From 8093b294e606f5fa1748ab060c56a6bed2650beb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ha=CC=8Akon=20Wiik=20A=CC=8Anes?= Date: Sat, 9 Nov 2024 21:12:18 +0100 Subject: [PATCH 01/14] Re-add kikuchipy to list MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Signed-off-by: Håkon Wiik Ånes --- extension_list.txt | 1 + 1 file changed, 1 insertion(+) 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 From 61c4ff2f015be0a895365c5ef1120f89f198e41c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ha=CC=8Akon=20Wiik=20A=CC=8Anes?= Date: Sat, 9 Nov 2024 21:12:31 +0100 Subject: [PATCH 02/14] Get MARKDOWN style from the sanctioned prettytable.TableStyle enum MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Signed-off-by: Håkon Wiik Ånes --- make_README.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) 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: From b29ad8d79116bd0741f2f2f0dbf2790b3b7cf59a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ha=CC=8Akon=20Wiik=20A=CC=8Anes?= Date: Sat, 9 Nov 2024 21:13:39 +0100 Subject: [PATCH 03/14] Update README with kikuchipy signals MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Signed-off-by: Håkon Wiik Ånes --- README.md | 86 ++++++++++++++++-------------- readme_source/1-readme_base.md | 2 +- readme_source/2-extension_table.md | 84 +++++++++++++++-------------- 3 files changed, 90 insertions(+), 82 deletions(-) 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/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 | From 7f0265359c250f7db1635539091a5b15dfb0e805 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ha=CC=8Akon=20Wiik=20A=CC=8Anes?= Date: Sat, 9 Nov 2024 21:18:02 +0100 Subject: [PATCH 04/14] Re-introduce kikuchipy tests MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Signed-off-by: Håkon Wiik Ånes --- .github/workflows/tests.yml | 16 +++++++--------- 1 file changed, 7 insertions(+), 9 deletions(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index f1ffa91..8c945ea 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: @@ -143,7 +142,7 @@ 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: | @@ -155,8 +154,7 @@ 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 @@ -184,7 +182,7 @@ jobs: if: ${{ always() }} run: | python -m pytest --pyargs hyperspy_gui_ipywidgets - + - name: Run hyperspy_gui_traitsui Test Suite if: ${{ always() }} # run the tests headlessly @@ -201,9 +199,9 @@ jobs: run: | python -m pytest --pyargs holospy - # - name: Run kikuchipy Test Suite - # run: | - # python -m pytest --pyargs kikuchipy + - name: Run kikuchipy Test Suite + run: | + python -m pytest --pyargs kikuchipy - name: Run LumiSpy Test Suite if: ${{ always() }} From 43d44bf28b7b28848204c1e5c66931d90679a834 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ha=CC=8Akon=20Wiik=20A=CC=8Anes?= Date: Sat, 9 Nov 2024 21:12:18 +0100 Subject: [PATCH 05/14] Re-add kikuchipy to list MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Signed-off-by: Håkon Wiik Ånes --- extension_list.txt | 1 + 1 file changed, 1 insertion(+) 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 From 34adcd503a4fbee783ae52009c371766f5824524 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ha=CC=8Akon=20Wiik=20A=CC=8Anes?= Date: Sat, 9 Nov 2024 21:12:31 +0100 Subject: [PATCH 06/14] Get MARKDOWN style from the sanctioned prettytable.TableStyle enum MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Signed-off-by: Håkon Wiik Ånes --- make_README.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) 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: From 4130ee64d5843e9caeb2085a304c1321444cecdd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ha=CC=8Akon=20Wiik=20A=CC=8Anes?= Date: Sat, 9 Nov 2024 21:13:39 +0100 Subject: [PATCH 07/14] Update README with kikuchipy signals MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Signed-off-by: Håkon Wiik Ånes --- README.md | 86 ++++++++++++++++-------------- readme_source/1-readme_base.md | 2 +- readme_source/2-extension_table.md | 84 +++++++++++++++-------------- 3 files changed, 90 insertions(+), 82 deletions(-) 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/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 | From 48790430068f55fade308c7cb280bd97a5bd85f9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ha=CC=8Akon=20Wiik=20A=CC=8Anes?