qmat 0.0.1__tar.gz

qmat-0.0.1/.github/workflows/ci_pipeline.yml

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+name: CI pipeline for qmat
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+
+jobs:
+  test-code:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python: ['3.8', '3.9', '3.10', '3.11', '3.12']
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: "${{ matrix.python }}"
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install .[test]
+    - name: Lint with flake8
+      run: |
+        # stop if there are Python syntax errors or undefined names
+        flake8 ./qmat ./tests --count --select=E9,F63,F7,F82 --show-source --statistics
+    - name: Run pytest with coverage
+      run: |
+        ./test.sh
+    - name: Upload coverage reports to Codecov
+      uses: codecov/codecov-action@v4
+      if: github.repository_owner == 'Parallel-in-Time' && matrix.python == '3.11'
+      with:
+        flags: smart-tests
+        verbose: true
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+
+  test-tutorials:
+    runs-on: ubuntu-latest
+    
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python 3.11
+      uses: actions/setup-python@v3
+      with:
+        python-version: "3.11"
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install .[test]
+    - name: Test with pytest-notebook
+      run: |
+        pytest ./docs/notebooks --nb-test-files -v
+  

qmat-0.0.1/.github/workflows/publish.yml

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+name: Publish qmat package 📦 to PyPI
+on:
+  workflow_dispatch:
+jobs:
+  publish:
+    name: Build and publish
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v3
+        with:
+          python-version: "3.11"
+      - name: Checkout repository
+        uses: actions/checkout@v2
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install build
+      - name: Build sdist
+        run: python -m build --sdist
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          password: ${{ secrets.PYPI_API_TOKEN }}

qmat-0.0.1/.gitignore

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+*.pyc
+*.swp
+env
+*.egg-info
+build
+
+# OSX
+.DS_Store
+.AppleDouble
+.LSOverride
+
+# Thumbnails
+._*
+
+# Spyder
+.spyproject
+
+*.xml
+
+# jupyter
+.ipynb_checkpoints
+
+# VSCode
+.vscode
+*.cpp
+
+# Pytest and coeverage stuff
+.benchmarks
+.pytest_cache
+.coverage*
+htmlcov
+sitecustomize.py
+
+# Doc
+docs/_build
+docs/site.webmanifest

qmat-0.0.1/LICENSE

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+BSD 2-Clause License
+
+Copyright (c) 2024, Parallel-in-Time (PinT) Algorithms
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

