FFT swap

.github/workflows/workflow.yml

@@ -4,7 +4,7 @@ on:
   pull_request:
     types: [opened, synchronize, reopened, ready_for_review]
   push:
-  
+
 
 jobs:
   check:
@@ -49,6 +49,8 @@ jobs:
     - name: Install dependencies
       run: |
         pip install tox tox-gh-actions
+        # Optional packages
+        pip install pyfftw  # `test_fft` runs for pyfftw when installed
     - name: Test with tox
       run: tox --skip-missing-interpreters false -e py${{ matrix.python-version }}-${{ matrix.pyenv }}
     - name: Upload Coverage to CodeCov
@@ -215,3 +217,32 @@ jobs:
           name: sphinx-docs
           path: docs/build
           retention-days: 7
+
+  osx_arm:
+    defaults:
+      run:
+        shell: bash -l {0}
+    needs: check
+    runs-on: macos-14
+    # Run on every code push, but only on review ready PRs
+    if: ${{ github.event_name == 'push' || github.event.pull_request.draft == false }}
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Conda
+      uses: conda-incubator/setup-miniconda@v2.3.0
+      with:
+        miniconda-version: "latest"
+        auto-update-conda: true
+        python-version: '3.8'
+        activate-environment: aspire
+        environment-file: environment-accelerate.yml
+        auto-activate-base: false
+    - name: Complete Install and Log Environment ${{ matrix.os }} Python ${{ matrix.python-version }}
+      run: |
+        conda info
+        conda list
+        conda install pyshtools  # debug depends issues
+        pip install -e ".[dev]"  # install aspire
+        pip freeze
+    - name: Test
+      run: python -m pytest -n3 --durations=50

environment-accelerate.yml

@@ -5,14 +5,11 @@ channels:
   - defaults
 
 dependencies:
-  - fftw
-  # There is a potential pyFFTW bug, pin to 0.12
-  #   https://github.com/pyFFTW/pyFFTW/issues/294
-  - pyfftw=0.12
   - pip
   - python=3.8
-  - numpy=1.23.5
-  - scipy=1.9.3
+  - pyshtools
+  - numpy=1.24.1
+  - scipy=1.10.1
   - scikit-learn
   - scikit-image
   - libblas=*=*accelerate

environment-default.yml

@@ -5,10 +5,6 @@ channels:
   - defaults
 
 dependencies:
-  - fftw
-  # There is a potential pyFFTW bug, pin to 0.12
-  #   https://github.com/pyFFTW/pyFFTW/issues/294
-  - pyfftw=0.12
   - pip
   - python=3.8
   - numpy=1.23.5

environment-intel.yml

@@ -5,10 +5,6 @@ channels:
   - defaults
 
 dependencies:
-  - fftw
-  # There is a potential pyFFTW bug, pin to 0.12
-  #   https://github.com/pyFFTW/pyFFTW/issues/294
-  - pyfftw=0.12
   - pip
   - python=3.8
   - numpy=1.23.5

environment-openblas.yml

@@ -5,10 +5,6 @@ channels:
   - defaults
 
 dependencies:
-  - fftw
-  # There is a potential pyFFTW bug, pin to 0.12
-  #   https://github.com/pyFFTW/pyFFTW/issues/294
-  - pyfftw=0.12
   - pip
   - python=3.8
   - numpy=1.23.5

pyproject.toml

@@ -39,12 +39,11 @@ dependencies = [
     "joblib",
     "matplotlib >= 3.2.0",
     "mrcfile",
-    "numpy>=1.21.5",
+    "numpy>=1.21.5, <2.0.0",
     "packaging",
     "pooch>=1.7.0",
     "pillow",
     "psutil",
-    "pyfftw",
     "pymanopt",
     "pyshtools<=4.10.4",  # 4.11.7 might have a packaging bug
     "PyWavelets",

src/aspire/config_default.yaml

@@ -3,7 +3,7 @@ common:
     # numeric module to use - one of numpy/cupy
     numeric: numpy
     # fft backend to use - one of pyfftw/scipy/cupy/mkl
-    fft: pyfftw
+    fft: scipy
 
     # Set cache directory for ASPIRE example data.
     # By default the cache location will be set by pooch.os_cache(),

src/aspire/numeric/pyfftw_fft.py

@@ -1,7 +1,11 @@
 import os
 from threading import Lock
 
-import pyfftw
+try:
+    import pyfftw
+except ModuleNotFoundError:
+    raise ModuleNotFoundError("Install `pyfftw` to use as a backend.")
+
 import pyfftw.interfaces.scipy_fftpack as scipy_fft
 
 from aspire.numeric.base_fft import FFT

tests/test_fft.py

@@ -1,12 +1,22 @@
+import logging
 from unittest import TestCase
 
 import numpy as np
 
 from aspire import config
 from aspire.numeric import fft_object, numeric_object
 
+logger = logging.getLogger(__name__)
 # Create test option combinations between numerical modules and FFT libs
-test_backends = [("numpy", "scipy"), ("numpy", "pyfftw")]
+test_backends = [("numpy", "scipy")]
+
+try:
+    import pyfftw  # noqa: F401
+
+    test_backends.append(("numpy", "pyfftw"))
+except ModuleNotFoundError:
+    logger.info("`pyfftw` module is not installed, skipping `pyfftw` FFT backend.")
+
 
 # Create Cupy fft backend if Cupy module is enabled and lib exits.
 if config["common"]["numeric"].as_str() == "cupy":

tests/test_synthetic_volume.py

@@ -136,4 +136,4 @@ def test_volume_symmetry(vol_fixture):
         corr = np.dot(rot_vol[0].flatten(), vol[0].flatten()) / np.dot(
             vol[0].flatten(), vol[0].flatten()
         )
-        assert abs(corr - 1) < 1e-5
+        assert abs(corr - 1) < 1.1e-5