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numpy 2 #2218

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bc8207f
misc numpy>=2 safety
casperdcl Sep 30, 2025
03051c5
bump numpy version
casperdcl Sep 30, 2025
849b0a7
dtype_like helper
casperdcl Sep 30, 2025
0356f32
bump astra-toolbox
casperdcl Sep 30, 2025
366826e
fix test precision
casperdcl Oct 1, 2025
6eb41b7
CI: test py3.12
casperdcl Oct 1, 2025
f3abd03
CI: bump actions
casperdcl Oct 24, 2025
46930e2
bump ccpi-regulariser
casperdcl Oct 24, 2025
d5b9813
Fix NaN usage in show_geometry function (#2246)
paskino Dec 8, 2025
f381c2a
astra-toolbox conda channel
casperdcl Dec 10, 2025
4006637
fix ccpi-regulariser CPU build string
casperdcl Jan 27, 2026
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32 changes: 16 additions & 16 deletions .github/workflows/build.yml
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Expand Up @@ -27,10 +27,10 @@ jobs:
runs-on: [self-hosted, python, cuda]
strategy:
matrix:
python-version: [3.11]
numpy-version: [1.25]
python-version: [3.12]
numpy-version: [1.26]
steps:
- uses: actions/checkout@v4
- uses: actions/checkout@v5
with: {fetch-depth: 0, submodules: recursive}
- id: reqs
name: set requirements
Expand Down Expand Up @@ -67,12 +67,12 @@ jobs:
matrix:
include:
- {python-version: '3.10', numpy-version: 1.23}
- {python-version: 3.12, numpy-version: 1.26}
- {python-version: 3.12, numpy-version: 2}
steps:
- uses: actions/checkout@v4
- uses: actions/checkout@v5
with: {fetch-depth: 0, submodules: recursive}
- name: set requirements
run: sed -ri -e '/ python /d' -e 's/(.* numpy) .*/\1=${{ matrix.numpy-version }}/' -e 's/=cuda*//' -e '/tigre/d' scripts/requirements-test.yml
run: sed -ri -e '/ python /d' -e 's/(.* numpy) .*/\1=${{ matrix.numpy-version }}/' -e 's/ cuda*//' -e '/tigre/d' scripts/requirements-test.yml
- uses: conda-incubator/setup-miniconda@v3
with:
python-version: ${{ matrix.python-version }}
Expand Down Expand Up @@ -109,8 +109,8 @@ jobs:
fi
fi
if $include_max; then
echo "include=[{'python-version': 3.12, 'os': 'ubuntu'}, {'python-version': 3.12, 'os': 'windows'}]" >> $GITHUB_OUTPUT
echo "include-numpy=[{'python-version': 3.12, 'numpy-version': 1.26, 'os': 'ubuntu'}, {'python-version': 3.12, 'numpy-version': 1.26, 'os': 'windows'}]" >> $GITHUB_OUTPUT
echo "include=[{'python-version': 3.13, 'os': 'ubuntu'}, {'python-version': 3.13, 'os': 'windows'}]" >> $GITHUB_OUTPUT
echo "include-numpy=[{'python-version': 3.13, 'numpy-version': 2, 'os': 'ubuntu'}, {'python-version': 3.13, 'numpy-version': 2, 'os': 'windows'}]" >> $GITHUB_OUTPUT
else
echo "include=[]" >> $GITHUB_OUTPUT
echo "include-numpy=[]" >> $GITHUB_OUTPUT
Expand All @@ -125,7 +125,7 @@ jobs:
os: ${{ fromJson(needs.conda-matrix.outputs.os) }}
include: ${{ fromJson(needs.conda-matrix.outputs.include) }}
steps:
- uses: actions/checkout@v4
- uses: actions/checkout@v5
with:
fetch-depth: 0
submodules: recursive
Expand Down Expand Up @@ -158,15 +158,15 @@ jobs:
os: ${{ fromJson(needs.conda-matrix.outputs.os) }}
include: ${{ fromJson(needs.conda-matrix.outputs.include-numpy) }}
steps:
- uses: actions/checkout@v4
- uses: actions/checkout@v5
- uses: conda-incubator/setup-miniconda@v3
with:
python-version: ${{ matrix.python-version }}
mamba-version: "*"
channels: conda-forge
conda-remove-defaults: "true"
- run: conda install boa
- uses: actions/download-artifact@v4
- uses: actions/download-artifact@v5
with:
name: cil-py${{ matrix.python-version }}-${{ matrix.os }}
path: dist
Expand All @@ -180,13 +180,13 @@ jobs:
runs-on: ubuntu-latest
needs: conda-test
steps:
- uses: actions/checkout@v4
- uses: actions/checkout@v5
- uses: conda-incubator/setup-miniconda@v3
with:
mamba-version: "*"
channels: conda-forge
conda-remove-defaults: "true"
- uses: actions/download-artifact@v4
- uses: actions/download-artifact@v5
with: {pattern: cil-py*-*, path: dist, merge-multiple: true}
- run: mamba install anaconda-client
- name: anaconda upload -c ccpi
Expand All @@ -205,7 +205,7 @@ jobs:
defaults: {run: {shell: 'bash -el {0}', working-directory: docs}}
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- uses: actions/checkout@v5
with:
fetch-depth: 0
submodules: recursive
Expand All @@ -229,7 +229,7 @@ jobs:
conda list
- run: pip install ..
