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Merge pull request #65 from hakonanes/enable-kikuchipy-again
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Re-enable kikuchipy
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@ericpre
ericpre authored Dec 12, 2024
2 parents 85c9e93 + 700589f commit 54122af
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25 changes: 16 additions & 9 deletions .github/workflows/tests.yml
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Expand Up @@ -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:
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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
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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: |
Expand All @@ -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
Expand Down Expand Up @@ -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
Expand All @@ -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() }}
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86 changes: 45 additions & 41 deletions README.md
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Expand Up @@ -21,53 +21,57 @@ 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. |

## 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 |


1 change: 1 addition & 0 deletions extension_list.txt
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@@ -1,5 +1,6 @@
exspy
holospy
hyperspy
kikuchipy
lumispy
pyxem
4 changes: 2 additions & 2 deletions make_README.py
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Expand Up @@ -2,7 +2,7 @@
import io
import os

from prettytable import MARKDOWN
from prettytable import TableStyle
import hyperspy.api as hs


Expand All @@ -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:
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2 changes: 1 addition & 1 deletion readme_source/1-readme_base.md
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Expand Up @@ -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. |
Expand Down
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