Merge branch 'main' into template-update-v2-YosefLab-treedata-v0.7.0

Author: colganwi

.codecov.yaml

@@ -6,8 +6,7 @@ coverage:
   status:
     project:
       default:
-        # Require 1% coverage, i.e., always succeed
-        target: 1
+        target: 85
     patch: false
     changes: false
 

.github/workflows/test.yaml

@@ -38,7 +38,8 @@ jobs:
                 | {
                     name: .key,
                     label: (if (.key | contains("pre")) then .key + " (PRE-RELEASE DEPENDENCIES)" else .key end),
-                    python: .value.python
+                    python: .value.python,
+                    allow_failure: (.key | contains("pre"))
                   }
               )')
           echo "envs=${ENVS_JSON}" | tee $GITHUB_OUTPUT
@@ -59,6 +60,8 @@ jobs:
     runs-on: ${{ matrix.os }}
     continue-on-error: ${{ contains(matrix.env.name, 'pre') }}  # make "all-green" pass even if pre-release job fails
 
+    continue-on-error: ${{ matrix.env.allow_failure }}
+
     steps:
       - uses: actions/checkout@v5
         with:
@@ -82,7 +85,11 @@ jobs:
           test -f .coverage || uvx hatch run ${{ matrix.env.name }}:cov-combine
           uvx hatch run ${{ matrix.env.name }}:cov-report   # report visibly
           uvx hatch run ${{ matrix.env.name }}:coverage xml # create report for upload
+          # Quick sanity check
+          grep -m1 'filename=' -n coverage.xml || { echo "coverage.xml missing filenames"; exit 1; }
       - name: Upload coverage
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV }}
         uses: codecov/codecov-action@v5
         with:
           fail_ci_if_error: true

.gitignore

@@ -2,6 +2,7 @@
 .DS_Store
 *~
 buck-out/
+*._*
 
 # Compiled files
 .venv/
@@ -19,3 +20,13 @@ __pycache__/
 # docs
 /docs/generated/
 /docs/_build/
+
+# IDEs
+/.idea/
+/.vscode/
+
+# Prettier
+/node_modules/
+
+# Environment
+environment.yml

.vscode/settings.json

@@ -15,4 +15,8 @@
     "python.analysis.typeCheckingMode": "basic",
     "python.testing.pytestEnabled": true,
     "python.testing.pytestArgs": ["-vv", "--color=yes"],
+    "python.analysis.diagnosticSeverityOverrides": {
+        "reportMissingImports": "none",
+        "reportGeneralTypeIssues": "none",
+    },
 }

CHANGELOG.md

@@ -12,4 +12,161 @@ and this project adheres to [Semantic Versioning][].
 
 ### Added
 
--   Basic tool, preprocessing and plotting functions
+### Changed
+
+### Fixed
+
+## [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

README.md

@@ -1,36 +1,40 @@
-# treedata
-
 [![Tests][badge-tests]][link-tests]
 [![Documentation][badge-docs]][link-docs]
+[![PyPI](https://img.shields.io/pypi/v/treedata.svg)](https://pypi.org/project/treedata)
+[![codecov](https://codecov.io/github/YosefLab/treedata/branch/main/graph/badge.svg?token=YPhuxlw4my)](https://codecov.io/github/YosefLab/treedata)
+[![PyPI Downloads](https://static.pepy.tech/personalized-badge/treedata?period=total&units=INTERNATIONAL_SYSTEM&left_color=GREY&right_color=GREEN&left_text=downloads)](https://pepy.tech/projects/treedata)
 
-[badge-tests]: https://img.shields.io/github/actions/workflow/status/colganwi/treedata/test.yaml?branch=main
-[link-tests]: https://github.com/YosefLab/treedata/actions/workflows/test.yml
+[badge-tests]: https://img.shields.io/github/actions/workflow/status/YosefLab/treedata/test.yaml?branch=main
+[link-tests]: https://github.com/YosefLab/treedata/actions/workflows/test.yaml
 [badge-docs]: https://img.shields.io/readthedocs/treedata
 
-anndata with trees
+<img
+  src="https://raw.githubusercontent.com/YosefLab/treedata/main/docs/_static/img/treedata_schema.svg"
+  class="dark-light" align="right" width="350" alt="image"
+/>
+
+# TreeData - AnnData with trees
 
-## Getting started
+TreeData is a lightweight wrapper around AnnData which adds two additional attributes, `obst` and `vart`, to store [nx.DiGraph] trees for observations and variables. TreeData has the same interface as AnnData and is fully compatible with [scverse] packages like [Scanpy].
 
-Please refer to the [documentation][link-docs]. In particular, the
+To learn more about TreeData, please refer to the [documentation][link-docs] or checkout the [getting started guide][link-getting-started].
 
--   [API documentation][link-api].
+See the [Pycea documentation](https://pycea.readthedocs.io/) to learn how TreeData can be used to analyze single-cell lineage tracing data.
 
 ## Installation
 
-You need to have Python 3.9 or newer installed on your system. If you don't have
+You need to have Python 3.10 or newer installed on your system. If you don't have
 Python installed, we recommend installing [Mambaforge](https://github.com/conda-forge/miniforge#mambaforge).
 
 There are several alternative options to install treedata:
 
-<!--
-1) Install the latest release of `treedata` from `PyPI <https://pypi.org/project/treedata/>`_:
+1. Install the latest release of `treedata` from [PyPI](https://pypi.org/project/treedata):
 
 ```bash
 pip install treedata
 ```
--->
 
-1. Install the latest development version:
+2. Install the latest development version:
 
 ```bash
 pip install git+https://github.com/YosefLab/treedata.git@main
@@ -42,15 +46,18 @@ See the [changelog][changelog].
 
 ## Contact
 
-For questions and help requests, you can reach out in the [scverse discourse][scverse-discourse].
-If you found a bug, please use the [issue tracker][issue-tracker].
+For questions and bug reports please use the [issue tracker][issue-tracker].
 
 ## Citation
 
 > t.b.a
 
+[scverse]: https://scverse.org/
+[Scanpy]: https://scanpy.readthedocs.io/
+[nx.DiGraph]: https://networkx.org/documentation/stable/reference/classes/digraph.html
 [scverse-discourse]: https://discourse.scverse.org/
-[issue-tracker]: https://github.com/colganwi/treedata/issues
-[changelog]: https://treedata.readthedocs.io/latest/changelog.html
+[issue-tracker]: https://github.com/YosefLab/treedata/issues
+[changelog]: https://treedata.readthedocs.io/en/latest/changelog.html
 [link-docs]: https://treedata.readthedocs.io
+[link-getting-started]: https://treedata.readthedocs.io/en/latest/notebooks/getting-started.html
 [link-api]: https://treedata.readthedocs.io/latest/api.html