GHA: Fix CI issues

.github/dependabot.yml

@@ -0,0 +1,6 @@
+version: 2
+updates:
+  - package-ecosystem: github-actions
+    directory: /
+    schedule:
+      interval: weekly

.github/workflows/main.yml

@@ -1,29 +1,76 @@
-name: github-CI
+name: main
 
-on: [push]
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+  workflow_dispatch:
 
 jobs:
-  build:
-
+  test:
     runs-on: ${{ matrix.os }}
     strategy:
+      fail-fast: false
       matrix:
-        os: [ubuntu-latest, macos-latest]
-        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
-    name: Python ${{ matrix.python-version }} example
+        os:
+          - ubuntu-latest
+          - macos-latest
+        mpi:
+          - mpich
+          - openmpi
+        py:
+          # - "3.7"
+          # - "3.8"
+          # - "3.9"
+          - "3.10"
+          - "3.11"
+          - "3.12"
 
     steps:
-    - uses: actions/checkout@v3
-    - run: git fetch --depth=1 origin +refs/tags/*:refs/tags/*
-    - name: setup-conda
-      uses: s-weigand/setup-conda@v1
+
+    - uses: actions/checkout@v4
+
+    - uses: actions/setup-python@v5
       with:
-          update-conda: true
-          python-version: ${{ matrix.python-version }}
-          conda-channels: anaconda, conda-forge
-    - run: conda --version
-    - run: which python
+        python-version: ${{ matrix.py }}
+
     - run: |
-        conda config --set always_yes yes
-        conda install -n root conda-build numpy fftw
-        conda build ./conf
+        # Install fftw
+        case $(uname) in
+          Linux)
+            sudo apt update
+            sudo apt install -y -q libfftw3-dev
+            ;;
+          Darwin)
+            export HOMEBREW_NO_INSTALLED_DEPENDENTS_CHECK=1
+            brew install fftw
+            ;;
+        esac
+
+    - run: python -m pip install -U pip build
+
+    - run: python -m build
+
+    - uses: mpi4py/setup-mpi@v1
+      with:
+        mpi: ${{ matrix.mpi }}
+
+    - run: pip install -vvv dist/mpi4py_fft-*.whl
+      env:
+        CFLAGS: "-O0"
+
+    - run: pip install -r conf/requirements-test.txt
+
+    - if: matrix.mpi == 'mpich' && startsWith(matrix.os, 'ubuntu')
+      run: ./runtests.sh
+      working-directory: tests
+
+    - if: matrix.mpi == 'mpich' && startsWith(matrix.os, 'ubuntu')
+      uses: codecov/codecov-action@v4
+      with:
+        use_oidc: true
+        files: test/coverage.xml
+        name: ${{ matrix.os }}-${{ matrix.mpi }}-${{ matrix.py }}

.gitignore

@@ -11,7 +11,6 @@ _templates/
 *.dat
 *.html
 *.xml
-*.txt
 *.h5
 *.nc
 *.xdmf

azure-pipelines.yml

@@ -1,35 +1,35 @@
 jobs:
-- job: macOS
-  displayName: macos-latest
-  pool:
-    vmImage: 'macos-latest'
-  strategy:
-    matrix:
-      Python37:
-        python.version: '3.7'
-      Python38:
-        python.version: '3.8'
-      Python39:
-        python.version: '3.9'
-      Python310:
-        python.version: '3.10'
-
-  steps:
-  - bash: echo "##vso[task.prependpath]$CONDA/bin"
-    displayName: Add conda to PATH
-
-  - bash: sudo chown -R $USER $CONDA
-    displayName: Take ownership of conda installation
-
-  - bash: |
-      conda config --add channels conda-forge
-      conda config --set always_yes yes
-      conda install -n root conda-build numpy fftw
-    displayName: Set up Anaconda
-
-  - bash: |
-      conda build --python $PYTHON_VERSION ./conf
-    displayName: Build and test
+# - job: macOS
+#   displayName: macos-latest
+#   pool:
+#     vmImage: 'macos-latest'
+#   strategy:
+#     matrix:
+#       Python37:
+#         python.version: '3.7'
+#       Python38:
+#         python.version: '3.8'
+#       Python39:
+#         python.version: '3.9'
+#       Python310:
+#         python.version: '3.10'
+#
+#   steps:
+#   - bash: echo "##vso[task.prependpath]$CONDA/bin"
+#     displayName: Add conda to PATH
+#
+#   - bash: sudo chown -R $USER $CONDA
+#     displayName: Take ownership of conda installation
+#
+#   - bash: |
+#       conda config --add channels conda-forge
+#       conda config --set always_yes yes
+#       conda install -n root conda-build numpy fftw
+#     displayName: Set up Anaconda
+#
+#   - bash: |
+#       conda build --python $PYTHON_VERSION ./conf
+#     displayName: Build and test
 
 - job: Ubuntu
   displayName: Ubuntu
@@ -45,6 +45,10 @@ jobs:
         python.version: '3.9'
       Python310:
         python.version: '3.10'
+      Python311:
+        python.version: '3.11'
+      Python312:
+        python.version: '3.12'
 
   steps:
   - bash: echo "##vso[task.prependpath]$CONDA/bin"
@@ -53,13 +57,16 @@ jobs:
   - bash: |
       conda config --add channels conda-forge
       conda config --set always_yes yes
-      conda install -n root conda-build numpy fftw
+      conda install -n root mpi4py mpich numpy fftw
     displayName: Set up Anaconda
 
