-Requires-Dist: h5py>=3; extra == "full-base"
-Requires-Dist: lxml; extra == "full-base"
 Requires-Dist: werkzeug; extra == "full-base"
 Requires-Dist: json-rpc; extra == "full-base"
 Requires-Dist: scipy; extra == "full-base"
 Requires-Dist: Pillow; extra == "full-base"
-Requires-Dist: glymur<0.14; extra == "full-base"
 Requires-Dist: resource; extra == "full-base"
-Requires-Dist: tifffile; extra == "full-base"
 Requires-Dist: hdf5plugin; extra == "full-base"
 Requires-Dist: pyicat_plus; extra == "full-base"
 Requires-Dist: ewoksnotify[full]; extra == "full-base"
-Requires-Dist: pyicat_plus; extra == "full-base"
 Provides-Extra: full-no-nabu
 Requires-Dist: orange-canvas-core; extra == "full-no-nabu"
 Requires-Dist: orange-widget-base; extra == "full-no-nabu"
 Requires-Dist: ewoks[orange]>=0.1.1; extra == "full-no-nabu"
-Requires-Dist: ewoksorange>=0.7.0rc0; extra == "full-no-nabu"
+Requires-Dist: ewoksorange==1.1; extra == "full-no-nabu"
 Requires-Dist: rsyncmanager; extra == "full-no-nabu"
 Requires-Dist: fabio; extra == "full-no-nabu"
-Requires-Dist: h5py>=3; extra == "full-no-nabu"
-Requires-Dist: lxml; extra == "full-no-nabu"
 Requires-Dist: werkzeug; extra == "full-no-nabu"
 Requires-Dist: json-rpc; extra == "full-no-nabu"
 Requires-Dist: scipy; extra == "full-no-nabu"
 Requires-Dist: Pillow; extra == "full-no-nabu"
-Requires-Dist: glymur<0.14; extra == "full-no-nabu"
 Requires-Dist: resource; extra == "full-no-nabu"
-Requires-Dist: tifffile; extra == "full-no-nabu"
 Requires-Dist: hdf5plugin; extra == "full-no-nabu"
 Requires-Dist: pyicat_plus; extra == "full-no-nabu"
 Requires-Dist: ewoksnotify[full]; extra == "full-no-nabu"
-Requires-Dist: pyicat_plus; extra == "full-no-nabu"
 Provides-Extra: full-no-cuda
 Requires-Dist: orange-canvas-core; extra == "full-no-cuda"
 Requires-Dist: orange-widget-base; extra == "full-no-cuda"
 Requires-Dist: ewoks[orange]>=0.1.1; extra == "full-no-cuda"
-Requires-Dist: ewoksorange>=0.7.0rc0; extra == "full-no-cuda"
+Requires-Dist: ewoksorange==1.1; extra == "full-no-cuda"
 Requires-Dist: rsyncmanager; extra == "full-no-cuda"
 Requires-Dist: fabio; extra == "full-no-cuda"
-Requires-Dist: h5py>=3; extra == "full-no-cuda"
-Requires-Dist: lxml; extra == "full-no-cuda"
 Requires-Dist: werkzeug; extra == "full-no-cuda"
 Requires-Dist: json-rpc; extra == "full-no-cuda"
 Requires-Dist: scipy; extra == "full-no-cuda"
 Requires-Dist: Pillow; extra == "full-no-cuda"
-Requires-Dist: glymur<0.14; extra == "full-no-cuda"
 Requires-Dist: resource; extra == "full-no-cuda"
-Requires-Dist: tifffile; extra == "full-no-cuda"
 Requires-Dist: hdf5plugin; extra == "full-no-cuda"
 Requires-Dist: pyicat_plus; extra == "full-no-cuda"
 Requires-Dist: ewoksnotify[full]; extra == "full-no-cuda"
-Requires-Dist: pyicat_plus; extra == "full-no-cuda"
 Requires-Dist: nabu>=2023.3.1dev; extra == "full-no-cuda"
 Provides-Extra: full
 Requires-Dist: orange-canvas-core; extra == "full"
 Requires-Dist: orange-widget-base; extra == "full"
 Requires-Dist: ewoks[orange]>=0.1.1; extra == "full"
-Requires-Dist: ewoksorange>=0.7.0rc0; extra == "full"
+Requires-Dist: ewoksorange==1.1; extra == "full"
 Requires-Dist: rsyncmanager; extra == "full"
 Requires-Dist: fabio; extra == "full"
-Requires-Dist: h5py>=3; extra == "full"
-Requires-Dist: lxml; extra == "full"
 Requires-Dist: werkzeug; extra == "full"
 Requires-Dist: json-rpc; extra == "full"
 Requires-Dist: scipy; extra == "full"
 Requires-Dist: Pillow; extra == "full"
-Requires-Dist: glymur<0.14; extra == "full"
 Requires-Dist: resource; extra == "full"
-Requires-Dist: tifffile; extra == "full"
 Requires-Dist: hdf5plugin; extra == "full"
 Requires-Dist: pyicat_plus; extra == "full"
 Requires-Dist: ewoksnotify[full]; extra == "full"
-Requires-Dist: pyicat_plus; extra == "full"
 Requires-Dist: nabu[full]>=2023.3.1dev; extra == "full"
 Requires-Dist: pycuda<2024.1.1; extra == "full"
 Requires-Dist: scikit-cuda; extra == "full"
@@ -123,22 +102,17 @@ Provides-Extra: doc
 Requires-Dist: orange-canvas-core; extra == "doc"
 Requires-Dist: orange-widget-base; extra == "doc"
 Requires-Dist: ewoks[orange]>=0.1.1; extra == "doc"
-Requires-Dist: ewoksorange>=0.7.0rc0; extra == "doc"
