Merge branch 'topic/default/ci-doc-nox' into 'branch/default'

CI with Nox

See merge request fluiddyn/transonic!128

.gitattributes

@@ -0,0 +1,3 @@
+# GitHub syntax highlighting
+pixi.lock linguist-language=YAML
+

.github/workflows/ci-linux.yml

@@ -0,0 +1,34 @@
+name: CI Linux
+
+on:
+  - push
+  - pull_request
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10", "3.11"]
+
+    steps:
+    - name: apt install
+      run: |
+        sudo apt install -y libopenmpi-dev
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install pdm nox
+    - name: Test with nox
+      run: |
+        nox -s test_without_pythran test_with_pythran
+    - uses: codecov/codecov-action@v3
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        fail_ci_if_error: false # optional (default = false)
+        verbose: true # optional (default = false)

.github/workflows/ci-windows.yml

@@ -0,0 +1,31 @@
+name: CI-windows
+
+on:
+  - push
+  - pull_request
+
+jobs:
+  tests:
+    runs-on: windows-2022
+    defaults:
+      run:
+        shell: bash -l {0}
+    strategy:
+      matrix:
+        python-version: ["3.11"]
+
+    steps:
+    - uses: actions/checkout@v2
+    - uses: prefix-dev/[email protected]
+      with:
+        pixi-version: v0.11.1
+        cache: false
+    - name: Tests
+      run: |
+        pixi run install-editable
+        pixi run pytest tests
+        pixi run mpirun -np 2 pytest tests
+        echo "TRANSONIC_BACKEND=python" >> $GITHUB_ENV
+        pixi run pytest tests
+        echo "TRANSONIC_BACKEND=numba" >> $GITHUB_ENV
+        pixi run pytest tests

.gitlab-ci.yml

@@ -1,4 +1,5 @@
 stages:
+  - pixi
   - image
   - lint
   - test
@@ -7,20 +8,25 @@ stages:
   - release
 
 variables:
-  CODECOV_TOKEN: b1c3afe7-4ef3-4c69-9656-78beec52ec16
-  OMPI_ALLOW_RUN_AS_ROOT: "1"
-  OMPI_ALLOW_RUN_AS_ROOT_CONFIRM: "1"
   PDM_CACHE_DIR: ${CI_PROJECT_DIR}/.pdm-cache
 
 image: registry.heptapod.net:443/fluiddyn/transonic/ci/default:stable
 
-before_script:
-  - export PATH=/root/.local/bin:$PATH
-  - pip install -U pdm tox tox-pdm --user
+
+pixi:test:
+  stage: pixi
+  image: registry.heptapod.net:443/fluiddyn/fluidsim/ci/default:pixi
+  script:
+    - pixi info
+    - pixi run install-editable
+    - pixi run pytest tests
+    - pixi run mpirun -np 2 pytest tests
+    - TRANSONIC_BACKEND=python pixi run pytest tests
+
 
 # Build an image for the above tasks; this should be a scheduled job, as
 # it is quite unnecessary to run on every invocation.
-CI image:
+image:build:
   stage: image
   tags:
     - container-registry-push
@@ -50,44 +56,48 @@ CI image:
       --single-snapshot
       --cleanup
       --destination registry.heptapod.net:443/fluiddyn/transonic/ci/$CI_COMMIT_HG_BRANCH:stable
+      # --destination registry.heptapod.net:443/fluiddyn/transonic/ci/default:stable
+
 
 validate_code:
   stage: lint
   needs:
-    - job: "CI image"
+    - job: "image:build"
       optional: true
   script:
     - pdm install -G dev
     - pdm run make lint
 
