pyotc 0.2.2__tar.gz

pyotc-0.2.2/.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Desktop (please complete the following information):**
+ - OS: [e.g. iOS]
+ - Browser [e.g. chrome, safari]
+ - Version [e.g. 22]
+
+**Smartphone (please complete the following information):**
+ - Device: [e.g. iPhone6]
+ - OS: [e.g. iOS8.1]
+ - Browser [e.g. stock browser, safari]
+ - Version [e.g. 22]
+
+**Additional context**
+Add any other context about the problem here.

pyotc-0.2.2/.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

pyotc-0.2.2/.github/workflows/README.md

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+# GitHub Actions Workflows
+
+This directory contains YAML workflows for GitHub Actions automation.
+
+## Workflows Overview
+- [build_and_publish.yml](build_and_publish.yml) – Deploys the project to production when a release is created.
+- [lint_and_test.yml](lint_and_test.yml) – Runs nox to check (ruff), format (ruff), and test (pytest) for a matrix of pythons.
+- [sphinx.yml](sphinx.yml) - Run sphinx documentation and deploys to github pages.
+

pyotc-0.2.2/.github/workflows/build_and_publish.yml

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+# This workflow will upload a Python Package to PyPI when a release is created
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: build and publish
+
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+  push:
+    branches:
+      - '77-fix-pypi-upload'
+
+permissions:
+  contents: read
+
+jobs:
+  uv-release-build:
+    name: uv-release-build
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+
+      - name: Run uv build
+        run: uv build
+      
+      - name: Upload distributions
+        uses: actions/upload-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+  pypi-publish:
+    runs-on: ubuntu-latest
+    needs:
+      - uv-release-build
+    permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing
+      id-token: write
+
+    # Dedicated environments with protections for publishing are strongly recommended.
+    # For more information, see: https://docs.github.com/en/actions/deployment/targeting-different-environments/using-environments-for-deployment#deployment-protection-rules
+    environment:
+      name: pypi
+      # OPTIONAL: uncomment and update to include your PyPI project URL in the deployment status:
+      # url: https://pypi.org/p/YOURPROJECT
+      #
+      # ALTERNATIVE: if your GitHub Release name is the PyPI project version string
+      # ALTERNATIVE: exactly, uncomment the following line instead:
+      # url: https://pypi.org/project/YOURPROJECT/${{ github.event.release.name }}
+
+    steps:
+      - name: Retrieve release distributions
+        uses: actions/download-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+      - name: Publish release distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          packages-dir: dist/

pyotc-0.2.2/.github/workflows/lint_and_test.yml

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+name: lint and test
+
+on:
+  push:
+
+jobs:
+  uv-nox:
+    name: uv-nox 
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: 'pip'
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+
+      - name: Install nox
+        run: pip install nox
+
+      - name: Install the project
+        run: uv sync --all-extras --dev
+
+      - name: Run nox sessions (lint format test)
+        run: python -m nox
+
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v5
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: ./coverage.xml
+          flags: unittests
+          name: codecov-umbrella
+          fail_ci_if_error: true

pyotc-0.2.2/.github/workflows/sphinx.yml

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+# Simple workflow for deploying static content to GitHub Pages
+# Obtained from github pages github actions dialog
+# deploys to pyotc.github.io/pyotc
+name: Deploy static content to Pages
+
+on:
+  # Runs on pushes targeting the default branch
+  push:
+    branches: ["main"]
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
+# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
+
+jobs:
+  # Single deploy job since we're just deploying
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Setup Pages
+        uses: actions/configure-pages@v5
+      - uses: actions/setup-python@v5
+      - name: Install dependencies
+        run: |
+          pip install sphinx sphinx_rtd_theme myst_parser
+          pip install .
+      - name: Sphinx build
+        run: |
+          sphinx-build docs _build
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: '_build'
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

pyotc-0.2.2/.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/
+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/
+cover/
+
+# 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/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .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
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__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/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+.idea/
+.DS_Store
+src/.DS_Store
+src/pyotc/.DS_Store
+src/pyotc/otc_backend/.DS_Store
+
+# pdf
+*.pdf

pyotc-0.2.2/.python-version

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+3.12

pyotc-0.2.2/AUTHORS.rst

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+=======
+Credits
+=======
+
+* Jay Hineman, @jhineman
+* Bongsoo Yi
+* Yuning Pan
+
+Contributors
+------------
+
+None yet. Why not be the first?

