geometric_kernels 0.2.3__tar.gz

geometric_kernels-0.2.3/.flake8

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+[flake8]
+max-line-length = 88
+select = C,E,F,W,B,B9
+# ignore:
+# E226 missing whitespace around arithmetic operator
+# W503 Line break occurred before a binary operator
+# W504 line break after binary operator
+# F811 redefinition because of multiple dispatch
+ignore = E203, E501, W503, E226, W503, W504, F811, F722
+max-complexity = 10
+exclude = __init__.py,.git,__pycache__,.mypy_cache,.pytest_cache

geometric_kernels-0.2.3/.gitattributes

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+*.ipynb linguist-vendored

geometric_kernels-0.2.3/.github/ISSUE_TEMPLATE/bugs-performance-issues.md

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+---
+name: Bug report (including performance and build issues)
+about: Help us find mistakes in the GeometricKernels code base
+labels: bug
+---
+
+<!-- Lines like this are comments and will be invisible -->
+
+# Bug / performance issue / build issue
+
+<!-- A clear and concise description of what the bug is. -->
+
+## To reproduce
+
+**Minimal, reproducible example**
+<!-- We need to be able to reproduce the bug by simply copy and pasting your code -->
+```python
+# This is the place for your code that reproduces the bug.
+# Please make sure it does not depend on external libraries (beyond GeometricKernels's own requirements) or specific datasets, and the smaller, the better :)
+# For help on how to write a good bug report, see https://stackoverflow.com/help/minimal-reproducible-example
+```
+
+**Stack trace, or error message**
+```
+// Paste the full stack trace/error message here
+```
+
+## Expected behavior
+
+<!-- A clear and concise description of what you expected to happen. -->
+
+## System information
+
+* GeometricKernels version
+* TensorFlow/PyTorch/Jax version
+* Python version
+* Operating system
+
+## Additional context
+
+<!-- Add any other context about the problem here. -->

geometric_kernels-0.2.3/.github/ISSUE_TEMPLATE/doc-issue.md

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+---
+name: Documentation or notebooks
+about: Let us know what would make the GeometricKernels documentation better
+---
+
+# Documentation/tutorial notebooks
+
+*Is there anything missing in the docs?*
+
+*Are there any mistakes in the docs?*
+
+*Is there a feature that needs some example code in a notebook?*
+
+*Do you know how to fix the docs?* If so, it'd be amazing if you'd be willing to directly contribute a pull request :)
+
+
+Links:
+* [latest GeometricKernels documentation](https://geometric-kernels.github.io/GeometricKernels/index.html)
+* [Landing page](https://geometric-kernels.github.io/)

geometric_kernels-0.2.3/.github/ISSUE_TEMPLATE/feature-request.md

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+---
+name: Feature request
+about: Suggest an idea for GeometricKernels
+labels: enhancement
+---
+
+<!-- Lines like this are comments and will be invisible -->
+
+# Feature request
+
+<!-- Please give a clear and concise description of your feature proposal! -->
+
+## Motivation
+
+**Is your feature request related to a problem?**
+<!-- A clear and concise description of the problem. For example: I'm always frustrated when [...] -->
+<!-- Are there relevant issues or other PRs? Please add links -->
+<!-- Who will benefit from this feature? -->
+
+## Proposal
+
+**Describe the solution you would like**
+<!-- A clear and concise description of what you want to happen. -->
+
+**What alternatives have you considered?**
+<!-- A clear and concise description of any alternative solutions or features you've considered. -->
+
+**Are you willing to open a pull request?** (We really appreciate contributions!)
+
+## Additional context
+
+<!-- Add any other context / information about your feature request here. -->

geometric_kernels-0.2.3/.github/ISSUE_TEMPLATE/other-issue.md

@@ -0,0 +1,4 @@
+---
+name: '"How do I do ..." and other issues'
+about: How-To Questions
+---

geometric_kernels-0.2.3/.github/workflows/docs.yaml

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+name: Docs
+
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  docs:
+    runs-on: ubuntu-latest
+    steps:
+      #----------------------------------------------
+      #       check-out repo and set-up python
+      #----------------------------------------------
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v4
+      with:
+        python-version: "3.10"
+      #----------------------------------------------
+      #       install
+      #----------------------------------------------
+    - name: Install dependencies
+      run: |
+        make install
+        pip install -r docs/requirements.txt
+    - name: Build documentation
+      run: |
+        make docs
+        ls -all docs/_build/html
+    - name: Clean
+      run: |
+        TMP_DIR=$(mktemp -d -p $(pwd))
+        mv docs/_build/html/* $TMP_DIR
+        rm -rf docs
+        mv $TMP_DIR docs
+        ls -all docs
+        touch docs/.nojekyll
+    - name: Push to GitHub
+      run: |
+        git add .
+        git add -f docs/autoapi/*
+        git config --global user.email "none"
+        git config --global user.name "github-actions-bot"
+        git commit -m "build documentation [ci skip]"
+        git push -f origin HEAD:gh-pages

