Small fixes before merge

.gitlab-ci.yml

@@ -96,7 +96,6 @@ tests_mpi:
     - job: "image:build"
       optional: true
   script:
-    - ls /usr/lib/x86_64-linux-gnu/libfftw3*
     - nox -s "tests(with_cov=True, with_mpi=True)"
 
 

Makefile

@@ -37,23 +37,6 @@ tests_mpi:
 tests_mpi4:
 	mpirun -np 4 pytest -s tests
 
-_tests_coverage:
-	mkdir -p .coverage
-	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 tests
-
-_report_coverage:
-	coverage combine
-	coverage report
-	coverage html
-	coverage xml
-	@echo "Code coverage analysis complete. View detailed report:"
-	@echo "file://${PWD}/.coverage/index.html"
-
-coverage: _tests_coverage _report_coverage
-
 clang-format:
 	find src_cpp/ -iname '*.h' -o -iname '*.cpp' | xargs clang-format -i
 

doc/index.md

@@ -24,8 +24,6 @@ perform Fast Fourier Transform (FFT) with different libraries, in particular
 - [pfft](https://github.com/mpip/pfft)
 - [p3dfft](https://github.com/sdsc/p3dfft)
 - [mpi4py-fft](https://bitbucket.org/mpi4py/mpi4py-fft)
-- [cufft](https://developer.nvidia.com/cufft) (fft library by CUDA
-  running on GPU)
 
 [pfft](https://github.com/mpip/pfft), [p3dfft](https://github.com/sdsc/p3dfft) and [mpi4py-fft](https://bitbucket.org/mpi4py/mpi4py-fft) are specialized in computing FFT
 efficiently on several cores of big clusters. The data can be split in pencils
@@ -110,6 +108,7 @@ journal = {Journal of Open Research Software}
 
 overview
 install
+plugins
 tutorials
 examples
 bench

doc/install.md

@@ -2,6 +2,14 @@
 
 # Installation and advice
 
+```{danger}
+
+We are working on a very deep reorganization of Fluidfft. Fluidfft 0.4.0, which
+should be released in the beginning of 2024, will work with plugins. This
+documentation is valid for Fluidfft <= 0.3.5. The new documentation should come soon.
+
+```
+
 ## Installation with pip
 
 To install fluidfft, you need a recent Python (>= 3.6) and a C++11 compiler

doc/plugins.md

@@ -0,0 +1 @@
+../plugins/README.md

pixi.toml

@@ -11,7 +11,6 @@ platforms = ["linux-64", "win-64", "osx-64"]
 
 [tasks]
 # use as `pixi run install-editable`
-# install-dependencies = "pixi install && pip install -e ./lib && pip install ../transonic"
 install-dependencies = "pixi install && pip install -e plugins/fluidfft-builder"
 install-editable = {cmd = "pip install -e . -v --no-build-isolation --no-deps", depends_on = ["install-dependencies"]}
 install-fftw = "pip install -e plugins/fluidfft-fftw --no-build-isolation -v"

plugins/README.md

@@ -1,14 +1,32 @@
 # Fluidfft plugins
 
-Directory containing the plugins, i.e. Python packages declaring the
-`fluidfft.plugins` entry point.
+The main Fluidfft package only contains pure Python FFT classes using other
+packages to perform the transforms.
 
-We should have
+The classes using in the background C++ Fluidfft classes are implemented in
+Fluidfft plugins. A plugin is a small Python packages defining entry points
+`fluidfft.plugins`.
+
+For example, the plugin `fluidfft-fftw` defines 3 sequential methods declared
+in its `pyproject.toml` file like this:
+
+```toml
+[project.entry-points."fluidfft.plugins"]
+
+"fft2d.with_fftw1d" = "fluidfft_fftw.fft2d.with_fftw1d"
+"fft2d.with_fftw2d" = "fluidfft_fftw.fft2d.with_fftw2d"
+"fft3d.with_fftw3d" = "fluidfft_fftw.fft3d.with_fftw3d"
+```
+
+The following plugins are implemented in Fluidfft repository:
 
-- [x] fluidfft-mpi4pyfft (cannot be tested because mpi4py-fft installation fails)
 - [x] fluidfft-fftw
-- [x] fluidfft-mpi_with_fftw
-- [x] fluidfft-fftwmpi
+- [x] fluidfft-mpi_with_fftw (parallel methods using the sequential FFTW3 library)
+- [x] fluidfft-fftwmpi (methods using the library `libfftw_mpi`)
+- [x] fluidfft-mpi4pyfft (cannot be tested because mpi4py-fft installation fails)
+
+We plan to soon also have:
+
 - [ ] fluidfft-p3dfft
 - [ ] fluidfft-pfft
 - [ ] fluidfft-pyvkfft (https://pyvkfft.readthedocs.io)

plugins/fluidfft-fftw/meson.build

@@ -15,17 +15,23 @@ py_mod = import('python')
 py = py_mod.find_installation('python3', pure: false)
 py_dep = py.dependency()
 