qmat-0.0.1/PKG-INFO

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+Metadata-Version: 2.3
+Name: qmat
+Version: 0.0.1
+Summary: Generation of Q-coefficients for Spectral Deferred Corrections (and other time-integration methods ...)
+Project-URL: Homepage, https://github.com/Parallel-in-Time/qmat
+Project-URL: Tracker, https://github.com/Parallel-in-Time/qmat/issues
+Maintainer-email: Thibaut Lunet <thibaut.lunet@tuhh.de>
+License: BSD 2-Clause License
+        
+        Copyright (c) 2024, Parallel-in-Time (PinT) Algorithms
+        
+        Redistribution and use in source and binary forms, with or without
+        modification, are permitted provided that the following conditions are met:
+        
+        1. Redistributions of source code must retain the above copyright notice, this
+           list of conditions and the following disclaimer.
+        
+        2. Redistributions in binary form must reproduce the above copyright notice,
+           this list of conditions and the following disclaimer in the documentation
+           and/or other materials provided with the distribution.
+        
+        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+        AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+        IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+        DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+        FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+        DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+        SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+        CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+        OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+        OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+License-File: LICENSE
+Classifier: Development Status :: 3 - Alpha
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Mathematics
+Requires-Python: >=3.8
+Requires-Dist: numpy
+Requires-Dist: scipy
+Provides-Extra: test
+Requires-Dist: coverage[toml]; extra == 'test'
+Requires-Dist: flake8; extra == 'test'
+Requires-Dist: matplotlib; extra == 'test'
+Requires-Dist: notebook; extra == 'test'
+Requires-Dist: pytest; extra == 'test'
+Requires-Dist: pytest-notebook; extra == 'test'
+Requires-Dist: pytest-timeout; extra == 'test'
+Description-Content-Type: text/markdown
+
+# QMat Package
+
+[![CI pipeline for qmat](https://github.com/Parallel-in-Time/qmat/actions/workflows/ci_pipeline.yml/badge.svg)](https://github.com/Parallel-in-Time/qmat/actions/workflows/ci_pipeline.yml)
+[![codecov](https://codecov.io/gh/Parallel-in-Time/qmat/graph/badge.svg?token=MO0LDVH5NN)](https://codecov.io/gh/Parallel-in-Time/qmat)
+
+`qmat` is a python package to generate matrix coefficients related to Collocation methods, Spectral Deferred Corrections (SDC), 
+and more general multi-stages time-integration methods (like Runge-Kutta, etc ...).
+
+It allows to generate $Q$-coefficients for multi-stages methods (equivalent to Butcher tables) :
+
+$$
+Q\text{-coefficients : }
+\begin{array}
+    {c|c}
+    \tau & Q \\
+    \hline
+    & w^\top
+\end{array}
+\quad \Leftrightarrow \quad
+\begin{array}
+    {c|c}
+    c & A \\
+    \hline
+    & b^\top
+\end{array}
+\quad\text{(Butcher table)}
+$$
+
+and many different **lower-triangular** approximation of the $Q$ matrix, named $Q_\Delta$,
+which are key elements for Spectral Deferred Correction (SDC), or more general Iterated Runge-Kutta Methods.
+
+
+
+## Installation
+
+🛠️ Still in construction, only installation from source is enable yet, see [current instructions ...](./docs/installation.md)
+
+## Basic usage
+
+📜 _If you are already familiar with those concepts, you can use this package like this :_
+
+```python
+from qmat import genQCoeffs, genQDeltaCoeffs
+
+# Coefficients or specific collocation method
+nodes, weights, Q = genQCoeffs("Collocation", nNodes=4, nodeType="LEGENDRE", quadType="RADAU-RIGHT")
+
+# QDelta matrix from Implicit-Euler based SDC
+QDelta = genQDeltaCoeffs("IE", nodes=nodes)
+
+# Butcher table of the classical explicit RK4 method
+c, b, A = genQCoeffs("ERK4")
+```
+
+> 🔔 _If you are not familiar with SDC or related methods, and want to learn more about it, checkout the 
+> [latest documentation build](https://qmat.readthedocs.io/en/latest/) and 
+in particular the [**step by step tutorials**](https://qmat.readthedocs.io/en/latest/notebooks.html)_
+
+
+For any contribution, please checkout out (very cool) [Contribution Guidelines](./docs/contributing.md)
+

