Merge branch 'topic/default/setup-plugins' into 'branch/default'

Entry point fluidfft.plugins

See merge request fluiddyn/fluidfft!49

.github/workflows/ci-linux.yml

@@ -12,9 +12,10 @@ jobs:
         python-version: [3.9, "3.10", "3.11"]
 
     steps:
+
     - name: apt install
       run: |
-        sudo apt install -y libfftw3-dev libfftw3-mpi-dev \
+        sudo apt-get install -y make libfftw3-dev libfftw3-mpi-dev \
           libhdf5-openmpi-dev openmpi-bin libopenmpi-dev \
           libopenblas-dev
 
@@ -37,8 +38,10 @@ jobs:
 
     - name: Run tests
       run: |
-        cp .github/fluidfft-site.cfg $HOME/.fluidfft-site.cfg
+        cp .github/fluidfft-site-seq.cfg $HOME/.fluidfft-site.cfg
         nox --session "tests(with_cov=True, with_mpi=False)"
+        make cleanall
+        cp .github/fluidfft-site-mpi.cfg $HOME/.fluidfft-site.cfg
         nox --session "tests(with_cov=True, with_mpi=True)"
         coverage xml
 

.github/workflows/ci-macos.yml

@@ -24,8 +24,9 @@ jobs:
         use-mamba: true
     - name: Install
       run: |
-        cp .github/fluidfft-site-macos.cfg $HOME/.fluidfft-site.cfg
+        cp .github/fluidfft-site-seq.cfg $HOME/.fluidfft-site.cfg
         pip install -e . -v --no-build-isolation --no-deps
+        pip install plugins/fluidfft-pyfftw
     - name: Tests
       run: |
-        pytest -v
+        pytest -v tests plugins/fluidfft-pyfftw

.github/workflows/ci-windows.yml

@@ -31,6 +31,7 @@ jobs:
       run: |
         cp .github/pythranrc-windows $HOME/.pythranrc
         pip install -e . -v --no-build-isolation --no-deps
+        pip install plugins/fluidfft-pyfftw
     - name: Tests
       run: |
-        pytest -v
+        pytest -v tests plugins/fluidfft-pyfftw

.readthedocs.yml

@@ -15,6 +15,7 @@ build:
     post_install:
       - pdm use -f $READTHEDOCS_VIRTUALENV_PATH
       - pdm sync -G doc --no-self
+      - pdm run pip install plugins/fluidfft-pyfftw
       - FLUIDFFT_TRANSONIC_BACKEND="python" pip install . -v --no-deps
 
 sphinx:

Makefile

@@ -1,10 +1,11 @@
-.PHONY: clean cleanall cleanmako cleancython develop build_ext_inplace list-sessions requirements
+.PHONY: clean cleanall cleanmako cleancython develop build_ext_inplace list-sessions tests
 
 develop: sync
 	pdm run pip install -e . --no-deps --no-build-isolation -v
 
 sync:
 	pdm sync --clean --no-self
+	pdm run pip install -e plugins/fluidfft-pyfftw
 
 clean:
 	rm -rf build
@@ -27,20 +28,20 @@ black:
 	pdm run black
 
 tests:
-	pytest -s src
+	pytest -s tests
 
 tests_mpi:
-	mpirun -np 2 pytest -s src
+	mpirun -np 2 pytest -s tests
 
 tests_mpi4:
-	mpirun -np 4 pytest -s src
+	mpirun -np 4 pytest -s tests
 
 _tests_coverage:
 	mkdir -p .coverage
-	coverage run -p -m pytest -s src
-	TRANSONIC_NO_REPLACE=1 coverage run -p -m pytest -s src
+	coverage run -p -m pytest -s tests
+	TRANSONIC_NO_REPLACE=1 coverage run -p -m pytest -s tests
 	# Using TRANSONIC_NO_REPLACE with mpirun in docker can block the tests
-	mpirun -np 2 --oversubscribe coverage run -p -m unittest discover src
+	mpirun -np 2 --oversubscribe coverage run -p -m unittest discover tests
 
