capytaine 2.3__tar.gz → 3.0.0a1__tar.gz

{capytaine-2.3 → capytaine-3.0.0a1}/.github/workflows/build_docs.yml

@@ -2,8 +2,6 @@ name: Build and deploy documentation
 
 on:
   push:
-    branches:
-      - master
     paths:
       - 'docs/**'
 
@@ -31,26 +29,26 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v4
 
-      - uses: actions/setup-python@v5
-        with:
-          python-version: '3.12'
+      - name: Set up Just
+        run: sudo apt install -y just
 
-      - name: Install Capytaine and other dependencies
-        run: pip install .[optional,docs]
+      - name: Set up UV
+        uses: astral-sh/setup-uv@v5
+        with:
+          enable-cache: true
 
       - name: Build documentation
-        run: cd docs && make
+        run: just build_docs
 
       - name: Deploy pages
         if: |
-          github.repository_owner == 'capytaine' &&
-          github.ref == 'refs/heads/master'
-        # Only deploy the version merged into the master branch of capytaine/capytaine
+          github.repository_owner == 'capytaine'
+        # Only deploy the version of capytaine/capytaine
         uses: JamesIves/github-pages-deploy-action@releases/v4
         with:
           folder: ./docs/_build/html/
           repository-name: capytaine/capytaine.github.io
           branch: main
-          target-folder: master/
+          target-folder: ${{ github.ref_name }}/
           clean: true
           token: ${{ secrets.TOKEN_PAGES }}

capytaine-3.0.0a1/.github/workflows/build_wheels.yaml

@@ -0,0 +1,103 @@
+name: Build wheels
+
+on:
+  workflow_dispatch:
+  push:
+    tags:
+      - v*
+  schedule:
+    - cron: '6 6 6/16 * *'  # On the 6th and 22nd of each month at 6:06
+
+
+jobs:
+  "build_wheels_on_windows":
+    name: Build wheels on Windows
+    runs-on: windows-2025
+
+    steps:
+      - uses: actions/checkout@v6
+
+      - uses: fortran-lang/setup-fortran@v1
+        with:
+          compiler: 'gcc'
+          version: '13'
+
+      - name: Build wheels
+        uses: pypa/cibuildwheel@v3.3.0
+        env:
+          CIBW_SKIP: "*win32* cp314t*"
+          CIBW_BEFORE_BUILD_WINDOWS: pip install delvewheel
+          CIBW_REPAIR_WHEEL_COMMAND_WINDOWS: "delvewheel show {wheel} && delvewheel repair -w {dest_dir} {wheel} --no-mangle-all"
+          # Package the DLL dependencies in the wheel for windows (done by default for the other platforms).
+          # delvewheel cannot mangle the libraries, stripping does not work.
+
+      - uses: actions/upload-artifact@v6
+        with:
+          name: wheels-windows
+          path: ./wheelhouse/*.whl
+
+  "build_wheels_on_ubuntu":
+    name: Build wheels on Ubuntu
+    runs-on: ubuntu-22.04
+
+    steps:
+      - uses: actions/checkout@v6
+
+      # No need to setup fortran, it won't be used by CIbuildwheel which is
+      # using a Manylinux container
+
+      - name: Build wheels on Ubuntu
+        uses: pypa/cibuildwheel@v3.3.0
+        env:
+          CIBW_SKIP: "*i686* *musllinux*"
+
+      - uses: actions/upload-artifact@v6
+        with:
+          name: wheels-ubuntu
+          path: ./wheelhouse/*.whl
+
+
+  "build_wheels_on_macos_intel":
+    name: Build wheels on MacOS Intel
+    runs-on: macos-15-intel
+
+    steps:
+      - uses: actions/checkout@v6
+
+      - uses: fortran-lang/setup-fortran@v1
+        with:
+          compiler: 'gcc'
+          version: '13'
+
+      - name: Build wheels
+        uses: pypa/cibuildwheel@v3.3.0
+        env:
+          CIBW_ENVIRONMENT: MACOSX_DEPLOYMENT_TARGET=15.0
+
+      - uses: actions/upload-artifact@v6
+        with:
+          name: wheels-macos-intel
+          path: ./wheelhouse/*.whl
+
+
+  "build_wheels_on_macos_arm":
+    name: Build wheels on MacOS ARM
+    runs-on: macos-14
+
+    steps:
+      - uses: actions/checkout@v6
+
+      - uses: fortran-lang/setup-fortran@v1
+        with:
+          compiler: 'gcc'
+          version: '13'
+
+      - name: Build wheels
+        uses: pypa/cibuildwheel@v3.3.0
+        env:
+          CIBW_ENVIRONMENT: MACOSX_DEPLOYMENT_TARGET=14.0
+
+      - uses: actions/upload-artifact@v6
+        with:
+          name: wheels-macos-arm
+          path: ./wheelhouse/*.whl

