capytaine 2.0__tar.gz → 2.2__tar.gz

capytaine-2.2/.github/workflows/build_docs.yml

@@ -0,0 +1,53 @@
+name: Build and deploy documentation
+
+on:
+  push:
+    branches:
+      - master
+    paths:
+      - 'docs/**'
+
+  pull_request:
+    paths:
+      - 'docs/**'
+
+  workflow_dispatch:
+
+
+# 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
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+
+      - name: Install Capytaine and other dependencies
+        run: pip install .[optional,docs]
+
+      - name: Build documentation
+        run: cd docs && make
+
+      - name: Deploy pages
+        if: github.ref == 'refs/heads/master'  # Only deploy the version merged into the master branch
+        uses: JamesIves/github-pages-deploy-action@releases/v4
+        with:
+          folder: ./docs/_build/html/
+          repository-name: capytaine/capytaine.github.io
+          branch: main
+          target-folder: master/
+          clean: true
+          token: ${{ secrets.TOKEN_PAGES }}

{capytaine-2.0 → capytaine-2.2}/.github/workflows/build_wheels.yaml

@@ -6,7 +6,7 @@ on:
     tags:
       - v*
   schedule:
-    - cron: '5 5 5/15 * *'  # On the 5th and 20th of each month at 5:05
+    - cron: '6 6 6/16 * *'  # On the 6th and 22nd of each month at 6:06
 
 
 jobs:
@@ -15,24 +15,20 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-20.04, macos-11, windows-2019]
+        os: [ubuntu-20.04, macos-12, macos-14, windows-2019]
+            # MacOS<=13 are Intel, while MacOS 14 is Apple Silicon
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      # From https://github.com/insarlab/PySolid/blob/18dcc0ffdc1aed88d9f4d87d9307284df14d26a7/.github/workflows/build-and-publish-to-pypi.yml
-      - name: Provide gfortran (macOS)
-        if: runner.os == 'macOS'
-        run: |
-          # https://github.com/actions/virtual-environments/issues/2524
-          # https://github.com/cbg-ethz/dce/blob/master/.github/workflows/pkgdown.yaml
-          sudo ln -s /usr/local/bin/gfortran-11 /usr/local/bin/gfortran
-          sudo mkdir /usr/local/gfortran
-          sudo ln -s /usr/local/Cellar/gcc@11/*/lib/gcc/11 /usr/local/gfortran/lib
-          gfortran --version
+      - uses: fortran-lang/setup-fortran@v1
+        id: setup-fortran
+        with:
+          compiler: 'gcc'
+          version: '13'
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.12.3
+        uses: pypa/cibuildwheel@v2.17.0
         env:
           CIBW_SKIP: "pp* *i686* *musllinux* *win32*"
         # Package the DLL dependencies in the wheel for windows (done by default for the other platforms).
@@ -44,6 +40,7 @@ jobs:
         #   output-dir: wheelhouse
         #   config-file: "{package}/pyproject.toml"
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
+          name: wheels-${{ matrix.os }}
           path: ./wheelhouse/*.whl

capytaine-2.2/.github/workflows/test_new_commits.yaml

@@ -0,0 +1,71 @@
+name: Build and test in fixed environments
+
+on:
+  push:
+    branches:
+      - 'master'
+    paths-ignore:
+      # Do not run if only the documentation has been changed
+      - 'docs/**'
+      - '**/*.md'
+  pull_request:
+    paths-ignore:
+      # Do not run if only the documentation has been changed
+      - 'docs/**'
+      - '**/*.md'
+
+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
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build_and_test:
+
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        python-version: ['3.8', '3.12']
+
+    steps:
+
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Set up nox
+      uses: wntrblm/nox@2024.03.02
+
+    - name: Run nox session
+      run: nox -s build_and_test_on_locked_env
+
+  compile_fortran:
+
+    runs-on: ubuntu-latest
+
+    steps:
+
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    - name: Set up Fortran
+      uses: fortran-lang/setup-fortran@v1
+      with:
+        compiler: 'gcc'
+        version: '13'
+
+    - name: Compile and run example
+      working-directory: capytaine/green_functions/libDelhommeau/
+      run: make example && examples/minimal/minimal_example.bin
+      # Soundness of the results is not tested, only that the compiling and
+      # execution are succeeding.