qmat-0.0.1/README.md

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+# QMat Package
+
+[![CI pipeline for qmat](https://github.com/Parallel-in-Time/qmat/actions/workflows/ci_pipeline.yml/badge.svg)](https://github.com/Parallel-in-Time/qmat/actions/workflows/ci_pipeline.yml)
+[![codecov](https://codecov.io/gh/Parallel-in-Time/qmat/graph/badge.svg?token=MO0LDVH5NN)](https://codecov.io/gh/Parallel-in-Time/qmat)
+
+`qmat` is a python package to generate matrix coefficients related to Collocation methods, Spectral Deferred Corrections (SDC), 
+and more general multi-stages time-integration methods (like Runge-Kutta, etc ...).
+
+It allows to generate $Q$-coefficients for multi-stages methods (equivalent to Butcher tables) :
+
+$$
+Q\text{-coefficients : }
+\begin{array}
+    {c|c}
+    \tau & Q \\
+    \hline
+    & w^\top
+\end{array}
+\quad \Leftrightarrow \quad
+\begin{array}
+    {c|c}
+    c & A \\
+    \hline
+    & b^\top
+\end{array}
+\quad\text{(Butcher table)}
+$$
+
+and many different **lower-triangular** approximation of the $Q$ matrix, named $Q_\Delta$,
+which are key elements for Spectral Deferred Correction (SDC), or more general Iterated Runge-Kutta Methods.
+
+
+
+## Installation
+
+🛠️ Still in construction, only installation from source is enable yet, see [current instructions ...](./docs/installation.md)
+
+## Basic usage
+
+📜 _If you are already familiar with those concepts, you can use this package like this :_
+
+```python
+from qmat import genQCoeffs, genQDeltaCoeffs
+
+# Coefficients or specific collocation method
+nodes, weights, Q = genQCoeffs("Collocation", nNodes=4, nodeType="LEGENDRE", quadType="RADAU-RIGHT")
+
+# QDelta matrix from Implicit-Euler based SDC
+QDelta = genQDeltaCoeffs("IE", nodes=nodes)
+
+# Butcher table of the classical explicit RK4 method
+c, b, A = genQCoeffs("ERK4")
+```
+
+> 🔔 _If you are not familiar with SDC or related methods, and want to learn more about it, checkout the 
+> [latest documentation build](https://qmat.readthedocs.io/en/latest/) and 
+in particular the [**step by step tutorials**](https://qmat.readthedocs.io/en/latest/notebooks.html)_
+
+
+For any contribution, please checkout out (very cool) [Contribution Guidelines](./docs/contributing.md)
+

qmat-0.0.1/docs/.readthedocs.yaml

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+version: "2"
+
+build:
+  os: "ubuntu-22.04"
+  tools:
+    python: "3.12"
+
+python:
+  install:
+    - requirements: docs/requirements.txt
+
+sphinx:
+  configuration: docs/conf.py

qmat-0.0.1/docs/Makefile

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+# Minimal makefile for Sphinx documentation
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SPHINXPROJ    = QMat
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

qmat-0.0.1/docs/_static/custom.css

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+.wy-nav-content {
+    padding: 1.618em 3.236em;
+    height: 100%;
+    max-width: 1000px;
+}
+
+p {
+    line-height: 24px;
+    font-size: 16px;
+    margin: 0 0 12px;
+}
+
+.nbinput, .nboutput {
+    margin-bottom: 12px !important;
+}
+
+.nboutput .output_area {
+    font-weight: bold;
+    color: #8a8a8a;
+}
+
+.rst-content {
+h1, h2, ol, ul {
+    margin-bottom: 12px !important;
+    }
+}
+
+blockquote {
+    padding: 5px 5px;
+    margin: 10px 0 12px 0 !important;
+    border-left: 4px solid #dfdfdf;
+    background: #eeeeee;
+    border-radius: 5px;
+}
+blockquote p {
+    margin-bottom: 0;
+}
+blockquote small {
+    display: block;
+    line-height: 19px;
+    color: #999999;
+}
+blockquote small:before {
+    content: '\2014 \00A0';
+}
+blockquote.pull-right {
+    float: right;
+    padding-right: 15px;
+    padding-left: 0;
+    border-right: 5px solid #eeeeee;
+    border-left: 0;
+}
+blockquote.pull-right p,
+blockquote.pull-right small {
+    text-align: right;
+}
+blockquote.pull-right small:before {
+    content: '';
+}
+blockquote.pull-right small:after {
+    content: '\00A0 \2014';
+}
+q:before,
+q:after,
+blockquote:before,
+blockquote:after {
+    content: "";
+}
+
+.rst-content div[class^="highlight"] {
+    margin: 1px 0 16px;
+}
+
+blockquote > div > div[class^="highlight"] {
+    margin: 8px 3px !important;
+}

