glass-box-umap 0.1.0a1

This package augments UMAP by computing exact feature contributions to the UMAP embedding.

[!WARNING] This repo is public but under intense reconstruction and is not ready for users. Please check back soon!

Glass Box UMAP

This repo contains a Python package called glass_box_umap.

This package augments UMAP by computing exact feature contributions to the UMAP embedding.

The publication for Glass Box UMAP can be found here.

Installation

# pip
pip install glass-box-umap

# uv
uv pip install glass-box-umap

Find complete installation instructions at docs/install.md.

Development

Environment setup

We use uv for dependency management and build tooling. First, install uv:

curl -LsSf https://astral.sh/uv/install.sh | sh

Make sure uv is installed and available. Verify this by checking which version you have:

uv --version

Then install the project with development dependencies:

uv sync --group dev

To also install documentation dependencies:

uv sync --group dev --group docs

This creates a virtual environment in .venv and installs all dependencies. The package itself is automatically installed in editable mode (equivalent to pip install -e .).

The easiest way to run code is to simply prefix commands with uv run (e.g., uv run <YOUR_COMMAND>). This executes the command inside the virtual environment automatically, so you don't need to activate it first.

Alternatively, if you prefer a traditional workflow, or are running from a different directory, you can manually source the activation script:

source .venv/bin/activate

Formatting and linting

To format the code, use the following command:

make format

To run the lint checks and type checking, use the following command:

make lint

Pre-commit hooks

We use pre-commit to run formatting and lint checks before each commit. To install the pre-commit hooks, use the following command:

pre-commit install

To run the pre-commit checks manually, use the following command:

make pre-commit

Testing

We use pytest for testing. The tests are found in the glass_box_umap/tests/ subpackage. To run the tests, use the following command:

make test

Managing dependencies

We use uv to manage dependencies. To add a new dependency:

uv add some-package

To add a new development dependency:

uv add --group dev some-dev-package

To update a dependency:

uv lock --upgrade-package some-package

Whenever you add or update a dependency, uv will automatically update both pyproject.toml and uv.lock. Make sure to commit changes to these files.

Documentation

We use Sphinx for documentation with the furo theme. We also use some Sphinx extensions (described below) to make the process of writing documentation easier.

To build the docs, first install pandoc. On macOS, this can be done using brew:

brew install pandoc

Then, build the docs using the following command:

uv run make docs

Note: the pandoc dependency is only required by the nbsphinx extension. If this extension is removed, there is no need to install pandoc.

sphinx-autoapi

This extension generates API docs automatically from the docstrings in the source code. To do so, it requires that docstrings adhere to the Google or Numpy style. This style is described in the Google Python Style Guide.

napolean

Rather than writing our docstrings in RST, we use this extension to convert Google and NumPy-style docstrings to RST at build time.

myst-parser

RST is complicated to write. This extension lets us write our docs in Markdown and then converts them to RST at build time.

nbsphinx

It is often convenient to write examples as Jupyter notebooks. This extension executes Jupyter notebooks and renders the results in the docs at build time. It requires pandoc, which can be installed using brew install pandoc.

Removing unused Sphinx extensions

To remove an unused extension, delete the corresponding line from the extensions list in docs/conf.py and delete the extension from the docs dependency group in pyproject.toml.

Publishing the package on PyPI

Publishing the package on PyPI requires that you have API tokens for the test and production PyPI servers. You can find these tokens in your PyPI account settings. Create a .env file by coping .env.copy and add your tokens to this file.

We use semantic versioning of the form MAJOR.MINOR.PATCH. See semver.org for more information. When you're ready to release a new version:

1. Update the version field in pyproject.toml to the new version number
2. Commit the change: git commit -am "Bump version to X.Y.Z"
3. Create a git tag matching the version:

RELEASE_VERSION=0.1.0
git tag -a v${RELEASE_VERSION} -m "Release version ${RELEASE_VERSION}"
git push origin v${RELEASE_VERSION}

Before creating the tag, make sure that your local git repository is on main, is up-to-date, and does not contain uncommitted changes!

If you need to delete a tag you've created:

git tag -d v${RELEASE_VERSION}

If you already pushed the deleted tag to GitHub, also delete it from the remote:

git push origin :refs/tags/v${RELEASE_VERSION}

Once you've created the correct new tag, build the package:

make build

You should see an output that looks like this:

Building glass-box-umap (0.1.0)
  - Building sdist
  - Built glass-box-umap-0.1.0.tar.gz
  - Building wheel

The build artifacts are written to the dist/ directory.

Make sure that the version number in the output from make build matches the one in pyproject.toml and the git tag!

If it does not, double-check that you updated the version field in pyproject.toml before creating the tag.

Next, check that you can publish the package to the PyPI test server:

make build-and-test-publish

The build-and-test-publish command calls uv build to build the package and then uv publish to upload the build artifacts to the test server.

Check that you can install the new version of the package from the test server:

pip install --index-url https://pypi.org/simple/ --extra-index-url https://test.pypi.org/simple/ glass-box-umap==${RELEASE_VERSION}

(For accurate installation testing: dependencies are installed from main PyPI (to avoid unreliable TestPyPI mirrors), while your package (not yet on main PyPI) is installed from TestPyPI.)

If everything looks good, build and publish the package to the prod PyPI server:

make build-and-publish

Finally, check that you can install the new version of the package from the prod PyPI server:

pip install glass-box-umap==${RELEASE_VERSION}