MAINT: trigger building of updated binaries; deprecate python 3.8 (#105)

* MAINT: trigger building of updated binaries; deprecate python 3.8

* MAINT: update github action versions

* MAINT: incremental removal of cgrappa; small formatting/type hinting updates

* STY: flake8 adjustments

* BLD: make build release by default

.github/workflows/build-python-package.yml

@@ -16,12 +16,12 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: [3.8, 3.9, '3.10', '3.11']
+        python-version: ['3.9', '3.10', '3.11', '3.12']
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Lint with flake8

.github/workflows/github-deploy.yml

@@ -12,23 +12,23 @@ on: workflow_dispatch
 #      - published
 
 env:
-  CIBW_SKIP: cp27-* pp27-* pp37-* pp38-* pp39-* pp310-* cp35-* cp36-* cp37-* cp*-win32 cp*-manylinux_i686 cp*-musl* cp312-*  # skip 3.12 for now until numpy releases
+  CIBW_SKIP: cp27-* pp27-* pp37-* pp38-* pp39-* pp310-* cp35-* cp36-* cp37-* cp38-* cp*-win32 cp*-manylinux_i686 cp*-musl*
 
 jobs:
   build_wheels:
     name: Build wheels on ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-20.04, windows-latest, macos-latest]
+        os: [ubuntu-latest, windows-latest, macos-latest]
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v5
         name: Install Python
         with:
-          python-version: '3.8'
+          python-version: '3.12'
 
       - name: Install cibuildwheel
         run: |
@@ -37,7 +37,7 @@ jobs:
 
       - name: Enable Developer Command Prompt
         if: runner.os == 'Windows'
-        uses: ilammy/msvc-dev-cmd@v1.12.0
+        uses: ilammy/msvc-dev-cmd@v1
 
       - name: Build wheels
         run: |
@@ -51,12 +51,12 @@ jobs:
     name: Build source distribution
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v5
         name: Install Python
         with:
-          python-version: '3.8'
+          python-version: '3.12'
 
       - name: Install dependencies
         run: |
@@ -79,7 +79,7 @@ jobs:
       id-token: write
     if: github.event_name == 'workflow_dispatch'
     steps:
-      - uses: actions/download-artifact@v2
+      - uses: actions/download-artifact@v4.1.7
         with:
           name: artifact
           path: dist

INSTALLATION.rst

@@ -1,3 +1,5 @@
+WARNING: this may contain outdated information.
+
 Windows 10 Installation
 =======================
 

meson.build

@@ -1,44 +1,60 @@
 project(
   'pygrappa',
-  'c', 'cpp',
-  version: '0.26.2',
-  license: '',
-  meson_version: '>= 0.64.0',
+  'c', 'cpp', 'cython',
+  version: '0.26.3',
+  license: 'MIT',
+  meson_version: '>= 1.5.0',
   default_options: [
-    'buildtype=debugoptimized',
+    'buildtype=release',
+    'b_ndebug=if-release',
     'c_std=c99',
     'cpp_std=c++14',
   ],
 )
 
 cc = meson.get_compiler('c')
 cpp = meson.get_compiler('cpp')
-cython = find_program('cython')
+cy = meson.get_compiler('cython')
+cython = find_program(cy.cmd_array()[0])
+if not cy.version().version_compare('>=3.0.8')
+  error('SciPy requires Cython >= 3.0.8')
+endif
 
 is_windows = host_machine.system() == 'windows'
 
 # https://mesonbuild.com/Python-module.html
-py_mod = import('python')
-py3 = py_mod.find_installation(pure: false)
+py3 = import('python').find_installation(pure: false)
 py3_dep = py3.dependency()
 
 # NumPy include directory - needed in all submodules
 incdir_numpy = run_command(py3,
-  [
-    '-c',
-    'import os; os.chdir(".."); import numpy; print(numpy.get_include())'
-  ],
-  check: true
+    [
+      '-c',
+      '''import os
+#os.chdir(os.path.join("..", "tools"))
+import numpy as np
+try:
+    incdir = os.path.relpath(np.get_include())
+except Exception:
+    incdir = np.get_include()
+print(incdir)
+    '''
+    ],
+    check: true
 ).stdout().strip()
+message(incdir_numpy)
 
 inc_np = include_directories(incdir_numpy)
 numpy_nodepr_api = '-DNPY_NO_DEPRECATED_API=NPY_1_9_API_VERSION'
 
