patch np1.20.0 deprecation

ThomasHoffmann77 · Dec 4, 2024 · 25dbff0 · 25dbff0
1 parent 90ee19c
commit 25dbff0
Showing 1 changed file with 18 additions and 0 deletions.
diff --git a/easybuild/easyconfigs/c/cryoCARE/cryoCARE-0.3.1_fix_np1.20.0deprecations.patch b/easybuild/easyconfigs/c/cryoCARE/cryoCARE-0.3.1_fix_np1.20.0deprecations.patch
@@ -0,0 +1,18 @@
+# Thomas Hoffmann, EMBL Heidelberg, [email protected]
+# cryoCARE has requirement numpy ~1.19.2, but we are using newer with SciPy-bundle
+# numpy.bool is deprecated sind v 1.20.0: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations.
+diff -ru cryoCARE_pip-0.3.1/cryocare/internals/CryoCAREDataModule.py cryoCARE_pip-0.3.1_fix_np1.20.0deprecations/cryocare/internals/CryoCAREDataModule.py
+--- cryoCARE_pip-0.3.1/cryocare/internals/CryoCAREDataModule.py	2023-12-11 10:19:20.000000000 +0100
++++ cryoCARE_pip-0.3.1_fix_np1.20.0deprecations/cryocare/internals/CryoCAREDataModule.py	2024-12-04 10:49:42.527101697 +0100
+@@ -121,9 +121,9 @@
+
+         # If no mask is specified, just create a one-mask
+         if mask_path is None:
+-            mask = np.ones(even.data.shape).astype(np.bool)
++            mask = np.ones(even.data.shape).astype(np.bool_)
+         else:
+-            mask = mrcfile.read(mask_path).astype(np.bool)
++            mask = mrcfile.read(mask_path).astype(np.bool_)
+
+             assert even.data.shape == mask.data.shape, '{} and {} tomogram / mask have different shapes.'.format(even_path,
+                                                                                                                  mask_path)