Merge branch 'topic/default/try-nox-pdm' into 'branch/default'

Topic/default/try nox pdm

See merge request fluiddyn/fluidsim!350

.github/workflows/ci.yml → .github/workflows/ci-linux.yml

@@ -1,4 +1,4 @@
-name: CI
+name: CI Linux
 
 on:
   - push
@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.9, "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11"]
 
     steps:
     - name: apt install
@@ -25,8 +25,17 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install tox tox-gh-actions
-    - name: Test with tox
+        pip install pdm nox
+    - name: Test with nox
       run: |
+        # needed to avoid a pdm/unearth bug
+        $(hg debuginstall -T '{pythonexe}') -m pip install hg-evolve hg-git --no-cache-dir --user
+        cp docker/hgrc $HOME/.hgrc
         cp .github/workflows/.fluidfft-site.cfg $HOME
-        tox
+        nox -s test_without_fft_and_pythran
+        nox -s test_with_fft_and_pythran
+    - uses: codecov/codecov-action@v3
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        fail_ci_if_error: true # optional (default = false)
+        verbose: true # optional (default = false)

.gitlab-ci.yml

@@ -2,12 +2,22 @@ stages:
   - image
   - lint
   - test
+  - report
+  - doc
 
 variables:
-  CODECOV_TOKEN: 4d2d8534-60ec-48b3-bf55-93b92f25913d
+  COVERAGE_DIR: .coverage_$CI_COMMIT_SHA
 
 image: registry.heptapod.net:443/fluiddyn/fluidsim/ci/default:stable
 
+# ugly workaround https://gitlab.com/gitlab-org/gitlab/-/issues/370052#note_1207556577
+workflow:
+  rules:
+    - if: $CI_PIPELINE_SOURCE == "merge_request_event"
+    - if: $CI_COMMIT_BRANCH && $CI_OPEN_MERGE_REQUESTS
+      when: never
+    - if: $CI_COMMIT_BRANCH
+
 # check_bug:
 #   image: fluiddyn/python3-stable:lastest
 #   script:
@@ -48,20 +58,83 @@ CI image:
       --cleanup
       --destination registry.heptapod.net:443/fluiddyn/fluidsim/ci/$CI_COMMIT_HG_BRANCH:stable
 
+
 validate_code:
   stage: lint
   needs:
     - job: "CI image"
       optional: true
   script:
-    - pdm install -G dev --no-self
-    - pdm run make lint
-    - pdm run make black_check
+    - echo "CI_COMMIT_HG_BRANCH $CI_COMMIT_HG_BRANCH"
+    - echo "CI_COMMIT_BRANCH $CI_COMMIT_BRANCH"
+    - nox -s validate_code
+
+
+test_without_fft_and_pythran:
+  stage: test
+  needs:
+    - job: "CI image"
+      optional: true
+  script:
+    - nox -s test_without_fft_and_pythran
+    - mkdir $COVERAGE_DIR
+    - cp -r .coverage/* $COVERAGE_DIR
+  artifacts:
+    paths:
+      - $COVERAGE_DIR/*
+    expire_in: 60 mins
 
-tests:
+test_with_fft_and_pythran:
   stage: test
   needs:
     - job: "CI image"
       optional: true
   script:
-    - tox -e py39,py39-fft,codecov
+    - nox -s test_with_fft_and_pythran
+    - mkdir $COVERAGE_DIR
+    - cp -r .coverage/* $COVERAGE_DIR
+  artifacts:
+    paths:
+      - $COVERAGE_DIR/*
+    expire_in: 60 mins
+
+
+report_coverage:
+  stage: report
+  rules:
+    - when: on_success
+  script:
+    - mv $COVERAGE_DIR .coverage
+    - pip install coverage
+    - coverage combine
+    - coverage report
+
+
+doc:build:
+  stage: doc
+  needs:
+    - job: "CI image"
+      optional: true
+  variables:
+    FLUIDFFT_TRANSONIC_BACKEND: "python"
+  script:
+    - python -m venv .venv
+    - . .venv/bin/activate
+    - pip install fluidfft
+    - pdm install -G doc -G fft -G test --no-self
+    - pip install . --config-settings=setup-args=-Dtransonic-backend=python
+    - pdm run xvfb-run --auto-servernum sphinx-build -b html -d doc/_build/doctrees doc doc/_build/html
+    - mkdir -p public/$CI_COMMIT_REF_NAME
+    - rsync -rvc --delete doc/_build/html/* public/$CI_COMMIT_REF_NAME/
+    # This directory can become too large leading to error.
+    # It can be purged with the botton "Clear runner caches"
+    # in https://foss.heptapod.net/fluiddyn/fluidsim/-/pipelines
+    - ls public
+    - echo "CI_COMMIT_REF_NAME="$CI_COMMIT_REF_NAME
+    - echo See https://fluiddyn.pages.heptapod.net/fluidsim/$CI_COMMIT_REF_NAME
+  artifacts:
+    name: "$CI_COMMIT_REF_NAME"
+    paths:
+      - public
+    expire_in: 5 days
+  when: always

