tomwer 1.3.16__tar.gz → 1.4.6__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- tomwer-1.4.6/LICENSE +29 -0
- tomwer-1.4.6/PKG-INFO +336 -0
- tomwer-1.4.6/README.rst +103 -0
- tomwer-1.4.6/pyproject.toml +10 -0
- tomwer-1.4.6/setup.cfg +174 -0
- tomwer-1.4.6/setup.py +4 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/__init__.py +10 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/orange/managedprocess.py +93 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/orange/settings.py +26 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/tests/TestAcquisition.py +220 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/tutorials/append_raw_darks_and_flats_frames_to_NXtomos.ows +44 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/tutorials/copy_reduced_darks_and_flats_meth1.ows +55 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/tutorials/drac_publication.ows +44 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/tutorials/id16b/ID16b_full_volume.ows +22 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/tutorials/id16b/ID16b_insitu.ows +302 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/tutorials/id16b/ID16b_normalization.ows +218 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/tutorials/simple_volume_to_slurm_reconstruction.ows +64 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/tutorials/test_cor.ows +19 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/tutorials/volume_casting_on_slurm.ows +54 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/widgets/__init__.py +41 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/widgets/cluster/FutureSupervisorOW.py +224 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/widgets/cluster/SlurmClusterOW.py +71 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/widgets/cluster/__init__.py +19 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/widgets/control/AdvancementOW.py +37 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/widgets/control/DataDiscoveryOW.py +231 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/widgets/control/DataListenerOW.py +381 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/widgets/control/DataSelectorOW.py +126 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/widgets/control/DataTransfertOW.py +196 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/widgets/control/DataValidatorOW.py +167 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/widgets/control/DataWatcherOW.py +178 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/widgets/control/EDF2NXTomomillOW.py +249 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/widgets/control/EmailOW.py +92 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/widgets/control/FilterOW.py +101 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/widgets/control/NXTomomillOW.py +337 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/widgets/control/NXtomoConcatenate.py +202 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/widgets/control/NotifierOW.py +108 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/widgets/control/ReduceDarkFlatSelectorOW.py +94 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/widgets/control/SingleTomoObjOW.py +142 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/widgets/control/TimerOW.py +110 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/widgets/control/TomoObjSeriesOW.py +58 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/widgets/control/VolumeSelector.py +120 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/widgets/control/__init__.py +18 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/widgets/control/icons/nxtomomill.svg +222 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/widgets/control/icons/reduced_darkflat_selector.png +344 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/widgets/control/icons/reduced_darkflat_selector.svg +59 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/widgets/control/icons/tomoobjseries.svg +138 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/widgets/dataportal/PublishProcessedDataOW.py +172 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/widgets/dataportal/__init__.py +18 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/widgets/debugtools/DatasetGeneratorOW.py +149 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/widgets/debugtools/ObjectInspectorOW.py +37 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/widgets/debugtools/__init__.py +17 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/widgets/edit/DarkFlatPatchOW.py +157 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/widgets/edit/ImageKeyEditorOW.py +106 