Merge pull request #111 from MPI-Dortmund/fix-install-problem

Update cuml and pandas
MPI-Dortmund · Oct 2, 2024 · c96b92e · c96b92e
2 parents 12d6323 + c2ba565
commit c96b92e
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Showing 6 changed files with 10 additions and 8 deletions.
diff --git a/conda_env_tomotwin.yml b/conda_env_tomotwin.yml
@@ -8,12 +8,12 @@ channels:
 dependencies:
   - pytorch[version='>=2.1']
   - torchvision
-  - pandas[version='<2']
+  - pandas
   - scipy
   - numpy
   - matplotlib
   - pytables
-  - cuml=23.12
+  - cuml=24.08
   - cuda-version=11.8
   - protobuf[version='>3.20']
   - tensorboard

diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -1,3 +1,4 @@
+sphinx<7
 sphinx-prompt
 sphinx-rtd-theme
 sphinxcontrib-youtube

diff --git a/docs/tutorials/text_modules/downscale_clustering.rst b/docs/tutorials/text_modules/downscale_clustering.rst
@@ -1,6 +1,6 @@
-.. include:: text_modules/downscale/first_paragraph.rst
+.. include:: downscale/first_paragraph.rst
 
 
 TomoTwin should be used to pick on tomograms without denoising or lowpass filtering. But you may use these tomograms for visualizing the picks in Napari. In this case, you should make sure the denoised/lowpass filtered tomogram has the same pixel size as the one you will pick on (downscaling it if necessary).
 
-.. include:: text_modules/downscale/boxsize_admonition.rst
+.. include:: downscale/boxsize_admonition.rst
diff --git a/docs/tutorials/text_modules/downscale_reference.rst b/docs/tutorials/text_modules/downscale_reference.rst
@@ -1,5 +1,5 @@
-.. include:: text_modules/downscale/first_paragraph.rst
+.. include:: downscale/first_paragraph.rst
 
 TomoTwin should be used to pick on tomograms without denoising or lowpass filtering. But you may use these tomograms to find the coordinates of your particle of interest for use as a reference. In this case, you should make sure the denoised/lowpass filtered tomogram has the same pixel size as the one you will pick on.
 
-.. include:: text_modules/downscale/boxsize_admonition.rst
+.. include:: downscale/boxsize_admonition.rst
diff --git a/setup.py b/setup.py
@@ -32,7 +32,8 @@
         "scikit-learn",
         "scikit-image",
         "pystardb>=0.4.2",
-        "pandas <= 2", # Because rapids does not support pandas > 1.5.3
+        "pandas",  # Because rapids does not support pandas > 1.5.3
+        "numexpr>=2.8.4",
         # "pytorch-metric-learning<1.7",
         "numba",
         "tabulate",

diff --git a/tomotwin/embed_main.py b/tomotwin/embed_main.py
@@ -76,7 +76,7 @@ def get_window_size(model_path: str) -> int:
     :return: Window size
     '''
 
-    checkpoint = torch.load(model_path)
+    checkpoint = torch.load(model_path, weights_only=False)
     if "window_size" in checkpoint["tomotwin_config"]:
         return int(checkpoint["tomotwin_config"]["window_size"][0])
     print("Can't find window size in model. Use window size of 37.")