+Requires-Dist: ewoksorange==1.1; extra == "doc"
 Requires-Dist: rsyncmanager; extra == "doc"
 Requires-Dist: fabio; extra == "doc"
-Requires-Dist: h5py>=3; extra == "doc"
-Requires-Dist: lxml; extra == "doc"
 Requires-Dist: werkzeug; extra == "doc"
 Requires-Dist: json-rpc; extra == "doc"
 Requires-Dist: scipy; extra == "doc"
 Requires-Dist: Pillow; extra == "doc"
-Requires-Dist: glymur<0.14; extra == "doc"
 Requires-Dist: resource; extra == "doc"
-Requires-Dist: tifffile; extra == "doc"
 Requires-Dist: hdf5plugin; extra == "doc"
 Requires-Dist: pyicat_plus; extra == "doc"
 Requires-Dist: ewoksnotify[full]; extra == "doc"
-Requires-Dist: pyicat_plus; extra == "doc"
 Requires-Dist: nabu>=2023.3.1dev; extra == "doc"
 Requires-Dist: Sphinx>=4.0.0; extra == "doc"
 Requires-Dist: nbsphinx; extra == "doc"
@@ -157,22 +131,17 @@ Provides-Extra: dev
 Requires-Dist: orange-canvas-core; extra == "dev"
 Requires-Dist: orange-widget-base; extra == "dev"
 Requires-Dist: ewoks[orange]>=0.1.1; extra == "dev"
-Requires-Dist: ewoksorange>=0.7.0rc0; extra == "dev"
+Requires-Dist: ewoksorange==1.1; extra == "dev"
 Requires-Dist: rsyncmanager; extra == "dev"
 Requires-Dist: fabio; extra == "dev"
-Requires-Dist: h5py>=3; extra == "dev"
-Requires-Dist: lxml; extra == "dev"
 Requires-Dist: werkzeug; extra == "dev"
 Requires-Dist: json-rpc; extra == "dev"
 Requires-Dist: scipy; extra == "dev"
 Requires-Dist: Pillow; extra == "dev"
-Requires-Dist: glymur<0.14; extra == "dev"
 Requires-Dist: resource; extra == "dev"
-Requires-Dist: tifffile; extra == "dev"
 Requires-Dist: hdf5plugin; extra == "dev"
 Requires-Dist: pyicat_plus; extra == "dev"
 Requires-Dist: ewoksnotify[full]; extra == "dev"
-Requires-Dist: pyicat_plus; extra == "dev"
 Requires-Dist: nabu[full]>=2023.3.1dev; extra == "dev"
 Requires-Dist: pycuda<2024.1.1; extra == "dev"
 Requires-Dist: scikit-cuda; extra == "dev"
@@ -184,22 +153,17 @@ Provides-Extra: dev-no-cuda
 Requires-Dist: orange-canvas-core; extra == "dev-no-cuda"
 Requires-Dist: orange-widget-base; extra == "dev-no-cuda"
 Requires-Dist: ewoks[orange]>=0.1.1; extra == "dev-no-cuda"
-Requires-Dist: ewoksorange>=0.7.0rc0; extra == "dev-no-cuda"
+Requires-Dist: ewoksorange==1.1; extra == "dev-no-cuda"
 Requires-Dist: rsyncmanager; extra == "dev-no-cuda"
 Requires-Dist: fabio; extra == "dev-no-cuda"
-Requires-Dist: h5py>=3; extra == "dev-no-cuda"
-Requires-Dist: lxml; extra == "dev-no-cuda"
 Requires-Dist: werkzeug; extra == "dev-no-cuda"
 Requires-Dist: json-rpc; extra == "dev-no-cuda"
 Requires-Dist: scipy; extra == "dev-no-cuda"
 Requires-Dist: Pillow; extra == "dev-no-cuda"
-Requires-Dist: glymur<0.14; extra == "dev-no-cuda"
 Requires-Dist: resource; extra == "dev-no-cuda"
-Requires-Dist: tifffile; extra == "dev-no-cuda"
 Requires-Dist: hdf5plugin; extra == "dev-no-cuda"
 Requires-Dist: pyicat_plus; extra == "dev-no-cuda"
 Requires-Dist: ewoksnotify[full]; extra == "dev-no-cuda"
-Requires-Dist: pyicat_plus; extra == "dev-no-cuda"
 Requires-Dist: nabu>=2023.3.1dev; extra == "dev-no-cuda"
 Requires-Dist: black; extra == "dev-no-cuda"
 Requires-Dist: flake8; extra == "dev-no-cuda"
@@ -209,22 +173,17 @@ Provides-Extra: test
 Requires-Dist: orange-canvas-core; extra == "test"
 Requires-Dist: orange-widget-base; extra == "test"
 Requires-Dist: ewoks[orange]>=0.1.1; extra == "test"
-Requires-Dist: ewoksorange>=0.7.0rc0; extra == "test"
+Requires-Dist: ewoksorange==1.1; extra == "test"
 Requires-Dist: rsyncmanager; extra == "test"
 Requires-Dist: fabio; extra == "test"
-Requires-Dist: h5py>=3; extra == "test"
-Requires-Dist: lxml; extra == "test"
 Requires-Dist: werkzeug; extra == "test"
 Requires-Dist: json-rpc; extra == "test"
 Requires-Dist: scipy; extra == "test"
 Requires-Dist: Pillow; extra == "test"
-Requires-Dist: glymur<0.14; extra == "test"
 Requires-Dist: resource; extra == "test"
-Requires-Dist: tifffile; extra == "test"
 Requires-Dist: hdf5plugin; extra == "test"
 Requires-Dist: pyicat_plus; extra == "test"
 Requires-Dist: ewoksnotify[full]; extra == "test"
-Requires-Dist: pyicat_plus; extra == "test"
 Requires-Dist: nabu>=2023.3.1dev; extra == "test"
 Requires-Dist: pytest-asyncio; extra == "test"
 Requires-Dist: tomoscan[test]>=2.2.0a6; extra == "test"