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/widgets/edit/ImageKeyUpgraderOW.py +109 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/widgets/edit/NXtomoEditorOW.py +127 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/widgets/edit/__init__.py +17 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/widgets/other/PythonScriptOW.py +827 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/widgets/other/__init__.py +17 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/widgets/reconstruction/AxisOW.py +530 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/widgets/reconstruction/CastNabuVolumeOW.py +203 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/widgets/reconstruction/DarkRefAndCopyOW.py +243 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/widgets/reconstruction/NabuHelicalPrepareWeightsDoubleOW.py +186 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/widgets/reconstruction/NabuOW.py +272 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/widgets/reconstruction/NabuVolumeOW.py +456 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/widgets/reconstruction/SAAxisOW.py +471 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/widgets/reconstruction/SADeltaBetaOW.py +386 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/widgets/reconstruction/SinoNormOW.py +262 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/widgets/reconstruction/__init__.py +19 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/widgets/stitching/ZStitchingConfigOW.py +118 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/widgets/stitching/__init__.py +17 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/widgets/utils.py +34 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/widgets/visualization/DataViewerOW.py +121 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/widgets/visualization/DiffViewerOW.py +53 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/widgets/visualization/NXtomoMetadataViewerOW.py +69 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/widgets/visualization/RadioStackOW.py +70 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/widgets/visualization/SampleMovedOW.py +89 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/widgets/visualization/SinogramViewerOW.py +65 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/widgets/visualization/SliceStackOW.py +85 -0
- tomwer-1.4.6/src/orangecontrib/tomwer/widgets/visualization/__init__.py +19 -0
- tomwer-1.4.6/src/tomwer/__init__.py +19 -0
- tomwer-1.4.6/src/tomwer/__main__.py +259 -0
- tomwer-1.4.6/src/tomwer/app/__init__.py +2 -0
- tomwer-1.4.6/src/tomwer/app/axis.py +196 -0
- tomwer-1.4.6/src/tomwer/app/canvas.py +57 -0
- tomwer-1.4.6/src/tomwer/app/canvas_launcher/config.py +120 -0
- tomwer-1.4.6/src/tomwer/app/canvas_launcher/environ.py +90 -0
- tomwer-1.4.6/src/tomwer/app/canvas_launcher/mainwindow.py +677 -0
- tomwer-1.4.6/src/tomwer/app/canvas_launcher/splash.py +24 -0
- tomwer-1.4.6/src/tomwer/app/canvas_launcher/utils.py +47 -0
- tomwer-1.4.6/src/tomwer/app/canvas_launcher/widgetsscheme.py +89 -0
- tomwer-1.4.6/src/tomwer/app/diffframe.py +107 -0
- tomwer-1.4.6/src/tomwer/app/imagekeyeditor.py +99 -0
- tomwer-1.4.6/src/tomwer/app/imagekeyupgrader.py +110 -0
- tomwer-1.4.6/src/tomwer/app/intensitynormalization.py +195 -0
- tomwer-1.4.6/src/tomwer/app/multicor.py +276 -0
- tomwer-1.4.6/src/tomwer/app/multipag.py +350 -0
- tomwer-1.4.6/src/tomwer/app/nabuapp.py +246 -0
- tomwer-1.4.6/src/tomwer/app/nxtomoeditor.py +111 -0
- tomwer-1.4.6/src/tomwer/app/patchrawdarkflat.py +130 -0
- tomwer-1.4.6/src/tomwer/app/radiostack.py +96 -0
- tomwer-1.4.6/src/tomwer/app/reducedarkflat.py +207 -0
- tomwer-1.4.6/src/tomwer/app/samplemoved.py +94 -0
- tomwer-1.4.6/src/tomwer/app/scanviewer.py +101 -0
- tomwer-1.4.6/src/tomwer/app/sinogramviewer.py +126 -0
- tomwer-1.4.6/src/tomwer/app/slicestack.py +90 -0
- tomwer-1.4.6/src/tomwer/app/stitching/common.py +418 -0
- tomwer-1.4.6/src/tomwer/app/stopdatalistener.py +42 -0
- tomwer-1.4.6/src/tomwer/app/ystitching.py +26 -0
- tomwer-1.4.6/src/tomwer/app/zstitching.py +26 -0
- tomwer-1.4.6/src/tomwer/core/__init__.py +2 -0
- tomwer-1.4.6/src/tomwer/core/cluster/__init__.py +4 -0
- tomwer-1.4.6/src/tomwer/core/cluster/cluster.py +148 -0
- tomwer-1.4.6/src/tomwer/core/futureobject.py +159 -0
- tomwer-1.4.6/src/tomwer/core/log/__init__.py +2 -0
- tomwer-1.4.6/src/tomwer/core/log/processlog.py +78 -0
- tomwer-1.4.6/src/tomwer/core/process/cluster/supervisor.py +61 -0
- tomwer-1.4.6/src/tomwer/core/process/conditions/filters.py +214 -0
- tomwer-1.4.6/src/tomwer/core/process/control/datalistener/datalistener.py +295 -0