.hgignore

@@ -18,6 +18,7 @@ __pycache__
 .pytest_cache/
 .mypy_cache/
 .coverage/
+.nox
 
 bench/launcher_*
 bench/SLURM*

.readthedocs.yml

@@ -1,24 +1,17 @@
-# Read the Docs configuration file
-# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
-
-# Required
 version: 2
 
-# Set the version of Python and other tools you might need
 build:
   os: ubuntu-22.04
   tools:
     python: "3.11"
+  jobs:
+    post_create_environment:
+      - pip install pdm pip -U
+    post_install:
+      - pdm use -f $READTHEDOCS_VIRTUALENV_PATH
+      - FLUIDFFT_TRANSONIC_BACKEND="python" pip install fluidfft
+      - pdm install -G doc -G fft -G test --no-self
+      - pip install . --config-settings=setup-args=-Dtransonic-backend=python
 
-# Build documentation in the doc directory with Sphinx
 sphinx:
   configuration: doc/conf.py
-
-python:
-  install:
-    - requirements: .readthedocs.req
-    - method: pip
-      path: .
-      extra_requirements:
-        - doc
-        - fft

Makefile

@@ -37,10 +37,16 @@ shortlog:
 	@hg log -M -r$(RELEASE): --template '- {desc|firstline} (:rev:`{node|short}`)\n'
 
 black:
-	black -l 82 fluidsim scripts bench doc lib --exclude "/(__pythran__|__python__|__numba__|doc/_build|\.ipynb_checkpoints/*)/"
+	pdm black
 
 black_check:
-	black --check -l 82 fluidsim scripts bench doc lib --exclude "/(__pythran__|__python__|__numba__|doc/_build|\.ipynb_checkpoints/*)/"
+	pdm black_check
+
+lint:
+	pdm lint
+
+validate_code:
+	pdm validate_code
 
 tests:
 	pytest -v lib
@@ -84,9 +90,6 @@ _report_coverage:
 coverage: _tests_coverage _report_coverage
 
 
-lint:
-	pylint -rn --rcfile=pylintrc --jobs=$(shell nproc) fluidsim --exit-zero
-
 define _init_coverage
 	rm -rf .coverage
 	mkdir -p .coverage

