capytaine 1.5.post1__tar.gz → 2.1__tar.gz

capytaine-2.1/.github/workflows/build_docs.yml

@@ -0,0 +1,46 @@
+name: Build and deploy documentation
+
+on:
+  push:
+    branches:
+      - master
+    paths:
+      - 'docs/**'
+
+  pull_request:
+    paths:
+      - 'docs/**'
+
+  workflow_dispatch:
+
+
+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-2.1/.github/workflows/build_wheels.yaml

@@ -0,0 +1,45 @@
+name: Build wheels
+
+on:
+  workflow_dispatch:
+  push:
+    tags:
+      - v*
+  schedule:
+    - cron: '5 5 5/15 * *'  # On the 5th and 20th of each month at 5:05
+
+
+jobs:
+  build_wheels:
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-20.04, macos-11, windows-2019]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: fortran-lang/setup-fortran@v1
+        id: setup-fortran
+        with:
+          compiler: 'gcc'
+          version: '13'
+
+      - name: Build wheels
+        uses: pypa/cibuildwheel@v2.17.0
+        env:
+          CIBW_SKIP: "pp* *i686* *musllinux* *win32*"
+        # Package the DLL dependencies in the wheel for windows (done by default for the other platforms).
+        # delvewheel cannot mangle the libraries, stripping does not work.
+          CIBW_BEFORE_BUILD_WINDOWS: pip install delvewheel
+          CIBW_REPAIR_WHEEL_COMMAND_WINDOWS: "delvewheel show {wheel} && delvewheel repair -w {dest_dir} {wheel} --no-mangle-all"
+        # with:
+        #   package-dir: .
+        #   output-dir: wheelhouse
+        #   config-file: "{package}/pyproject.toml"
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: wheels-${{ matrix.os }}
+          path: ./wheelhouse/*.whl

capytaine-2.1/.github/workflows/test_new_commits.yaml

@@ -0,0 +1,44 @@
+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
+
+jobs:
+  build_and_test:
+
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        python-version: ['3.8', '3.11']
+
+    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_locked_env

capytaine-2.1/.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: ['3.7', '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

capytaine-2.1/.gitignore

@@ -0,0 +1,153 @@
+.idea/
+pytest/Nemoh_verification_cases/*/results/
+docs/_static/
+docs/developer_manual/api/*.rst
+.pytest_cache/
+.vscode/
+*.ogv
+
+# Created by https://www.gitignore.io/api/python,fortran
+
+### Fortran ###
+# Prerequisites
+*.d
+
+# Compiled Object files
+*.slo
+*.lo
+*.o
+*.obj
+
+# Precompiled Headers
+*.gch
+*.pch
+
+# Compiled Dynamic libraries
+*.so
+*.dylib
+*.dll
+
+# Fortran module files
+*.mod
+*.smod
+
+# Compiled Static libraries
+*.lai
+*.la
+*.a
+*.lib
+
+# Executables
+*.exe
+*.out
+*.app
+
+### Python ###
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+wheelhouse/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*,cover
+.hypothesis/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# dotenv
+.env
+
+# virtualenv
+.venv
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# End of https://www.gitignore.io/api/python,fortran
+pytest/io_legacy_cases/single_body/Hydrostatics.dat
+pytest/io_legacy_cases/single_body/KH.dat
+pytest/io_legacy_cases/single_body_list/Hydrostatics.dat
+pytest/io_legacy_cases/single_body_list/KH.dat
+pytest/io_legacy_cases/two_bodies_list/Hydrostatics_0.dat
+pytest/io_legacy_cases/two_bodies_list/Hydrostatics_1.dat
+pytest/io_legacy_cases/two_bodies_list/KH_0.dat
+pytest/io_legacy_cases/two_bodies_list/KH_1.dat

capytaine-2.1/.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"]

capytaine-2.1/.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-2.1/CONTRIBUTING.md

@@ -0,0 +1,51 @@
+# How to contribute
+
+Thank you for your interest into Capytaine.
+Here are some things you should know before you go further.
+
+## Contact
+
+The best place to report a bug or to propose an enhancement is the [issue
+tracker](https://github.com/mancellin/capytaine/issues) of Capytaine's Github
+repository.
+
+The [discussion page](https://github.com/mancellin/capytaine/discussions) can
+also be used to ask questions and submit ideas.
+
+## Submitting changes
+
+Pull requests are welcome.
+Before submitting one, please take a look at the following points:
+
+* To submit a pull request (PR), you will need to fork the repository. Then, it is
+  recommended to create a new branch in your fork dedicated to your bug fix or
+  new feature. Once the PR has been accepted, the content of the branch will be
+  squashed into a single commit on the master branch. Afterward, the branch can
+  be deleted (or forgotten).
+
+* For simple modifications (e.g. typos) the whole process above can be done
+  automatically by Github by using its edition functionality (the pencil icon
+  on the top left of Github's file viewer).
+
+* The Github repository includes tests in the `pytest` directory.
+  Tests can be run with the `pytest` module (`python -m pytest`).
+  Before submitting a change of the code, make sure that all tests are passing.
+  If you'd like to add a feature, please add the relevant tests to the `pytest`
+  directory.
+
+* All modifications of the code are listed in the `docs/changelog.rst`.
+  If you submit a bug fix or a new feature, please add a line in the changelog.
+
+* New features should also be documented in the user manual (`docs/user_manual/`).
+  Please add a short documentation of the feature in the relevant page.
+
+* The code follows the [PEP8](https://pep8.org/) guidelines for code style.
+  Indentation is done with four spaces.
+  Try to avoid trailing whitespaces whenever possible.
+
+The whole of Capytaine is currently licensed under the terms of the General
+Public License (GPL). In the future, some modules might be extracted and
+released with another free software license, such as the Apache License. If
+your contribution cannot be released under another license (because it includes
+code from another GPL package or just because you don't want to), please tell
+us explicitly.

capytaine-2.1/Dockerfile

@@ -0,0 +1,13 @@
+FROM ubuntu:jammy
+
+RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y \
+                git \
+                gfortran \
+                python3 \
+                python3-pip \
+                ipython3 \
+                && rm -rf /var/lib/apt/lists/*
+
+WORKDIR /home/user/
+ADD ./ ./capytaine/
+RUN pip install ./capytaine

capytaine-2.1/Makefile

@@ -0,0 +1,30 @@
+install:
+	pip install .
+
+develop:
+	pip install meson-python ninja "numpy>=2.0.0rc1,<2.3" charset-normalizer # No installed from pyproject.toml in this case...
+	pip install --no-build-isolation -e .
+
+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