- tomwer-1.4.6/src/tomwer/core/process/control/datalistener/rpcserver.py +276 -0
- tomwer-1.4.6/src/tomwer/core/process/control/datawatcher/datawatcher.py +432 -0
- tomwer-1.4.6/src/tomwer/core/process/control/datawatcher/datawatcherobserver.py +648 -0
- tomwer-1.4.6/src/tomwer/core/process/control/datawatcher/datawatcherprocess.py +228 -0
- tomwer-1.4.6/src/tomwer/core/process/control/datawatcher/edfdwprocess.py +174 -0
- tomwer-1.4.6/src/tomwer/core/process/control/datawatcher/hdf5dwprocess.py +58 -0
- tomwer-1.4.6/src/tomwer/core/process/control/datawatcher/status.py +52 -0
- tomwer-1.4.6/src/tomwer/core/process/control/emailnotifier.py +136 -0
- tomwer-1.4.6/src/tomwer/core/process/control/nxtomoconcatenate.py +129 -0
- tomwer-1.4.6/src/tomwer/core/process/control/nxtomomill.py +202 -0
- tomwer-1.4.6/src/tomwer/core/process/control/scanlist.py +24 -0
- tomwer-1.4.6/src/tomwer/core/process/control/scantransfer.py +641 -0
- tomwer-1.4.6/src/tomwer/core/process/control/scanvalidator.py +260 -0
- tomwer-1.4.6/src/tomwer/core/process/control/tests/test_concatenate_nxtomos.py +81 -0
- tomwer-1.4.6/src/tomwer/core/process/control/timer.py +79 -0
- tomwer-1.4.6/src/tomwer/core/process/control/tomoobjseries.py +12 -0
- tomwer-1.4.6/src/tomwer/core/process/drac/binning.py +37 -0
- tomwer-1.4.6/src/tomwer/core/process/drac/dracbase.py +170 -0
- tomwer-1.4.6/src/tomwer/core/process/drac/gallery.py +109 -0
- tomwer-1.4.6/src/tomwer/core/process/drac/output.py +12 -0
- tomwer-1.4.6/src/tomwer/core/process/drac/processeddataset.py +147 -0
- tomwer-1.4.6/src/tomwer/core/process/drac/publish.py +118 -0
- tomwer-1.4.6/src/tomwer/core/process/drac/rawdataset.py +142 -0
- tomwer-1.4.6/src/tomwer/core/process/drac/tests/test_gallery.py +71 -0
- tomwer-1.4.6/src/tomwer/core/process/drac/tests/test_icat_processed_dataset.py +80 -0
- tomwer-1.4.6/src/tomwer/core/process/drac/tests/test_icat_raw_dataset.py +90 -0
- tomwer-1.4.6/src/tomwer/core/process/edit/darkflatpatch.py +121 -0
- tomwer-1.4.6/src/tomwer/core/process/edit/imagekeyeditor.py +238 -0
- tomwer-1.4.6/src/tomwer/core/process/edit/nxtomoeditor.py +307 -0
- tomwer-1.4.6/src/tomwer/core/process/edit/tests/test_darkflatpatch.py +243 -0
- tomwer-1.4.6/src/tomwer/core/process/edit/tests/test_imagekey_editor.py +99 -0
- tomwer-1.4.6/src/tomwer/core/process/output.py +59 -0
- tomwer-1.4.6/src/tomwer/core/process/reconstruction/__init__.py +4 -0
- tomwer-1.4.6/src/tomwer/core/process/reconstruction/axis/anglemode.py +21 -0
- tomwer-1.4.6/src/tomwer/core/process/reconstruction/axis/axis.py +461 -0
- tomwer-1.4.6/src/tomwer/core/process/reconstruction/axis/mode.py +274 -0
- tomwer-1.4.6/src/tomwer/core/process/reconstruction/axis/params.py +798 -0
- tomwer-1.4.6/src/tomwer/core/process/reconstruction/axis/projectiontype.py +10 -0
- tomwer-1.4.6/src/tomwer/core/process/reconstruction/axis/side.py +8 -0
- tomwer-1.4.6/src/tomwer/core/process/reconstruction/darkref/darkrefs.py +476 -0
- tomwer-1.4.6/src/tomwer/core/process/reconstruction/darkref/darkrefscopy.py +361 -0
- tomwer-1.4.6/src/tomwer/core/process/reconstruction/darkref/params.py +273 -0
- tomwer-1.4.6/src/tomwer/core/process/reconstruction/nabu/castvolume.py +239 -0
- tomwer-1.4.6/src/tomwer/core/process/reconstruction/nabu/nabucommon.py +688 -0
- tomwer-1.4.6/src/tomwer/core/process/reconstruction/nabu/nabuscores.py +714 -0
- tomwer-1.4.6/src/tomwer/core/process/reconstruction/nabu/nabuslices.py +887 -0
- tomwer-1.4.6/src/tomwer/core/process/reconstruction/nabu/nabuvolume.py +575 -0
- tomwer-1.4.6/src/tomwer/core/process/reconstruction/nabu/plane.py +19 -0
- tomwer-1.4.6/src/tomwer/core/process/reconstruction/nabu/settings.py +35 -0
- tomwer-1.4.6/src/tomwer/core/process/reconstruction/nabu/target.py +8 -0
- tomwer-1.4.6/src/tomwer/core/process/reconstruction/nabu/test/test_castvolume.py +116 -0
- tomwer-1.4.6/src/tomwer/core/process/reconstruction/nabu/test/test_nabu_utils.py +277 -0
- tomwer-1.4.6/src/tomwer/core/process/reconstruction/nabu/test/test_nabunormalization.py +199 -0
- tomwer-1.4.6/src/tomwer/core/process/reconstruction/nabu/utils.py +516 -0
- tomwer-1.4.6/src/tomwer/core/process/reconstruction/normalization/normalization.py +334 -0
- tomwer-1.4.6/src/tomwer/core/process/reconstruction/normalization/params.py +134 -0
- tomwer-1.4.6/src/tomwer/core/process/reconstruction/output.py +103 -0
- tomwer-1.4.6/src/tomwer/core/process/reconstruction/params_cache.py +36 -0
- tomwer-1.4.6/src/tomwer/core/process/reconstruction/paramsbase.py +183 -0
- tomwer-1.4.6/src/tomwer/core/process/reconstruction/saaxis/params.py +134 -0
- tomwer-1.4.6/src/tomwer/core/process/reconstruction/saaxis/saaxis.py +828 -0
