Add function to export spatialdata to legacy anndata format

.github/workflows/test_and_deploy.yaml

@@ -49,7 +49,7 @@ jobs:
                   pip install pytest-cov
             - name: Install dependencies
               run: |
-                  pip install -e ".[dev,test]"
+                  pip install --pre -e ".[dev,test]"
             - name: Test
               env:
                   MPLBACKEND: agg

.readthedocs.yaml

@@ -13,3 +13,4 @@ python:
           path: .
           extra_requirements:
               - doc
+              - pre

CHANGELOG.md

@@ -15,7 +15,8 @@ and this project adheres to [Semantic Versioning][].
 -   (MCMICRO) support for TMAs (such as the data of exemplar-002)
 -   (Xenium) support for post-xenium aligned images (IF, HE)
 -   (Xenium) reader for the selection coordinates file from the Xenium Explorer
--   DBiT-seq reader
+-   (DBiT-seq) reader
+-   converter functions `experimental.to_legacy_anndata()` and `experimental.from_legacy_anndata()`
 -   (Visium) support for raw reads (capture locations not under tissue)
 
 ### Fixed

docs/api.md

@@ -25,6 +25,8 @@ I/O for the `spatialdata` project.
     dbit
 ```
 
+### Conversion functions
+
 ### Utility functions
 
 ```{eval-rst}
@@ -34,3 +36,17 @@ I/O for the `spatialdata` project.
     xenium_aligned_image
     xenium_explorer_selection
 ```
+
+### Experimental readers
+
+### Experimental conversion functions
+
+```{eval-rst}
+.. currentmodule:: spatialdata_io.experimental
+
+.. autosummary::
+    :toctree: generated
+
+    from_legacy_anndata
+    to_legacy_anndata
+```

docs/conf.py

@@ -9,6 +9,9 @@
 from datetime import datetime
 from importlib.metadata import metadata
 from pathlib import Path
+import spatialdata_io.experimental
+
+_ = spatialdata_io.experimental
 
 HERE = Path(__file__).parent
 sys.path.insert(0, str(HERE / "extensions"))

pyproject.toml

@@ -22,6 +22,8 @@ urls.Documentation = "https://spatialdata-io.readthedocs.io/"
 urls.Source = "https://github.com/scverse/spatialdata-io"
 urls.Home-page = "https://github.com/scverse/spatialdata-io"
 dependencies = [
+    "anndata",
+    "numpy",
     "spatialdata",
     "scikit-image",
     "h5py",
@@ -53,6 +55,10 @@ test = [
     "pytest",
     "pytest-cov",
 ]
+# this will be used by readthedocs and will make pip also look for pre-releases, generally installing the latest available version
+pre = [
+    "spatialdata>=0.1.0-pre0"
+]
 
 [tool.coverage.run]
 source = ["spatialdata_io"]