{tomwer-1.5.1 → tomwer-1.5.2}/setup.cfg

@@ -34,12 +34,11 @@ install_requires =
 	setuptools
 	psutil
 	silx[full] >=2.1.1
-	tomoscan>=2.2.0a6
+	tomoscan[full_no_compression_plugins]>=2.2.0a6
 	nxtomo>=2.0.0dev2
 	nxtomomill>=1.2.0dev1
 	processview>=1.5.0
 	ewoks>=0.1.1
-	ewokscore<1.1.0
 	sluurp>=0.4.1
 	packaging
 	pint
@@ -99,22 +98,17 @@ full_base =
 	orange-canvas-core
 	orange-widget-base
 	ewoks[orange]>=0.1.1
-	ewoksorange >= 0.7.0rc0
+	ewoksorange == 1.1
 	rsyncmanager
 	fabio
-	h5py>=3
-	lxml
 	werkzeug
 	json-rpc
 	scipy
 	Pillow
-	glymur<0.14  # for python3.9 until https://github.com/quintusdias/glymur/issues/688 is fixed
 	resource
-	tifffile
 	hdf5plugin
 	pyicat_plus
 	ewoksnotify[full]
-	pyicat_plus
 full_no_nabu = 
 	%(full_base)s
 full_no_cuda = 