- tomwer-1.4.6/src/tomwer/core/process/reconstruction/sadeltabeta/params.py +78 -0
- tomwer-1.4.6/src/tomwer/core/process/reconstruction/sadeltabeta/sadeltabeta.py +836 -0
- tomwer-1.4.6/src/tomwer/core/process/reconstruction/scores/params.py +184 -0
- tomwer-1.4.6/src/tomwer/core/process/reconstruction/scores/scores.py +198 -0
- tomwer-1.4.6/src/tomwer/core/process/reconstruction/tests/test_axis.py +46 -0
- tomwer-1.4.6/src/tomwer/core/process/reconstruction/tests/test_darkref.py +33 -0
- tomwer-1.4.6/src/tomwer/core/process/reconstruction/tests/test_params_cache.py +37 -0
- tomwer-1.4.6/src/tomwer/core/process/reconstruction/tests/test_saaxis.py +91 -0
- tomwer-1.4.6/src/tomwer/core/process/reconstruction/tests/test_sadeltabeta.py +48 -0
- tomwer-1.4.6/src/tomwer/core/process/reconstruction/tests/test_utils.py +29 -0
- tomwer-1.4.6/src/tomwer/core/process/reconstruction/utils/cor.py +16 -0
- tomwer-1.4.6/src/tomwer/core/process/script/python.py +61 -0
- tomwer-1.4.6/src/tomwer/core/process/script/tests/test_script.py +41 -0
- tomwer-1.4.6/src/tomwer/core/process/stitching/metadataholder.py +186 -0
- tomwer-1.4.6/src/tomwer/core/process/stitching/nabustitcher.py +188 -0
- tomwer-1.4.6/src/tomwer/core/process/stitching/tests/test_metadataholder.py +17 -0
- tomwer-1.4.6/src/tomwer/core/process/task.py +130 -0
- tomwer-1.4.6/src/tomwer/core/process/tests/test_conditions.py +65 -0
- tomwer-1.4.6/src/tomwer/core/process/tests/test_dark_and_flat.py +359 -0
- tomwer-1.4.6/src/tomwer/core/process/tests/test_data_listener.py +88 -0
- tomwer-1.4.6/src/tomwer/core/process/tests/test_data_transfer.py +354 -0
- tomwer-1.4.6/src/tomwer/core/process/tests/test_data_watcher.py +39 -0
- tomwer-1.4.6/src/tomwer/core/process/tests/test_nabu.py +460 -0
- tomwer-1.4.6/src/tomwer/core/process/tests/test_normalization.py +79 -0
- tomwer-1.4.6/src/tomwer/core/process/tests/test_timer.py +51 -0
- tomwer-1.4.6/src/tomwer/core/process/utils.py +85 -0
- tomwer-1.4.6/src/tomwer/core/process/visualization/dataviewer.py +14 -0
- tomwer-1.4.6/src/tomwer/core/process/visualization/diffviewer.py +14 -0
- tomwer-1.4.6/src/tomwer/core/process/visualization/imagestackviewer.py +13 -0
- tomwer-1.4.6/src/tomwer/core/process/visualization/radiostack.py +13 -0
- tomwer-1.4.6/src/tomwer/core/process/visualization/samplemoved.py +12 -0
- tomwer-1.4.6/src/tomwer/core/process/visualization/sinogramviewer.py +12 -0
- tomwer-1.4.6/src/tomwer/core/process/visualization/slicestack.py +12 -0
- tomwer-1.4.6/src/tomwer/core/process/visualization/tests/test_data_viewer.py +12 -0
- tomwer-1.4.6/src/tomwer/core/process/visualization/tests/test_diff_viewer.py +12 -0
- tomwer-1.4.6/src/tomwer/core/process/visualization/tests/test_image_stack_viewer.py +14 -0
- tomwer-1.4.6/src/tomwer/core/process/visualization/tests/test_radio_stack.py +12 -0
- tomwer-1.4.6/src/tomwer/core/process/visualization/tests/test_sample_moved.py +14 -0
- tomwer-1.4.6/src/tomwer/core/process/visualization/tests/test_sinogram_viewer.py +13 -0
- tomwer-1.4.6/src/tomwer/core/process/visualization/tests/test_slice_stack.py +13 -0
- tomwer-1.4.6/src/tomwer/core/process/visualization/tests/test_volume_viewer.py +12 -0
- tomwer-1.4.6/src/tomwer/core/process/visualization/volumeviewer.py +11 -0
- tomwer-1.4.6/src/tomwer/core/resourcemanager.py +33 -0
- tomwer-1.4.6/src/tomwer/core/scan/__init__.py +6 -0
- tomwer-1.4.6/src/tomwer/core/scan/blissscan.py +233 -0
- tomwer-1.4.6/src/tomwer/core/scan/edfscan.py +582 -0
- tomwer-1.4.6/src/tomwer/core/scan/hdf5scan.py +26 -0
- tomwer-1.4.6/src/tomwer/core/scan/nxtomoscan.py +516 -0
- tomwer-1.4.6/src/tomwer/core/scan/scanbase.py +706 -0
- tomwer-1.4.6/src/tomwer/core/scan/scanfactory.py +226 -0
- tomwer-1.4.6/src/tomwer/core/scan/tests/test_edf.py +25 -0
- tomwer-1.4.6/src/tomwer/core/scan/tests/test_future_scan.py +35 -0
- tomwer-1.4.6/src/tomwer/core/scan/tests/test_nxtomoscan.py +143 -0
- tomwer-1.4.6/src/tomwer/core/settings.py +171 -0
- tomwer-1.4.6/src/tomwer/core/tests/test_scanutils.py +26 -0
- tomwer-1.4.6/src/tomwer/core/tests/test_utils.py +272 -0
- tomwer-1.4.6/src/tomwer/core/tomwer_object.py +55 -0
- tomwer-1.4.6/src/tomwer/core/utils/__init__.py +2 -0
- tomwer-1.4.6/src/tomwer/core/utils/char.py +17 -0
- tomwer-1.4.6/src/tomwer/core/utils/deprecation.py +109 -0
- tomwer-1.4.6/src/tomwer/core/utils/dictutils.py +12 -0
- tomwer-1.4.6/src/tomwer/core/utils/ftseriesutils.py +44 -0
- tomwer-1.4.6/src/tomwer/core/utils/gpu.py +18 -0
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tomwer-1.4.6/LICENSE
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The Tomwer library goal is to provide some useful process for acquisition/reconstruction automation.