{capytaine-2.3 → capytaine-3.0.0a1}/.github/workflows/test_new_commits.yaml

@@ -16,7 +16,6 @@ on:
 
 env:
   FORCE_COLOR: 3
-  # Colors for nox
 
 # The following block is meant to cancel the workflow if a newer commit is pushed on the pull request
 # From https://stackoverflow.com/questions/66335225/how-to-cancel-previous-runs-in-the-pr-when-you-push-new-commitsupdate-the-curre
@@ -25,28 +24,35 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
-  build_and_test:
+  "build_and_test":
 
     runs-on: ubuntu-latest
 
     strategy:
       matrix:
-        python-version: ['3.8', '3.12']
+        python-version: ['38', '313']
 
     steps:
 
     - name: Checkout repository
       uses: actions/checkout@v4
 
+    # - name: Set up Just
+    #   uses: extractions/setup-just@v3
+    #   with:
+    #       just-version: 1.40
+    - name: Set up Just
+      run: sudo apt install -y just
+
     - name: Set up UV
       uses: astral-sh/setup-uv@v5
       with:
         enable-cache: true
 
-    - name: Run nox session
-      run: uvx nox --force-python ${{ matrix.python-version }} -s build_and_test_on_locked_env
+    - name: Run tests
+      run: just test_in_py${{ matrix.python-version }}_reference_env
 
-  compile_fortran:
+  "compile_fortran":
 
     runs-on: ubuntu-latest
 
@@ -66,11 +72,11 @@ jobs:
     #     version: '13'
 
     - name: Compile and run example
-      working-directory: capytaine/green_functions/libDelhommeau/
+      working-directory: libs/libDelhommeau/
       run: make example && examples/minimal/minimal_example.bin
       # Soundness of the results is not tested, only that the compiling and
       # execution are succeeding.
 
     - name: Run simple benchmark
-      working-directory: capytaine/green_functions/libDelhommeau/
+      working-directory: libs/libDelhommeau/
       run: make run_bench_rankine && make run_bench_waves

capytaine-3.0.0a1/.github/workflows/test_with_latest_dependencies.yaml

@@ -0,0 +1,48 @@
+name: Build and test using latest available dependencies
+
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: '5 5 5/15 * *'  # On the 5th and 20th of each month at 5:05
+
+env:
+  FORCE_COLOR: 3
+
+jobs:
+  "test_in_latest_env":
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    - name: Set up UV
+      uses: astral-sh/setup-uv@v5
+      with:
+        enable-cache: true
+
+    - name: Set up Just
+      run: sudo apt install -y just
+
+    - name: Run tests
+      run: just test_in_latest_env
+
+  "test_in_nightly_env":
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    - name: Set up UV
+      uses: astral-sh/setup-uv@v5
+      with:
+        enable-cache: true
+
+    - name: Set up Just
+      run: sudo apt install -y just
+
+    - name: Run tests
+      run: just test_in_nightly_env

capytaine-3.0.0a1/.pre-commit-config.yaml

@@ -0,0 +1,25 @@
+exclude: "pytest/.*/.*"
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: "v6.0.0"
+    hooks:
+      - id: check-added-large-files  # Prevent giant files from being committed
+      - id: check-ast  # Simply check whether files parse as valid python
+      - id: check-case-conflict  # Check for filenames that would conflict on a case-insensitive filesystem
+      - id: check-illegal-windows-names  # Check for filenames that could not exist on Windows
+      - id: check-merge-conflict  # Check for files that contain merge conflict strings
+      - id: check-symlinks  # Checks for symlinks which do not point to anything
+      - id: check-toml  # Attempts to load all TOML files to verify syntax
+      - id: check-yaml  # Attempts to load all YAML files to verify syntax
+      - id: debug-statements  # Check for calls to breakpoint()
+      - id: end-of-file-fixer  # Makes sure files end in a newline and only a newline
+      - id: no-commit-to-branch  # Disallow commiting directly to "master"
+      - id: mixed-line-ending  # Check the kind of line ending (LF or CRLF)
+      - id: trailing-whitespace  # Trim trailing whitespaces
+
+  - repo: https://github.com/codespell-project/codespell
+    rev: "v2.4.1"
+    hooks:
+      - id: codespell
+        additional_dependencies:
+        - tomli