tomwer-1.5.2/src/orangecontrib/tomwer/tutorials/untitled.ows

@@ -0,0 +1,15 @@
+<?xml version='1.0' encoding='utf-8'?>
+<scheme version="2.0" title="" description="">
+	<nodes>
+		<node id="0" name="nabu slice reconstruction" qualified_name="orangecontrib.tomwer.widgets.reconstruction.NabuOW.NabuOW" project_name="tomwer" version="" title="nabu slice reconstruction" position="(234.0, 102.0)" />
+	</nodes>
+	<links />
+	<annotations />
+	<thumbnail />
+	<node_properties>
+		<properties node_id="0" format="literal">{'_ewoks_default_inputs': {'data': None, 'nabu_params': {'preproc': {'flatfield': 1, 'double_flatfield': 0, 'dff_sigma': 0.0, 'ccd_filter_enabled': 0, 'ccd_filter_threshold': 0.04, 'take_logarithm': True, 'log_min_clip': 1e-06, 'log_max_clip': 10.0, 'sino_rings_correction': 'None', 'sino_rings_options': 'sigma=1.0 ; levels=10 ; padding=False', 'tilt_correction': '', 'autotilt_options': '', 'normalize_srcurrent': 1, 'rotate_projections_center': '', 'flat_distortion_correction_enabled': True, 'flat_distortion_params': "tile_size=100; interpolation_kind='linear'; padding_mode='edge'; correction_spike_threshold=None", 'detector_distortion_correction': False, 'detector_distortion_correction_options': {'map_x': '', 'map_z': ''}}, 'reconstruction': {'method': 'FBP', 'slice_plane': 'XY', 'angles_file': '', 'axis_correction_file': '', 'angle_offset': 0.0, 'fbp_filter_type': 'ramlak', 'padding_type': 'edges', 'iterations': 200, 'optim_algorithm': 'chambolle-pock', 'weight_tv': 0.01, 'preconditioning_filter': 1, 'positivity_constraint': 1, 'rotation_axis_position': '', 'translation_movements_file': '', 'clip_outer_circle': 1, 'centered_axis': 1, 'start_x': 0, 'end_x': -1, 'start_y': 0, 'end_y': -1, 'start_z': 0, 'end_z': -1, 'enable_halftomo': 0}, 'dataset': {'binning': 1, 'binning_z': 1, 'projections_subsampling': 1, 'exclude_projections': ''}, 'tomwer_slices': 'middle', 'output': {'file_format': 'hdf5', 'location': '', 'output_dir_mode': 'same folder as scan'}, 'phase': {'method': 'None', 'unsharp_coeff': 0, 'unsharp_sigma': 0, 'ctf_geometry': ' z1_v=None; z1_h=None; detec_pixel_size=None; magnification=True', 'beam_shape': 'parallel', 'ctf_advanced_params': ' length_scale=1e-05; lim1=1e-05; lim2=0.2; normalize_by_mean=True'}, 'gpu_mem_fraction': 0.9, 'cpu_mem_fraction': 0.9, 'configuration_level': 'advanced', 'mode_locked': False, 'cluster_config': None}}, 'controlAreaVisible': True, 'savedWidgetGeometry': b'\x01\xd9\xd0\xcb\x00\x03\x00\x00\x00\x00\t\xb8\x00\x00\x00\xdb\x00\x00\x0c\xb4\x00\x00\x03!\x00\x00\t\xb8\x00\x00\x00\xdb\x00\x00\x0c\xb4\x00\x00\x03!\x00\x00\x00\x01\x00\x00\x00\x00\x07\x80\x00\x00\t\xb8\x00\x00\x00\xdb\x00\x00\x0c\xb4\x00\x00\x03!', '__version__': 1}</properties>
+	</node_properties>
+	<session_state>
+		<window_groups />
+	</session_state>
+</scheme>

{tomwer-1.5.1 → tomwer-1.5.2}/src/orangecontrib/tomwer/widgets/cluster/FutureSupervisorOW.py

@@ -206,6 +206,8 @@ class FutureTomwerObjectObserverWidget(
             return
         elif future_tomo_obj.status == "error":
             state = DatasetState.FAILED
+            if future_tomo_obj.job_id is None:
+                details = "Job submission to Slurm has failed. This is likely due to an invalid configuration request, such as requesting a GPU on a partition that does not support GPUs. Please review your configuration and try again."
         elif future_tomo_obj.status == "pending":
             details = "\n".join([details, "pending"])
             state = DatasetState.PENDING

{tomwer-1.5.1 → tomwer-1.5.2}/src/tomwer/app/canvas_launcher/config.py

@@ -9,7 +9,11 @@ import logging
 import tomwer.version
 from tomwer.gui import icons
 
-from ewoksorange.pkg_meta import iter_entry_points
+try:
+    from ewoksorange.pkg_meta import entry_points
+except ImportError:
+    # ewoksorange < 2.0
+    from ewoksorange.pkg_meta import iter_entry_points as entry_points
 from . import environ
 from .splash import getIcon, splash_screen
 from .widgetsscheme import WidgetsScheme
@@ -82,7 +86,7 @@ class TomwerConfig(config.Config):
             return entry.name.lower() not in ("ewoks demo",)
 
         try:
-            all_eps = filter(accept_extension, iter_entry_points(group=WIDGETS_ENTRY))
+            all_eps = filter(accept_extension, entry_points(group=WIDGETS_ENTRY))
         except Exception as e:
             _logger.error(f"fail to find add-ons. Error is {e}")
         return iter(all_eps)

{tomwer-1.5.1 → tomwer-1.5.2}/src/tomwer/core/process/reconstruction/nabu/utils.py

@@ -342,6 +342,7 @@ class _NabuPhaseMethod(Enum):
     PAGANIN = "Paganin"
     CTF = "CTF"
     NONE = "None"
+    CONE = "cone"
 
     @classmethod
     def from_value(cls, value):

{tomwer-1.5.1 → tomwer-1.5.2}/src/tomwer/gui/reconstruction/nabu/nabuconfig/ctf.py

@@ -9,8 +9,6 @@ from tomwer.gui.reconstruction.nabu.nabuconfig import base
 from tomwer.gui.utils.illustrations import _IllustrationWidget
 from tomwer.gui.utils.scrollarea import QComboBoxIgnoreWheel
 