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Tomwer is distributed under the MIT license.
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Tomwer is using the Qt library. A word of caution is to be provided. If users develop and distribute software using modules accessing Qt by means of Riverbank Computing Qt bindings PyQt4 or PyQt5, those users will be conditioned by the license of their PyQt4/5 software (GPL or commercial). If the end user does not own a commercial license of PyQt4 or PyQt5 and wishes to be free of any distribution condition, (s)he should be able to use PySide because it uses the LGPL license.
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It can also be used as an Orange3 add-on. If you wan't to distribute Orange you must stick to there license (GNU [GPL-3.0]+ license)
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The MIT license follows:
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Copyright (c) European Synchrotron Radiation Facility (ESRF)
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Permission is hereby granted, free of charge, to any person obtaining a copy of
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this software and associated documentation files (the "Software"), to deal in
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the Software without restriction, including without limitation the rights to
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use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
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the Software, and to permit persons to whom the Software is furnished to do so,
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subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
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COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
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CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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Metadata-Version: 2.2
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Name: tomwer
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Version: 1.4.6
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Summary: "tomography workflow tools"
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Home-page: https://gitlab.esrf.fr/tomotools/tomwer
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Author: Henri Payno, Pierre Paleo, Pierre-Olivier Autran, Jérôme Lesaint, Alessandro Mirone
|
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Author-email: henri.payno@esrf.fr, pierre.paleo@esrf.fr, pierre-olivier.autran@esrf.fr, jerome.lesaint@esrf.fr, mirone@esrf.fr
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License: MIT
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Project-URL: Bug Tracker, https://gitlab.esrf.fr/tomotools/tomwer/-/issues
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Keywords: orange3 add-on,ewoks
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Classifier: Intended Audience :: Education
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Classifier: Intended Audience :: Science/Research
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Classifier: License :: OSI Approved :: MIT License
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Classifier: Programming Language :: Python :: 3
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Classifier: Environment :: X11 Applications :: Qt
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Classifier: Operating System :: POSIX
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Classifier: Topic :: Software Development :: Libraries :: Python Modules
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.. image:: doc/img/tomwer.png
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:alt: Tomwer Logo
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:align: left
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:width: 400px
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Introduction
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------------
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**Tomwer** provides tools to automate acquisition and reconstruction processes for tomography. The package includes:
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- A library to individually access each acquisition process.
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- Graphical User Interface (GUI) applications to control key processes such as reconstruction and data transfer, which can be executed as standalone applications.
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- An Orange add-on to help users define custom workflows (`Orange3 <http://orange.biolab.si>`_).
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Tomwer relies on `Nabu <https://gitlab.esrf.fr/tomotools/nabu>`_ for tomographic reconstruction.
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**Note**: Currently, the software is only compatible with Linux.
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Documentation
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-------------
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The latest version of the documentation is available `here <https://tomotools.gitlab-pages.esrf.fr/tomwer/>`_.
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Installation
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------------
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Step 1: Installing Tomwer
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'''''''''''''''''''''''''
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|
263
|
+
To install Tomwer with all features:
|
264
|
+
|
265
|
+
.. code-block:: bash
|
266
|
+
|
267
|
+
pip install tomwer[full]
|
268
|
+
|
269
|
+
Alternatively, you can install the latest development branch from the repository:
|
270
|
+
|
271
|
+
.. code-block:: bash
|
272
|
+
|
273
|
+
pip install git+https://gitlab.esrf.fr/tomotools/tomwer/#egg=tomwer[full]
|
274
|
+
|
275
|
+
|
276
|
+
Step 2: (Optional) Update Orange-CANVAS-CORE and Orange-WIDGET-BASE
|
277
|
+
''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
|
278
|
+
|
279
|
+
If you need access to additional 'processing' wheels and 'reprocess action,' you may want to update these Orange forks. This is optional, as the project works with the native Orange libraries.
|
280
|
+
|
281
|
+
.. code-block:: bash
|
282
|
+
|
283
|
+
pip install git+https://github.com/payno/orange-canvas-core --no-deps --upgrade
|
284
|
+
pip install git+https://github.com/payno/orange-widget-base --no-deps --upgrade
|
285
|
+
|
286
|
+
|
287
|
+
Launching Applications
|
288
|
+
-----------------------
|
289
|
+
|
290
|
+
After installation, Tomwer includes several applications. You can launch an application by running:
|
291
|
+
|
292
|
+
.. code-block:: bash
|
293
|
+
|
294
|
+
tomwer <appName> [options]
|
295
|
+
|
296
|
+
- If you run `tomwer` without arguments, a manual page will be displayed.