+
 step_without_pythran:
   stage: test
   needs:
-    - job: "CI image"
+    - job: "image:build"
       optional: true
   script:
-    - tox -e py310,codecov
+    - nox -s test_without_pythran
 
 step_pythran_then_cython:
   stage: test
   needs:
-    - job: "CI image"
+    - job: "image:build"
       optional: true
   script:
-    - tox -e py310-pythran,py310-cython,codecov
+    - nox -s test_with_pythran test_with_cython
 
 step_pythran_cython:
   stage: test
   needs:
-    - job: "CI image"
+    - job: "image:build"
       optional: true
   script:
-    - tox -e py310-pythran-cython
+    - nox -s test_with_pythran_cython
+
 
 pages:
   stage: publish
   needs:
-    - job: "CI image"
+    - job: "image:build"
       optional: true
   script:
     - pdm install -G doc
@@ -107,6 +117,7 @@ pages:
     expire_in: 5 days
   when: always
 
+
 build:package:
   stage: build
   before_script:
@@ -126,6 +137,7 @@ build:package:
     paths:
       - ${PDM_CACHE_DIR}
 
+
 # manually set PDM_PUBLISH_PASSWORD in web interface to your pypi API token
 release:package:
   stage: release

.hgignore

@@ -12,11 +12,13 @@ doc/**.zip
 
 *.so
 
-build/*
+build
 dist/*.tar.gz
 dist*
-.tox/*
-.coverage/*
+.tox
+.coverage
+.nox
+.pixi
 
 **/tmp*.py
 

CHANGES.md

@@ -1,12 +1,14 @@
 # Release notes
 
-## Future
-
-See the [ROADMAP.md file](https://transonic.readthedocs.io/en/latest/roadmap.html).
-
 % Unreleased_
 % -----------
 
+## [0.6.0] (unpublished)
+
+- Support for [Meson build](https://transonic.readthedocs.io/en/latest/packaging.html)
+  through `transonic --meson`
+- Support for Python 3.12
+
 ## [0.5.3] (2023-08-21)
 
 - [!110](https://foss.heptapod.net/fluiddyn/transonic/-/merge_requests/110)

Makefile

@@ -2,7 +2,7 @@
 COV=pytest --cov --cov-config=pyproject.toml
 
 develop:
-	pdm install
+	pdm sync --clean
 
 black:
 	black -l 82 src _transonic_testing data_tests tests

README.md

@@ -5,6 +5,7 @@
 [![Documentation status](https://readthedocs.org/projects/transonic/badge/?version=latest)](http://transonic.readthedocs.org)
 ![Supported Python versions](https://img.shields.io/pypi/pyversions/transonic.svg)
 [![Heptapod CI](https://foss.heptapod.net/fluiddyn/transonic/badges/branch/default/pipeline.svg)](https://foss.heptapod.net/fluiddyn/transonic/-/pipelines)
+[![Github Actions](https://github.com/fluiddyn/transonic/actions/workflows/ci.yml/badge.svg?branch=branch/default)](https://github.com/fluiddyn/transonic/actions)
 [![mybinder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/fluiddyn/transonic/branch/default?urlpath=lab/tree/doc/ipynb/executed)
 [![sonarcloud](https://sonarcloud.io/api/project_badges/measure?project=fluiddyn_transonic&metric=alert_status)](https://sonarcloud.io/dashboard?id=fluiddyn_transonic)
 

data_tests/package_for_test_meson/meson.build

@@ -4,31 +4,10 @@
 
 project('package_for_test_meson', 'cpp')
 
-py = import('python').find_installation(pure: false)
-
-# Taken from Scipy
-
-# This uses the path as is, and avoids running the interpreter.
-incdir_numpy = meson.get_external_property('numpy-include-dir', 'not-given')
-if incdir_numpy == 'not-given'
-  # see also what is done in Scipy and Fluidsim (more robust)
-  incdir_numpy = run_command(py,
-    [
-      '-c',
-      '''import numpy as np
-incdir = np.get_include()
-print(incdir)
-  '''
-    ],
-    check: true
-  ).stdout().strip()
-
-else
-  _incdir_numpy_abs = incdir_numpy
-endif
-
-inc_np = include_directories(incdir_numpy)
-np_dep = declare_dependency(include_directories: inc_np)
+# https://mesonbuild.com/Python-module.html
+py_mod = import('python')
+py = py_mod.find_installation('python3', pure: false)
+py_dep = py.dependency()
 
 backend = get_option('transonic-backend')
 