-from .reconstruction import AnglesFileWidget as Filewidget
-
 
 def nabu_param_ligne_to_dict(str_ligne: str) -> dict:
     ddict = {}
@@ -324,10 +322,6 @@ class CTFConfig(qt.QGroupBox, base._NabuStageConfigBase):
         self._geometryWidget = CTFGeometry(parent=self, title="geometry")
         self.layout().addRow(self._geometryWidget)
         self.registerWidget(self._geometryWidget, "optional")
-        # translation file
-        self._translationFile = Filewidget(self)
-        self.layout().addRow("translation file", self._translationFile)
-        self.registerWidget(self._translationFile, "optional")
         # advanced parameters
         self._advancedParamsWidget = CTFAdvancedParams(
             parent=self, title="advanced parameters"
@@ -338,7 +332,6 @@ class CTFConfig(qt.QGroupBox, base._NabuStageConfigBase):
         # connect signal / slot
         self._geometryWidget.sigConfChanged.connect(self._confChanged)
         self._advancedParamsWidget.sigConfChanged.connect(self._confChanged)
-        self._translationFile._qle.textEdited.connect(self._confChanged)
 
     def _confChanged(self, *args, **kwargs):
         self.sigConfChanged.emit("phase")
@@ -346,11 +339,8 @@ class CTFConfig(qt.QGroupBox, base._NabuStageConfigBase):
     def getConfiguration(self) -> dict:
         ddict = self._geometryWidget.getConfiguration()
         ddict.update(self._advancedParamsWidget.getConfiguration())
-        ddict["ctf_translations_file"] = self._translationFile.getFile()
         return ddict
 
     def setConfiguration(self, ddict):
         self._geometryWidget.setConfiguration(ddict=ddict)
         self._advancedParamsWidget.setConfiguration(ddict=ddict)
-        if "ctf_translations_file" in ddict:
-            self._translationFile.setFile(ddict["ctf_translations_file"])

tomwer-1.5.2/src/tomwer/gui/reconstruction/nabu/nabuconfig/tests/test_NabuConfiguration.py

@@ -0,0 +1,42 @@
+from __future__ import annotations
+
+from tomwer.tests.conftest import qtapp  # noqa F401
+from tomwer.gui.reconstruction.nabu.nabuconfig.nabuconfig import (
+    NabuConfiguration,
+)
+from nabu.pipeline.config import _extract_nabuconfig_keyvals
+from nabu.pipeline.fullfield.nabu_config import (
+    nabu_config as nabu_fullfield_default_config,
+)
+
+
+def test_NabuConfiguration(
+    qtapp,  # noqa F811
+):
+    """Test that the 'NabuConfiguration' produce only keys understandable by nabu"""
+    widget = NabuConfiguration(parent=None)
+
+    tomwer_config = widget.getConfiguration()
+    nabu_config = _extract_nabuconfig_keyvals(nabu_fullfield_default_config)
+
+    tomwer_section_keys = set(tomwer_config.keys())
+    nabu_section_keys = set(nabu_config.keys())
+    tomwer_section_keys.remove("tomwer_slices")
+    assert tomwer_section_keys.issubset(
+        nabu_section_keys
+    ), f"tomwer provide sections undefined by nabu: {tomwer_section_keys - nabu_section_keys}"
+
+    for section_key in nabu_config.keys():
+        if section_key in tomwer_config:
+            nabu_sub_section_keys = set(nabu_config[section_key].keys())
+            tomwer_sub_section_keys = set(tomwer_config[section_key].keys())
+            if section_key == "phase":
+                # this key is pop by tomwer before calling nabu. It is used internally only
+                tomwer_sub_section_keys.remove("beam_shape")
+            elif section_key == "reconstruction":
+                tomwer_sub_section_keys.remove("slice_plane")
+            elif section_key == "output":
+                tomwer_sub_section_keys.remove("output_dir_mode")
+            assert tomwer_sub_section_keys.issubset(
+                nabu_sub_section_keys
+            ), f"tomwer provides keys undefined by nabu: {tomwer_sub_section_keys - nabu_sub_section_keys}"

{tomwer-1.5.1 → tomwer-1.5.2}/src/tomwer/gui/reconstruction/nabu/test/test_ctf.py

@@ -29,12 +29,10 @@ class TestFutureSupervisorOW(TestCaseQt):
         assert config == {
             "ctf_geometry": " z1_v=None; z1_h=None; detec_pixel_size=None; magnification=True",
             "ctf_advanced_params": " length_scale=1e-05; lim1=1e-05; lim2=0.2; normalize_by_mean=True",
-            "ctf_translations_file": "",
             "beam_shape": "parallel",
         }
 
         config["beam_shape"] = "cone"
-        config["ctf_translations_file"] = "my_file.txt"
         config["ctf_geometry"] = (
             " z1_v=10.2; z1_h=3.6; detec_pixel_size=1e-05; magnification=False"
         )

