Merge pull request #30 from mpi4py/dalcinl/cython3

dalcinl · web-flow · commit ad9a610b9c53 · 2024-04-24T20:47:21.000+03:00
Add pyproject.toml and support Cython 3
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -0,0 +1,6 @@
+version: 2
+updates:
+  - package-ecosystem: github-actions
+    directory: /
+    schedule:
+      interval: weekly
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -1,29 +1,77 @@
-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"]
-    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:
+        files: test/coverage.xml
+        name: ${{ matrix.os }}-${{ matrix.mpi }}-${{ matrix.py }}
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
diff --git a/.gitignore b/.gitignore
@@ -11,7 +11,6 @@ _templates/
 *.dat
 *.html
 *.xml
-*.txt
 *.h5
 *.nc
 *.xdmf
diff --git a/Makefile b/Makefile
@@ -1,7 +1,7 @@
 VERSION=$(shell python3 -c "import mpi4py_fft; print(mpi4py_fft.__version__)")
 
 default:
-	python setup.py build_ext -i
+	python setup.py build build_ext -i
 
 pip:
 	rm -f dist/*
@@ -15,6 +15,6 @@ tag:
 publish: tag pip
 
 clean:
-	git clean mpi4py_fft -fx
+	git clean -dxf mpi4py_fft
 	cd docs && make clean && cd ..
-	@rm -rf *.egg-info/ build/ dist/ .eggs/
+	@rm -rf *.egg-info/ build/ dist/ .eggs/
diff --git a/azure-pipelines.yml b/azure-pipelines.yml
diff --git a/conf/meta.yaml b/conf/meta.yaml
@@ -16,7 +16,7 @@ requirements:
     - {{ compiler('cxx') }}
   host:
     - python
-    - cython <3.0
+    - cython
     - numpy
     - pip
     - fftw
@@ -25,7 +25,7 @@ requirements:
   run:
     - python
     - mpi4py
-    - mpich 4.0.2
+    - mpich
     - {{ pin_compatible('numpy') }}
     - fftw
     - hdf5 * mpi_*
diff --git a/conf/requirements-test.txt b/conf/requirements-test.txt
@@ -0,0 +1,3 @@
+coverage
+pyfftw; sys_platform == 'linux' and python_version < '3.12'
+scipy
diff --git a/mpi4py_fft/fftw/fftw_xfftn.pxd b/mpi4py_fft/fftw/fftw_xfftn.pxd
@@ -1,4 +1,5 @@
-cdef extern from "fftw3.h":
+# cython: language_level=3str
+cdef extern from "fftw3.h" nogil:
 
     ctypedef struct fftw_complex_struct:
         pass
@@ -12,15 +13,15 @@ cdef extern from "fftw3.h":
 
     void fftw_destroy_plan(fftw_plan)
 
-    void fftw_execute_dft(fftw_plan, void *_in, void *_out) nogil
+    void fftw_execute_dft(fftw_plan, void *_in, void *_out)
 
-    void fftw_execute_dft_c2r(fftw_plan, void *_in, void *_out) nogil
+    void fftw_execute_dft_c2r(fftw_plan, void *_in, void *_out)
 
-    void fftw_execute_dft_r2c(fftw_plan, void *_in, void *_out) nogil
+    void fftw_execute_dft_r2c(fftw_plan, void *_in, void *_out)
 
-    void fftw_execute_r2r(fftw_plan, void *_in, void *_out) nogil
+    void fftw_execute_r2r(fftw_plan, void *_in, void *_out)
 
-    void fftw_execute(fftw_plan) nogil
+    void fftw_execute(fftw_plan)
 
     void fftw_init_threads()
 
@@ -43,7 +44,7 @@ cdef extern from "fftw3.h":
     void fftw_print_plan(fftw_plan)
 
 
-cdef extern from "fftw_planxfftn.h":
+cdef extern from "fftw_planxfftn.h" nogil:
 
     ctypedef double fftw_real
 
@@ -57,4 +58,4 @@ cdef extern from "fftw_planxfftn.h":
                              int      kind[],
                              unsigned flags)
 
-ctypedef void (*generic_function)(void *plan, void *_in, void *_out) nogil
+ctypedef void (*generic_function)(void *plan, void *_in, void *_out) noexcept nogil
diff --git a/mpi4py_fft/fftw/fftw_xfftn.pyx b/mpi4py_fft/fftw/fftw_xfftn.pyx
@@ -1,5 +1,5 @@
-cimport fftw_xfftn
-#cython: language_level=3
+# cython: language_level=3str
+from . cimport fftw_xfftn
 cimport numpy as np
 from .utilities import *
 import numpy as np
@@ -26,16 +26,16 @@ cpdef void cleanup():
     fftw_cleanup()
     fftw_cleanup_threads()
 
-cdef void _fftw_execute_dft(void *plan, void *_in, void *_out) nogil:
+cdef void _fftw_execute_dft(void *plan, void *_in, void *_out) noexcept nogil:
     fftw_execute_dft(<fftw_plan>plan, <fftw_complex *>_in, <fftw_complex *>_out)
 
-cdef void _fftw_execute_dft_r2c(void *plan, void *_in, void *_out) nogil:
+cdef void _fftw_execute_dft_r2c(void *plan, void *_in, void *_out) noexcept nogil:
     fftw_execute_dft_r2c(<fftw_plan>plan, <fftw_real *>_in, <fftw_complex *>_out)
 
-cdef void _fftw_execute_dft_c2r(void *plan, void *_in, void *_out) nogil:
+cdef void _fftw_execute_dft_c2r(void *plan, void *_in, void *_out) noexcept nogil:
     fftw_execute_dft_c2r(<fftw_plan>plan, <fftw_complex *>_in, <fftw_real *>_out)
 
-cdef void _fftw_execute_r2r(void *plan, void *_in, void *_out) nogil:
+cdef void _fftw_execute_r2r(void *plan, void *_in, void *_out) noexcept nogil:
     fftw_execute_r2r(<fftw_plan>plan, <fftw_real *>_in, <fftw_real *>_out)
 
 cdef generic_function _get_execute_function(kind):
diff --git a/mpi4py_fft/fftw/utilities.pyx b/mpi4py_fft/fftw/utilities.pyx
@@ -1,4 +1,4 @@
-#cython: language_level=3
+#cython: language_level=3str
 
 cimport numpy as np
 import numpy as np
diff --git a/pyproject.toml b/pyproject.toml
@@ -0,0 +1,3 @@
+[build-system]
+requires = ["setuptools >= 42", "numpy", "cython >= 0.29.32"]
+build-backend = "setuptools.build_meta"
diff --git a/setup.py b/setup.py
diff --git a/tests/runtests.sh b/tests/runtests.sh
diff --git a/tests/test_mpifft.py b/tests/test_mpifft.py

-Original file line number
+Diff line change
 *.dat
 *.html
 *.xml
 -*.txt
 *.h5
 *.nc
 *.xdmf
Original file line number	Diff line number	Diff line change
`@@ -0,0 +1,3 @@`
	`1`	`+coverage`
	`2`	`+pyfftw; sys_platform == 'linux' and python_version < '3.12'`
	`3`	`+scipy`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-#cython: language_level=3`
	`1`	`+#cython: language_level=3str`
`2`	`2`
`3`	`3`	`cimport numpy as np`
`4`	`4`	`import numpy as np`