diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index a28d3b8..43a5bcd 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -62,8 +62,7 @@ jobs: PYTHON_VERSION: '3.11' env: - # EXTENSION: hyperspy-gui-ipywidgets hyperspy-gui-traitsui kikuchipy lumispy pyxem exspy holospy - EXTENSION: hyperspy-gui-ipywidgets hyperspy-gui-traitsui lumispy pyxem exspy holospy + EXTENSION: hyperspy-gui-ipywidgets hyperspy-gui-traitsui kikuchipy lumispy pyxem exspy holospy TEST_DEPS: pytest pytest-xdist pytest-rerunfailures pytest-mpl filelock defaults: run: @@ -85,6 +84,11 @@ jobs: run: | mamba install pip pyqt ${{ env.TEST_DEPS }} + - name: Install numpy 1.x + run: | + # remove when pyxem support numpy 2 + mamba install numpy=1 + - name: Conda info run: | conda info @@ -141,7 +145,7 @@ jobs: if: contains(matrix.HYPERSPY_VERSION, 'RnMajor') run: | pip install "hyperspy[all] @ git+https://github.com/hyperspy/hyperspy.git@RELEASE_next_major" - + - name: Install Extension Release if: contains(matrix.EXTENSION_VERSION, 'release') run: | @@ -153,8 +157,7 @@ jobs: pip install git+https://github.com/hyperspy/exspy.git pip install git+https://github.com/hyperspy/holospy.git pip install git+https://github.com/lumispy/lumispy.git - # uncomment when kikuchipy supports hyperspy 2 - # pip install git+https://github.com/pyxem/kikuchipy.git + pip install git+https://github.com/pyxem/kikuchipy.git pip install git+https://github.com/pyxem/pyxem.git pip install git+https://github.com/hyperspy/hyperspy_gui_ipywidgets.git pip install git+https://github.com/hyperspy/hyperspy_gui_traitsui.git @@ -182,7 +185,7 @@ jobs: if: ${{ always() }} run: | python -m pytest --pyargs hyperspy_gui_ipywidgets - + - name: Run hyperspy_gui_traitsui Test Suite if: ${{ always() }} # run the tests headlessly @@ -199,9 +202,13 @@ jobs: run: | python -m pytest --pyargs holospy - # - name: Run kikuchipy Test Suite - # run: | - # python -m pytest --pyargs kikuchipy + - name: Run kikuchipy Test Suite + if: ${{ always() }} + # Run the tests headlessly. + # Unskip test when https://github.com/pyxem/kikuchipy/issues/707 is fixed and + # released. + run: | + xvfb-run python -m pytest --pyargs kikuchipy -k "not test_not_allow_download_raises" - name: Run LumiSpy Test Suite if: ${{ always() }} diff --git a/README.md b/README.md index 25d10ce..2e5a758 100644 --- a/README.md +++ b/README.md @@ -21,7 +21,7 @@ and send us a pull request. | [holospy](https://github.com/hyperspy/holospy) | Electron holography | | [hyperspy-gui-ipywidgets](https://github.com/hyperspy/hyperspy_gui_ipywidgets) | ipywidgets widgets for HyperSpy | | [hyperspy-gui-traitsui](https://github.com/hyperspy/hyperspy_gui_traitsui) | traitsui widgets for HyperSpy | -| [kikuchipy](https://github.com/kikuchipy/kikuchipy) | Processing, simulating and indexing of electron backscatter diffraction patterns | +| [kikuchipy](https://github.com/pyxem/kikuchipy) | Processing, simulating and indexing of electron backscatter diffraction patterns | | [LumiSpy](https://github.com/lumispy/lumispy) | Analysis of luminescence spectroscopy data | | [pyxem](https://github.com/pyxem/pyxem) | Multi-dimensional diffraction microscopy | | [rosettasciio](https://github.com/hyperspy/rosettasciio) | Reading and writing of scientific data formats. | @@ -29,45 +29,49 @@ and send us a pull request. ## List of `signal_type` classes provided by the different HyperSpy extensions in alphabetical order -| signal_type | aliases | class name | package | -| :-------------------------: | :-----------------------------------------------------------------------: | :-------------------------: | :-----: | -| beam_shift | | BeamShift | pyxem | -| CL_SEM | CLSEM, cathodoluminescence SEM | CLSEMSpectrum | lumispy | -| CL_STEM | CLSTEM, cathodoluminescence STEM | CLSTEMSpectrum | lumispy | -| CL | CLSpectrum, cathodoluminescence | CLSpectrum | lumispy | -| correlation | | Correlation1D | pyxem | -| correlation | | Correlation2D | pyxem | -| dpc | | DPCSignal1D | pyxem | -| dpc | | DPCSignal2D | pyxem | -| DielectricFunction | dielectric function | DielectricFunction | exspy | -| diffraction | | Diffraction1D | pyxem | -| diffraction | | Diffraction2D | pyxem | -| diffraction_variance | | DiffractionVariance1D | pyxem | -| diffraction_variance | | DiffractionVariance2D | pyxem | -| diffraction_vectors | | DiffractionVectors | pyxem | -| diffraction_vectors | | DiffractionVectors1D | pyxem | -| diffraction_vectors | | DiffractionVectors2D | pyxem | -| tensor_field | | DisplacementGradientMap | pyxem | -| EDS_SEM | | EDSSEMSpectrum | exspy | -| EDS_TEM | | EDSTEMSpectrum | exspy | -| EELS | TEM EELS | EELSSpectrum | exspy | -| EL | ELSpectrum, electroluminescence | ELSpectrum | lumispy | -| electron_diffraction | | ElectronDiffraction1D | pyxem | -| electron_diffraction | | ElectronDiffraction2D | pyxem | -| hologram | | HologramImage | holospy | -| insitu_diffraction | | InSituDiffraction2D | pyxem | -| labeled_diffraction_vectors | | LabeledDiffractionVectors2D | pyxem | -| Luminescence | LuminescenceSpectrum | LumiSpectrum | lumispy | -| Transient | TRLumi, TR luminescence, time-resolved luminescence | LumiTransient | lumispy | -| TransientSpec | TRLumiSpec, TR luminescence spectrum, time-resolved luminescence spectrum | LumiTransientSpectrum | lumispy | -| orientation_map | | OrientationMap | pyxem | -| PL | PLSpectrum, photoluminescence | PLSpectrum | lumispy | -| pair_distribution_function | | PairDistributionFunction1D | pyxem | -| polar_diffraction | | PolarDiffraction2D | pyxem | -| polar_vectors | | PolarVectors | pyxem | -| power | | Power2D | pyxem | -| reduced_intensity | | ReducedIntensity1D | pyxem | -| vector_matching | | VectorMatchingResults | pyxem | -| virtual_dark_field | | VirtualDarkFieldImage | pyxem | +| signal_type | aliases | class name | package | +| :-------------------------: | :-----------------------------------------------------------------------: | :-------------------------: | :-------: | +| beam_shift | | BeamShift | pyxem | +| CL_SEM | CLSEM, cathodoluminescence SEM | CLSEMSpectrum | lumispy | +| CL_STEM | CLSTEM, cathodoluminescence STEM | CLSTEMSpectrum | lumispy | +| CL | CLSpectrum, cathodoluminescence | CLSpectrum | lumispy | +| correlation | | Correlation1D | pyxem | +| correlation | | Correlation2D | pyxem | +| dpc | | DPCSignal1D | pyxem | +| dpc | | DPCSignal2D | pyxem | +| DielectricFunction | dielectric function | DielectricFunction | exspy | +| diffraction | | Diffraction1D | pyxem | +| diffraction | | Diffraction2D | pyxem | +| diffraction_variance | | DiffractionVariance1D | pyxem | +| diffraction_variance | | DiffractionVariance2D | pyxem | +| diffraction_vectors | | DiffractionVectors | pyxem | +| diffraction_vectors | | DiffractionVectors1D | pyxem | +| diffraction_vectors | | DiffractionVectors2D | pyxem | +| tensor_field | | DisplacementGradientMap | pyxem | +| EBSD | electron_backscatter_diffraction | EBSD | kikuchipy | +| EBSDMasterPattern | ebsd_master_pattern, master_pattern | EBSDMasterPattern | kikuchipy | +| ECPMasterPattern | ecp_master_pattern | ECPMasterPattern | kikuchipy | +| EDS_SEM | | EDSSEMSpectrum | exspy | +| EDS_TEM | | EDSTEMSpectrum | exspy | +| EELS | TEM EELS | EELSSpectrum | exspy | +| EL | ELSpectrum, electroluminescence | ELSpectrum | lumispy | +| electron_diffraction | | ElectronDiffraction1D | pyxem | +| electron_diffraction | | ElectronDiffraction2D | pyxem | +| hologram | | HologramImage | holospy | +| insitu_diffraction | | InSituDiffraction2D | pyxem | +| labeled_diffraction_vectors | | LabeledDiffractionVectors2D | pyxem | +| Luminescence | LuminescenceSpectrum | LumiSpectrum | lumispy | +| Transient | TRLumi, TR luminescence, time-resolved luminescence | LumiTransient | lumispy | +| TransientSpec | TRLumiSpec, TR luminescence spectrum, time-resolved luminescence spectrum | LumiTransientSpectrum | lumispy | +| orientation_map | | OrientationMap | pyxem | +| PL | PLSpectrum, photoluminescence | PLSpectrum | lumispy | +| pair_distribution_function | | PairDistributionFunction1D | pyxem | +| polar_diffraction | | PolarDiffraction2D | pyxem | +| polar_vectors | | PolarVectors | pyxem | +| power | | Power2D | pyxem | +| reduced_intensity | | ReducedIntensity1D | pyxem | +| vector_matching | | VectorMatchingResults | pyxem | +| VirtualBSEImage | virtual_backscatter_electron_image | VirtualBSEImage | kikuchipy | +| virtual_dark_field | | VirtualDarkFieldImage | pyxem | diff --git a/extension_list.txt b/extension_list.txt index 99c99a3..3402bcf 100644 --- a/extension_list.txt +++ b/extension_list.txt @@ -1,5 +1,6 @@ exspy holospy hyperspy +kikuchipy lumispy pyxem diff --git a/make_README.py b/make_README.py index 847cf10..136e005 100644 --- a/make_README.py +++ b/make_README.py @@ -2,7 +2,7 @@ import io import os -from prettytable import MARKDOWN +from prettytable import TableStyle import hyperspy.api as hs @@ -11,7 +11,7 @@ # Get the information from hyperspy f = io.StringIO() with contextlib.redirect_stdout(f): - hs.print_known_signal_types(style=MARKDOWN) + hs.print_known_signal_types(style=TableStyle.MARKDOWN) table_ascii = f.getvalue() with open(os.path.join(readme_source_folder, '2-extension_table.md'), "w") as f: diff --git a/readme_source/1-readme_base.md b/readme_source/1-readme_base.md index f6f40d6..01c9765 100644 --- a/readme_source/1-readme_base.md +++ b/readme_source/1-readme_base.md @@ -21,7 +21,7 @@ and send us a pull request. | [holospy](https://github.com/hyperspy/holospy) | Electron holography | | [hyperspy-gui-ipywidgets](https://github.com/hyperspy/hyperspy_gui_ipywidgets) | ipywidgets widgets for HyperSpy | | [hyperspy-gui-traitsui](https://github.com/hyperspy/hyperspy_gui_traitsui) | traitsui widgets for HyperSpy | -| [kikuchipy](https://github.com/kikuchipy/kikuchipy) | Processing, simulating and indexing of electron backscatter diffraction patterns | +| [kikuchipy](https://github.com/pyxem/kikuchipy) | Processing, simulating and indexing of electron backscatter diffraction patterns | | [LumiSpy](https://github.com/lumispy/lumispy) | Analysis of luminescence spectroscopy data | | [pyxem](https://github.com/pyxem/pyxem) | Multi-dimensional diffraction microscopy | | [rosettasciio](https://github.com/hyperspy/rosettasciio) | Reading and writing of scientific data formats. | diff --git a/readme_source/2-extension_table.md b/readme_source/2-extension_table.md index 5b91d2e..3a48609 100644 --- a/readme_source/2-extension_table.md +++ b/readme_source/2-extension_table.md @@ -1,40 +1,44 @@ -| signal_type | aliases | class name | package | -| :-------------------------: | :-----------------------------------------------------------------------: | :-------------------------: | :-----: | -| beam_shift | | BeamShift | pyxem | -| CL_SEM | CLSEM, cathodoluminescence SEM | CLSEMSpectrum | lumispy | -| CL_STEM | CLSTEM, cathodoluminescence STEM | CLSTEMSpectrum | lumispy | -| CL | CLSpectrum, cathodoluminescence | CLSpectrum | lumispy | -| correlation | | Correlation1D | pyxem | -| correlation | | Correlation2D | pyxem | -| dpc | | DPCSignal1D | pyxem | -| dpc | | DPCSignal2D | pyxem | -| DielectricFunction | dielectric function | DielectricFunction | exspy | -| diffraction | | Diffraction1D | pyxem | -| diffraction | | Diffraction2D | pyxem | -| diffraction_variance | | DiffractionVariance1D | pyxem | -| diffraction_variance | | DiffractionVariance2D | pyxem | -| diffraction_vectors | | DiffractionVectors | pyxem | -| diffraction_vectors | | DiffractionVectors1D | pyxem | -| diffraction_vectors | | DiffractionVectors2D | pyxem | -| tensor_field | | DisplacementGradientMap | pyxem | -| EDS_SEM | | EDSSEMSpectrum | exspy | -| EDS_TEM | | EDSTEMSpectrum | exspy | -| EELS | TEM EELS | EELSSpectrum | exspy | -| EL | ELSpectrum, electroluminescence | ELSpectrum | lumispy | -| electron_diffraction | | ElectronDiffraction1D | pyxem | -| electron_diffraction | | ElectronDiffraction2D | pyxem | -| hologram | | HologramImage | holospy | -| insitu_diffraction | | InSituDiffraction2D | pyxem | -| labeled_diffraction_vectors | | LabeledDiffractionVectors2D | pyxem | -| Luminescence | LuminescenceSpectrum | LumiSpectrum | lumispy | -| Transient | TRLumi, TR luminescence, time-resolved luminescence | LumiTransient | lumispy | -| TransientSpec | TRLumiSpec, TR luminescence spectrum, time-resolved luminescence spectrum | LumiTransientSpectrum | lumispy | -| orientation_map | | OrientationMap | pyxem | -| PL | PLSpectrum, photoluminescence | PLSpectrum | lumispy | -| pair_distribution_function | | PairDistributionFunction1D | pyxem | -| polar_diffraction | | PolarDiffraction2D | pyxem | -| polar_vectors | | PolarVectors | pyxem | -| power | | Power2D | pyxem | -| reduced_intensity | | ReducedIntensity1D | pyxem | -| vector_matching | | VectorMatchingResults | pyxem | -| virtual_dark_field | | VirtualDarkFieldImage | pyxem | +| signal_type | aliases | class name | package | +| :-------------------------: | :-----------------------------------------------------------------------: | :-------------------------: | :-------: | +| beam_shift | | BeamShift | pyxem | +| CL_SEM | CLSEM, cathodoluminescence SEM | CLSEMSpectrum | lumispy | +| CL_STEM | CLSTEM, cathodoluminescence STEM | CLSTEMSpectrum | lumispy | +| CL | CLSpectrum, cathodoluminescence | CLSpectrum | lumispy | +| correlation | | Correlation1D | pyxem | +| correlation | | Correlation2D | pyxem | +| dpc | | DPCSignal1D | pyxem | +| dpc | | DPCSignal2D | pyxem | +| DielectricFunction | dielectric function | DielectricFunction | exspy | +| diffraction | | Diffraction1D | pyxem | +| diffraction | | Diffraction2D | pyxem | +| diffraction_variance | | DiffractionVariance1D | pyxem | +| diffraction_variance | | DiffractionVariance2D | pyxem | +| diffraction_vectors | | DiffractionVectors | pyxem | +| diffraction_vectors | | DiffractionVectors1D | pyxem | +| diffraction_vectors | | DiffractionVectors2D | pyxem | +| tensor_field | | DisplacementGradientMap | pyxem | +| EBSD | electron_backscatter_diffraction | EBSD | kikuchipy | +| EBSDMasterPattern | ebsd_master_pattern, master_pattern | EBSDMasterPattern | kikuchipy | +| ECPMasterPattern | ecp_master_pattern | ECPMasterPattern | kikuchipy | +| EDS_SEM | | EDSSEMSpectrum | exspy | +| EDS_TEM | | EDSTEMSpectrum | exspy | +| EELS | TEM EELS | EELSSpectrum | exspy | +| EL | ELSpectrum, electroluminescence | ELSpectrum | lumispy | +| electron_diffraction | | ElectronDiffraction1D | pyxem | +| electron_diffraction | | ElectronDiffraction2D | pyxem | +| hologram | | HologramImage | holospy | +| insitu_diffraction | | InSituDiffraction2D | pyxem | +| labeled_diffraction_vectors | | LabeledDiffractionVectors2D | pyxem | +| Luminescence | LuminescenceSpectrum | LumiSpectrum | lumispy | +| Transient | TRLumi, TR luminescence, time-resolved luminescence | LumiTransient | lumispy | +| TransientSpec | TRLumiSpec, TR luminescence spectrum, time-resolved luminescence spectrum | LumiTransientSpectrum | lumispy | +| orientation_map | | OrientationMap | pyxem | +| PL | PLSpectrum, photoluminescence | PLSpectrum | lumispy | +| pair_distribution_function | | PairDistributionFunction1D | pyxem | +| polar_diffraction | | PolarDiffraction2D | pyxem | +| polar_vectors | | PolarVectors | pyxem | +| power | | Power2D | pyxem | +| reduced_intensity | | ReducedIntensity1D | pyxem | +| vector_matching | | VectorMatchingResults | pyxem | +| VirtualBSEImage | virtual_backscatter_electron_image | VirtualBSEImage | kikuchipy | +| virtual_dark_field | | VirtualDarkFieldImage | pyxem |