Cupy 13.6 + numpy 2.3 environment related changes

conda-recipe/environment/environment.yml

@@ -0,0 +1,132 @@
+name: httomo
+channels:
+  - astra-toolbox
+  - conda-forge
+dependencies:
+  - _libgcc_mutex=0.1=conda_forge
+  - _openmp_mutex=4.5=2_gnu
+  - aom=3.9.1=hac33072_0
+  - astra-toolbox=2.4.1=py312hf5d4436_0
+  - blosc=1.21.6=he440d0b_1
+  - brunsli=0.1=hd1e3526_2
+  - bzip2=1.0.8=hda65f42_8
+  - c-ares=1.34.6=hb03c661_0
+  - c-blosc2=2.22.0=hc31b594_1
+  - ca-certificates=2026.1.4=hbd8a1cb_0
+  - cached-property=1.5.2=hd8ed1ab_1
+  - cached_property=1.5.2=pyha770c72_1
+  - charls=2.4.2=h59595ed_0
+  - cuda-cccl_linux-64=12.9.27=ha770c72_0
+  - cuda-cudart=12.9.79=h5888daf_0
+  - cuda-cudart-dev_linux-64=12.9.79=h3f2d84a_0
+  - cuda-cudart-static_linux-64=12.9.79=h3f2d84a_0
+  - cuda-cudart_linux-64=12.9.79=h3f2d84a_0
+  - cuda-nvrtc=12.9.86=hecca717_1
+  - cuda-version=12.9=h4f385c5_3
+  - cupy=13.6.0=py312h0317cef_2
+  - cupy-core=13.6.0=py312h16a6543_2
+  - dav1d=1.2.1=hd590300_0
+  - fastrlock=0.8.3=py312h8285ef7_2
+  - fftw=3.3.10=nompi_h3b011a4_111
+  - giflib=5.2.2=hd590300_0
+  - h5py=3.11.0=mpi_openmpi_py312h7cdcccc_1
+  - hdf5=1.14.3=mpi_openmpi_hf5a2fd3_4
+  - icu=78.1=h33c6efd_0
+  - imagecodecs=2026.1.1=py312ha4965bc_0
+  - imageio=2.37.0=pyhfb79c49_0
+  - importlib-metadata=8.7.0=pyhe01879c_1
+  - jxrlib=1.1=hd590300_3
+  - keyutils=1.6.3=hb9d3cd8_0
+  - krb5=1.21.3=h659f571_0
+  - lazy-loader=0.4=pyhd8ed1ab_2
+  - lcms2=2.17=h717163a_0
+  - ld_impl_linux-64=2.45=default_hbd61a6d_105
+  - lerc=4.0.0=h0aef613_1
+  - libaec=1.1.4=h3f801dc_0
+  - libastra=2.4.1=cuda_12_0
+  - libavif16=1.3.0=h6395336_2
+  - libblas=3.11.0=5_h4a7cf45_openblas
+  - libbrotlicommon=1.2.0=hb03c661_1
+  - libbrotlidec=1.2.0=hb03c661_1
+  - libbrotlienc=1.2.0=hb03c661_1
+  - libcblas=3.11.0=5_h0358290_openblas
+  - libcublas=12.9.1.4=h676940d_1
+  - libcufft=11.4.1.4=hecca717_1
+  - libcurand=10.3.10.19=h676940d_1
+  - libcurl=8.18.0=h4e3cde8_0
+  - libcusolver=11.7.5.82=h676940d_2
+  - libcusparse=12.5.10.65=hecca717_2
+  - libdeflate=1.25=h17f619e_0
+  - libedit=3.1.20250104=pl5321h7949ede_0
+  - libev=4.33=hd590300_2
+  - libexpat=2.7.3=hecca717_0
+  - libffi=3.5.2=h9ec8514_0
+  - libfreetype=2.14.1=ha770c72_0
+  - libfreetype6=2.14.1=h73754d4_0
