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

Fluidfft plugins

See merge request fluiddyn/fluidfft!50

.flake8

@@ -0,0 +1,2 @@
+[flake8]
+ignore = E501,E225,E226,E303,E201,E202,E203,W503

.github/workflows/ci-linux.yml

@@ -36,15 +36,25 @@ jobs:
         # cython is for coverage
         python -m pip install coverage cython
 
-    - name: Run tests
+    - name: Run sequential tests with nox
       run: |
-        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
+        mv .coverage/coverage.xml coverage_without_mpi.xml
+
+    - name: Run parallel tests with nox
+      run: |
         nox --session "tests(with_cov=True, with_mpi=True)"
+        mv .coverage/coverage.xml coverage_with_mpi.xml
+
+    - name: Produce coverage xml
+      run: |
         coverage xml
 
     - name: Upload coverage to codecov
       if: ${{ success() }}
       uses: codecov/codecov-action@v3
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        fail_ci_if_error: false # optional (default = false)
+        verbose: true # optional (default = false)
+        files: coverage_without_mpi.xml,coverage_with_mpi.xml

.github/workflows/ci-pixi.yml

@@ -0,0 +1,32 @@
+name: CI Pixi
+
+on:
+  - push
+  - pull_request
+
+jobs:
+  tests:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ["windows-2022", "macos-latest"]
+        python-version: ["3.9", "3.10", "3.11"]
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+    - uses: actions/checkout@v3
+    - uses: prefix-dev/[email protected]
+      with:
+        pixi-version: v0.11.1
+        cache: false
+    - name: Install
+      run: |
+        pixi run install-editable
+        # C++ code is not yet compatible with Windows
+        # pixi run pip install plugins/fluidfft-fftw -v --no-build-isolation --no-deps
+    - name: Tests
+      run: |
+        pixi run pytest -v tests
+        # pixi run pytest -v plugins/fluidfft-fftw

.gitlab-ci.yml

@@ -23,15 +23,17 @@ workflow:
     - if: $CI_COMMIT_BRANCH
 
 
-# pixi-test:
-#   stage: pixi
-#   image: $DOCKER_IMAGE_PATH:pixi
-#   script:
-#     - pixi info
-#     # - rm -rf ../transonic
-#     # - hg clone https://foss.heptapod.net/fluiddyn/transonic ../transonic
-#     - pixi run install-editable
-#     - pixi run pytest -v
+pixi-test:
+  stage: pixi
+  image: registry.heptapod.net:443/fluiddyn/fluidsim/ci/default:pixi
+  script:
+    - pixi info
+    - pixi run install-editable
+    - pixi run pip install plugins/fluidfft-fftw -v --no-build-isolation --no-deps
+    - pixi run pytest -v tests
+    - pixi run pytest -v plugins/fluidfft-fftw
+    # - pixi run pip install plugins/fluidfft-mpi_with_fftw -v --no-build-isolation --no-deps
+    # - pixi run mpirun -np 2 pytest -v plugins/fluidfft-mpi_with_fftw
 
 
 # Build an image for the other tasks; this should be a scheduled job, as
@@ -85,7 +87,6 @@ tests_seq:
     - job: "image:build"
       optional: true
   script:
-    - cp site.cfg.files/site.cfg.docker_seq site.cfg
     - nox -s "tests(with_cov=True, with_mpi=False)"
 
 
@@ -95,7 +96,6 @@ tests_mpi:
     - job: "image:build"
       optional: true
   script:
-    - cp site.cfg.files/site.cfg.docker_mpi site.cfg
     - nox -s "tests(with_cov=True, with_mpi=True)"
 
 
@@ -104,8 +104,6 @@ pages:
   needs:
     - job: "image:build"
       optional: true
-  variables:
-    FLUIDFFT_TRANSONIC_BACKEND: "python"
   script:
     - nox -s doc
     - mkdir -p public/$CI_COMMIT_REF_NAME

.hgignore

@@ -23,7 +23,6 @@ src_cy/fft*_pxd.pxd
 src/**/*.pyx
 src/**/*.pxd
 src/**/*.cpp
-src/**/*.cu
 
 __pycache__
 
@@ -53,6 +52,7 @@ site.cfg
 .tox
 .nox
 .venv
+.pixi
 .cache
 .mypy_cache
 **/__pythran__/*
@@ -79,3 +79,5 @@ doc/tmp/*
 .vscode
 
 .pdm-python
+
+src/fluidfft/build_conf.txt

.readthedocs.yml

@@ -15,8 +15,8 @@ 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
+      - pdm run python -c "from fluidfft_builder import create_fake_modules as c; c()"
+      - pdm run pip install . --no-deps -C setup-args=-Dtransonic-backend=python
 
 sphinx:
   configuration: doc/conf.py

Makefile

@@ -1,11 +1,18 @@
-.PHONY: clean cleanall cleanmako cleancython develop build_ext_inplace list-sessions tests
+.PHONY: clean cleanall develop list-sessions tests doc
 
 develop: sync
+	pdm run python -c "from fluidfft_builder import create_fake_modules as c; c()"
 	pdm run pip install -e . --no-deps --no-build-isolation -v
+	pdm run pip install -e plugins/fluidfft-fftw --no-build-isolation -v
+
+develop_mpi_with_fftw:
+	pdm run pip install -e plugins/fluidfft-mpi_with_fftw --no-build-isolation -v
+
+develop_fftwmpi:
+	pdm run pip install -e plugins/fluidfft-fftwmpi --no-build-isolation -v
 
 sync:
 	pdm sync --clean --no-self
-	pdm run pip install -e plugins/fluidfft-pyfftw
 
 clean:
 	rm -rf build
@@ -16,13 +23,7 @@ cleanso:
 cleanpythran:
 	find src -name __pythran__ -type d -exec rm -rf "{}" +
 
-cleancython:
-	find src -name "*_cy.cpp" -delete
-
-cleanmako:
-	python -c "from src_cy.make_files_with_mako import clean_files as c; c()"
-
-cleanall: clean cleanso cleanmako cleancython cleanpythran
+cleanall: clean cleanso cleanpythran
 
 black:
 	pdm run black
@@ -36,23 +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
 
@@ -63,6 +47,9 @@ list-sessions:
 lock:
 	pdm lock -G :all
 
+doc:
+	nox -s doc
+
 # Catch-all target: route all unknown targets to nox sessions
 %:
 	@nox --version 2>/dev/null || pip install nox

README.md

@@ -60,7 +60,7 @@ Click on the links to know more:
     P3DFFT, PFFT (for 3D solvers) either using a package manager or
     [from
     source](https://fluidfft.readthedocs.io/en/latest/install/fft_libs.html)
-3.  Python packages `fluiddyn mako cython pyfftw pythran mpi4py`
+3.  Python packages `fluiddyn cython pyfftw pythran mpi4py`
 4.  [A C++11 compiler and BLAS
     libraries](https://github.com/serge-sans-paille/pythran#installation)
     and

doc/conf.py

@@ -15,7 +15,6 @@
 import os
 from pathlib import Path
 import subprocess
-from runpy import run_path
 import getpass
 from subprocess import call
 
@@ -94,9 +93,6 @@ def save_fig_scaling(dir_name, dim, n0, n1, n2=None):
 except OSError:
     print("Can not find doxygen to generate the documentation of the cpp code.")
 
-run_path("../src_cy/create_fake_mod_for_doc.py")
-
-
 # -- General configuration ----------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.

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