 _report_coverage:
 	coverage combine

doc/ipynb/tuto_fft2d_seq.md

@@ -21,12 +21,11 @@ If you really want performance, first benchmark the different methods for an arr
 
 ```{code-cell} ipython3
 import numpy as np
-from fluidfft.fft2d import methods_seq
-from fluidfft import import_fft_class
+from fluidfft import get_methods, import_fft_class
 ```
 
 ```{code-cell} ipython3
-print(methods_seq)
+print(get_methods(ndim=2, sequential=True))
 ```
 
 We import a class and instantiate it:

doc/ipynb/tuto_fft3d_seq.md

@@ -17,12 +17,11 @@ In this tutorial, we present how to use fluidfft to perform 3D fft in sequential
 
 ```{code-cell} ipython3
 import numpy as np
-from fluidfft.fft3d import methods_seq
-from fluidfft import import_fft_class
+from fluidfft import get_methods, import_fft_class
 ```
 
 ```{code-cell} ipython3
-print(methods_seq)
+print(get_methods(ndim=3, sequential=True))
 ```
 
 We import a class and instantiate it:

noxfile.py

@@ -52,14 +52,16 @@ def tests(session, with_mpi, with_cov):
     session.install("-e", ".", "--no-deps", "-v", silent=False)
     session.run("ls", "src/fluidfft/fft3d", silent=False, external=True)
 
+    session.install("-e", "plugins/fluidfft-pyfftw")
+
     def run_command(command, **kwargs):
         session.run(*command.split(), **kwargs)
 
     if with_cov:
         cov_path = Path.cwd() / ".coverage"
         cov_path.mkdir(exist_ok=True)
 
-    command = "pytest -v -s"
+    command = "pytest -v -s tests"
     if with_cov:
         command += (
             " --cov --cov-config=setup.cfg --no-cov-on-fail --cov-report=term-missing"
@@ -70,12 +72,10 @@ def run_command(command, **kwargs):
 
     if with_mpi:
         if with_cov:
-            command = (
-                "mpirun -np 2 --oversubscribe coverage run -p -m pytest --exitfirst src"
-            )
+            command = "mpirun -np 2 --oversubscribe coverage run -p -m pytest -v -s --exitfirst tests"
 
         else:
-            command = "mpirun -np 2 --oversubscribe pytest src"
+            command = "mpirun -np 2 --oversubscribe pytest -v -s tests"
 
         # Using TRANSONIC_NO_REPLACE with mpirun in docker can block the tests
         run_command(command, external=True)
@@ -92,6 +92,7 @@ def doc(session):
     session.install(
         "-e", ".", "--no-deps", env={"FLUIDFFT_TRANSONIC_BACKEND": "python"}
     )
+    session.install("-e", "plugins/fluidfft-pyfftw")
 
     session.chdir("doc")
     session.run("make", "cleanall", external=True)

plugins/README.md

@@ -0,0 +1,21 @@
+# Fluidfft plugins
+
+Directory containing the plugins, i.e. Python packages declaring the
+`fluidfft.plugins` entry point.
+
+We should have
+
+- [x] fluidfft-mpi4pyfft (cannot be tested because mpi4py-fft installation fails)
+- [ ] fluidfft-fftw
+- [ ] fluidfft-mpi_with_fftw
+- [ ] fluidfft-fftwmpi
+- [ ] fluidfft-p3dfft
+- [ ] fluidfft-pfft
+- [ ] fluidfft-pyvkfft (https://pyvkfft.readthedocs.io)
+
+Currently, we have only one tested plugin (fluidfft-pyfftw), which was written to
+design and test the plugin machinery. However, I (PA) think that this (pure Python)
+code will have to go back in fluidfft. Pyfftw can just be an optional dependency
+for fluidfft.
+
+TODO: When we have other plugins, move back the code using pyfftw inside fluidfft.