geometric_kernels-0.2.3/.github/workflows/publish-pypi.yaml

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+name: Publish-PyPI
+
+on:
+  push:
+    tags: v[0-9]+.[0-9]+.[0-9]+*
+
+jobs:
+  upload-pypi:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+      - name: Install flit
+        run: |
+          pip install flit
+      - name: Create pip package
+        run: |
+          flit build
+      - name: Publish to PyPI
+        run: |
+          flit publish
+        env:
+          FLIT_INDEX_URL: ${{ secrets.PYPI_INDEX_URL }}
+          FLIT_PASSWORD: ${{ secrets.PYPI_TOKEN }}
+          FLIT_USERNAME: __token__

geometric_kernels-0.2.3/.github/workflows/quality-checks.yaml

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+name: QualityChecks
+
+on:
+  push:
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  check-and-test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
+      fail-fast: false
+
+    name: Python-${{ matrix.python-version }}
+    steps:
+      #----------------------------------------------
+      #       check-out repo and set-up python
+      #----------------------------------------------
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+      #----------------------------------------------
+      #       install
+      #----------------------------------------------
+    - name: Install dependencies
+      run: GK_REQUIREMENTS=test_requirements-${{ matrix.python-version }}.txt make install
+      #----------------------------------------------
+      #       Lint and test
+      #----------------------------------------------
+    - name: Run lint
+      run: make lint
+    - name: Run tests
+      run: make test

geometric_kernels-0.2.3/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# 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/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+docs/generated/
+docs/autoapi/
+docs/bin
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# Emacs backup files
+*~
+
+# Vim swp files
+*.swp
+
+# Mac OS
+.DS_Store
+
+# Idea
+/.idea/

geometric_kernels-0.2.3/CHANGELOG.md

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+# CHANGELOG
+
+## v0.2.3 - 16.01.2025
+* Constraint version of plum-dispatch because of wesselb/lab#23
+
+## v0.2.2 - 29.11.2024
+* Replace opt_einsum's contract with lab's einsum for better backend-independence by @vabor112 in https://github.com/geometric-kernels/GeometricKernels/pull/145
+* Hypersphere space small improvements by @vabor112 in https://github.com/geometric-kernels/GeometricKernels/pull/142
+* The Hypercube space for binary vectors and labeled unweighted graphs by @vabor112 in https://github.com/geometric-kernels/GeometricKernels/pull/141
+* Fix algorithm selecting signatures and add precomputed characters for SO(9), SU(7), SU(8), SU(9) by @imbirik in https://github.com/geometric-kernels/GeometricKernels/pull/151
+* Revise tests and numerous fixes by @vabor112 in https://github.com/geometric-kernels/GeometricKernels/pull/149
+
+## v0.2.1 - 08.08.2024
+ Minor release with mostly cosmetic changes:
+* Add "If you have a question" section to README.md by @vabor112 in https://github.com/geometric-kernels/GeometricKernels/pull/131
+* Github cosmetics by @stoprightthere in https://github.com/geometric-kernels/GeometricKernels/pull/133
+* Replace all references to "gpflow" organization with "geometric-kernels" organization by @vabor112 in https://github.com/geometric-kernels/GeometricKernels/pull/134
+* Use fit_gpytorch_model or fit.fit_gpytorch_mll depening on the botorсh version by @vabor112 in https://github.com/geometric-kernels/GeometricKernels/pull/137
+* Add a missing type cast and fix a typo in kernels/karhunen_loeve.py by @vabor112 in https://github.com/geometric-kernels/GeometricKernels/pull/136
+* Minor documentation improvements by @vabor112 in https://github.com/geometric-kernels/GeometricKernels/pull/135
+* Add citation to the preprint of the GeometricKernels paper by @vabor112 in https://github.com/geometric-kernels/GeometricKernels/pull/138
+* Add citation file by @aterenin in https://github.com/geometric-kernels/GeometricKernels/pull/140
+* Fix dependencies (Version 0.2.1) by @stoprightthere in https://github.com/geometric-kernels/GeometricKernels/pull/143
+
+## v0.2 - 21.04.2024
+ New geometric kernel that *just works*, `kernels.MaternGeometricKernel`. Relies on *(hopefully)* sensible defaults we defined. Mostly by @stoprightthere.
+
+New spaces, based on Azangulov et al. ([2022](https://arxiv.org/abs/2208.14960), [2023](https://arxiv.org/abs/2301.13088)), mostly by @imbirik and @stoprightthere:
+- hyperbolic spaces $\mathbb{H}_n$ in `spaces.Hyperbolic`,
+- manifolds of symmetric positive definite matrices $\mathrm{SPD}(n)$ endowed with the affine-invariant Riemannian metric in `spaces.SymmetricPositiveDefiniteMatrices`,
+- special orthogonal groups $\mathrm{SO}(n)$ in `spaces.SpecialOrthogonal`.
+- special unitary groups $\mathrm{SU}(n)$ in `spaces.SpecialUnitary`.
+
+New package `geometric_kernels.feature_maps` for (approximate) finite-dimensional feature maps. Mostly by @stoprightthere.
+
+New small package `geometric_kernels.sampling` for efficient sampling from geometric Gaussian process priors. Based on the (approximate) finite-dimensional feature maps. Mostly by @stoprightthere.
+
+Examples/Tutorials improvements, mostly by @vabor112:
+- new Jupyter notebooks `Graph.ipynb`, `Hyperbolic.ipynb`, `Hypersphere.ipynb`, `Mesh.ipynb`, `SPD.ipynb`, `SpecialOrthogonal.ipynb`, `SpecialUnitary.ipynb`, `Torus.ipynb` featuring tutorials on all the spaces in the library,
+- new Jupyter notebooks `backends/JAX_Graph.ipynb`, `backends/PyTorch_Graph.ipynb`, `backends/TensorFlow_Graph.ipynb` showcasing how to use all the backends supported by the library,
+- new Jupyter notebooks `frontends/GPflow.ipynb`, `frontends/GPJax.ipynb`, `frontends/GPyTorch.ipynb` showcasing how to use all the frontends supported by the library,
+- other notebooks updated and grouped together in `other/` folder.
+
+
+Documentation improvements, mostly by @vabor112:
+- all docstrings throughout the library revised,
+- added new documentation pages describing the basic theoretical concepts, in `docs/theory`,
+- notebooks are now rendered as part of the documentation, you can refer to them from the docstrings and other documentation pages,
+- introduced a more or less unified style for docstrings.
+
+Other:
+- refactoring and bug fixes,
+- added type hints throughout the library and enabled `mypy`,
+- updated frontends (with limited suppot for GPJax due to conflicting dependencies),
+- improved `spaces.ProductDiscreteSpectrumSpace` and `kernels.ProductGeometricKernel`,
+- filtered out or fixed some annoying external warnings,
+- added a new banner for `README.md` and for our [landing page](https://geometric-kernels.github.io/), courtesy of @aterenin,
+- example notebooks are now run as tests,
+- we now support Python 3.8, 3.9, 3.10, 3.11 and have test workflows for all the supported Python versions,
+- we now provide a PyPI package,
+- [LAB](https://github.com/wesselb/lab) is now a lightweight dependency, thanks to @wesselb,
+- kernels are now normalized to have unit outputscale by default.
+
+## v0.1-alpha - 20.10.2022
+Alpha release.