qmat-0.0.1/docs/conf.py

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+# -*- coding: utf-8 -*-
+#
+# Configuration file for the Sphinx documentation builder.
+#
+# This file does only contain a selection of the most common options. For a
+# full list see the documentation:
+# http://www.sphinx-doc.org/en/master/config
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('.'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'QMat Package'
+copyright = '2024 PinT Community'
+author = 'PinT Community'
+
+# The short X.Y version
+version = ''
+# The full version, including alpha/beta/rc tags
+release = ''
+
+
+# -- General configuration ---------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    'sphinx.ext.mathjax',
+    'autoapi.extension',
+    'sphinx.ext.viewcode',
+    'sphinx.ext.napoleon',
+    'sphinx.ext.extlinks',
+    'nbsphinx',
+    'sphinx_rtd_theme',
+    'sphinx_gallery.load_style',
+    'sphinxcontrib.video',
+    'myst_parser',
+    'sphinx_favicon',
+]
+
+myst_enable_extensions = [
+    "amsmath",
+    "dollarmath",
+]
+
+favicons = [
+    "android-chrome-192x192.png",
+    "android-chrome-512x512.png",
+    "apple-touch-icon.png",
+    "favicon-16x16.png",
+    "favicon-32x32.png",
+    "favicon.ico",
+]
+
+add_module_names = False
+autoapi_type = 'python'
+autoapi_dirs = ['../qmat']
+autoapi_file_patterns = ['*.py']
+autoapi_options = ['members', 'undoc-members']
+autoapi_python_class_content = 'both'
+autoapi_add_toctree_entry = False
+
+napoleon_use_param = False
+napoleon_use_keyword = False
+napoleon_use_ivar = True
+
+extlinks = {'repo': ('https://github.com/Parallel-in-Time/qmat/tree/main/%s', None)}
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix(es) of source filenames.
+source_suffix = ['.rst', '.md']
+
+# The master toctree document.
+master_doc = 'index'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = 'en'
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path .
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'default'
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'sphinx_rtd_theme'
+html_logo = 'sdc_logo.png'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#
+html_theme_options = {
+    "collapse_navigation": "false"
+}
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+html_css_files = [
+    'custom.css',
+]
+
+# Custom sidebar templates, must be a dictionary that maps document names
+# to template names.
+#
+# The default sidebars (for documents that don't match any pattern) are
+# defined by theme itself.  Builtin themes are using these templates by
+# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
+# 'searchbox.html']``.
+#
+# html_sidebars = {}
+
+
+# -- Options for HTMLHelp output ---------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'qmatdoc'
+
+
+# -- Options for nbsphinx galleries
+# Using _images/ is a hack to get relocated images which have been included in the pages
+nbsphinx_thumbnails = {
+    
+}

qmat-0.0.1/docs/contributing.md

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+# Contributing
+
+📜 _Package is currently developed with an open-source philosophy, so any relevant contribution is welcome_
+
+## General rules
+
+Ideally, your code implementation should be :
+
+- _**simple** enough so your grandma can understand it_
+- _**beautiful** enough to make your cousin in art school want to read it_
+- _**efficient** enough such that you spend more time analyzing your plots than coding and running experiments_
+
+Of course, that's an ideal goal ... but nothing prevents to aim at the sky when reaching the top of the mountain 🚡
+
+Recommended approach is to **fork this repository**, create a new branch in your fork, and open a **pull request** when ready.
+This will automatically trigger the CI pipeline that :
+
+1. check linting with `flake8`
+2. run all the tests defined in the `tests` folder, and upload a coverage report to `codecov`
+3. test all the tutorials located in the [notebook folder](https://github.com/Parallel-in-Time/qmat/tree/main/docs/notebooks) 
+
+Current coverage is at 100%, so no untested line will be accepted 😇.
+
+> 📣 Know that no code styling formatter (like `black`, or else ...) will ever be imposed in CI, as long as I'm still breathing !
+
+## Base recipes
+
+_A few base memo on how to develop this package ..._
+
+- [General code structure](./devdoc/structure.md)
+- [Add a Runge-Kutta scheme](./devdoc/addRK.md)
+- [Testing your changes](./devdoc/testing.md)
+- [Update this documentation](./devdoc/updateDoc.md)
+
+```{eval-rst}
+.. toctree::
+    :maxdepth: 1
+    :hidden:
+
+    devdoc/structure
+    devdoc/addRK
+    devdoc/testing
+    devdoc/updateDoc
+```