v1.4.0

This release adds Shadow DOM support, changing widget rendering behavior. The HiGlass viewer is now rendered within a ShadowDOM root, isolating its CSS styling from that of the containing document. Consumers who inspect el.children or rely on document-level styles will be affected.

What's changed

• Render HiGlass viewer inside Shadow DOM by @manzt in #208
• Fix page scrolling when using mouse wheel to zoom in Jupyter notebooks by @kaspermunch in #194
• Raise minimum Python to 3.10 by @manzt in #207

Maintenance

• Set minimum uv version in pyproject.toml by @manzt in #203
• Unpin uv version in docs workflows by @manzt in #205
• Replace pkg_resources with packaging for version parsing by @manzt in #206
• Typecheck project with ty by @manzt in #204
• chore(deps): bump actions/checkout from 5 to 6 in the actions group across 1 directory by @dependabot[bot] in #209
• Add widget.js smoke test by @manzt in #202

New Contributors

• @kaspermunch made their first contribution in #194

Full Changelog: v1.3.5...v1.4.0

v1.3.5

Bug fixes

• Inline esm.sh URLs in widget.js by @manzt in #201

Full Changelog: v1.3.4...v1.3.5

Sequence logo track support

Updated docs for multivec tracks and added a literal for sequence-logo tracks

v1.3.3

What's Changed

• Add hg.chromsizes helper @pkerpedjiev in #187

import higlass as hg

ts = hg.chromsizes('chromSizes_hg19_reordered.tsv')

hg.view(
    (ts.track('horizontal-chromosome-labels'), 'top'),
    (ts.track('horizontal-chromosome-labels'), 'left'),
)

Full Changelog: v1.3.2...v1.3.3

v1.3.2

What's Changed

• fix: Resolve jupyter server tile sources in combined tracks by @pkerpedjiev in #186

Full Changelog: v1.3.1...v1.3.2

v1.3.1

What's Changed

• feat(widget): Batch tile requests within an animation frame by @manzt in #181

Full Changelog: v1.3.0...v1.3.1

v1.3.0

This release deliberately contains backwards-incompatible changes. To avoid automatically picking up releases like this, you can pin the exact version of higlass-python in your pyproject.toml or requirements.txt file .

• Switch to Jupyter comms-based server (remove hg.server) by @manzt in #145

HiGlass now uses Jupyter's built-in communication system to serve tilesets, removing the need for hg.server. Previously, hg.server ran a background HTTP server, but it caused issues on remote machines (e.g., authentication, port configuration).

This update removes hg.server and replaces it with a Jupyter comms-based approach, leveraging existing WebSocket connections. This makes HiGlass more robust across different environments and simplifies setup.

If HiGlass already works for you, nothing should change! If you previously used hg.server.enable_proxy, you can simple remove that line in your code:

-- hg.server.enable_proxy() 

This is a new feature, so please report any issues!

• Add higlass.Tileset for making custom tilesets by @manzt in #172, #177

With the removal of hg.server, HiGlass now provides a simpler way to define custom tilesets.

Instead of hg.server.add(tileset), you can now subclass hg.Tileset:

from dataclasses import dataclass

import higlass as hg
from clodius.tiles import cooler

@dataclass
class MyCustomCoolerTileset(hg.Tileset):
    path: str
    datatype = "matrix"

    def tiles(self, tile_ids):
        return cooler.tiles(self.path, tile_ids)

    def info(self):
        return cooler.tileset_info(self.path)

tileset = MyCustomCoolerTileset("test.mcool")
hg.view(tileset.track())

hg.Tileset automatically registers the tileset via Jupyter comms and provides a .track() method to create a HiGlass track with the correct tileset information.

• Remove higlass.fuse by @manzt in #175

higlass.fuse was an incomplete and poorly documented feature that added complexity without clear benefits. Filehandle-like interfaces now provide a more reliable alternative. If you relied on this feature, please open an issue!

Full Changelog: v1.2.1...v1.3.0

v1.2.1

What's Changed

• Allow file pointers in tileset loaders by @pkerpedjiev in #161
• Suppress right-click event propagation by @manzt in #160
• Properly deep-copy pydantic models with model_copy(deep=True) by @pkerpedjiev in #163

Full Changelog: v1.2.0...v1.2.1

v1.2.0

What's Changed

• Breaking: Migrate to higlass-schema v0.2.0 (pydantic v2) by @manzt in #155
• Shorter automatic uids for Tracks and Views by @manzt in #157
• Upgrade HiGlass front-end to v1.13 by @manzt in #158

Full Changelog: v1.1.2...v1.2.0

This release does not introduce changes to the higlass-python API itself. However, it migrates the core data objects created and modified by the higlass-python API from Pydantic v1 to Pydantic v2. We are marking this as a breaking release, as some methods and attributes on these objects are now deprecated.

Libraries relying on higlass-schema (Pydantic models for Python) may encounter breaking changes if they use methods that have changed between Pydantic v1 and v2. We expect this update to improve compatibility and make it easier to use higlass-python in environments that depend on Pydantic v2 (which are increasing).

v1.1.2

What's Changed

• Pin higlass-schema version upper bound for <v1.2 by @manzt in #156

Full Changelog: v1.1.0...v1.1.2