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.
-
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.
- Click "Choose a tag", then type a new tag in the format
-
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).
-
Document significant changes
- Add migration steps or noteworthy updates.
- Ensure PR titles are clear and consistent.
2 maintainers
Release files for higlass-python 1.4.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| higlass_python-1.4.0.tar.gz | 2.3 MB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| higlass_python-1.4.0-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 2.3 MB
Release files / higlass_python-1.4.0.tar.gz
| Download URL | higlass_python-1.4.0.tar.gz |
|---|---|
| Size | 2.3 MB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
bf250e8baa2f3667f715a585805191cec5ab0bd8d93392abcdfe43aa430daef3
|
|
BLAKE2b-256 checksum How to use checksums |
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|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/6.1.0 CPython/3.13.7
|
Provenance
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PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Mar 1, 2026.
Transparency logRelease files / higlass_python-1.4.0-py3-none-any.whl
| Download URL | higlass_python-1.4.0-py3-none-any.whl |
|---|---|
| Size | 24.2 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
fa1d5ed4924b73bf391ee9342c82560c71942e980f799b338faf7c07c4c8a1e8
|
|
BLAKE2b-256 checksum How to use checksums |
5c2906b523f00c0d2238658db9033f9be66e4ba859cab414f8bd69a38646ddac
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/6.1.0 CPython/3.13.7
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Mar 1, 2026.
Transparency log
