Merge branch 'main' into multislice-updated

mjo22 · Dec 6, 2024 · cd595a4 · cd595a4
2 parents 0fd73c2 + b4d678d
commit cd595a4
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diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
@@ -26,15 +26,15 @@ jobs:
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v5
         with:
-          lfs: true
+#          lfs: true
           python-version: ${{ matrix.python-version }}
-      - name: Install Git LFS
-        run: |
-          sudo apt-get update
-          sudo apt-get install git-lfs
-          git lfs install
-      - name: Pull LFS Files
-        run: git lfs pull
+#      - name: Install Git LFS
+#        run: |
+#          sudo apt-get update
+#          sudo apt-get install git-lfs
+#          git lfs install
+#      - name: Pull LFS Files
+#        run: git lfs pull
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip

diff --git a/.gitignore b/.gitignore
@@ -1,3 +1,8 @@
+# generate-starfile-and-mrcs tutorial generated data
+docs/examples/relion_dataset.star
+docs/examples/relion_dataset.star~
+docs/examples/relion_dataset_particles/
+
 .vscode/settings.json
 *.swp
 *_version.py

diff --git a/docs/api/simulator/potential_integrators.md b/docs/api/simulator/potential_integrators.md
@@ -26,16 +26,6 @@
 
 ---
 
-::: cryojax.simulator.EwaldSphereExtraction
-        options:
-            members:
-                - __init__
-                - compute_fourier_integrated_potential
-                - extract_voxels_from_spline_coefficients
-                - extract_voxels_from_grid_points
-
----
-
 ::: cryojax.simulator.NufftProjection
         options:
             members:

diff --git a/docs/examples/cross-correlation-search.ipynb b/docs/examples/cross-correlation-search.ipynb
diff --git a/docs/examples/data/groel_chainA.pdb b/docs/examples/data/groel_chainA.pdb
diff --git a/docs/examples/read-dataset.ipynb b/docs/examples/read-dataset.ipynb