capytaine-2.2/.github/workflows/test_with_latest_dependencies.yaml

@@ -0,0 +1,35 @@
+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
+  # Colors for nox
+
+jobs:
+  build_and_test:
+
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        python-version: ['3.8', '3.12']
+
+    steps:
+
+    - name: Checkout repository and submodules
+      uses: actions/checkout@v4
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Set up nox
+      uses: wntrblm/nox@2024.03.02
+
+    - name: Run nox session
+      run: nox -s build_and_test_on_latest_env editable_build_and_test_on_latest_env

{capytaine-2.0 → capytaine-2.2}/.gitignore

@@ -1,5 +1,5 @@
 .idea/
-examples/**/results*
+pytest/Nemoh_verification_cases/*/results/
 docs/_static/
 docs/developer_manual/api/*.rst
 .pytest_cache/

capytaine-2.2/.pre-commit-config.yaml

@@ -0,0 +1,40 @@
+exclude: "pytest/.*/.*"
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: "v4.4.0"
+    hooks:
+      # Prevent giant files from being committed
+      - id: check-added-large-files
+      # Simply check whether files parse as valid python
+      - id: check-ast
+      # Check for files with names that would conflict on a case-insensitive filesystem like MacOS HFS+ or Windows FAT
+      - id: check-case-conflict
+      # Check for files that contain merge conflict strings
+      - id: check-merge-conflict
+      # Checks for symlinks which do not point to anything
+      - id: check-symlinks
+      # Attempts to load all TOML files to verify syntax
+      - id: check-toml
+      # Attempts to load all YAML files to verify syntax
+      - id: check-yaml
+      # Check for calls to breakpoint()
+      - id: debug-statements
+      # Makes sure files end in a newline and only a newline
+      - id: end-of-file-fixer
+      # Disallow commiting directly to "master"
+      - id: no-commit-to-branch
+      # Check the kind of line ending (LF or CRLF)
+      - id: mixed-line-ending
+      # Trim trailing whitespaces
+      - id: trailing-whitespace
+
+  # - repo: https://github.com/astral-sh/ruff-pre-commit
+  #   rev: "v0.0.291"
+  #   hooks:
+  #     - id: ruff
+
+  - repo: https://github.com/codespell-project/codespell
+    rev: "v2.2.5"
+    hooks:
+      - id: codespell
+        args: ["-L", "ba,informations,inout,ist,lamda,ment,noe,periode,sur", "--skip", "capytaine/green_functions/libDelhommeau/src/old_Prony_decomposition.f90"]

capytaine-2.2/.zenodo.json

@@ -0,0 +1,15 @@
+{
+    "title": "Capytaine",
+    "upload_type": "software",
+    "creators": [
+        {
+            "affiliation": "Eurobios Mews Labs",
+            "name": "Matthieu Ancellin",
+            "orcid": "0000-0002-0316-3230"
+        },
+        {
+            "name": "the Capytaine contributors"
+        }
+    ],
+    "access_right": "open"
+}

capytaine-2.2/Makefile

@@ -0,0 +1,30 @@
+install:
+	pip install .
+
+develop:
+	pip install -r editable_install_requirements.txt
+	pip install --no-build-isolation --editable .
+
+TEMP_DIR := $(shell mktemp -d)
+test_fortran_compilation:
+	# Compile the Fortran code without parallelism for easier reading of the errors.
+	# It is assumed that meson and ninja are already installed.
+	meson setup --wipe $(TEMP_DIR) && meson compile -C $(TEMP_DIR) -j 1
+
+test:
+	# Build and test the current repository in a fixed environment.
+	nox -s build_and_test_on_locked_env
+
+clean:
+	rm -f capytaine/green_functions/libs/*.so
+	rm -rf build/
+	rm -rf dist/
+	rm -rf capytaine.egg-info/
+	rm -rf docs/_build
+	rm -rf .pytest_cache/
+	rm -rf .nox/
+	rm -rf .venv/
+	rm -rf __pycache__ */__pycache__ */*/__pycache__ */*/*/__pycache__
+	rm -rf ${HOME}/.cache/capytaine/*
+
+.PHONY: install develop test clean test_fortran_compilation