+cython_args = ['-3', '--fast-fail', '--output-file', '@OUTPUT@', '--include-dir', '@BUILD_ROOT@', '@INPUT@']
+if cy.version().version_compare('>=3.1.0')
+  cython_args += ['-Xfreethreading_compatible=True']
+endif
+cython_cplus_args = ['--cplus'] + cython_args
 
-cython_cli = find_program('pygrappa/utils/cythoner.py')
-
-cython_gen_cpp = generator(cython_cli,
-  arguments : ['@INPUT@', '@OUTPUT@', '--cplus'],
+cython_gen_cpp = generator(cython,
+  arguments : cython_cplus_args,
   output : '@[email protected]',
   depends : [])
 

pygrappa/__init__.py

@@ -1,4 +1,4 @@
-'''Bring functions up to the correct level.'''
+"""Bring functions up to the correct level."""
 
 # GRAPPA
 from .mdgrappa import mdgrappa  # NOQA

pygrappa/cgsense.py

@@ -1,4 +1,4 @@
-'''Python implementation of iterative and CG-SENSE.'''
+"""Python implementation of iterative and CG-SENSE."""
 
 from time import time
 import logging
@@ -8,25 +8,25 @@
 
 
 def _fft(x0, axes=None):
-    '''Utility Forward FFT function.
-    '''
+    """Utility Forward FFT function.
+    """
     if axes is None:
         axes = np.arange(x0.ndim-1)
     return np.fft.fftshift(np.fft.fftn(np.fft.ifftshift(
         x0, axes=axes), axes=axes), axes=axes)
 
 
 def _ifft(x0, axes=None):
-    '''Utility Inverse FFT function.
-    '''
+    """Utility Inverse FFT function.
+    """
     if axes is None:
         axes = np.arange(x0.ndim-1)
     return np.fft.ifftshift(np.fft.ifftn(np.fft.fftshift(
         x0, axes=axes), axes=axes), axes=axes)
 
 
-def cgsense(kspace, sens, coil_axis=-1):
-    '''Conjugate Gradient SENSE for arbitrary Cartesian acquisitions.
+def cgsense(kspace, sens, coil_axis: int = -1):
+    """Conjugate Gradient SENSE for arbitrary Cartesian acquisitions.
 
     Parameters
     ----------
@@ -65,7 +65,7 @@ def cgsense(kspace, sens, coil_axis=-1):
            Resonance in Medicine: An Official Journal of the
            International Society for Magnetic Resonance in Medicine
            46.4 (2001): 638-651.
-    '''
+    """
     # Make sure coils are in the back
     kspace = np.moveaxis(kspace, coil_axis, -1)
 
@@ -98,13 +98,13 @@ def cgsense(kspace, sens, coil_axis=-1):
     # => E : (sx*sy, sx*sy)
 
     def _AH(x0):
-        '''kspace -> imspace'''
+        """kspace -> imspace"""
         x0 = np.reshape(x0, kspace.shape)
         res = np.sum(sens.conj()*_ifft(x0), axis=-1)
         return np.reshape(res, (-1,))
 
     def _A(x0):
-        '''imspace -> kspace'''
+        """imspace -> kspace"""
         res = np.reshape(x0, dims)
         res = _fft(res[..., None]*sens)*mask[..., None]
         return np.reshape(res, (-1,))
@@ -122,7 +122,3 @@ def E(x0):
     logging.info('CG-SENSE took %g sec', (time() - t0))
 
     return np.reshape(x, dims).astype(tipe)
-
-
-if __name__ == '__main__':
-    pass

pygrappa/coils.py

@@ -1,12 +1,12 @@
-'''Coil estimation strategies.'''
+"""Coil estimation strategies."""
 
 import numpy as np
 from scipy.linalg import eigh
 from skimage.filters import threshold_li
 
 
-def walsh(imspace, mask=None, coil_axis=-1):
-    '''Stochastic matched filter coil combine.
+def walsh(imspace, mask=None, coil_axis: int = -1):
+    """Stochastic matched filter coil combine.
 