- name: checkout docs
uses: actions/checkout@v4
uses: actions/checkout@v5
with:
path: docs/build
ref: gh-pages
Expand Down Expand Up @@ -262,7 +262,7 @@ jobs:
contents: read
packages: write
steps:
- uses: actions/checkout@v4
- uses: actions/checkout@v5
with:
fetch-depth: 0
submodules: recursive
Expand Down
4 changes: 4 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -7,6 +7,10 @@
- Dependencies:
- olefile and dxchange are optional dependencies, instead of required (#2209)
- improve `tqdm` notebook support (#2241)
- Added support for numpy 2
- Update to CCPi-Regularisation toolkit 25.0.0
- Added support for python 3.13
- Added support for astra-toolbox 2.4
- Documentation:
- Render the user showcase notebooks in the documentation (#2189)
- Enhancements:
Expand Down
4 changes: 2 additions & 2 deletions Dockerfile
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Expand Up @@ -9,13 +9,13 @@ LABEL org.opencontainers.image.source=https://github.com/TomographicImaging/CIL
LABEL org.opencontainers.image.licenses="Apache-2.0 AND BSD-3-Clause AND GPL-3.0"

# CUDA-specific packages
ARG CIL_EXTRA_PACKAGES="tigre=2.6 astra-toolbox=2.1.0=cuda*"
ARG CIL_EXTRA_PACKAGES="tigre=2.6 astra-toolbox::astra-toolbox=2.4=cuda* ccpi::ccpi-regulariser=25.0.0=cuda*"
# build & runtime dependencies
# TODO: sync scripts/create_local_env_for_cil_development.sh, scripts/requirements-test.yml, recipe/meta.yaml (e.g. missing libstdcxx-ng _openmp_mutex pip)?
# vis. https://github.com/TomographicImaging/CIL/pull/1590
COPY --chown="${NB_USER}" scripts/requirements-test.yml environment.yml
# channel_priority: https://stackoverflow.com/q/58555389
RUN sed -ri '/tigre|astra-toolbox| python /d' environment.yml \
RUN sed -ri -e '/tigre| python /d' -e 's/ cuda*//' environment.yml \
&& for pkg in 'jupyter-server-proxy>4.1.0' $CIL_EXTRA_PACKAGES; do echo " - $pkg" >> environment.yml; done \
&& conda config --env --set channel_priority strict \
&& for ch in defaults nvidia ccpi https://software.repos.intel.com/python/conda conda-forge; do conda config --env --add channels $ch; done \
Expand Down
11 changes: 5 additions & 6 deletions README.md
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Expand Up @@ -19,7 +19,7 @@ Binary installation of CIL can be achieved with `conda`.
We recommend using either [`miniconda`](https://docs.conda.io/projects/miniconda/en/latest) or [`miniforge`](https://github.com/conda-forge/miniforge), which are both minimal installers for `conda`. We also recommend a `conda` version of at least `23.10` for quicker installation.

