Changelog

Changelog#

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[Unreleased]#

Added#

Changed#

Fixed#

[0.3.1] - 2026-07-08#

Added#

Changed#

  • Require anndata>=0.13 (and consequently Python >=3.12, which anndata 0.13 requires) (#88)

Fixed#

  • TreeData.__getitem__ now delegates anndata.acc accessor indexers (AdRef, MapAcc, RefAcc) to AnnData.__getitem__ instead of routing them through _normalize_indices. This fixes an IndexError: Unknown indexer from obs_vector/var_vector (and any var_names/layer column lookup) under anndata ≥ 0.13 (#88)

[0.3.0] - 2026-07-07#

Added#

Changed#

  • Require zarr>=3 (anndata 0.13 no longer supports zarr <3). Removed the dead zarr<3 (ZARR_V2) code branches and the dead anndata<0.11 (USE_EXPERIMENTAL) code branches now that the supported floors exceed them (#88)

  • Zarr writes now store obst/vart in a columnar layout (one array per node/edge attribute key) instead of a single JSON scalar. Dense numeric/boolean columns use native dtypes; ragged or complex columns fall back to per-element JSON. This fixes a TypeError: string too large to store inside array crash when writing large trees to zarr v3 (#86)

  • dtype parameter in TreeData.__init__ is now deprecated; passing it raises a FutureWarning and has no effect, matching anndata’s removal of this argument

  • obsm, varm, layers, raw, shape, filename, filemode, asview, and related parameters in TreeData.__init__ are now keyword-only, matching the anndata 0.13.x API

  • Added compatibility with anndata 0.13.x: removed dtype from internal _init_as_actual call, which was removed from AnnData in 0.13.x

  • Added compatibility with anndata 0.13.x “Unify X and layers” change: layers.copy() and dict(layers) no longer include the internal None key (used to store X) in _mutated_copy and write routines

Fixed#

  • Fixed UserWarning: Duplicate name: 'zarr.json' spam when writing to a zarr ZipStore by staging the write in a MemoryStore and copying to the ZipStore once (#86)

  • read_zarr now auto-detects .zip paths and opens them as a ZipStore (#86)

  • Node/edge attributes explicitly set to None are now preserved through a zarr round-trip and kept distinct from absent attributes (#86)

  • Rewriting into an existing zarr group now removes trees that are no longer present, so the persisted tree set matches the TreeData being written (#86)

[0.2.5] - 2026-04-20#

Added#

Changed#

  • Updated anndata dependency (#75)

Fixed#

  • Removed pathlib dependency (#83)

[0.2.4] - 2025-11-05#

Added#

Changed#

  • Deprecated TreeData.obst_keys and TreeData.vart_keys for consistency with AnnData (https://github.com/scverse/anndata/pull/2093) (#73)

Fixed#

  • Added support for zarr v3 (#73)

  • Eliminated deprecations warnings from AnnData>=0.12.0 (#73)

[0.2.3] - 2025-10-14#

Added#

Changed#

  • Optimized tree overlap detection to speed up copying and subsetting with many trees (#66)

  • Switch to hatch with v0.0.6 template update (#61)

Fixed#

  • Fixed codecov configuration (#64)

[0.2.2] - 2025-09-18#

Added#

  • tdata.has_overlap parameter to check whether the TreeData object contains overlapping trees (#59)

Changed#

  • Default value for tdata.allow_overlap is now True (#60)

Fixed#

[0.2.1] - 2025-07-10#

Added#

  • support for instantiating TreeData objects with only the tree structure (#56)

Changed#

  • Updated docs to clarify all the ways TreeData can be instantiated (#56)

Fixed#

[0.2.0] - 2025-06-16#

Added#

  • alignment parameter which allows for obs_names and var_names aligned to either the leaves, nodes, or a subset of leaves and nodes in trees stored in the obst and vart fields. Added a tutorial describing how alignment works (#55)

Changed#

  • read_h5ad and write_h5ad and been renamed read_h5td and write_h5td to clarify that the treedata format differs from anndata. read_h5ad and write_h5ad will be removed in v1.0.0 (#56)

Fixed#

  • Fixed typing issues (#51)

[0.1.3] - 2025-01-20#

Added#

Changed#

Fixed#

  • Fixed typing issues (#51)

  • Fixed ImportError: zarr-python major version > 2 is not supported' error with Python 12 (#46)

[0.1.2] - 2024-12-02#

Added#

Changed#

Fixed#

  • Fixed KeyError: "Unable to synchronously open object (object 'X' doesn't exist)"' when reading h5ad without X field (#40)

[0.1.1] - 2024-11-25#

Added#

  • Axis in td.concat can now be specified with obs and var (#40)

Changed#

Fixed#

  • Fixed ImportError: cannot import name '_resolve_dim' from 'anndata._core.merge' caused by anndata update (#40)

[0.1.0] - 2024-09-27#

Added#

Changed#

  • Encoding of treedata attributes in h5ad and zarr files. label, allow_overlap, obst, and vart are now separate fields in the file. (#31)

Fixed#

  • TreeData objects with .raw specified can now be read (#31)

[0.0.4] - 2024-09-02#

Added#

Changed#

Fixed#

  • Fixed typing bug introduced by anndata update (#29)

[0.0.3] - 2024-08-21#

Added#

  • Add concatenation tutorial to documentation (#27)

Changed#

  • obst and vart create local copy of nx.DiGraphs that are added (#26)

  • TreeData.label value remains the same after td.concat as long as all label values are the same for all objects (#27)

Fixed#

  • Fixed bug which caused key to be listed twice in label column after value update in obst or vart (#26)

[0.0.2] - 2024-06-18#

Changed#

  • Empty trees are now allowed to avoid error on subsetting (#13)

  • How trees are stored in h5ad and zarr files (#16)

  • Format of label column with multiple trees ([1,2] -> 1,2) (#16)

Fixed#

  • Fixed issue with slow read/write of large trees

[0.0.1] - 2024-05-13#

Added#

  • TreeData class for storing and manipulating trees

  • Read/write trees to h5ad and zarr files

  • Concatenate trees with similar API to AnnData