   - bash: |
-      conda build --no-test --python $PYTHON_VERSION ./conf
-      conda create --name mpi4py_fft_env mpi4py_fft_test coverage scipy pyfftw=0.12 python=$PYTHON_VERSION --use-local
+      conda create --name mpi4py_fft_env \
+        python=$PYTHON_VERSION \
+        mpi4py mpich numpy fftw \
+        pyfftw scipy coverage
       source activate mpi4py_fft_env
+      pip install -vvv --no-deps .
       pip install codecov
       cd tests && ./runtests.sh
     displayName: Build and test

conf/requirements-test.txt

@@ -0,0 +1,3 @@
+coverage
+pyfftw; sys_platform == 'linux' and python_version < '3.12'
+scipy

tests/runtests.sh

@@ -1,47 +1,35 @@
 #!/bin/sh
 set -e
 
-PY=$(python -c 'import sys; print(sys.version_info.major)')
-export OMPI_MCA_plm=isolated
-export OMPI_MCA_btl_vader_single_copy_mechanism=none
-export OMPI_MCA_rmaps_base_oversubscribe=yes
+export OMPI_MCA_plm_ssh_agent=false
+export OMPI_MCA_pml=ob1
+export OMPI_MCA_btl=tcp,self
+export OMPI_MCA_mpi_yield_when_idle=true
+export OMPI_MCA_btl_base_warn_component_unused=false
+export OMPI_MCA_rmaps_base_oversubscribe=true
+export PRTE_MCA_rmaps_default_mapping_policy=:oversubscribe
 
-if [ $PY -eq 3 ]; then
-    # coverage only for python version 3
+python -m coverage erase
 
-    python -m coverage erase
+python -m coverage run -m test_fftw
+python -m coverage run -m test_libfft
+python -m coverage run -m test_io
+python -m coverage run -m test_darray
 
-    python -m coverage run -m test_fftw
-    python -m coverage run -m test_libfft
-    python -m coverage run -m test_io
-    python -m coverage run -m test_darray
-    mpiexec -n  2 python -m coverage run -m test_pencil
+mpiexec -n  2 python -m coverage run -m test_pencil
+#mpiexec -n  4 python -m coverage test_pencil.py
+#mpiexec -n  8 python -m coverage test_pencil.py
 
-    #mpiexec -n  4 python -m coverage test_pencil.py
-    #mpiexec -n  8 python -m coverage test_pencil.py
-    mpiexec -n  2 python -m coverage run -m test_mpifft
-    #mpiexec -n  4 python -m coverage test_mpifft.py
-    # mpiexec -n  8 python -m coverage test_mpifft.py
-    # mpiexec -n 12 python -m coverage test_mpifft.py
-    mpiexec -n 2 python -m coverage run spectral_dns_solver.py
-    mpiexec -n 2 python -m coverage run -m test_io
-    #mpiexec -n 4 python -m coverage run -m test_io
-    mpiexec -n 2 python -m coverage run -m test_darray
-    #mpiexec -n 4 python -m coverage run -m test_darray
+mpiexec -n  2 python -m coverage run -m test_mpifft
+#mpiexec -n  4 python -m coverage test_mpifft.py
+#mpiexec -n  8 python -m coverage test_mpifft.py
+#mpiexec -n 12 python -m coverage test_mpifft.py
+mpiexec -n 2 python -m coverage run spectral_dns_solver.py
 
-    python -m coverage combine
+mpiexec -n 2 python -m coverage run -m test_io
+#mpiexec -n 4 python -m coverage run -m test_io
+mpiexec -n 2 python -m coverage run -m test_darray
+#mpiexec -n 4 python -m coverage run -m test_darray
 
-else
-    python test_fftw.py
-    python test_libfft.py
-    mpiexec -n  2 python test_pencil.py
-    #mpiexec -n  4 python test_pencil.py
-    #mpiexec -n  8 python test_pencil.py
-    mpiexec -n  2 python test_mpifft.py
-    #mpiexec -n  4 python test_mpifft.py
-    # mpiexec -n  8 python test_mpifft.py
-    # mpiexec -n 12 python test_mpifft.py
-    mpiexec -n 2 python test_io.py
-    mpiexec -n 2 python test_darray.py
-    mpiexec -n 2 python spectral_dns_solver.py
-fi
+python -m coverage combine
+python -m coverage xml

tests/test_mpifft.py

@@ -152,8 +152,8 @@ def test_mpifft():
                                         fft.backward.input_array.shape)
                                 assert (fft.backward.output_pencil.subshape ==
                                         fft.backward.output_array.shape)
-                                assert np.alltrue(np.array(fft.global_shape(True)) == np.array(fft.forward.output_pencil.shape))
-                                assert np.alltrue(np.array(fft.global_shape(False)) == np.array(fft.forward.input_pencil.shape))
+                                assert np.all(np.array(fft.global_shape(True)) == np.array(fft.forward.output_pencil.shape))
+                                assert np.all(np.array(fft.global_shape(False)) == np.array(fft.forward.input_pencil.shape))
                                 ax = -1 if axes is None else axes[-1] if isinstance(axes[-1], int) else axes[-1][-1]
                                 assert fft.forward.input_pencil.substart[ax] == 0
                                 assert fft.backward.output_pencil.substart[ax] == 0

tests/test_speed.py

@@ -1,15 +1,10 @@
 from time import time
 import numpy as np
+import pyfftw
 import scipy.fftpack as sp
 from mpi4py_fft import fftw
 import pickle
 
-try:
-    import pyfftw
-except ImportError:
-    print('pyFFTW not available')
-    raise SystemExit(0)
-
 try:
     #fftw.import_wisdom('wisdom.dat')
     pyfftw.import_wisdom(pickle.load(open('pyfftw.wisdom', 'rb')))