+  - libgcc=15.2.0=he0feb66_16
+  - libgcc-ng=15.2.0=h69a702a_16
+  - libgfortran=15.2.0=h69a702a_16
+  - libgfortran-ng=15.2.0=h69a702a_16
+  - libgfortran5=15.2.0=h68bc16d_16
+  - libgomp=15.2.0=he0feb66_16
+  - libhwy=1.3.0=h4c17acf_1
+  - libjpeg-turbo=3.1.2=hb03c661_0
+  - libjxl=0.11.1=hf08fa70_5
+  - liblapack=3.11.0=5_h47877c9_openblas
+  - liblzma=5.8.1=hb9d3cd8_2
+  - libnghttp2=1.67.0=had1ee68_0
+  - libnpp=12.4.1.87=h676940d_1
+  - libnsl=2.0.1=hb9d3cd8_1
+  - libnvjitlink=12.9.86=hecca717_2
+  - libopenblas=0.3.30=pthreads_h94d23a6_4
+  - libpng=1.6.53=h421ea60_0
+  - libsqlite=3.51.1=hf4e2dac_1
+  - libssh2=1.11.1=hcf80075_0
+  - libstdcxx=15.2.0=h934c35e_16
+  - libstdcxx-ng=15.2.0=hdf11a46_16
+  - libtiff=4.7.1=h9d88235_1
+  - libtomo=1.15.3=cuda12.9h1234567_101
+  - libuuid=2.41.3=h5347b49_0
+  - libwebp-base=1.6.0=hd42ef1d_0
+  - libxcb=1.17.0=h8a09558_0
+  - libxcrypt=4.4.36=hd590300_1
+  - libzlib=1.3.1=hb9d3cd8_2
+  - libzopfli=1.0.3=h9c3ff4c_0
+  - lz4-c=1.10.0=h5888daf_1
+  - mpi=1.0=openmpi
+  - mpi4py=4.1.1=py312hd140a38_102
+  - ncurses=6.5=h2d0b736_3
+  - networkx=3.6.1=pyhcf101f3_0
+  - nomkl=1.0=h5ca1d4c_0
+  - numexpr=2.14.1=py312h88efc94_101
+  - numpy=2.3.5=py312h33ff503_1
+  - openjpeg=2.5.4=h55fea9a_0
+  - openjph=0.26.0=h8d634f6_0
+  - openmpi=4.1.6=hc5af2df_101
+  - openssl=3.6.0=h26f9b46_0
+  - packaging=25.0=pyh29332c3_1
+  - pillow=12.1.0=py312h50c33e8_0
+  - pip=25.3=pyh8b19718_0
+  - pthread-stubs=0.4=hb9d3cd8_1002
+  - python=3.12.12=hd63d673_1_cpython
+  - python_abi=3.12=8_cp312
+  - pywavelets=1.9.0=py312h4f23490_2
+  - rav1e=0.7.1=h8fae777_3
+  - readline=8.3=h853b02a_0
+  - scikit-image=0.25.2=py312hf79963d_2
+  - scipy=1.16.3=py312h54fa4ab_2
+  - setuptools=80.9.0=pyhff2d567_0
+  - snappy=1.2.2=h03e3b7b_1
+  - svt-av1=3.1.2=hecca717_0
+  - tifffile=2025.1.10=pyhd8ed1ab_0
+  - tk=8.6.13=noxft_ha0e22de_103
+  - tomopy=1.15.3=pyhd8ed1ab_1
+  - tzdata=2025c=hc9c84f9_1
+  - wheel=0.45.1=pyhd8ed1ab_1
+  - xorg-libxau=1.0.12=hb03c661_1
+  - xorg-libxdmcp=1.1.5=hb03c661_1
+  - zfp=1.0.1=h909a3a2_5
+  - zipp=3.23.0=pyhcf101f3_1
+  - zlib=1.3.1=hb9d3cd8_2
+  - zlib-ng=2.3.2=hceb46e0_1
+  - zstd=1.5.7=hb78ec9c_6

httomo/base_block.py

@@ -121,4 +121,4 @@ def is_gpu(self) -> bool:
 