geometric_kernels-0.2.3/CITATION.bib

@@ -0,0 +1,6 @@
+@article{mostowsky2024,
+      title = {The GeometricKernels Package: Heat and Matérn Kernels for Geometric Learning on Manifolds, Meshes, and Graphs},
+      author = {Peter Mostowsky and Vincent Dutordoir and Iskander Azangulov and Noémie Jaquier and Michael John Hutchinson and Aditya Ravuri and Leonel Rozo and Alexander Terenin and Viacheslav Borovitskiy},
+      year = {2024},
+      journal = {arXiv:2407.08086},
+}

geometric_kernels-0.2.3/CITATION.cff

@@ -0,0 +1,29 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+title: "GeometricKernels"
+authors:
+- name: "GeometricKernels Contributors"
+preferred-citation:
+  type: "article"
+  title: "The GeometricKernels Package: Heat and Matérn Kernels for Geometric Learning on Manifolds, Meshes, and Graphs"
+  authors:
+  - family-names: "Mostowsky"
+    given-names: "Peter"
+  - family-names: "Dutordoir"
+    given-names: "Vincent"
+  - family-names: "Azangulov"
+    given-names: "Iskander"
+  - family-names: "Jaquier"
+    given-names: "Noémie"
+  - family-names: "Hutchinson"
+    given-names: "Michael John"
+  - family-names: "Ravuri"
+    given-names: "Aditya"
+  - family-names: "Rozo"
+    given-names: "Leonel"
+  - family-names: "Terenin"
+    given-names: "Alexander"
+  - family-names: "Borovitskiy"
+    given-names: "Viacheslav"
+  year: "2024"
+  journal: "arXiv:2407.08086"

geometric_kernels-0.2.3/CODE_OF_CONDUCT.md

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+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, religion, or sexual identity
+and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the
+  overall community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or
+  advances of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email
+  address, without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement (the [project maintainers](CONTRIBUTING.md#who-are-we?)).
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series
+of actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or
+permanent ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior,  harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within
+the community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.0, available at
+https://www.contributor-covenant.org/version/2/0/code_of_conduct.html.
+
+Community Impact Guidelines were inspired by [Mozilla's code of conduct
+enforcement ladder](https://github.com/mozilla/diversity).
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see the FAQ at
+https://www.contributor-covenant.org/faq. Translations are available at
+https://www.contributor-covenant.org/translations.