Merge pull request #64 from jat255/add_etspy

Add ETSpy to known extensions list
hyperspy · Jan 4, 2025 · 7e40ade · 7e40ade
2 parents 5461df7 + 939093e
commit 7e40ade
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Showing 5 changed files with 20 additions and 4 deletions.
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -58,7 +58,7 @@ jobs:
             USE_MAMBA: true
 
     env:
-      EXTENSION: hyperspy-gui-ipywidgets hyperspy-gui-traitsui kikuchipy lumispy pyxem exspy holospy
+      EXTENSION: hyperspy-gui-ipywidgets hyperspy-gui-traitsui kikuchipy lumispy pyxem exspy holospy etspy
       TEST_DEPS: pytest pytest-xdist pytest-rerunfailures pytest-mpl filelock
       PYTHON_VERSION: '3.12'
     defaults:
@@ -79,7 +79,9 @@ jobs:
 
       - name: Install pip, pyqt, orix and Test dependencies
         run: |
-          mamba install pip pyqt orix ${{ env.TEST_DEPS }}
+          # astra-toolbox from pypi.org only works with gpu
+          # ffmpeg is a missing dependencies from etspy, see https://github.com/usnistgov/etspy/issues/25
+          mamba install pip pyqt orix astra-toolbox ffmpeg ${{ env.TEST_DEPS }}
 
       - name: Install dask 2024.11.2
         run: |
@@ -159,6 +161,7 @@ jobs:
           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
+          pip install git+https://github.com/usnistgov/etspy.git
 
       - name: Clear conda and pip cache
         run: |
@@ -219,3 +222,9 @@ jobs:
         if: ${{ always() }}
         run: |
           python -m pytest --pyargs pyxem
+
+      - name: Run ETSpy Test Suite
+        if: ${{ always() }}
+        # Test needs to be fixed, see https://github.com/usnistgov/etspy/issues/24
+        run: |
+          python -m pytest --pyargs etspy -n 2 -k "not test_version"
diff --git a/README.md b/README.md
@@ -24,7 +24,8 @@ and send us a pull request.
 | [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.                                        |
+| [rosettasciio](https://github.com/hyperspy/rosettasciio)                       | Reading and writing of scientific data formats                                         |
+| [etspy](https://github.com/usnistgov/etspy)                                    | Electron tomography processing and reconstruction tools                               |
 
 ## List of `signal_type` classes provided by the different HyperSpy extensions in alphabetical order
 
@@ -69,7 +70,9 @@ and send us a pull request.
 |      polar_diffraction      |                                                                           |      PolarDiffraction2D     |   pyxem   |
 |        polar_vectors        |                                                                           |         PolarVectors        |   pyxem   |
 |            power            |                                                                           |           Power2D           |   pyxem   |
+|           RecStack          |                            Reconstructed stack                            |           RecStack          |   etspy   |
 |      reduced_intensity      |                                                                           |      ReducedIntensity1D     |   pyxem   |
+|          TomoStack          |                  Tomography, Tomography stack, TiltStack                  |          TomoStack          |   etspy   |
 |       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
@@ -4,3 +4,4 @@ hyperspy
 kikuchipy
 lumispy
 pyxem
+etspy
diff --git a/readme_source/1-readme_base.md b/readme_source/1-readme_base.md
@@ -24,6 +24,7 @@ and send us a pull request.
 | [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.                                        |
+| [rosettasciio](https://github.com/hyperspy/rosettasciio)                       | Reading and writing of scientific data formats                                         |
+| [etspy](https://github.com/usnistgov/etspy)                                    | Electron tomography processing and reconstruction tools                               |
 
 ## List of `signal_type` classes provided by the different HyperSpy extensions in alphabetical order
diff --git a/readme_source/2-extension_table.md b/readme_source/2-extension_table.md
@@ -38,7 +38,9 @@
 |      polar_diffraction      |                                                                           |      PolarDiffraction2D     |   pyxem   |
 |        polar_vectors        |                                                                           |         PolarVectors        |   pyxem   |
 |            power            |                                                                           |           Power2D           |   pyxem   |
+|           RecStack          |                            Reconstructed stack                            |           RecStack          |   etspy   |
 |      reduced_intensity      |                                                                           |      ReducedIntensity1D     |   pyxem   |
+|          TomoStack          |                  Tomography, Tomography stack, TiltStack                  |          TomoStack          |   etspy   |
 |       vector_matching       |                                                                           |    VectorMatchingResults    |   pyxem   |
 |       VirtualBSEImage       |                     virtual_backscatter_electron_image                    |       VirtualBSEImage       | kikuchipy |
 |      virtual_dark_field     |                                                                           |    VirtualDarkFieldImage    |   pyxem   |
-Original file line number
+Diff line change
@@ Expand Up / @@ -4,3 +4,4 @@ hyperspy @@
     kikuchipy
     lumispy
     pyxem
+    etspy