geometric_kernels 0.2__tar.gz

geometric_kernels-0.2/.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/.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/.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://gpflow.github.io/GeometricKernels/index.html)
+* [Landing page](https://geometric-kernels.github.io/)

geometric_kernels-0.2/.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/.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/.github/workflows/docs.yaml

@@ -0,0 +1,48 @@
+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: Doctests
+      run: |
+        make doctest
+    - 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/.github/workflows/quality-checks.yaml

@@ -0,0 +1,37 @@
+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/.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/CHANGELOG.md

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+# CHANGELOG
+
+## 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/CODE_OF_CONDUCT.md

@@ -0,0 +1,127 @@
+# 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.

geometric_kernels-0.2/CONTRIBUTING.md

@@ -0,0 +1,79 @@
+# Contribution guidelines
+
+### Who are we?
+
+*Maintainers* (in alphabetical order: Viacheslav Borovitskiy, Vincent Dutordoir, Peter Mostowsky) steer the project, keep the community thriving, and manage contributions.
+
+*Contributors* (you?) submit issues, make pull requests, answer questions on Slack, and more.
+
+Community is important to us, and we want everyone to feel welcome and be able to contribute to their fullest. Our [code of conduct](CODE_OF_CONDUCT.md) gives an overview of what that means.
+
+Here is the list of original contributors to the project (in alphabetical order): Viacheslav Borovitskiy, Vincent Dutordoir, Michael Hutchinson, Noemie Jaquier,  Peter Mostowsky, Aditya Ravuri, Alexander Terenin.
+
+### Reporting a bug
+
+Finding and fixing bugs helps us provide robust functionality to all users. You can either submit a bug report or, if you know how to fix the bug yourself, you can submit a bug fix. We gladly welcome either, but a fix is likely to be released sooner, simply because others may not have time to quickly implement a fix themselves. If you're interested in implementing it, but would like help in doing so, you can send [the maintainers](#who-are-we) an email or open an [issue](https://github.com/GPflow/GeometricKernels/issues/new).
+
+We use GitHub issues for bug reports. You can use the [issue template](https://github.com/GPflow/GeometricKernels/issues/new) to start writing yours. Once you've submitted it, the maintainers will take a look as soon as possible, ideally within the week, and get back to you about how to proceed. If it's a small easy fix, they may implement it then and there. For fixes that are more involved, they will discuss with you about how urgent the fix is, with the aim of providing some timeline of when you can expect to see it.
+
+If you'd like to submit a bug fix, [open a pull request](https://github.com/GPflow/GeometricKernels/compare). We recommend you discuss your changes with the community before you begin working on them (e.g. via issues), so that questions and suggestions can be made early on.
+
+### Requesting a feature
+
+GeometricKernels is built on features added and improved by the community. You can submit a feature request either as an issue or, if you can implement the change yourself, as a pull request. We gladly welcome either, but a pull request is likely to be released sooner, simply because others may not have time to quickly implement it themselves.
+
+We use GitHub issues for feature requests. You can use the [issue template](https://github.com/GPflow/GeometricKernels/issues/new) to start writing yours. Once you've submitted it, the maintainers will take a look as soon as possible, ideally within the week, and get back to you about how to proceed. If it's a small easy feature that is backwards compatible, they may implement it then and there. For features that are more involved, they will discuss with you about a timeline for implementing it. Features that are not backwards compatible are likely to take longer to reach a release. It may become apparent during discussions that a feature doesn't lie within the scope of GeometricKernels, in which case we will discuss alternative options with you, such as adding it as a notebook or an external extension to GeometricKernels.
+
+If you'd like to submit a pull request, [open a pull request](https://github.com/GPflow/GeometricKernels/compare). We recommend you discuss your changes with the community before you begin working on them (e.g. via issues), so that questions and suggestions can be made early on.
+
+### Pull request guidelines
+
+- Limit the pull request to the smallest useful feature or enhancement, or the smallest change required to fix a bug. This makes it easier for reviewers to understand why each change was made, and makes reviews quicker.
+- Where appropriate, include [documentation](#documentation), [type hints](#type-checking), and [tests](#tests). See those sections for more details.
+- Pull requests that modify or extend the code should include appropriate tests, or be covered by already existing tests. In particular:
+  - New features should include a demonstration of how to use the new API, and should include sufficient tests to give confidence that the feature works as expected.
+  - Bug fixes should include tests to verify that the updated code works as expected and defend against future regressions.
+  - When refactoring code, verify that existing tests are adequate.
+- In commit messages, be descriptive but to the point. Comments such as "further fixes" obscure the more useful information.
+
+### Documentation
+
+GeometricKernels has two primary sources of documentation: the notebooks and the API reference.
+
+For the API reference, we document Python code inline, using [reST markup](https://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html). See [here](docs/README.md) for details on the documentation build. All parts of the public API need docstrings (indeed anything without docstrings won't appear in the built documentation). Similarly, don't add docstrings to private functionality, else it will appear in the documentation website. Use code comments sparingly, as they incur a maintenance cost and tend to drift out of sync with the corresponding code.
+
+### Quality checks
+
+We use [make](https://www.gnu.org/software/make/manual/make.html#toc-Overview-of-make) to run our commands. This guide assumes you have this installed.
+
+#### Type and format checking
+
+We use [type hints](https://docs.python.org/3/library/typing.html) for documentation and static type checking with [mypy](http://mypy-lang.org). We format all Python code, other than the notebooks, with [black](https://black.readthedocs.io/en/stable/), [flake8](https://flake8.pycqa.org/en/latest/), and [isort](https://pycqa.github.io/isort/). You may need to run these before pushing changes, with (in the repository root)
+
+Run the type and format checkers (black, flake8 and mypy) with
+```bash
+$ make lint
+```
+
+The formatter (isort and black) can be run with
+```bash
+$ make format
+```
+
+#### Tests
+
+We write and run tests with [pytest](https://pytest.org).
+
+Run tests with
+```bash
+$ make test
+```
+
+#### Continuous integration
+
+[GitHub actions](https://github.com/GPflow/GeometricKernels/blob/main/.github/workflows/quality-checks.yaml) will automatically run the quality checks against pull requests to the develop branch. The GitHub repository is set up such that these need to pass in order to merge.
+
+
+# License
+
+[Apache License 2.0](LICENSE)