{tomwer-1.5.1 → tomwer-1.5.2}/src/tomwer/gui/reconstruction/tests/test_nabu.py

@@ -150,7 +150,6 @@ class TestNabuPhaseConfig(TestCaseQt):
             "beam_shape": "parallel",
             "ctf_advanced_params": " length_scale=1e-05; lim1=1e-05; lim2=0.2; normalize_by_mean=True",
             "ctf_geometry": " z1_v=None; z1_h=None; detec_pixel_size=None; magnification=True",
-            "ctf_translations_file": "",
         }
         self.assertEqual(self.nabuWidget.getConfiguration(), ini_conf)
 
@@ -165,7 +164,6 @@ class TestNabuPhaseConfig(TestCaseQt):
             "beam_shape": "cone",
             "ctf_advanced_params": " length_scale=1e-05; lim1=1e-05; lim2=0.2; normalize_by_mean=True",
             "ctf_geometry": " z1_v=0.0; z1_h=0.0; detec_pixel_size=None; magnification=True",
-            "ctf_translations_file": "",
         }
         self.nabuWidget.setConfiguration(conf)
         self.nabuWidget.show()

{tomwer-1.5.1 → tomwer-1.5.2}/src/tomwer/version.py

@@ -77,7 +77,7 @@ RELEASE_LEVEL_VALUE = {
 
 MAJOR = 1
 MINOR = 5
-MICRO = 1
+MICRO = 2
 RELEV = "final"  # <16
 SERIAL = 0  # <16
 

{tomwer-1.5.1 → tomwer-1.5.2}/src/tomwer.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: tomwer
-Version: 1.5.1
+Version: 1.5.2
 Summary: "tomography workflow tools"
 Home-page: https://gitlab.esrf.fr/tomotools/tomwer
 Author: Henri Payno, Pierre Paleo, Pierre-Olivier Autran, Jérôme Lesaint, Alessandro Mirone
@@ -25,12 +25,11 @@ Requires-Dist: numpy
 Requires-Dist: setuptools
 Requires-Dist: psutil
 Requires-Dist: silx[full]>=2.1.1
-Requires-Dist: tomoscan>=2.2.0a6
+Requires-Dist: tomoscan[full_no_compression_plugins]>=2.2.0a6
 Requires-Dist: nxtomo>=2.0.0dev2
 Requires-Dist: nxtomomill>=1.2.0dev1
 Requires-Dist: processview>=1.5.0
 Requires-Dist: ewoks>=0.1.1
-Requires-Dist: ewokscore<1.1.0
 Requires-Dist: sluurp>=0.4.1
 Requires-Dist: packaging
 Requires-Dist: pint
@@ -39,83 +38,63 @@ Provides-Extra: full-base
 Requires-Dist: orange-canvas-core; extra == "full-base"
 Requires-Dist: orange-widget-base; extra == "full-base"
 Requires-Dist: ewoks[orange]>=0.1.1; extra == "full-base"
-Requires-Dist: ewoksorange>=0.7.0rc0; extra == "full-base"
+Requires-Dist: ewoksorange==1.1; extra == "full-base"
 Requires-Dist: rsyncmanager; extra == "full-base"
 Requires-Dist: fabio; extra == "full-base"
-Requires-Dist: h5py>=3; extra == "full-base"
-Requires-Dist: lxml; extra == "full-base"
 Requires-Dist: werkzeug; extra == "full-base"
 Requires-Dist: json-rpc; extra == "full-base"
 Requires-Dist: scipy; extra == "full-base"
 Requires-Dist: Pillow; extra == "full-base"
-Requires-Dist: glymur<0.14; extra == "full-base"
 Requires-Dist: resource; extra == "full-base"
-Requires-Dist: tifffile; extra == "full-base"
 Requires-Dist: hdf5plugin; extra == "full-base"
 Requires-Dist: pyicat_plus; extra == "full-base"
 Requires-Dist: ewoksnotify[full]; extra == "full-base"
-Requires-Dist: pyicat_plus; extra == "full-base"
 Provides-Extra: full-no-nabu
 Requires-Dist: orange-canvas-core; extra == "full-no-nabu"
 Requires-Dist: orange-widget-base; extra == "full-no-nabu"
 Requires-Dist: ewoks[orange]>=0.1.1; extra == "full-no-nabu"
-Requires-Dist: ewoksorange>=0.7.0rc0; extra == "full-no-nabu"
+Requires-Dist: ewoksorange==1.1; extra == "full-no-nabu"
 Requires-Dist: rsyncmanager; extra == "full-no-nabu"
 Requires-Dist: fabio; extra == "full-no-nabu"
-Requires-Dist: h5py>=3; extra == "full-no-nabu"
-Requires-Dist: lxml; extra == "full-no-nabu"
 Requires-Dist: werkzeug; extra == "full-no-nabu"
 Requires-Dist: json-rpc; extra == "full-no-nabu"