|
297
|
+
- For application-specific help, run:
|
298
|
+
|
299
|
+
.. code-block:: bash
|
300
|
+
|
301
|
+
tomwer <appName> --help
|
302
|
+
|
303
|
+
|
304
|
+
Tomwer Canvas - Orange Canvas
|
305
|
+
-----------------------------
|
306
|
+
|
307
|
+
You can launch the Orange canvas to create workflows using the available building blocks:
|
308
|
+
|
309
|
+
.. code-block:: bash
|
310
|
+
|
311
|
+
tomwer canvas
|
312
|
+
|
313
|
+
- Alternatively, you can use `orange-canvas`.
|
314
|
+
- If you're using a virtual environment, remember to activate it:
|
315
|
+
|
316
|
+
.. code-block:: bash
|
317
|
+
|
318
|
+
source myvirtualenv/bin/activate
|
319
|
+
|
320
|
+
|
321
|
+
Building Documentation
|
322
|
+
-----------------------
|
323
|
+
|
324
|
+
To build the documentation:
|
325
|
+
|
326
|
+
.. code-block:: bash
|
327
|
+
|
328
|
+
sphinx-build doc build/html
|
329
|
+
|
330
|
+
The documentation will be generated in `doc/build/html`, and the entry point is `index.html`. To view the documentation in a browser:
|
331
|
+
|
332
|
+
.. code-block:: bash
|
333
|
+
|
334
|
+
firefox build/html/index.html
|
335
|
+
|
336
|
+
**Note**: Building the documentation requires `sphinx` to be installed, which is not a hard dependency of Tomwer. If needed, install it separately.
|
tomwer-1.4.6/README.rst
ADDED
@@ -0,0 +1,103 @@
|
|
1
|
+
.. image:: doc/img/tomwer.png
|
2
|
+
:alt: Tomwer Logo
|
3
|
+
:align: left
|
4
|
+
:width: 400px
|
5
|
+
|
6
|
+
Introduction
|
7
|
+
------------
|
8
|
+
|
9
|
+
**Tomwer** provides tools to automate acquisition and reconstruction processes for tomography. The package includes:
|
10
|
+
|
11
|
+
- A library to individually access each acquisition process.
|
12
|
+
- Graphical User Interface (GUI) applications to control key processes such as reconstruction and data transfer, which can be executed as standalone applications.
|
13
|
+
- An Orange add-on to help users define custom workflows (`Orange3 <http://orange.biolab.si>`_).
|
14
|
+
|
15
|
+
Tomwer relies on `Nabu <https://gitlab.esrf.fr/tomotools/nabu>`_ for tomographic reconstruction.
|
16
|
+
|
17
|
+
**Note**: Currently, the software is only compatible with Linux.
|
18
|
+
|
19
|
+
Documentation
|
20
|
+
-------------
|
21
|
+
|
22
|
+
The latest version of the documentation is available `here <https://tomotools.gitlab-pages.esrf.fr/tomwer/>`_.
|
23
|
+
|
24
|
+
Installation
|
25
|
+
------------
|
26
|
+
|
27
|
+
Step 1: Installing Tomwer
|
28
|
+
'''''''''''''''''''''''''
|
29
|
+
|
30
|
+
To install Tomwer with all features:
|
31
|
+
|
32
|
+
.. code-block:: bash
|
33
|
+
|
34
|
+
pip install tomwer[full]
|
35
|
+
|
36
|
+
Alternatively, you can install the latest development branch from the repository:
|
37
|
+
|
38
|
+
.. code-block:: bash
|
39
|
+
|
40
|
+
pip install git+https://gitlab.esrf.fr/tomotools/tomwer/#egg=tomwer[full]
|
41
|
+
|
42
|
+
|
43
|
+
Step 2: (Optional) Update Orange-CANVAS-CORE and Orange-WIDGET-BASE
|
44
|
+
''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
|
45
|
+
|
46
|
+
If you need access to additional 'processing' wheels and 'reprocess action,' you may want to update these Orange forks. This is optional, as the project works with the native Orange libraries.
|
47
|
+
|
48
|
+
.. code-block:: bash
|
49
|
+
|
50
|
+
pip install git+https://github.com/payno/orange-canvas-core --no-deps --upgrade
|
51
|
+
pip install git+https://github.com/payno/orange-widget-base --no-deps --upgrade
|
52
|
+
|
53
|
+
|
54
|
+
Launching Applications
|
55
|
+
-----------------------
|
56
|
+
|
57
|
+
After installation, Tomwer includes several applications. You can launch an application by running:
|
58
|
+
|
59
|
+
.. code-block:: bash
|
60
|
+
|
61
|
+
tomwer <appName> [options]
|
62
|
+
|
63
|
+
- If you run `tomwer` without arguments, a manual page will be displayed.
