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[RELEASE] v2.1.0 #197

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Merged
nightwnvol merged 6 commits into from
Jan 21, 2025
Merged

[RELEASE] v2.1.0 #197

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145a689
fix: UserWarning from dipy.core.gradients.gradient_table
nightwnvol Jan 20, 2025
8a1fa66
build: update numpy dependency; bump to v2.1.0
nightwnvol Jan 20, 2025
6a8138d
docs: update CHANGELOG.md
nightwnvol Jan 20, 2025
fd5ec27
ci: add cp313 wheels; bump cibuildwheel to v2.22.0
nightwnvol Jan 20, 2025
a3868d3
ci: bump macos x86_64 runners to v13
nightwnvol Jan 20, 2025
2f76e35
ci: bump macos runner to v13
nightwnvol Jan 20, 2025
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32 changes: 20 additions & 12 deletions .github/workflows/build_wheels.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@ jobs:
build_windows_wheels:
strategy:
matrix:
py: [cp36, cp37, cp38, cp39, cp310, cp311, cp312]
py: [cp36, cp37, cp38, cp39, cp310, cp311, cp312, cp313]
arch:
- [AMD64, win_amd64, x64]
- [x86, win32, x86]
Expand All @@ -29,7 +29,7 @@ jobs:
python setup_site.py openblas libopenblas ${{ github.workspace }}\OpenBLAS\lib ${{ github.workspace }}\OpenBLAS\include

- name: Build wheel ${{ matrix.py }}-${{ matrix.arch[1] }}
uses: pypa/cibuildwheel@v2.19.1
uses: pypa/cibuildwheel@v2.22.0
env:
CIBW_PLATFORM: windows
CIBW_BUILD: ${{ matrix.py }}-${{ matrix.arch[1] }}
Expand All @@ -53,31 +53,35 @@ jobs:
[
{
py: cp36,
arch: [x86_64, macosx_x86_64, 12.0, macos-12]
arch: [x86_64, macosx_x86_64, 12.0, macos-13]
},
{
py: cp37,
arch: [x86_64, macosx_x86_64, 12.0, macos-12]
arch: [x86_64, macosx_x86_64, 12.0, macos-13]
},
{
py: cp38,
arch: [x86_64, macosx_x86_64, 12.0, macos-12]
arch: [x86_64, macosx_x86_64, 12.0, macos-13]
},
{
py: cp39,
arch: [x86_64, macosx_x86_64, 12.0, macos-12]
arch: [x86_64, macosx_x86_64, 12.0, macos-13]
},
{
py: cp310,
arch: [x86_64, macosx_x86_64, 12.0, macos-12]
arch: [x86_64, macosx_x86_64, 12.0, macos-13]
},
{
py: cp311,
arch: [x86_64, macosx_x86_64, 12.0, macos-12]
arch: [x86_64, macosx_x86_64, 12.0, macos-13]
},
{
py: cp312,
arch: [x86_64, macosx_x86_64, 12.0, macos-12]
arch: [x86_64, macosx_x86_64, 12.0, macos-13]
},
{
py: cp313,
arch: [x86_64, macosx_x86_64, 12.0, macos-13]
},
{
py: cp38,
Expand All @@ -98,6 +102,10 @@ jobs:
{
py: cp312,
arch: [arm64, macosx_arm64, 12.0, macos-14]
},
{
py: cp313,
arch: [arm64, macosx_arm64, 12.0, macos-14]
}
]
name: ${{ matrix.config.py }}-${{ matrix.config.arch[1] }}
Expand Down Expand Up @@ -125,7 +133,7 @@ jobs:
python3 setup_site.py openblas openblas ${{ github.workspace }}/OpenBLAS/lib ${{ github.workspace }}/OpenBLAS/include

- name: Build wheel ${{ matrix.config.py }}-${{ matrix.config.arch[1] }}
uses: pypa/cibuildwheel@v2.19.1
uses: pypa/cibuildwheel@v2.22.0
env:
CIBW_ENVIRONMENT_MACOS: >
MACOSX_DEPLOYMENT_TARGET=${{ matrix.config.arch[2] }}
Expand All @@ -145,7 +153,7 @@ jobs:
build_linux_wheels:
strategy:
matrix:
py: [cp36, cp37, cp38, cp39, cp310, cp311, cp312]
py: [cp36, cp37, cp38, cp39, cp310, cp311, cp312, cp313]
arch:
- [x86_64, manylinux_x86_64, amd64]
- [aarch64, manylinux_aarch64, arm64]
Expand Down Expand Up @@ -173,7 +181,7 @@ jobs:
platforms: ${{ matrix.arch[2] }}

- name: Build wheel ${{ matrix.py }}-${{ matrix.arch[1] }}
uses: pypa/cibuildwheel@v2.19.1
uses: pypa/cibuildwheel@v2.22.0
env:
CIBW_PLATFORM: linux
CIBW_BUILD: ${{ matrix.py }}-${{ matrix.arch[1] }}
Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/compile_openblas_macos.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@ jobs:
strategy:
matrix:
arch:
- [x86_64, SANDYBRIDGE, 12.0, macos-12]
- [x86_64, SANDYBRIDGE, 12.0, macos-13]
- [arm64, ARMV8, 12.0, macos-14]
name: ${{ matrix.arch[0] }}
runs-on: ${{ matrix.arch[3] }}
Expand Down
10 changes: 10 additions & 0 deletions CHANGELOG.md
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@@ -1,6 +1,16 @@
# Change Log
### All notable changes to `AMICO` will be documented in this file.

## `v2.1.0`<br>_2025-01-20_
### 🛠️Changed
- Support for `numpy>=2.0.0`

### 🐛Fixed
- `UserWarning`: pass `bvals` and `bvecs` as keyword args in `dipy.core.gradients.gradient_table`

---
---

## `v2.0.3`<br>_2024-07-04_
### 🐛Fixed
- Wrong diffusivity value in the `set()` method of the `NODDI` model (typo introduced in f070c23)
Expand Down
2 changes: 1 addition & 1 deletion amico/core.py
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Original file line number Diff line number Diff line change
Expand Up @@ -432,7 +432,7 @@ def fit( self ) :
if self.get_config('doMergeB0'):
gtab = gradient_table( np.hstack((0,self.scheme.b[self.scheme.dwi_idx])), np.vstack((np.zeros((1,3)),self.scheme.raw[self.scheme.dwi_idx,:3])) )
else:
gtab = gradient_table( self.scheme.b, self.scheme.raw[:,:3] )
gtab = gradient_table( bvals=self.scheme.b, bvecs=self.scheme.raw[:,:3] )
DTI = dti.TensorModel( gtab, fit_method=self.get_config('DTI_fit_method'))
else :
if not isfile( pjoin(self.get_config('DATA_path'), peaks_filename) ):
Expand Down
4 changes: 2 additions & 2 deletions setup.cfg
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
[metadata]
name = dmri-amico
version = 2.0.3
version = 2.1.0
url = https://github.com/daducci/AMICO
download_url = https://pypi.org/project/dmri-amico
project_urls =
Expand Down Expand Up @@ -34,7 +34,7 @@ keywords =
[options]
zip_safe = False
install_requires =
numpy>=1.19.5, <2.0.0
numpy>=1.19.5
scipy>=1.5.4
dipy>=1.4.1
threadpoolctl>=3.1.0
Expand Down
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