pyotc-0.2.2/CHANGELOG.md

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+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [Unreleased]
+
+## [0.2.2] - 2025-10-10
+* Add github actions build wheels and upload them to pypi.
+
+## [0.2.1] - 2025-10-10
+* Fix verion in `pyproject.toml`
+
+## [0.2.0] - 2025-10-02
+
+### Added
+* [RELEASE.md](./RELEASE.md)
+* Install with `uv`
+* `pytest` testing
+* `nox` for linting (`ruff`), formating (`ruff`), and testing (`pytest`)
+* [sphinx documentation](https://pyotc.github.io/pyotc/)
+* github actions running `nox` and generating documentation
+* sparse versions of exact otc
+* entropic otc
+
+### Changed
+* Use `md` vs `rst` in most cases
+
+### Removed
+* makefiles from cookie cutter
+
+## [0.1.0] - 2024-02-27
+
+### Added
+* Initial cookiecutter template
+* Basic algorithm
+
+[unreleased]: https://github.com/pyotc/pyotc
+[0.1.0]: https://github.com/pyotc/pyotc/tree/v0.1.0

pyotc-0.2.2/CONTRIBUTING.md

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+# Contributing
+
+Contributions are welcome, and they are greatly appreciated! Every little bit helps, and credit will always be given.
+
+You can contribute in many ways:
+
+## Types of Contributions
+
+### Report Bugs
+
+Report bugs at [https://github.com/pyotc/pyotc/issues](https://github.com/pyotc/pyotc/issues).
+
+If you are reporting a bug, please include:
+
+- Your operating system name and version.
+- Any details about your local setup that might be helpful in troubleshooting.
+- Detailed steps to reproduce the bug.
+
+### Fix Bugs
+
+Look through the GitHub issues for bugs. Anything tagged with "bug" and "help wanted" is open to whoever wants to implement it.
+
+### Implement Features
+
+Look through the GitHub issues for features. Anything tagged with "enhancement" and "help wanted" is open to whoever wants to implement it.
+
+See improvements listed in the [issues](https://github.com/pyotc/pyotc/issues).
+
+### Write Documentation
+
+`pyotc` could always use more documentation, whether as part of the official `pyotc` docs, in docstrings, or even on the web in blog posts, articles, and such.
+
+### Submit Feedback
+
+The best way to send feedback is to file an issue at [https://github.com/pyotc/pyotc/issues](https://github.com/pytoc/pyotc/issues).
+
+If you are proposing a feature:
+
+- Explain in detail how it would work.
+- Keep the scope as narrow as possible, to make it easier to implement.
+- Remember that this is a volunteer-driven project, and that contributions are welcome! :)
+
+## Get Started!
+
+Ready to contribute? Here's how to set up `pyotc` for local development.
+
+1. Fork the `pyotc` repo on GitHub.
+2. Clone your fork locally:
+
+    ```shell
+    git clone git@github.com:your_name_here/pyotc.git
+    ```
+
+3. Install your local copy into a virtualenv. See the [install directions](INSTALL.md)
+
+4. Create a branch for local development:
+
+    ```shell
+    git checkout -b name-of-your-bugfix-or-feature
+    ```
+
+   Now you can make your changes locally.
+
+5. When you're done making changes use [nox](nox) to lint, format, and test.
+
+6. Commit your changes and push your branch to GitHub:
+
+    ```shell
+    git add .
+    git commit -m "Your detailed description of your changes."
+    git push origin name-of-your-bugfix-or-feature
+    ```
+
+7. Submit a pull request through the GitHub website.
+
+## Pull Request Guidelines
+
+Before you submit a pull request, check that it meets these guidelines:
+
+0. Run `nox` in the root directory. Other [nox cli](https://nox.thea.codes/en/stable/usage.html#command-line-usage) options are avaiable. We use this same workflow in github actions. This should install, lint, format, and test your code.
+1. Include new tests for new functionality.
+2. Include new documentation for new functionality.
+3. Include updates to the [changelog](./CHANGELOG.md).
+4. Prepare to [help other review your changes](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/getting-started/helping-others-review-your-changes).
+
+## `uv` workflow
+
+### Adding dependencies with `uv`
+If you're adding true dependency, say for example `pytorch`, this is done simply with
+```bash
+uv add pytorch
+```
+See also documentation on [adding dependencies](https://docs.astral.sh/uv/concepts/projects/dependencies/#adding-dependencies)
+
+If you're adding a [development dependency](https://docs.astral.sh/uv/concepts/projects/dependencies/#development-dependencies) (e.g `pytest`) there is a little extra
+```bash
+uv add --dev pytest
+```
+
+### Running nox via `uv` as tool
+```bash
+# in project root
+uv tool run nox
+```
+*Note that this uses `nox` in isolation and should mimic what is done in [github actions](.github/workflows/nox.yml)*
+
+### Running ruff format via `uv`
+```bash
+# in project root
+uv tool run ruff format
+```
+*Note that this uses `ruff` in isolation and should mimic what is done in [github actions](.github/workflows/nox.yml)*
+*Ruff in particular on your system, vs as tool, may be divergent.*
+
+
+### Tagged releases
+We adhere to the following release process described in the template available in [RELEASE.md](RELEASE.md).