{capytaine-2.0 → capytaine-2.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: capytaine
-Version: 2.0
+Version: 2.2
 Summary: Python BEM solver for linear potential flow, based on Nemoh
 Author-Email: Matthieu Ancellin <matthieu.ancellin@eurobios.com>
 License:                     GNU GENERAL PUBLIC LICENSE
@@ -683,43 +683,60 @@ Classifier: Intended Audience :: Science/Research
 Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
 Classifier: Topic :: Scientific/Engineering
 Project-URL: Repository, https://github.com/capytaine/capytaine
-Requires-Python: >=3.7
-Requires-Dist: numpy
+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: xarray
-Requires-Dist: pytest; extra == "ci"
-Requires-Dist: hypothesis; extra == "ci"
-Provides-Extra: ci
+Requires-Dist: rich
+Requires-Dist: matplotlib; extra == "optional"
+Requires-Dist: joblib>=1.3; extra == "optional"
+Requires-Dist: meshio; extra == "optional"
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: sphinx; extra == "docs"
+Requires-Dist: sphinx-toolbox; extra == "docs"
+Requires-Dist: sphinxcontrib-proof; extra == "docs"
+Requires-Dist: sphinxcontrib-mermaid; extra == "docs"
+Provides-Extra: optional
+Provides-Extra: test
+Provides-Extra: docs
 Description-Content-Type: text/markdown
 
 # Capytaine: a linear potential flow BEM solver with Python.
 
-[![DOI](http://joss.theoj.org/papers/10.21105/joss.01341/status.svg)](https://doi.org/10.21105/joss.01341)
-![CI status](https://github.com/capytaine/capytaine/actions/workflows/tests.yaml/badge.svg?event=push)
+![CI status](https://github.com/capytaine/capytaine/actions/workflows/test_new_commits.yaml/badge.svg?event=push)
+![CI status](https://github.com/capytaine/capytaine/actions/workflows/test_with_latest_dependencies.yaml/badge.svg)
+
 
 Capytaine is Python package for the simulation of the interaction between water waves and floating bodies in frequency domain.
 It is built around a full rewrite of the open source Boundary Element Method (BEM) solver Nemoh for the linear potential flow wave theory.
 
 ## Installation
 
+[![PyPI](https://img.shields.io/pypi/v/capytaine)](https://pypi.org/project/capytaine)
+[![Conda-forge](https://img.shields.io/conda/vn/conda-forge/capytaine)](https://github.com/conda-forge/capytaine-feedstock)
+
 Packages for Windows, macOS and Linux are available on PyPI:
 
 ```bash
 pip install capytaine
 ```
-and Conda-forge:
+and Conda-forge
+
 ```bash
 conda install -c conda-forge capytaine
 ```
 
 ## Documentation
 
-[https://ancell.in/capytaine/latest/](https://ancell.in/capytaine/latest/)
+[https://capytaine.github.io/](https://capytaine.github.io/)
+
+[![DOI](http://joss.theoj.org/papers/10.21105/joss.01341/status.svg)](https://doi.org/10.21105/joss.01341)
 
 ## License
 
-Copyright (C) 2017-2023, Matthieu Ancellin
+Copyright (C) 2017-2024, Matthieu Ancellin
 
 Since April 2022, the development of Capytaine is funded by the Alliance for Sustainable Energy, LLC, Managing and Operating Contractor for the National Renewable Energy Laboratory (NREL) for the U.S. Department of Energy.
 
@@ -727,7 +744,8 @@ This program is free software: you can redistribute it and/or modify it under th
 
 This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.
 
