Merge pull request #27 from YosefLab/concat-tutorial

Concat tutorial

CHANGELOG.md

@@ -14,11 +14,22 @@ and this project adheres to [Semantic Versioning][].
 
 ### Changed
 
+### Fixed
+
+## [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 `tree_label` column after value update in `obst` or `vart` (#26)
+-   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
 

docs/index.md

@@ -9,6 +9,9 @@
 notebooks/getting-started
 
 api.md
+
+notebooks/concatenation
+
 changelog.md
 contributing.md
 references.md

pyproject.toml

@@ -4,7 +4,7 @@ requires = ["hatchling"]
 
 [project]
 name = "treedata"
-version = "0.0.2"
+version = "0.0.3"
 description = "anndata with trees"
 readme = "README.md"
 requires-python = ">=3.10"

src/treedata/_core/merge.py

@@ -3,6 +3,7 @@
 from __future__ import annotations
 
 import typing
+import warnings
 from collections.abc import (
     Callable,
     Collection,
@@ -100,7 +101,16 @@ def concat(
         fill_value=fill_value,
         pairwise=pairwise,
     )
-    tdata = TreeData(adata, allow_overlap=True)
+
+    # Create new TreeData object
+    label = {t.label for t in tdatas if t.label is not None}
+    if len(label) > 1:
+        warnings.warn("Multiple label values found. Setting to `tree`.", stacklevel=2)
+        label = "tree"
+    else:
+        label = next(iter(label), None)
+    allow_overlap = any(t.allow_overlap for t in tdatas)
+    tdata = TreeData(adata, allow_overlap=allow_overlap, label=label)
 
     # Trees for concatenation axis
     concat_trees = [getattr(t, f"{dim}t") for t in tdatas]