pyotc-0.2.2/INSTALL.md

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+# Install
+We expect pyotc to be pip-installable across all platforms.
+
+## Install for usage
+### From pypi
+
+```pip install pyotc```
+[TODO#26](https://github.com/pyotc/pyotc/issues/26)
+
+### From github
+
+```pip install https://github.com/pyotc/pyotc.git```
+
+## Install for development
+We test in venvs provided by [uv](https://docs.astral.sh/uv/) via [nox](https://nox.thea.codes/en/stable/usage.html#changing-the-sessions-default-backend). It's helpful, but not strictly necessary to do the same.
+
+```bash
+git clone https://github.com/pyotc/pyotc.git
+cd pyotc
+pip install -e .
+```
+
+### `uv` workflow
+[Install the uv tool](https://docs.astral.sh/uv/getting-started/installation/).
+
+Then
+
+```bash
+git clone https://github.com/pyotc/pyotc.git
+cd pyotc
+uv sync
+uv pip install -e .
+```
+
+To verify your installation, run
+```bash
+uv run pytest
+```
+
+
+

pyotc-0.2.2/LICENSE

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+MIT License
+
+Copyright (c) 2024, Jay Hineman
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+

pyotc-0.2.2/MANIFEST.in

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+include AUTHORS.md
+include CONTRIBUTING.md
+include HISTORY.md
+include LICENSE
+include README.md
+
+recursive-include tests *
+recursive-exclude * __pycache__
+recursive-exclude * *.py[co]
+
+recursive-include docs *.rst conf.py Makefile make.bat *.jpg *.png *.gif

pyotc-0.2.2/PKG-INFO

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+Metadata-Version: 2.4
+Name: pyotc
+Version: 0.2.2
+Summary: Perform optimal transition coupling (OTC) in python.
+Author: Jay Hineman, Yuning Pan, Bongsoo Yi
+License: MIT license
+License-File: AUTHORS.rst
+License-File: LICENSE
+Requires-Python: >=3.10
+Requires-Dist: matplotlib>=3.10.0
+Requires-Dist: networkx>=3.4.2
+Requires-Dist: numpy>=2.2.1
+Requires-Dist: pot>=0.9.5
+Description-Content-Type: text/markdown
+
+# pyotc
+[![codecov](https://codecov.io/github/pyotc/pyotc/graph/badge.svg?token=52QPNW0AP7)](https://codecov.io/github/pyotc/pyotc)
+
+A python implementations of optimal transport coupling algorithms.
+
+## Documentation
+Find sphinx documentation [here](https://pyotc.github.io/pyotc/).
+
+## Install
+See [install instructions](INSTALL.md)
+
+## Run Tests
+With a `uv` setup one can simply
+```bash
+uv run pytest
+```
+Otherwise, in `pip` installed context with deps met, `pytest` should behave as expected.
+
+## Contributing
+Guidelines for contribution to `pyotc` are provided in [CONTRIBUTING.md](./CONTRIBUTING.md).
+
+## Changelog
+A summary of changes and guide to versioning are recoreded in [CHANGELOG.md](./CHANGELOG.md).