From 145a6896532ba1b2e45eb4c206709f59c1faf461 Mon Sep 17 00:00:00 2001 From: nightwnvol Date: Mon, 20 Jan 2025 11:23:05 +0100 Subject: [PATCH 1/6] fix: UserWarning from dipy.core.gradients.gradient_table --- amico/core.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/amico/core.py b/amico/core.py index 3c0b39c..07ac65c 100644 --- a/amico/core.py +++ b/amico/core.py @@ -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) ): From 8a1fa663b8fce39f1bb2069b9096d154382c7dad Mon Sep 17 00:00:00 2001 From: nightwnvol Date: Mon, 20 Jan 2025 11:23:50 +0100 Subject: [PATCH 2/6] build: update numpy dependency; bump to v2.1.0 --- setup.cfg | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/setup.cfg b/setup.cfg index bfd89bc..fd9da4b 100644 --- a/setup.cfg +++ b/setup.cfg @@ -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 = @@ -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 From 6a8138d185205cce34c1bb033805ebba52646014 Mon Sep 17 00:00:00 2001 From: nightwnvol Date: Mon, 20 Jan 2025 11:24:20 +0100 Subject: [PATCH 3/6] docs: update CHANGELOG.md --- CHANGELOG.md | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 109b0ea..a37735f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,6 +1,16 @@ # Change Log ### All notable changes to `AMICO` will be documented in this file. +## `v2.1.0`
_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`
_2024-07-04_ ### 🐛Fixed - Wrong diffusivity value in the `set()` method of the `NODDI` model (typo introduced in f070c23) From fd5ec27d62692f058b48d9e783acb4084bb83ba7 Mon Sep 17 00:00:00 2001 From: nightwnvol Date: Mon, 20 Jan 2025 11:26:52 +0100 Subject: [PATCH 4/6] ci: add cp313 wheels; bump cibuildwheel to v2.22.0 --- .github/workflows/build_wheels.yml | 18 +++++++++++++----- 1 file changed, 13 insertions(+), 5 deletions(-) diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml index c3cf833..b71db9a 100644 --- a/.github/workflows/build_wheels.yml +++ b/.github/workflows/build_wheels.yml @@ -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] @@ -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] }} @@ -79,6 +79,10 @@ jobs: py: cp312, arch: [x86_64, macosx_x86_64, 12.0, macos-12] }, + { + py: cp313, + arch: [x86_64, macosx_x86_64, 12.0, macos-12] + }, { py: cp38, arch: [arm64, macosx_arm64, 12.0, macos-14] @@ -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] }} @@ -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] }} @@ -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] @@ -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] }} From a3868d3aa9a39b542f07ce2fd7ef71892c831f47 Mon Sep 17 00:00:00 2001 From: nightwnvol Date: Mon, 20 Jan 2025 12:05:45 +0100 Subject: [PATCH 5/6] ci: bump macos x86_64 runners to v13 --- .github/workflows/build_wheels.yml | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml index b71db9a..5524ba1 100644 --- a/.github/workflows/build_wheels.yml +++ b/.github/workflows/build_wheels.yml @@ -53,35 +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-12] + arch: [x86_64, macosx_x86_64, 12.0, macos-13] }, { py: cp38, From 2f76e35dc711f2b6aafda0035b69d9f49bf9c07f Mon Sep 17 00:00:00 2001 From: nightwnvol Date: Mon, 20 Jan 2025 12:46:58 +0100 Subject: [PATCH 6/6] ci: bump macos runner to v13 --- .github/workflows/compile_openblas_macos.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/compile_openblas_macos.yml b/.github/workflows/compile_openblas_macos.yml index eef9e11..10f0ea8 100644 --- a/.github/workflows/compile_openblas_macos.yml +++ b/.github/workflows/compile_openblas_macos.yml @@ -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] }}