-It is based on [Nemoh](https://lheea.ec-nantes.fr/logiciels-et-brevets/nemoh-presentation-192863.kjsp), which has been developed by Gérard Delhommeau, Aurélien Babarit et al., (École Centrale de Nantes) and is distributed under the Apache License 2.0.
+It is based on version 2 of [Nemoh](https://lheea.ec-nantes.fr/logiciels-et-brevets/nemoh-presentation-192863.kjsp), which has been developed by Gérard Delhommeau, Aurélien Babarit et al., (École Centrale de Nantes) and was distributed under the Apache License 2.0.
+
+Some core Fortran routines of Capytaine coming from Nemoh version 2 are also available under the Apache License 2.0. They can be found in the [`capytaine/green_functions/libDelhommeau`](https://github.com/capytaine/capytaine/tree/master/capytaine/green_functions/libDelhommeau) directory of Capytaine's repository.
 
-It includes code from [meshmagick](https://github.com/LHEEA/meshmagick/) by François Rongère (École
-Centrale de Nantes), licensed under the GNU General Public License (GPL).
+Capytaine includes code from [meshmagick](https://github.com/LHEEA/meshmagick/) by François Rongère (École Centrale de Nantes), licensed under the GNU General Public License (GPL).

{capytaine-2.0 → capytaine-2.2}/README.md

@@ -1,30 +1,37 @@
 # Capytaine: a linear potential flow BEM solver with Python.
 
-[![DOI](http://joss.theoj.org/papers/10.21105/joss.01341/status.svg)](https://doi.org/10.21105/joss.01341)
-![CI status](https://github.com/capytaine/capytaine/actions/workflows/tests.yaml/badge.svg?event=push)
+![CI status](https://github.com/capytaine/capytaine/actions/workflows/test_new_commits.yaml/badge.svg?event=push)
+![CI status](https://github.com/capytaine/capytaine/actions/workflows/test_with_latest_dependencies.yaml/badge.svg)
+
 
 Capytaine is Python package for the simulation of the interaction between water waves and floating bodies in frequency domain.
 It is built around a full rewrite of the open source Boundary Element Method (BEM) solver Nemoh for the linear potential flow wave theory.
 
 ## Installation
 
+[![PyPI](https://img.shields.io/pypi/v/capytaine)](https://pypi.org/project/capytaine)
+[![Conda-forge](https://img.shields.io/conda/vn/conda-forge/capytaine)](https://github.com/conda-forge/capytaine-feedstock)
+
 Packages for Windows, macOS and Linux are available on PyPI:
 
 ```bash
 pip install capytaine
 ```
-and Conda-forge:
+and Conda-forge
+
 ```bash
 conda install -c conda-forge capytaine
 ```
 
 ## Documentation
 
-[https://ancell.in/capytaine/latest/](https://ancell.in/capytaine/latest/)
+[https://capytaine.github.io/](https://capytaine.github.io/)
+
+[![DOI](http://joss.theoj.org/papers/10.21105/joss.01341/status.svg)](https://doi.org/10.21105/joss.01341)
 
 ## License
 
-Copyright (C) 2017-2023, Matthieu Ancellin
+Copyright (C) 2017-2024, Matthieu Ancellin
 
 Since April 2022, the development of Capytaine is funded by the Alliance for Sustainable Energy, LLC, Managing and Operating Contractor for the National Renewable Energy Laboratory (NREL) for the U.S. Department of Energy.
 
@@ -32,7 +39,8 @@ This program is free software: you can redistribute it and/or modify it under th
 
 This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.
 
-It is based on [Nemoh](https://lheea.ec-nantes.fr/logiciels-et-brevets/nemoh-presentation-192863.kjsp), which has been developed by Gérard Delhommeau, Aurélien Babarit et al., (École Centrale de Nantes) and is distributed under the Apache License 2.0.
+It is based on version 2 of [Nemoh](https://lheea.ec-nantes.fr/logiciels-et-brevets/nemoh-presentation-192863.kjsp), which has been developed by Gérard Delhommeau, Aurélien Babarit et al., (École Centrale de Nantes) and was distributed under the Apache License 2.0.
+
+Some core Fortran routines of Capytaine coming from Nemoh version 2 are also available under the Apache License 2.0. They can be found in the [`capytaine/green_functions/libDelhommeau`](https://github.com/capytaine/capytaine/tree/master/capytaine/green_functions/libDelhommeau) directory of Capytaine's repository.
 