#### Create a conda environment with CIL
We maintain an environment file with the required packages to run the [CIL demos](https://github.com/TomographicImaging/CIL-Demos) which you can use to create a new environment. This will have specific and tested versions of all dependencies that are outlined in the table below:
We maintain an environment file with the required packages to run the [CIL demos](https://github.com/TomographicImaging/CIL-Demos) which you can use to create a new environment. This will have specific and tested versions of all dependencies that are outlined in the table below:

```sh
conda env create -f https://tomographicimaging.github.io/scripts/env/cil_demos.yml
Expand Down Expand Up @@ -47,13 +47,13 @@ While building the CIL package we test with specific versions of dependencies. T

| Package | Tested Version | Conda install command | Description | License |
|----|----|--------|--------|----|
| [Python](https://www.python.org/) | 3.10 - 3.12 | `"python>=3.10,<=3.12"` || [PSF-2.0](https://docs.python.org/3/license.html) |
| [Numpy](https://github.com/numpy/numpy) | 1.23 - 1.26 | `"numpy>=1.23,<2"` || [BSD-3-Clause](https://numpy.org/doc/stable/license.html) |
| [Python](https://www.python.org/) | 3.10 - 3.13 | `"python>=3.10,<=3.13"` || [PSF-2.0](https://docs.python.org/3/license.html) |
| [Numpy](https://github.com/numpy/numpy) | 1.23 - 2.3 | `"numpy>=1.23,<=2.3"` || [BSD-3-Clause](https://numpy.org/doc/stable/license.html) |
| [IPP](https://www.intel.com/content/www/us/en/developer/tools/oneapi/ipp.html#gs.gxwq5p) | 2021.12 | `-c https://software.repos.intel.com/python/conda ipp=2021.12` | The Intel Integrated Performance Primitives Library (required for the CIL recon class). | [ISSL](http://www.intel.com/content/www/us/en/developer/articles/license/end-user-license-agreement.html) |
|--|--| **Optional dependencies** |--|--|
| [ASTRA toolbox](http://www.astra-toolbox.com) | 2.1 | CPU: `conda-forge::astra-toolbox=2.1=py*` <br> GPU: `conda-forge::astra-toolbox=2.1=cuda*` | CT projectors, FBP and FDK. | [GPL-3.0](https://github.com/astra-toolbox/astra-toolbox/blob/master/COPYING) |
| [ASTRA toolbox](http://www.astra-toolbox.com) | 2.1 - 2.4 | CPU: `astra-toolbox::astra-toolbox=2.4=py*` <br> GPU: `astra-toolbox::astra-toolbox=2.4=cuda*` | CT projectors, FBP and FDK. | [GPL-3.0](https://github.com/astra-toolbox/astra-toolbox/blob/master/COPYING) |
| [TIGRE](https://github.com/CERN/TIGRE) | 2.6 | `ccpi::tigre=2.6` | CT projectors, FBP and FDK. | [BSD-3-Clause](https://github.com/CERN/TIGRE/blob/master/LICENSE.txt) |
| [CCPi Regularisation Toolkit](https://github.com/TomographicImaging/CCPi-Regularisation-Toolkit) | 24.0.1 | `ccpi::ccpi-regulariser=24.0.1` | Toolbox of regularisation methods. | [Apache-2.0](https://github.com/TomographicImaging/CCPi-Regularisation-Toolkit/blob/master/LICENSE) |
| [CCPi Regularisation Toolkit](https://github.com/TomographicImaging/CCPi-Regularisation-Toolkit) | 25.0.0 | CPU: `ccpi::ccpi-regulariser=25.0.0=cpu*` <br> GPU: `ccpi::ccpi-regulariser=25.0.0=cuda*` | Toolbox of regularisation methods. | [Apache-2.0](https://github.com/TomographicImaging/CCPi-Regularisation-Toolkit/blob/master/LICENSE) |
| [TomoPhantom](https://github.com/dkazanc/TomoPhantom) | [2.0.0](https://github.com/dkazanc/TomoPhantom/releases/tag/v2.0.0) | `ccpi::tomophantom=2.0.0` | Generates phantoms to use as test data. | [Apache-2.0](https://github.com/dkazanc/TomoPhantom/blob/master/LICENSE) |
| [ipykernel](https://github.com/ipython/ipykernel) || `ipykernel` | Provides the IPython kernel to run Jupyter notebooks. | [BSD-3-Clause](https://github.com/ipython/ipykernel/blob/main/LICENSE) |
| [ipywidgets](https://github.com/jupyter-widgets/ipywidgets) || `ipywidgets` | Enables visualisation tools within jupyter noteboooks. | [BSD-3-Clause](https://github.com/jupyter-widgets/ipywidgets/blob/main/LICENSE) |