     @property
     def is_cpu(self) -> bool:
-        return getattr(self._data, "device", None) is None
+        return self._data.device == "cpu"

httomo/methods.py

@@ -37,7 +37,7 @@ def calculate_stats(
     """
 
     # do this whereever the data is at the moment (GPU/CPU)
-    if getattr(data, "device", None) is not None:
+    if data.device != "cpu":
         # GPU
         data = xp.nan_to_num(data, copy=False, nan=0.0, posinf=0, neginf=0)
     else:
@@ -181,7 +181,7 @@ def _save_dataset_data(
 ):
     start = np.array(global_index)
     stop = start + np.array(data.shape)
-    assert getattr(data, "device", None) is None, "data must be on CPU for saving"
+    assert data.device == "cpu", "data must be on CPU for saving"
     assert stop[0] <= dataset.shape[0]
     assert stop[1] <= dataset.shape[1]
     assert stop[2] <= dataset.shape[2]

httomo/runner/auxiliary_data.py

@@ -70,7 +70,7 @@ def set_flats(self, flats: generic_array) -> None:
         self._flats = flats
 
     def set_angles(self, angles: np.ndarray) -> None:
-        assert getattr(angles, "device", None) is None, "Angles must be a CPU array"
+        assert angles.device == "cpu", "Angles must be a CPU array"
         self._angles = angles
 
     def _get_field(self, field: str, gpu=False) -> generic_array:

pyproject.toml

@@ -38,8 +38,8 @@ requires-python = ">=3.10"
 dynamic = ["version"]
 dependencies = [
     "click",
-    "cupy",
-    "numpy",
+    "cupy==13.6.*",
+    "numpy==2.3.*",
     "hdf5plugin",
     "httomo-backends",
     "loguru",

tests/method_wrappers/test_images.py

@@ -79,7 +79,7 @@ def save_to_images(data, out_dir, comm_rank, axis, file_format):
 def test_images_leaves_gpudata(mocker: MockerFixture, dummy_block: DataSetBlock):
     class FakeModule:
         def save_to_images(data, out_dir, offset):
-            assert getattr(data, "device", None) is None  # make sure it's on CPU
+            assert data.device == "cpu"  # make sure it's on CPU
 
     mocker.patch(
         "httomo.method_wrappers.generic.import_module", return_value=FakeModule

tests/method_wrappers/test_save_intermediate.py

@@ -157,7 +157,7 @@ def save_intermediate_data(
             angles: np.ndarray,
         ):
             assert isinstance(data, np.ndarray)
-            assert getattr(data, "device", None) is None
+            assert data.device == "cpu"
 
     mocker.patch(
         "httomo.method_wrappers.generic.import_module", return_value=FakeModule

tests/method_wrappers/test_stats_calc.py

@@ -128,9 +128,9 @@ class FakeModule:
         def calculate_stats(data, comm):
             # regardless of dataset input, we want device data if gpu enabled
             if gpu_enabled:
-                assert getattr(data, "device", None) is not None
+                assert data.device != "cpu"
             else:
-                assert getattr(data, "device", None) is None
+                assert data.device == "cpu"
             return (1.2, 3.1, 42.0, 10)
 
     mocker.patch(

tests/test_base_block.py

@@ -255,7 +255,7 @@ def test_to_cpu_transfers_the_data_back():
 
     assert block.is_gpu is False
     assert block.is_cpu is True
-    assert getattr(block.data, "device", None) is None
+    assert block.data.device == "cpu"
 
 
 def test_transfer_to_cpu_with_no_gpu(mocker: MockerFixture):
@@ -270,7 +270,7 @@ def test_transfer_to_cpu_with_no_gpu(mocker: MockerFixture):
 
     assert block.is_gpu is False
     assert block.is_cpu is True
-    assert getattr(block.data, "device", None) is None
+    assert block.data.device == "cpu"
 
 
 def test_to_cpu_twice_has_no_effect():