-It includes code from [meshmagick](https://github.com/LHEEA/meshmagick/) by François Rongère (École
-Centrale de Nantes), licensed under the GNU General Public License (GPL).
+Capytaine includes code from [meshmagick](https://github.com/LHEEA/meshmagick/) by François Rongère (École Centrale de Nantes), licensed under the GNU General Public License (GPL).

{capytaine-2.0 → capytaine-2.2}/capytaine/__about__.py

@@ -1,14 +1,14 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 __all__ = ["__title__", "__description__", "__version__", "__author__", "__uri__", "__license__"]
 
 __title__ = "capytaine"
 __description__ = """Python BEM solver for linear potential flow, based on Nemoh"""
 
-__version__ = "2.0"
+__version__ = "2.2"
 
 __author__ = "Matthieu Ancellin"
-__uri__ = "https://github.com/mancellin/capytaine"
+__uri__ = "https://github.com/capytaine/capytaine"
 __license__ = "GPL-3.0"
 
 

{capytaine-2.0 → capytaine-2.2}/capytaine/__init__.py

@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-# coding: utf-8
 # Copyright (C) 2017-2019 Matthieu Ancellin
 # See LICENSE file at <https://github.com/mancellin/capytaine>
 
@@ -24,10 +22,14 @@ from capytaine.bodies.predefined.rectangles import Rectangle, RectangularParalle
 
 from capytaine.bem.problems_and_results import RadiationProblem, DiffractionProblem
 from capytaine.bem.solver import BEMSolver
-from capytaine.bem.engines import BasicMatrixEngine, HierarchicalToeplitzMatrixEngine
+from capytaine.bem.engines import BasicMatrixEngine, HierarchicalToeplitzMatrixEngine, HierarchicalPrecondMatrixEngine
 from capytaine.green_functions.delhommeau import Delhommeau, XieDelhommeau
 
 from capytaine.post_pro.free_surfaces import FreeSurface
 
 from capytaine.io.mesh_loaders import load_mesh
 from capytaine.io.xarray import assemble_dataset
+
+from capytaine.ui.rich import set_logging
+
+set_logging(level="WARNING")

{capytaine-2.0 → capytaine-2.2}/capytaine/bem/airy_waves.py

@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-# coding: utf-8
 """Computing the potential and velocity of Airy wave."""
 # Copyright (C) 2017-2019 Matthieu Ancellin
 # See LICENSE file at <https://github.com/mancellin/capytaine>
@@ -27,7 +25,8 @@ def airy_waves_potential(points, pb):
     x, y, z = points.T
     k = pb.wavenumber
     h = pb.water_depth
-    wbar = x * np.cos(pb.wave_direction) + y * np.sin(pb.wave_direction)
+    beta = pb.encounter_wave_direction
+    wbar = x * np.cos(beta) + y * np.sin(beta)
 
     if 0 <= k*h < 20:
         cih = np.cosh(k*(z+h))/np.cosh(k*h)
@@ -61,8 +60,9 @@ def airy_waves_velocity(points, pb):
     x, y, z = points.T
     k = pb.wavenumber
     h = pb.water_depth
+    beta = pb.encounter_wave_direction
 
-    wbar = x * np.cos(pb.wave_direction) + y * np.sin(pb.wave_direction)
+    wbar = x * np.cos(beta) + y * np.sin(beta)
 
     if 0 <= k*h < 20:
         cih = np.cosh(k*(z+h))/np.cosh(k*h)
@@ -104,5 +104,3 @@ def airy_waves_free_surface_elevation(points, pb):
     """
     points, output_shape = _normalize_free_surface_points(points)
     return 1j * pb.omega / pb.g * airy_waves_potential(points, pb).reshape(output_shape)
-
-