capytaine-3.0.0a1/Justfile

@@ -0,0 +1,189 @@
+set shell := ["bash", "-c"]
+set windows-shell := ["powershell.exe", "-c"]
+
+default:
+    just --list
+
+# Run the recipe below in a clean virtual environment to install Capytaine in
+# editable mode.
+editable_install:
+    uv pip install -r pyproject.toml \
+        --extra optional \
+        --group editable_install \
+        --group dev
+    uv pip install --no-build-isolation --editable .
+
+# Define the temporary directory differently based on OS
+TEMP_DIR := if os_family() == 'windows' {
+    `$temp = Join-Path $env:TEMP ('capytainedev-' + [System.IO.Path]::GetRandomFileName()); New-Item -ItemType Directory -Path $temp -Force | Out-Null; Write-Output $temp`
+} else {
+    `mktemp --directory --tmpdir capytainedev-XXXXX`
+}
+
+ENV := "MPLBACKEND=pdf CAPYTAINE_PROGRESS_BAR=False CAPYTAINE_CACHE_DIR=" + TEMP_DIR + "/cache/"
+
+TEST_DIR := justfile_directory() / 'pytest'
+NEMOH_CASES := TEST_DIR / 'Nemoh_verification_cases' / 'Cylinder'
+
+EXAMPLES_DIR := justfile_directory() / 'docs' / 'examples' / 'src'
+EXAMPLES_FILES := ' \
+    A1_single_body_hydrodynamics.py \
+    A2_multibody.py \
+    A3_finite_depth_flap.py \
+    A4_forward_speed_on_vertical_cylinder.py \
+    A7_custom_dofs.py \
+    A8_convergence_study.py \
+    A10_elasticity_of_beam.py \
+    A11_parametric_study_depth.py \
+    B1_pressure_on_hull.py \
+    B2_haskind.py \
+    B3_free_surface_elevation.py \
+    B4_kochin.py \
+    B5_plot_velocity_in_domain.py \
+    B8_pressure_infinite_frequency.py \
+    C5_plot_influence_matrix.py \
+    C8_compare_Green_functions.py \
+    C9_custom_Green_function.py \
+'
+
+## Reason for skipping some example files:
+# A5_benchmark_plane_symmetries.py \
+# A6_benchmark_axisymmetric_mesh.py \
+# A9_test_irregular_frequency_removal.py \ # Slow
+# B6_animate_free_surface.py  \           # Requires VTK
+# B7_boat_animation.py  \                 # Requires VTK
+# C6_axisymmetric_buoy.py  \              # Requires VTK
+# C10_custom_linear_solver_on_gpu.py \    # Requires torch
+
+# Run the test suite and the example files assuming a virtual environment with
+# Capytaine installed has been activated
+[unix]
+_test:
+    #!/usr/bin/env bash
+    set -euxo pipefail
+    uv pip list | grep -Ei "numpy|xarray|capytaine" || true
+    cd {{TEMP_DIR}}
+    export {{ENV}}
+    python -c "import capytaine; print(capytaine.__version__)"
+    python -m pytest {{TEST_DIR}}
+    capytaine --help
+    capytaine {{NEMOH_CASES}}/Nemoh.cal
+    capytaine {{NEMOH_CASES}}/Nemoh_v3.cal
+    set +x  # Stop displaying commands
+    for f in {{EXAMPLES_FILES}}; do
+        echo -e "\n---> Running $f";
+        python {{EXAMPLES_DIR}}/$f;
+    done
+
+# Simplified version of the above, working on Windows
+[windows]
+_test:
+    #! powershell
+    cd {{TEMP_DIR}}
+    python -c "import capytaine; print(capytaine.__version__)"
+    python -m pytest {{TEST_DIR}}
+    capytaine --help
+    capytaine {{NEMOH_CASES}}/Nemoh.cal
+    capytaine {{NEMOH_CASES}}/Nemoh_v3.cal
+
+_install_and_test:
+    uv pip install --no-deps --no-build-isolation .
+    just _test
+
+
+# In the recipes below, we have
+#
+#    --no-editable --with "capytaine @ ." -- just _test
+#
+# or
+#
+#    --no-editable -- just _install_and_test
+#
+# because the default behavior of uv is to install the local project in
+# editable mode, but we don't want that because of an incompatibility with
+# meson-python (https://github.com/astral-sh/uv/issues/10214)
+#
+# besides, we have --no-default-groups because uv loads by default the `dev`
+# dependency-group from pyproject.toml, but we don't need it here and it can
+# actually cause issue in CI.
+
+test_in_latest_env:
+    uv run \
+        --isolated --no-default-groups \
+        --no-editable --with "capytaine[optional] @ ." \
+        --group test \
+        -- \
+        just _test
+
+# In the recipe below,
+# "--index-strategy unsafe-best-match" means uv should not ignore wheels
+# from PyPI during universal resolution
+
+test_in_nightly_env:
+    uv run \
+        --isolated --no-default-groups \
+        --python 3.14 \
+        --pre --extra-index-url https://pypi.anaconda.org/scientific-python-nightly-wheels/simple \
+        --index-strategy unsafe-best-match \
+        --no-editable --with "capytaine @ ." \
+        --group test \
+        -- \
+        just _test
+
+
+test_in_py38_reference_env:
+    uv run \
+        --isolated --no-default-groups \
+        --python 3.8 \
+        --no-editable \
+        --with-requirements {{TEST_DIR}}/envs/2023-08-01-py3.8.txt \
+        -- \
+        just _install_and_test
+
+test_in_py313_reference_env:
+    uv run \
+        --isolated --no-default-groups \
+        --python 3.13 \
+        --no-editable \
+        --with-requirements {{TEST_DIR}}/envs/2025-11-25-py3.13.txt \
+        -- \
+        just _install_and_test
+
+# How the requirements files from the above recipes where generated.
+create_test_env_file python="3.8" date="2023-08-01":
+    uv pip compile \
+        pyproject.toml \
+        --python-version {{python}} \
+        --group test \
+        --group editable_install \
+        --extra optional \
+        --exclude-newer {{date}} \
+        -o {{TEST_DIR}}/envs/{{date}}-py{{python}}.txt
+
+
+# Compile the Fortran code without parallelism for easier reading of the errors.
+test_fortran_compilation:
+    # It is assumed that meson and ninja are already installed (e.g. with editable_install).
+    meson setup --wipe {{TEMP_DIR}}/build && meson compile -C {{TEMP_DIR}}/build -j 1
+
+
+build_docs:
+    uv run \
+        --isolated \
+        --no-editable --with "capytaine[optional] @ ." \
+        --group docs \
+        -- \
+        make --directory="./docs/"
+
+
+clean:
+    rm -f src/capytaine/green_functions/libs/*.so
+    rm -rf build/
+    rm -rf dist/
+    rm -rf src/capytaine.egg-info/
+    rm -rf docs/_build
+    rm -rf .pytest_cache/
+    rm -rf .venv/
+    rm -rf __pycache__ */__pycache__ */*/__pycache__ */*/*/__pycache__
+    rm -rf $HOME/.cache/capytaine/*
+    rm -rf /tmp/capytainedev-*/