Expand All @@ -62,7 +62,6 @@ While building the CIL package we test with specific versions of dependencies. T
|[olefile](https://github.com/decalage2/olefile)|>= 0.46|`olefile>=0.46`|Package to process Microsoft OLE2 files, used to read ZEISS data files.|[BSD-style (custom)](https://github.com/decalage2/olefile?tab=License-1-ov-file)|
|[dxchange](https://github.com/data-exchange/dxchange)||`dxchange`|Provides an interface with TomoPy for loading tomography data.|[BSD-style (custom)](https://github.com/data-exchange/dxchange?tab=License-1-ov-file)|


### Docker

Finally, CIL can be run via a Jupyter Notebook enabled Docker container:
Expand Down
24 changes: 12 additions & 12 deletions Wrappers/Python/cil/framework/acquisition_data.py
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Expand Up @@ -27,7 +27,7 @@
class AcquisitionData(DataContainer, Partitioner):
"""
DataContainer for holding 2D or 3D sinogram

Parameters
----------
array : numpy.ndarray or DataContainer
Expand All @@ -36,10 +36,10 @@ class AcquisitionData(DataContainer, Partitioner):
If True, the array will be deep copied. If False, the array will be shallow copied.
geometry : AcquisitionGeometry
The geometry of the data. If the dtype of the array and geometry are different, the geometry dtype will be overridden.

**kwargs:
dtype : numpy.dtype
Specify the data type of the AcquisitionData array, this is useful if you pass None to array and want to over-ride the dtype of the geometry.
Specify the data type of the AcquisitionData array, this is useful if you pass None to array and want to over-ride the dtype of the geometry.
If an array is passed, dtype must match the dtype of the array.

"""
Expand Down Expand Up @@ -84,7 +84,7 @@ def __init__(self,
if dtype is None:
dtype = geometry.dtype
array = numpy.empty(geometry.shape, dtype)

elif issubclass(type(array) , DataContainer):
array = array.as_array()

Expand All @@ -107,12 +107,12 @@ def __eq__(self, other):
'''
Check if two AcquisitionData objects are equal. This is done by checking if the geometry, data and dtype are equal.
Also, if the other object is a numpy.ndarray, it will check if the data and dtype are equal.

Parameters
----------
other: AcquisitionData or numpy.ndarray
The object to compare with.

Returns
-------
bool
Expand All @@ -123,12 +123,12 @@ def __eq__(self, other):
if numpy.array_equal(self.as_array(), other.as_array()) \
and self.geometry == other.geometry \
and self.dtype == other.dtype:
return True
return True
elif numpy.array_equal(self.as_array(), other) and self.dtype==other.dtype:
return True
else:
return False

def _get_slice(self, **kwargs):
'''
Functionality of get_slice
Expand Down Expand Up @@ -165,8 +165,8 @@ def _get_slice(self, **kwargs):
return out
else:
return AcquisitionData(out.array, deep_copy=False, geometry=geometry_new)


def get_slice(self, *args, **kwargs):
'''
Returns a new AcquisitionData of a single slice in the requested direction.
Expand Down Expand Up @@ -205,10 +205,10 @@ def get_slice(self, *args, **kwargs):
raise TypeError(f"Cannot use 'projection' for geometries that use angles. Use 'angle' instead.")
elif key not in AcquisitionDimension and key != 'force':
raise TypeError(f"'{key}' not in allowed labels {AcquisitionDimension}.")

if args:
warnings.warn("Positional arguments for get_slice are deprecated. Use keyword arguments instead.", DeprecationWarning, stacklevel=2)

num_args = len(args)

if num_args > 0:
Expand Down
4 changes: 1 addition & 3 deletions Wrappers/Python/cil/framework/block.py
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Expand Up @@ -733,9 +733,7 @@ def __neg__(self):
return -1 * self

def dot(self, other):
#
tmp = [ self.containers[i].dot(other.containers[i]) for i in range(self.shape[0])]
return sum(tmp)
return sum(self.containers[i].dot(other.containers[i]) for i in range(self.shape[0]))

def __len__(self):

Expand Down
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