 Requires-Dist: scipy; extra == "full-no-nabu"
 Requires-Dist: Pillow; extra == "full-no-nabu"
-Requires-Dist: glymur<0.14; extra == "full-no-nabu"
 Requires-Dist: resource; extra == "full-no-nabu"
-Requires-Dist: tifffile; extra == "full-no-nabu"
 Requires-Dist: hdf5plugin; extra == "full-no-nabu"
 Requires-Dist: pyicat_plus; extra == "full-no-nabu"
 Requires-Dist: ewoksnotify[full]; extra == "full-no-nabu"
-Requires-Dist: pyicat_plus; extra == "full-no-nabu"
 Provides-Extra: full-no-cuda
 Requires-Dist: orange-canvas-core; extra == "full-no-cuda"
 Requires-Dist: orange-widget-base; extra == "full-no-cuda"
 Requires-Dist: ewoks[orange]>=0.1.1; extra == "full-no-cuda"
-Requires-Dist: ewoksorange>=0.7.0rc0; extra == "full-no-cuda"
+Requires-Dist: ewoksorange==1.1; extra == "full-no-cuda"
 Requires-Dist: rsyncmanager; extra == "full-no-cuda"
 Requires-Dist: fabio; extra == "full-no-cuda"
-Requires-Dist: h5py>=3; extra == "full-no-cuda"
-Requires-Dist: lxml; extra == "full-no-cuda"
 Requires-Dist: werkzeug; extra == "full-no-cuda"
 Requires-Dist: json-rpc; extra == "full-no-cuda"
 Requires-Dist: scipy; extra == "full-no-cuda"
 Requires-Dist: Pillow; extra == "full-no-cuda"
-Requires-Dist: glymur<0.14; extra == "full-no-cuda"
 Requires-Dist: resource; extra == "full-no-cuda"
-Requires-Dist: tifffile; extra == "full-no-cuda"
 Requires-Dist: hdf5plugin; extra == "full-no-cuda"
 Requires-Dist: pyicat_plus; extra == "full-no-cuda"
 Requires-Dist: ewoksnotify[full]; extra == "full-no-cuda"
-Requires-Dist: pyicat_plus; extra == "full-no-cuda"
 Requires-Dist: nabu>=2023.3.1dev; extra == "full-no-cuda"
 Provides-Extra: full
 Requires-Dist: orange-canvas-core; extra == "full"
 Requires-Dist: orange-widget-base; extra == "full"
 Requires-Dist: ewoks[orange]>=0.1.1; extra == "full"
-Requires-Dist: ewoksorange>=0.7.0rc0; extra == "full"
+Requires-Dist: ewoksorange==1.1; extra == "full"
 Requires-Dist: rsyncmanager; extra == "full"
 Requires-Dist: fabio; extra == "full"
-Requires-Dist: h5py>=3; extra == "full"
-Requires-Dist: lxml; extra == "full"
 Requires-Dist: werkzeug; extra == "full"
 Requires-Dist: json-rpc; extra == "full"
 Requires-Dist: scipy; extra == "full"
 Requires-Dist: Pillow; extra == "full"
-Requires-Dist: glymur<0.14; extra == "full"
 Requires-Dist: resource; extra == "full"
-Requires-Dist: tifffile; extra == "full"
 Requires-Dist: hdf5plugin; extra == "full"
 Requires-Dist: pyicat_plus; extra == "full"
 Requires-Dist: ewoksnotify[full]; extra == "full"
-Requires-Dist: pyicat_plus; extra == "full"
 Requires-Dist: nabu[full]>=2023.3.1dev; extra == "full"
 Requires-Dist: pycuda<2024.1.1; extra == "full"
 Requires-Dist: scikit-cuda; extra == "full"
@@ -123,22 +102,17 @@ Provides-Extra: doc
 Requires-Dist: orange-canvas-core; extra == "doc"
 Requires-Dist: orange-widget-base; extra == "doc"
 Requires-Dist: ewoks[orange]>=0.1.1; extra == "doc"
-Requires-Dist: ewoksorange>=0.7.0rc0; extra == "doc"
+Requires-Dist: ewoksorange==1.1; extra == "doc"
 Requires-Dist: rsyncmanager; extra == "doc"
 Requires-Dist: fabio; extra == "doc"
-Requires-Dist: h5py>=3; extra == "doc"
-Requires-Dist: lxml; extra == "doc"
 Requires-Dist: werkzeug; extra == "doc"
 Requires-Dist: json-rpc; extra == "doc"
 Requires-Dist: scipy; extra == "doc"
 Requires-Dist: Pillow; extra == "doc"
-Requires-Dist: glymur<0.14; extra == "doc"
 Requires-Dist: resource; extra == "doc"
-Requires-Dist: tifffile; extra == "doc"
 Requires-Dist: hdf5plugin; extra == "doc"
 Requires-Dist: pyicat_plus; extra == "doc"
 Requires-Dist: ewoksnotify[full]; extra == "doc"