plugins/fluidfft-mpi4pyfft/LICENSE

@@ -0,0 +1,21 @@
+The MIT License (MIT)
+
+Copyright (c) 2024 Pierre Augier
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

plugins/fluidfft-mpi4pyfft/pyproject.toml

@@ -0,0 +1,20 @@
+[build-system]
+requires = ["flit_core >=3.2,<4"]
+build-backend = "flit_core.buildapi"
+
+[project]
+name = "fluidfft_mpi4pyfft"
+version = "0.0.1"
+description = "Fluidfft plugin using mpi4pyfft"
+authors = [{name = "Pierre Augier", email = "pierre.augier@univ-grenoble-alpes.fr"}]
+license = {file = "LICENSE"}
+classifiers = ["License :: OSI Approved :: MIT License"]
+dependencies = ["fluidfft", "mpi4py-fft"]
+
+[project.urls]
+Home = "https://fluidfft.readthedocs.io"
+
+[project.entry-points."fluidfft.plugins"]
+
+"fft3d.mpi_with_mpi4pyfft" = "fluidfft_mpi4pyfft.mpi_with_mpi4pyfft"
+"fft3d.mpi_with_mpi4pyfft_slab" = "fluidfft_mpi4pyfft.fft3d.mpi_with_mpi4pyfft_slab"

src/fluidfft/fft3d/mpi_with_mpi4pyfft.py → plugins/fluidfft-mpi4pyfft/src/fluidfft_mpi4pyfft/mpi_with_mpi4pyfft.py

@@ -3,7 +3,7 @@
 from mpi4py import MPI
 from mpi4py_fft import PFFT, newDistArray
 
-from .base import BaseFFTMPI
+from fluidfft.fft3d.base import BaseFFTMPI
 
 
 class FFT3DMPIWithMPI4PYFFT(BaseFFTMPI):

plugins/fluidfft-mpi4pyfft/tests/test_with_mpi4pyfft.py

@@ -0,0 +1,12 @@
+from unittest import TestCase
+
+from fluidfft.fft3d.testing import complete_test_class_3d
+
+
+class Tests(TestCase):
+    pass
+
+
+methods = ["fft3d.mpi_with_mpi4pyfft", "fft3d.mpi_with_mpi4pyfft_slab"]
+for method in methods:
+    complete_test_class_3d(method, Tests)

plugins/fluidfft-pyfftw/LICENSE

@@ -0,0 +1,21 @@
+The MIT License (MIT)
+
+Copyright (c) 2024 Pierre Augier
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

plugins/fluidfft-pyfftw/pyproject.toml

@@ -0,0 +1,20 @@
+[build-system]
+requires = ["flit_core >=3.2,<4"]
+build-backend = "flit_core.buildapi"
+
+[project]
+name = "fluidfft_pyfftw"
+version = "0.0.1"
+description = "Fluidfft plugin using pyfftw"
+authors = [{name = "Pierre Augier", email = "pierre.augier@univ-grenoble-alpes.fr"}]
+license = {file = "LICENSE"}
+classifiers = ["License :: OSI Approved :: MIT License"]
+dependencies = ["fluidfft", "pyfftw"]
+
+[project.urls]
+Home = "https://foss.heptapod.net/fluiddyn/fluidfft"
+
+[project.entry-points."fluidfft.plugins"]
+
+"fft2d.with_pyfftw" = "fluidfft_pyfftw.fft2d"
+"fft3d.with_pyfftw" = "fluidfft_pyfftw.fft3d"

src/fluidfft/fft2d/with_pyfftw.py → plugins/fluidfft-pyfftw/src/fluidfft_pyfftw/fft2d.py

@@ -1,5 +1,5 @@
-"""Class using pyfftw (:mod:`fluidfft.fft2d.with_pyfftw`)
-=========================================================
+"""Class using pyfftw
+=====================
 
 .. autoclass:: FFT2DWithPYFFTW
    :members:

src/fluidfft/fft3d/with_pyfftw.py → plugins/fluidfft-pyfftw/src/fluidfft_pyfftw/fft3d.py

@@ -1,5 +1,5 @@
-"""Class using pyfftw (:mod:`fluidfft.fft3d.with_pyfftw`)
-=========================================================
+"""Class using pyfftw
+=====================
 
 .. autoclass:: FFT3DWithPYFFTW
    :members:

plugins/fluidfft-pyfftw/tests/test_with_pyfftw.py

@@ -0,0 +1,12 @@
+from unittest import TestCase
+
+from fluidfft.fft3d.testing import complete_test_class_3d
+from fluidfft.fft2d.testing import complete_test_class_2d
+
+
+class Tests(TestCase):
+    pass
+
+
+complete_test_class_2d("fft2d.with_pyfftw", Tests)
+complete_test_class_3d("fft3d.with_pyfftw", Tests)