     Parameters
     ----------
@@ -31,7 +31,7 @@ def walsh(imspace, mask=None, coil_axis=-1):
            imagery." Magnetic Resonance in Medicine: An Official
            Journal of the International Society for Magnetic
            Resonance in Medicine 43.5 (2000): 682-690.
-    '''
+    """
     imspace = np.moveaxis(imspace, coil_axis, -1)
     ncoils = imspace.shape[-1]
     ns = np.prod(imspace.shape[:-1])

pygrappa/examples/basic_cgrappa.py

@@ -1,11 +1,12 @@
-'''Basic CGRAPPA example using Shepp-Logan phantom.'''
+"""Basic CGRAPPA example using Shepp-Logan phantom."""
 
 import numpy as np
 import matplotlib.pyplot as plt
 from phantominator import shepp_logan
 
 from pygrappa import cgrappa
 
+
 if __name__ == '__main__':
 
     # Generate fake sensitivity maps: mps

pygrappa/examples/basic_cgsense.py

@@ -1,4 +1,4 @@
-'''Basic usage of CG-SENSE implementation.'''
+"""Basic usage of CG-SENSE implementation."""
 
 import numpy as np
 import matplotlib.pyplot as plt
@@ -8,6 +8,7 @@
 from pygrappa import cgsense
 from pygrappa.utils import gaussian_csm
 
+
 if __name__ == '__main__':
 
     N, nc = 128, 4

pygrappa/examples/basic_gfactor.py

@@ -1,11 +1,12 @@
-'''Simple g-factor maps.'''
+"""Simple g-factor maps."""
 
 import numpy as np
 import matplotlib.pyplot as plt
 
 from pygrappa import gfactor, gfactor_single_coil_R2
 from pygrappa.utils import gaussian_csm
 
+
 if __name__ == '__main__':
 
     # Make circle

pygrappa/examples/basic_grappa.py

@@ -1,11 +1,12 @@
-'''Basic GRAPPA example using Shepp-Logan phantom.'''
+"""Basic GRAPPA example using Shepp-Logan phantom."""
 
 import numpy as np
 import matplotlib.pyplot as plt
 from phantominator import shepp_logan
 
 from pygrappa import grappa
 
+
 if __name__ == '__main__':
 
     # Generate fake sensitivity maps: mps

pygrappa/examples/basic_grappaop.py

@@ -1,4 +1,4 @@
-'''Basic usage of the GRAPPA operator.'''
+"""Basic usage of the GRAPPA operator."""
 
 import numpy as np
 import matplotlib.pyplot as plt
@@ -8,7 +8,7 @@
 except ImportError:
     from skimage.measure import compare_nrmse
 
-from pygrappa import cgrappa, grappaop
+from pygrappa import mdgrappa, grappaop
 from pygrappa.utils import gaussian_csm
 
 
@@ -51,7 +51,7 @@ def normalize(x0):
     kspace4x1[3::4, ...] = 0
 
     # Compare to regular ol' GRAPPA
-    grecon4x1 = cgrappa(kspace4x1, calib, kernel_size=(4, 5))
+    grecon4x1 = mdgrappa(kspace4x1, calib, kernel_size=(4, 5))
 
     # Get a GRAPPA operator and do the recon
     Gx, Gy = grappaop(calib)
@@ -65,7 +65,7 @@ def normalize(x0):
     kspace2x2 = kspace.copy()
     kspace2x2[1::2, ...] = 0
     kspace2x2[:, 1::2, :] = 0
-    grecon2x2 = cgrappa(kspace2x2, calib, kernel_size=(4, 5))
+    grecon2x2 = mdgrappa(kspace2x2, calib, kernel_size=(4, 5))
     recon2x2 = kspace2x2.copy()
     recon2x2[1::2, ...] = recon2x2[::2, ...] @ Gx
     recon2x2[:, 1::2, :] = recon2x2[:, ::2, :] @ Gy

pygrappa/examples/basic_gridding.py

@@ -1,4 +1,4 @@
-'''Demonstrate how to grid non-Cartesian data.
+"""Demonstrate how to grid non-Cartesian data.
 
 Notes
 -----
@@ -22,7 +22,7 @@
        NFFT 3---a software library for various nonequispaced fast
        Fourier transforms." ACM Transactions on Mathematical Software
        (TOMS) 36.4 (2009): 19.
-'''
+"""
 
 from time import time
 

pygrappa/examples/basic_hpgrappa.py

@@ -1,4 +1,4 @@
-'''Basic hp-GRAPPA usage.'''
+"""Basic hp-GRAPPA usage."""
 
 import numpy as np
 from mpl_toolkits.mplot3d import Axes3D  # pylint: disable=W0611 # NOQA
@@ -8,6 +8,7 @@
 from pygrappa import hpgrappa, mdgrappa
 from pygrappa.utils import gaussian_csm
 
+
 if __name__ == '__main__':
 
     # The much abused Shepp-Logan phantom