-incdir_numpy = run_command('transonic-get-include', 'numpy', check: true).stdout().strip()
+incdir_numpy = run_command(
+  'transonic-get-include', 'numpy', check: true
+).stdout().strip()
 inc_np = include_directories(incdir_numpy)
 np_dep = declare_dependency(include_directories: inc_np)
 
 fftw_dep = dependency('fftw3', static: false)
 
 dependencies = [fftw_dep, np_dep]
 
-include_path_fluidfft_builder = run_command('fluidfft-builder-print-include-dir').stdout().strip()
+include_path_fluidfft_builder = run_command(
+  'fluidfft-builder-print-include-dir', check: true
+).stdout().strip()
 
-include_path_cy = run_command('fluidfft-builder-print-include-dir-cython').stdout().strip()
+include_path_cy = run_command(
+  'fluidfft-builder-print-include-dir-cython', check: true
+).stdout().strip()
 add_project_arguments('-I', include_path_cy, language : 'cython')
 
 subdir('src/fluidfft_fftw')

plugins/fluidfft-fftw/src/fluidfft_fftw/fft2d/meson.build

@@ -33,4 +33,4 @@ foreach dim : ['1', '2']
     subdir: 'fluidfft_fftw/fft2d',
   )
 
-endforeach
+endforeach

plugins/fluidfft-fftwmpi/meson.build

@@ -24,16 +24,22 @@ py_mod = import('python')
 py = py_mod.find_installation('python3', pure: false)
 py_dep = py.dependency()
 
-incdir_numpy = run_command('transonic-get-include', 'numpy', check: true).stdout().strip()
+incdir_numpy = run_command(
+  'transonic-get-include', 'numpy', check: true
+).stdout().strip()
 inc_np = include_directories(incdir_numpy)
 np_dep = declare_dependency(include_directories: inc_np)
 
 dependencies = [fftw_dep, mpi_dep, fftwmpi_dep, np_dep]
 link_args = ['-lfftw3_mpi']
 
-include_path_fluidfft_builder = run_command('fluidfft-builder-print-include-dir').stdout().strip()
+include_path_fluidfft_builder = run_command(
+  'fluidfft-builder-print-include-dir', check: true
+).stdout().strip()
 
-include_path_cy = run_command('fluidfft-builder-print-include-dir-cython').stdout().strip()
+include_path_cy = run_command(
+  'fluidfft-builder-print-include-dir-cython', check: true
+).stdout().strip()
 add_project_arguments('-I', include_path_cy, language : 'cython')
 
 subdir('src/fluidfft_fftwmpi')

plugins/fluidfft-mpi_with_fftw/meson.build

@@ -18,15 +18,21 @@ py_dep = py.dependency()
 fftw_dep = dependency('fftw3', static: false)
 mpi_dep = dependency('mpi', language: 'cpp')
 
-incdir_numpy = run_command('transonic-get-include', 'numpy', check: true).stdout().strip()
+incdir_numpy = run_command(
+  'transonic-get-include', 'numpy', check: true
+).stdout().strip()
 inc_np = include_directories(incdir_numpy)
 np_dep = declare_dependency(include_directories: inc_np)
 
 dependencies = [fftw_dep, mpi_dep, np_dep]
 
-include_path_fluidfft_builder = run_command('fluidfft-builder-print-include-dir').stdout().strip()
+include_path_fluidfft_builder = run_command(
+  'fluidfft-builder-print-include-dir', check: true
+).stdout().strip()
 
-include_path_cy = run_command('fluidfft-builder-print-include-dir-cython').stdout().strip()
+include_path_cy = run_command(
+  'fluidfft-builder-print-include-dir-cython', check: true
+).stdout().strip()
 add_project_arguments('-I', include_path_cy, language : 'cython')
 
 subdir('src/fluidfft_mpi_with_fftw')

plugins/pure_cpp/2d/run_benchs.py

@@ -72,22 +72,16 @@ def call_bash(commands):
 
 for cls in classes:
     src += (
-        "\nnb_procs['"
-        + cls
-        + "'] = "
+        f"\nnb_procs['{cls}'] = "
         + repr(np.array(nb_procs[cls]))
-        + "\ntimes_fft['"
-        + cls
-        + "'] = "
+        + f"\ntimes_fft['{cls}'] = "
         + repr(np.array(times_fft[cls]))
-        + "\ntimes_ifft['"
-        + cls
-        + "'] = "
+        + "\ntimes_ifft['{cls}'] = "
         + repr(np.array(times_ifft[cls]))
     )
 
 if not os.path.exists(output_dir):
     os.mkdir(output_dir)
 
-with open(output_dir + "/bench.py", "w") as f:
-    f.write(src + "\n")
+with open(output_dir + "/bench.py", "w", encoding="utf8") as file:
+    file.write(src + "\n")