= Date: Sat, 9 Nov 2024 21:18:02 +0100 Subject: [PATCH 08/14] Re-introduce kikuchipy tests MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Signed-off-by: Håkon Wiik Ånes --- .github/workflows/tests.yml | 16 +++++++--------- 1 file changed, 7 insertions(+), 9 deletions(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index a28d3b8..1d32493 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: @@ -141,7 +140,7 @@ 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 +152,7 @@ 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 +180,7 @@ 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 +197,9 @@ jobs: run: | python -m pytest --pyargs holospy - # - name: Run kikuchipy Test Suite - # run: | - # python -m pytest --pyargs kikuchipy + - name: Run kikuchipy Test Suite + run: | + python -m pytest --pyargs kikuchipy - name: Run LumiSpy Test Suite if: ${{ always() }} From 64ddd353bef859db2dafb3f2c6555c752debd0ba Mon Sep 17 00:00:00 2001 From: Eric Prestat Date: Tue, 12 Nov 2024 16:44:50 +0000 Subject: [PATCH 09/14] Tests are not package with kikuchipy, test only for dev version --- .github/workflows/tests.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 1d32493..b268406 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -198,6 +198,8 @@ jobs: python -m pytest --pyargs holospy - name: Run kikuchipy Test Suite + # tests are not package with kikuchipy, test only for dev version + if: contains(matrix.EXTENSION_VERSION, 'dev') run: | python -m pytest --pyargs kikuchipy From 31d18a533b10f6199885d17443556a3e616c180c Mon Sep 17 00:00:00 2001 From: Eric Prestat Date: Fri, 15 Nov 2024 10:00:42 +0000 Subject: [PATCH 10/14] Pin numpy<2 until pyxem supports numpy 2 --- .github/workflows/tests.yml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index b268406..82b9584 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -84,6 +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 From 68c1a4bd1a9d5b16887b9e0cdb6fdd5e6561f68c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ha=CC=8Akon=20Wiik=20A=CC=8Anes?= Date: Sun, 1 Dec 2024 08:40:13 +0100 Subject: [PATCH 11/14] Also run kikuchipy tests when release version is installed MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Signed-off-by: Håkon Wiik Ånes --- .github/workflows/tests.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index a10e9f1..3ba8deb 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -203,6 +203,7 @@ jobs: python -m pytest --pyargs holospy - name: Run kikuchipy Test Suite + if: ${{ always() }} run: | python -m pytest --pyargs kikuchipy From 057b6568dd3aa6a0e635ecd27905732244b843fb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ha=CC=8Akon=20Wiik=20A=CC=8Anes?= Date: Sun, 1 Dec 2024 10:13:18 +0100 Subject: [PATCH 12/14] Skip PyVista test and test with incorrect paths MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Signed-off-by: Håkon Wiik Ånes --- .github/workflows/tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 3ba8deb..4b0e873 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -205,7 +205,7 @@ jobs: - name: Run kikuchipy Test Suite if: ${{ always() }} run: | - python -m pytest --pyargs kikuchipy + python -m pytest --pyargs kikuchipy -k "not test_spherical_pyvista and not test_not_allow_download_raises" - name: Run LumiSpy Test Suite if: ${{ always() }} From 90e43cc2434733d33ee7cd0a23f67db17ced7066 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ha=CC=8Akon=20Wiik=20A=CC=8Anes?= Date: Sun, 1 Dec 2024 10:40:28 +0100 Subject: [PATCH 13/14] Run tests in head-less mode since PyVista is installed MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Signed-off-by: Håkon Wiik Ånes --- .github/workflows/tests.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 4b0e873..6fb09f6 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -204,8 +204,9 @@ jobs: - name: Run kikuchipy Test Suite if: ${{ always() }} + # run the tests headlessly run: | - python -m pytest --pyargs kikuchipy -k "not test_spherical_pyvista and not test_not_allow_download_raises" + xvfb-run python -m pytest --pyargs kikuchipy -k "not test_spherical_pyvista and not test_not_allow_download_raises" - name: Run LumiSpy Test Suite if: ${{ always() }} From 700589f0a67719ae37ff6692a1239c5651b20ce1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ha=CC=8Akon=20Wiik=20A=CC=8Anes?= Date: Sun, 8 Dec 2024 13:24:01 +0100 Subject: [PATCH 14/14] Unskip PyVista test (we have a virtual frame buffer), explain remaining skip MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Signed-off-by: Håkon Wiik Ånes --- .github/workflows/tests.yml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 6fb09f6..43a5bcd 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -204,9 +204,11 @@ jobs: - name: Run kikuchipy Test Suite if: ${{ always() }} - # run the tests headlessly + # 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_spherical_pyvista and not test_not_allow_download_raises" + xvfb-run python -m pytest --pyargs kikuchipy -k "not test_not_allow_download_raises" - name: Run LumiSpy Test Suite if: ${{ always() }}