-Requires-Dist: pyicat_plus; extra == "doc"
 Requires-Dist: nabu>=2023.3.1dev; extra == "doc"
 Requires-Dist: Sphinx>=4.0.0; extra == "doc"
 Requires-Dist: nbsphinx; extra == "doc"
@@ -157,22 +131,17 @@ Provides-Extra: dev
 Requires-Dist: orange-canvas-core; extra == "dev"
 Requires-Dist: orange-widget-base; extra == "dev"
 Requires-Dist: ewoks[orange]>=0.1.1; extra == "dev"
-Requires-Dist: ewoksorange>=0.7.0rc0; extra == "dev"
+Requires-Dist: ewoksorange==1.1; extra == "dev"
 Requires-Dist: rsyncmanager; extra == "dev"
 Requires-Dist: fabio; extra == "dev"
-Requires-Dist: h5py>=3; extra == "dev"
-Requires-Dist: lxml; extra == "dev"
 Requires-Dist: werkzeug; extra == "dev"
 Requires-Dist: json-rpc; extra == "dev"
 Requires-Dist: scipy; extra == "dev"
 Requires-Dist: Pillow; extra == "dev"
-Requires-Dist: glymur<0.14; extra == "dev"
 Requires-Dist: resource; extra == "dev"
-Requires-Dist: tifffile; extra == "dev"
 Requires-Dist: hdf5plugin; extra == "dev"
 Requires-Dist: pyicat_plus; extra == "dev"
 Requires-Dist: ewoksnotify[full]; extra == "dev"
-Requires-Dist: pyicat_plus; extra == "dev"
 Requires-Dist: nabu[full]>=2023.3.1dev; extra == "dev"
 Requires-Dist: pycuda<2024.1.1; extra == "dev"
 Requires-Dist: scikit-cuda; extra == "dev"
@@ -184,22 +153,17 @@ Provides-Extra: dev-no-cuda
 Requires-Dist: orange-canvas-core; extra == "dev-no-cuda"
 Requires-Dist: orange-widget-base; extra == "dev-no-cuda"
 Requires-Dist: ewoks[orange]>=0.1.1; extra == "dev-no-cuda"
-Requires-Dist: ewoksorange>=0.7.0rc0; extra == "dev-no-cuda"
+Requires-Dist: ewoksorange==1.1; extra == "dev-no-cuda"
 Requires-Dist: rsyncmanager; extra == "dev-no-cuda"
 Requires-Dist: fabio; extra == "dev-no-cuda"
-Requires-Dist: h5py>=3; extra == "dev-no-cuda"
-Requires-Dist: lxml; extra == "dev-no-cuda"
 Requires-Dist: werkzeug; extra == "dev-no-cuda"
 Requires-Dist: json-rpc; extra == "dev-no-cuda"
 Requires-Dist: scipy; extra == "dev-no-cuda"
 Requires-Dist: Pillow; extra == "dev-no-cuda"
-Requires-Dist: glymur<0.14; extra == "dev-no-cuda"
 Requires-Dist: resource; extra == "dev-no-cuda"
-Requires-Dist: tifffile; extra == "dev-no-cuda"
 Requires-Dist: hdf5plugin; extra == "dev-no-cuda"
 Requires-Dist: pyicat_plus; extra == "dev-no-cuda"
 Requires-Dist: ewoksnotify[full]; extra == "dev-no-cuda"
-Requires-Dist: pyicat_plus; extra == "dev-no-cuda"
 Requires-Dist: nabu>=2023.3.1dev; extra == "dev-no-cuda"
 Requires-Dist: black; extra == "dev-no-cuda"
 Requires-Dist: flake8; extra == "dev-no-cuda"
@@ -209,22 +173,17 @@ Provides-Extra: test
 Requires-Dist: orange-canvas-core; extra == "test"
 Requires-Dist: orange-widget-base; extra == "test"
 Requires-Dist: ewoks[orange]>=0.1.1; extra == "test"
-Requires-Dist: ewoksorange>=0.7.0rc0; extra == "test"
+Requires-Dist: ewoksorange==1.1; extra == "test"
 Requires-Dist: rsyncmanager; extra == "test"
 Requires-Dist: fabio; extra == "test"
-Requires-Dist: h5py>=3; extra == "test"
-Requires-Dist: lxml; extra == "test"
 Requires-Dist: werkzeug; extra == "test"
 Requires-Dist: json-rpc; extra == "test"
 Requires-Dist: scipy; extra == "test"
 Requires-Dist: Pillow; extra == "test"
-Requires-Dist: glymur<0.14; extra == "test"
 Requires-Dist: resource; extra == "test"
-Requires-Dist: tifffile; extra == "test"
 Requires-Dist: hdf5plugin; extra == "test"
 Requires-Dist: pyicat_plus; extra == "test"
 Requires-Dist: ewoksnotify[full]; extra == "test"
-Requires-Dist: pyicat_plus; extra == "test"
 Requires-Dist: nabu>=2023.3.1dev; extra == "test"
 Requires-Dist: pytest-asyncio; extra == "test"
 Requires-Dist: tomoscan[test]>=2.2.0a6; extra == "test"