|
64
|
+
- For application-specific help, run:
|
65
|
+
|
66
|
+
.. code-block:: bash
|
67
|
+
|
68
|
+
tomwer <appName> --help
|
69
|
+
|
70
|
+
|
71
|
+
Tomwer Canvas - Orange Canvas
|
72
|
+
-----------------------------
|
73
|
+
|
74
|
+
You can launch the Orange canvas to create workflows using the available building blocks:
|
75
|
+
|
76
|
+
.. code-block:: bash
|
77
|
+
|
78
|
+
tomwer canvas
|
79
|
+
|
80
|
+
- Alternatively, you can use `orange-canvas`.
|
81
|
+
- If you're using a virtual environment, remember to activate it:
|
82
|
+
|
83
|
+
.. code-block:: bash
|
84
|
+
|
85
|
+
source myvirtualenv/bin/activate
|
86
|
+
|
87
|
+
|
88
|
+
Building Documentation
|
89
|
+
-----------------------
|
90
|
+
|
91
|
+
To build the documentation:
|
92
|
+
|
93
|
+
.. code-block:: bash
|
94
|
+
|
95
|
+
sphinx-build doc build/html
|
96
|
+
|
97
|
+
The documentation will be generated in `doc/build/html`, and the entry point is `index.html`. To view the documentation in a browser:
|
98
|
+
|
99
|
+
.. code-block:: bash
|
100
|
+
|
101
|
+
firefox build/html/index.html
|
102
|
+
|
103
|
+
**Note**: Building the documentation requires `sphinx` to be installed, which is not a hard dependency of Tomwer. If needed, install it separately.
|
@@ -0,0 +1,10 @@
|
|
1
|
+
[build-system]
|
2
|
+
requires = [
|
3
|
+
"setuptools>=46.4",
|
4
|
+
"wheel",
|
5
|
+
]
|
6
|
+
build-backend = "setuptools.build_meta"
|
7
|
+
|
8
|
+
[tool.pytest.ini_options]
|
9
|
+
# consider_namespace_packages = true # for pytest>=8.1
|
10
|
+
addopts = "--import-mode=importlib" # for all pytest versions, pytest-cov needs `pip install -e .`
|
tomwer-1.4.6/setup.cfg
ADDED
@@ -0,0 +1,174 @@
|
|
1
|
+
[metadata]
|
2
|
+
name = tomwer
|
3
|
+
version = attr: tomwer.__version__
|
4
|
+
author = Henri Payno, Pierre Paleo, Pierre-Olivier Autran, Jérôme Lesaint, Alessandro Mirone
|
5
|
+
author_email = henri.payno@esrf.fr, pierre.paleo@esrf.fr, pierre-olivier.autran@esrf.fr, jerome.lesaint@esrf.fr, mirone@esrf.fr
|
6
|
+
description = "tomography workflow tools"
|
7
|
+
long_description = file: README.rst
|
8
|
+
long_description_content_type = text/x-rst
|
9
|
+
license = MIT
|
10
|
+
url = https://gitlab.esrf.fr/tomotools/tomwer
|
11
|
+
project_urls =
|
12
|
+
Bug Tracker = https://gitlab.esrf.fr/tomotools/tomwer/-/issues
|
13
|
+
classifiers =
|
14
|
+
Intended Audience :: Education
|
15
|
+
Intended Audience :: Science/Research
|
16
|
+
License :: OSI Approved :: MIT License
|
17
|
+
Programming Language :: Python :: 3
|
18
|
+
Environment :: Console
|
19
|
+
Environment :: X11 Applications :: Qt
|
20
|
+
Operating System :: POSIX
|
21
|
+
Natural Language :: English
|
22
|
+
Topic :: Scientific/Engineering :: Physics
|
23
|
+
Topic :: Software Development :: Libraries :: Python Modules
|
24
|
+
keywords =
|
25
|
+
orange3 add-on,ewoks
|
26
|
+
|
27
|
+
[options]
|
28
|
+
package_dir =
|
29
|
+
=src
|
30
|
+
packages = find_namespace:
|
31
|
+
python_requires = >=3.6
|
32
|
+
install_requires =
|
33
|
+
numpy
|
34
|
+
setuptools
|
35
|
+
psutil
|
36
|
+
silx[full] >= 2.0
|
37
|
+
tomoscan>=2.1.0a18
|
38
|
+
nxtomo>=1.3.0dev4
|
39
|
+
nxtomomill>=1.1.0a0
|
40
|
+
processview>=1.5.0
|
41
|
+
ewoks>=0.1.1
|
42
|
+
sluurp>=0.4.1
|
43
|
+
packaging
|
44
|
+
pyunitsystem>=2.0.0a
|
45
|
+
tqdm
|
46
|
+
|
47
|
+
[options.packages.find]
|
48
|
+
where = src
|
49
|
+
|
50
|
+
[options.entry_points]
