higlass-python 1.3.3

Python bindings for HiGlass

higlass-python 🔎

A fresh Python library for higlass built on top of higlass-schema and anywidget.

Installation

pip install higlass-python

Usage

import higlass as hg

# Remote data source (tileset)
tileset1 = hg.remote(
    uid="CQMd6V_cRw6iCI_-Unl3PQ",
    server="https://higlass.io/api/v1/",
    name="Rao et al. (2014) GM12878 MboI (allreps) 1kb",
)

# Local tileset
tileset2 = hg.cooler("../data/dataset.mcool")

# Create a `hg.HeatmapTrack` for each tileset
track1 = tileset1.track("heatmap")
track2 = tileset2.track("heatmap")

# Create two independent `hg.View`s, one for each heatmap
view1 = hg.view(track1, width=6)
view2 = hg.view(track2, width=6)

# Lock zoom & location for each `View`
view_lock = hg.lock(view1, view2)

# Concatenate views horizontally and apply synchronization lock
(view1 | view2).locks(view_lock)

To learn more about the new API, check out the updated documentation.

Upgrade Guide

higlass-python v1.0 is a total rewrite of our prior implementation, aimed to offer a more ergonomic and flexible API. While this might present challenges when upgrading existing code, we've prepared documentation to guide you through the new API usage.

If you find a missing feature, please open an issue – we're committed to supporting your use cases with the new API.

Despite the large changes in v1.0, we will strive to avoid breaking changes going forward. However, because of the complete rewrite, the v1.0 release doesn't strictly adhere to semantic versioning. You can think of it as a pre-1.0 release, with breaking changes and new features included in minor releases, and bug fixes in patch releases.

We will aim for strict semantic versioning with the v2.0 release. Your feedback and understanding are greatly appreciated.

Development

higlass-python is primarily a Python project, but it includes JavaScript for the anywidget-based front-end code (src/higlass/widget.js). We use uv for Python development and deno for linting and type-checking JavaScript.

All formatting, linting, and tests are enforced in CI.

Commands Cheatsheet

All commands are run from the root of the project, from a terminal:

Python

Command	Action
uv run jupyter lab	Run Jupyter lab with current package state
uv run ruff check --fix && uv run ruff format	Lint and apply formatting
uv run check	Check linting rules
uv run ruff format --check	Check formatting
uv run pytest	Run unit tests
uv run docs/build.py	Build the documentation in docs/_build/html

JavaScript

Command	Action
deno fmt	Format code
deno lint --fix	Lint and auto-fix issues
deno check src/higlass/widget.js	Typecheck .js with TypeScript

Changelog

Check the GitHub Releases for a detailed changelog.

Release

Releases are managed via the GitHub UI.

Draft a new release:

1. Create a tag

   • Click "Choose a tag", then type a new tag in the format v[major].[minor].[patch] to create it.
   • Note: The UI is not obvious about this. You can create a tag here, not just select one. Tag creation triggers a workflow to publish to PyPI.

2. Generate release notes

   • Click "Generate Release Notes" to auto-summarize changes from merged PRs.
   • Edit to exclude irrelevant changes for end users (e.g., docs or CI).

3. Document significant changes

   • Add migration steps or noteworthy updates.
   • Ensure PR titles are clear and consistent.