@@ -40,24 +19,47 @@ endif
 
 use_pythran = backend.contains('pythran')
 if use_pythran
+  incdir_numpy = run_command(
+    py,
+    [
+      '-c',
+      '''import os
+import numpy as np
+try:
+  incdir = os.path.relpath(np.get_include())
+except Exception:
+  incdir = np.get_include()
+print(incdir)'''
+    ],
+    check: true
+  ).stdout().strip()
 
-  pythran = find_program('pythran', native: true)
+  inc_np = include_directories(incdir_numpy)
+  np_dep = declare_dependency(include_directories: inc_np)
 
-  # This external-property may not be needed if we can use the native include
-  # dir, see https://github.com/serge-sans-paille/pythran/issues/1394
-  incdir_pythran = meson.get_external_property('pythran-include-dir', 'not-given')
-  if incdir_pythran == 'not-given'
-    incdir_pythran = run_command(py,
+  incdir_pythran = run_command(
+      py,
       [
         '-c',
-      '''import pythran
-incdir = pythran.get_include()
-print(incdir)
-'''
+        '''import os
+import pythran;
+incdir = os.path.dirname(pythran.__file__)
+try:
+  incdir = os.path.relpath(incdir)
+except Exception:
+  pass
+print(incdir)'''
       ],
       check: true
     ).stdout().strip()
-  endif
+
+  pythran = find_program('pythran', native: true)
+
+  cpp_args_pythran = [
+    '-DENABLE_PYTHON_MODULE',
+    '-D__PYTHRAN__=3',
+    '-DPYTHRAN_BLAS_NONE'
+  ]
 
   if get_option('use-xsimd') == true
     # xsimd is unvendored from pythran by conda-forge, and due to a compiler
@@ -68,22 +70,21 @@ print(incdir)
       include_directories: incdir_pythran,
       dependencies: xsimd_dep,
     )
+    cpp_args_pythran += ['-DUSE_XSIMD']
   else
     pythran_dep = declare_dependency(
       include_directories: incdir_pythran,
     )
   endif
 
-  cpp_args_pythran = [
-    '-DENABLE_PYTHON_MODULE',
-    '-D__PYTHRAN__=3',
-    '-DPYTHRAN_BLAS_NONE'
-  ]
-
   pythran_complex_hook = get_option('pythran-complex-hook')
+  if pythran_complex_hook == 'os-dependent'
+    pythran_complex_hook = host_machine.system() == 'linux'
+  endif
 
-else
-  pythran_dep = []
+  if get_option('native')
+    cpp_args_pythran += ['-march=native', '-Ofast']
+  endif
 
 endif
 

data_tests/package_for_test_meson/meson.options

@@ -4,12 +4,24 @@ option(
     value: 'pythran,python,numba',
     description:
       'pythran,python,numba (default), cython, numpy, numba; ' +
-      'or comma separated value representing multi-backends'
+      'or comma separated value representing multi-backends',
 )
-option('use-xsimd', type: 'boolean', value: true, description: 'use xsimd')
 option(
-    'pythran-complex-hook',
+    'native',
+    type: 'boolean',
+    value: false,
+    description: 'Performance oriented and not portable build',
+)
+option(
+    'use-xsimd',
     type: 'boolean',
     value: true,
-    description: 'Pythran complex_hook option'
+    description: 'Turns on xsimd vectorization',
+)
+option(
+    'pythran-complex-hook',
+    type: 'combo',
+    choices: ['os-dependent', 'true', 'false'],
+    value: 'os-dependent',
+    description: 'Pythran complex_hook option',
 )

data_tests/saved__backend__/cython/block_fluidsim.py

@@ -11,7 +11,7 @@ def rk2_step0(state_spect_n12, state_spect, tendencies_n, diss2, dt):
     #     float64[][] diss2;
     #     float dt
     # )
-    state_spect_n12[:] = (state_spect + ((dt / 2) * tendencies_n)) * diss2
+    state_spect_n12[:] = (state_spect + dt / 2 * tendencies_n) * diss2
 
 
 arguments_blocks = {