|
51
|
+
console_scripts =
|
52
|
+
tomwer=tomwer.__main__:main
|
53
|
+
orange3.addon =
|
54
|
+
tomwer-add-on=orangecontrib.tomwer
|
55
|
+
orange.widgets =
|
56
|
+
tomwer=orangecontrib.tomwer.widgets
|
57
|
+
orangecanvas.examples =
|
58
|
+
tomo_examples=orangecontrib.tomwer.examples
|
59
|
+
orange.widgets.tutorials =
|
60
|
+
tomo_tutorials=orangecontrib.tomwer.tutorials
|
61
|
+
tomo_tutorials_id16b=orangecontrib.tomwer.tutorials.id16b
|
62
|
+
orange.canvas.help =
|
63
|
+
html-index=orangecontrib.tomwer.widgets:WIDGET_HELP_PATH
|
64
|
+
ewoks.tasks.class =
|
65
|
+
tomwer.core.process.*.*=tomwer
|
66
|
+
|
67
|
+
[options.package_data]
|
68
|
+
tomwer.resources =
|
69
|
+
gui/icons/*.png
|
70
|
+
gui/icons/*.svg
|
71
|
+
gui/icons/*.npy
|
72
|
+
gui/illustrations/*.svg
|
73
|
+
gui/illustrations/*.png
|
74
|
+
orangecontrib.tomwer =
|
75
|
+
tutorials/*.ows
|
76
|
+
tutorials/id16b/*.ows
|
77
|
+
widgets/icons/*.png
|
78
|
+
widgets/icons/*.svg
|
79
|
+
widgets/cluster/icons/*.png
|
80
|
+
widgets/cluster/icons/*.svg
|
81
|
+
widgets/control/icons/*.png
|
82
|
+
widgets/control/icons/*.svg
|
83
|
+
widgets/debugtools/icons/*.png
|
84
|
+
widgets/debugtools/icons/*.svg
|
85
|
+
widgets/edit/icons/*.png
|
86
|
+
widgets/edit/icons/*.svg
|
87
|
+
widgets/dataportal/icons/*.png
|
88
|
+
widgets/dataportal/icons/*.svg
|
89
|
+
widgets/reconstruction/icons/*.png
|
90
|
+
widgets/reconstruction/icons/*.svg
|
91
|
+
widgets/visualization/icons/*.png
|
92
|
+
widgets/visualization/icons/*.svg
|
93
|
+
widgets/other/icons/*.png
|
94
|
+
widgets/other/icons/*.svg
|
95
|
+
|
96
|
+
[options.extras_require]
|
97
|
+
full_base =
|
98
|
+
orange-canvas-core
|
99
|
+
orange-widget-base
|
100
|
+
ewoks[orange]>=0.1.1
|
101
|
+
ewoksorange >= 0.7.0rc0
|
102
|
+
rsyncmanager
|
103
|
+
fabio
|
104
|
+
h5py>=3
|
105
|
+
lxml
|
106
|
+
werkzeug
|
107
|
+
json-rpc
|
108
|
+
scipy
|
109
|
+
Pillow
|
110
|
+
glymur
|
111
|
+
resource
|
112
|
+
tifffile
|
113
|
+
hdf5plugin
|
114
|
+
pyicat_plus
|
115
|
+
ewoksnotify[full]
|
116
|
+
pyicat_plus
|
117
|
+
full_no_nabu =
|
118
|
+
%(full_base)s
|
119
|
+
full_no_cuda =
|
120
|
+
%(full_base)s
|
121
|
+
nabu>=2023.3.1dev
|
122
|
+
full =
|
123
|
+
%(full_base)s
|
124
|
+
nabu[full]>=2023.3.1dev
|
125
|
+
pycuda<2024.1.1
|
126
|
+
scikit-cuda
|
127
|
+
doc =
|
128
|
+
%(full_no_cuda)s
|
129
|
+
Sphinx>=4.0.0
|
130
|
+
nbsphinx
|
131
|
+
pandoc
|
132
|
+
jupyterlab
|
133
|
+
pydata_sphinx_theme
|
134
|
+
sphinx-design
|
135
|
+
sphinx-autodoc-typehints
|
136
|
+
sphinxcontrib-youtube
|
137
|
+
dev_spec =
|
138
|
+
black
|
139
|
+
flake8
|
140
|
+
timeout-decorator
|
141
|
+
pyopencl
|
142
|
+
dev =
|
143
|
+
%(full)s
|
144
|
+
%(dev_spec)s
|
145
|
+
dev_no_cuda =
|
146
|
+
%(full_no_cuda)s
|
147
|
+
%(dev_spec)s
|
148
|
+
test =
|
149
|
+
%(full_no_cuda)s
|
150
|
+
pytest-asyncio
|
151
|
+
tomoscan[test]>=2.1.0a18
|
152
|
+
setup_requires =
|
153
|
+
setuptools
|
154
|
+
numpy>=1.12
|
155
|
+
|
156
|
+
[build_sphinx]
|
157
|
+
source-dir = ./doc
|
158
|
+
|
159
|
+
[flake8]
|
160
|
+
ignore = E501,W503,E203,E265,E266,E712,E262
|
161
|
+
max-line-length = 88
|
162
|
+
exclude =
|
163
|
+
.eggs
|
164
|
+
doc/ext
|
165
|
+
|
166
|
+
[coverage:run]
|
167
|
+
omit =
|
168
|
+
setup.py
|
169
|
+
*/test/*
|
170
|
+
|
171
|
+
[egg_info]
|
172
|
+
tag_build =
|
173
|
+
tag_date = 0
|
174
|
+
|
tomwer-1.4.6/setup.py
ADDED