README.md

@@ -0,0 +1,100 @@
+# ![FluidSim](https://foss.heptapod.net/fluiddyn/fluidsim/raw/branch/default/doc/logo.svg)
+
+[![Latest version](https://badge.fury.io/py/fluidsim.svg)](https://pypi.python.org/pypi/fluidsim/)
+![Supported Python versions](https://img.shields.io/pypi/pyversions/fluidsim.svg)
+[![Documentation status](https://readthedocs.org/projects/fluidsim/badge/?version=latest)](http://fluidsim.readthedocs.org)
+[![Chat room](https://img.shields.io/matrix/fluiddyn-users:matrix.org.svg)](https://matrix.to/#/#fluiddyn-users:matrix.org)
+[![Code coverage](https://codecov.io/gh/fluiddyn/fluidsim/branch/branch%2Fdefault/graph/badge.svg)](https://codecov.io/gh/fluiddyn/fluidsim)
+[![Heptapod CI](https://foss.heptapod.net/fluiddyn/fluidsim/badges/branch/default/pipeline.svg)](https://foss.heptapod.net/fluiddyn/fluidsim/-/pipelines)
+[![Github Actions](https://github.com/fluiddyn/fluidsim/actions/workflows/ci.yml/badge.svg?branch=branch/default)](https://github.com/fluiddyn/fluidsim/actions)
+
+Fluidsim is an extensible framework for studying fluid dynamics with
+numerical simulations using Python. Fluidsim is an object-oriented
+library to develop solvers (mainly using pseudo-spectral methods) by
+writing mainly Python code. The result is **very efficient** even
+compared to a pure Fortran or C++ code since the time-consuming tasks
+are performed by optimized compiled functions.
+
+**Documentation**: <https://fluidsim.readthedocs.io>
+
+## Getting started
+
+To try fluidsim without installation:
+[![Binder notebook](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/fluiddyn/fluidsim/branch%2Fdefault?urlpath=lab/tree/doc/ipynb)
+
+For a **basic installation** it should be sufficient to run:
+
+    pip install fluidsim
+
+or with conda:
+
+    conda install -c conda-forge fluidsim
+
+Much more detailed instructions are given in [the
+documentation](https://fluidsim.readthedocs.io/en/latest/install.html).
+
+## How does it work?
+
+Fluidsim is a
+[HPC](https://en.wikipedia.org/wiki/High-performance_computing) code. It
+is part of the wider project
+[FluidDyn](https://pypi.python.org/pypi/fluiddyn/) and its
+pseudospectral solvers rely on the library
+[fluidfft](http://fluidfft.readthedocs.io) to use very efficient FFT
+libraries. Fluidfft is written in C++, Cython and Python. Fluidfft and
+fluidsim take advantage of
+[Pythran](https://github.com/serge-sans-paille/pythran), an
+ahead-of-time compiler which produces very efficient binaries by
+compiling Python via C++11.
+
+An advantage of a CFD code written mostly in Python is that, to run
+simulations and analyze the results, the users communicate (possibly
+interactively) together and with the machine with Python, which is
+nowadays among the best languages to do these tasks. Moreover, it is
+much simpler and faster than with pure Fortran or C++ codes to add any
+complicated analysis or to write a modified solver. Fluidsim can also be
+used to extend existing solvers with Python interfaces such as
+[Basilisk](http://basilisk.fr).
+
+We have created fluidsim to be **easy and nice to use and to develop**,
+**efficient** and **robust**.
+
+*Keywords and ambitions*: fluid dynamics research with Python (>=3.6);
+modular, object-oriented, collaborative, tested and documented, free and
+open-source software.
+
+## License
+
+FluidSim is distributed under the
+[CeCILL](http://www.cecill.info/index.en.html) License, a GPL compatible
+french license.
+
+## Metapapers and citations
+
+If you use FluidSim to produce scientific articles, please cite our
+metapapers presenting the [FluidDyn
+project](https://openresearchsoftware.metajnl.com/articles/10.5334/jors.237/),
+[FluidFFT](https://openresearchsoftware.metajnl.com/articles/10.5334/jors.238/),
+and
+[FluidSim](https://openresearchsoftware.metajnl.com/articles/10.5334/jors.239/):
+
+    @article{fluiddyn, doi = {10.5334/jors.237}, year = {2019}, publisher
+    = {Ubiquity Press, Ltd.}, volume = {7}, author = {Pierre Augier and
+    Ashwin Vishnu Mohanan and Cyrille Bonamy}, title = {{FluidDyn}: A
+    Python Open-Source Framework for Research and Teaching in Fluid
+    Dynamics by Simulations, Experiments and Data Processing}, journal =
+    {Journal of Open Research Software} }
+
+    @article{fluidfft, doi = {10.5334/jors.238}, year = {2019}, publisher
+    = {Ubiquity Press, Ltd.}, volume = {7}, author = {Ashwin Vishnu
+    Mohanan and Cyrille Bonamy and Pierre Augier}, title = {{FluidFFT}:
+    Common {API} (C\$mathplusmathplus\$ and Python) for Fast Fourier
+    Transform {HPC} Libraries}, journal = {Journal of Open Research
+    Software} }
+
+    @article{fluidsim, doi = {10.5334/jors.239}, year = {2019}, publisher
+    = {Ubiquity Press, Ltd.}, volume = {7}, author = {Mohanan, Ashwin
+    Vishnu and Bonamy, Cyrille and Linares, Miguel Calpe and Augier,
+    Pierre}, title = {{FluidSim}: {Modular}, {Object}-{Oriented} {Python}
+    {Package} for {High}-{Performance} {CFD} {Simulations}}, journal =
+    {Journal of Open Research Software} }