{capytaine-2.3 → capytaine-3.0.0a1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: capytaine
-Version: 2.3
+Version: 3.0.0a1
 Summary: Python BEM solver for linear potential flow, based on Nemoh
 Author-Email: Matthieu Ancellin <matthieu.ancellin@mews-labs.com>
 License:                     GNU GENERAL PUBLIC LICENSE
@@ -689,26 +689,20 @@ Requires-Python: >=3.8
 Requires-Dist: numpy>=1.20; python_version >= "3.9"
 Requires-Dist: numpy>=1.24; python_version == "3.8"
 Requires-Dist: scipy
-Requires-Dist: pandas>=1.3
+Requires-Dist: pandas<3,>=1.3
 Requires-Dist: xarray
 Requires-Dist: rich
 Provides-Extra: optional
 Requires-Dist: matplotlib; extra == "optional"
+Requires-Dist: vtk; extra == "optional"
+Requires-Dist: pyvista; extra == "optional"
+Requires-Dist: psutil; extra == "optional"
 Requires-Dist: joblib>=1.3; extra == "optional"
+Requires-Dist: threadpoolctl; extra == "optional"
 Requires-Dist: meshio; extra == "optional"
+Requires-Dist: trimesh; extra == "optional"
+Requires-Dist: h5py; extra == "optional"
 Requires-Dist: netcdf4; extra == "optional"
-Requires-Dist: vtk; extra == "optional"
-Provides-Extra: more-optional
-Requires-Dist: pygmsh; extra == "more-optional"
-Requires-Dist: gmsh; extra == "more-optional"
-Provides-Extra: test
-Requires-Dist: pytest; extra == "test"
-Requires-Dist: capytaine[optional]; extra == "test"
-Provides-Extra: docs
-Requires-Dist: sphinx; extra == "docs"
-Requires-Dist: sphinx-toolbox; extra == "docs"
-Requires-Dist: sphinxcontrib-proof; extra == "docs"
-Requires-Dist: sphinxcontrib-mermaid; extra == "docs"
 Description-Content-Type: text/markdown
 
 # Capytaine: a linear potential flow BEM solver with Python.

{capytaine-2.3 → capytaine-3.0.0a1}/docs/Makefile

@@ -28,4 +28,4 @@ test: show
 
 autodoc:
 	rm -rf developer_manual/api/capytaine*.rst
-	sphinx-apidoc -o developer_manual/api/ ../capytaine --separate --doc-project "API documentation"
+	sphinx-apidoc -o developer_manual/api/ ../src/capytaine --separate --doc-project "API documentation"