Merge branch 'main' into feature/gpu_ci

scverse · Jul 25, 2023 · a3d23c9 · a3d23c9
2 parents 0429840 + 0c4c0b0
commit a3d23c9
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Showing 10 changed files with 30 additions and 9 deletions.
diff --git a/.gitignore b/.gitignore
@@ -12,10 +12,10 @@ __pycache__/
 /*.egg-info/
 /requirements*.lock
 /.python-version
+/hatch.toml
 
 # Tests and coverage
-/.pytest_cache/
-/.cache/
+/*cache/
 /data/
 /tmp.zarr/
 test.h5ad

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -5,7 +5,7 @@ repos:
       - id: black
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: "v0.0.278"
+    rev: "v0.0.280"
     hooks:
       - id: ruff
         args: ["--fix"]

diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -5,6 +5,7 @@ build:
     python: "3.10"
 sphinx:
   configuration: docs/conf.py
+  fail_on_warning: true # do not change or you will be fired
 python:
   install:
     - method: pip

diff --git a/anndata/_core/views.py b/anndata/_core/views.py
@@ -349,7 +349,7 @@ def __copy__(self) -> AwkArray:
             array = self
             # makes a shallow copy and removes the reference to the original AnnData object
             array = ak.with_parameter(self, _PARAM_NAME, None)
-            array = ak.with_parameter(array, "__array__", None)
+            array = ak.with_parameter(array, "__list__", None)
             return array
 
     @as_view.register(AwkArray)
@@ -367,7 +367,7 @@ def as_view_awkarray(array, view_args):
                 "Please open an issue in the AnnData repo and describe your use-case."
             )
         array = ak.with_parameter(array, _PARAM_NAME, (parent_key, attrname, keys))
-        array = ak.with_parameter(array, "__array__", "AwkwardArrayView")
+        array = ak.with_parameter(array, "__list__", "AwkwardArrayView")
         return array
 
     ak.behavior["AwkwardArrayView"] = AwkwardArrayView

diff --git a/anndata/tests/test_awkward.py b/anndata/tests/test_awkward.py
@@ -147,8 +147,20 @@ def test_view(key):
 def test_view_of_awkward_array_with_custom_behavior():
     """Currently can't create view of arrays with custom __name__ (in this case "string")
     See https://github.com/scverse/anndata/pull/647#discussion_r963494798_"""
+
+    from uuid import uuid4
+
+    BEHAVIOUR_ID = str(uuid4())
+
+    class ReversibleArray(ak.Array):
+        def reversed(self):
+            return self[..., ::-1]
+
+    ak.behavior[BEHAVIOUR_ID] = ReversibleArray
     adata = gen_adata((3, 3), varm_types=(), obsm_types=(), layers_types=())
-    adata.obsm["awk_string"] = ak.Array(["AAA", "BBB", "CCC"])
+    adata.obsm["awk_string"] = ak.with_parameter(
+        ak.Array(["AAA", "BBB", "CCC"]), "__list__", BEHAVIOUR_ID
+    )
     adata_view = adata[:2]
 
     with pytest.raises(NotImplementedError):

diff --git a/docs/conf.py b/docs/conf.py
@@ -98,7 +98,7 @@
 
 def setup(app: Sphinx):
     # Don’t allow broken links. DO NOT CHANGE THIS LINE, fix problems instead.
-    app.warningiserror = False
+    app.warningiserror = True
 
 
 intersphinx_mapping = dict(

diff --git a/docs/release-notes/0.9.2.md b/docs/release-notes/0.9.2.md
@@ -1,8 +1,9 @@
-### 0.9.2 {small}`the future`
+### 0.9.2 {small}`2023-07-25`
 
 ```{rubric} Bugfix
 ```
 
+* Views of `awkward.Array`s now work with `awkward>=2.3` {pr}`1040` {user}`ivirshup`
 * Fix ufuncs of views like `adata.X[:10].cov(axis=0)` returning views {pr}`1043` {user}`flying-sheep`
 * Fix instantiating AnnData where `.X` is a `DataFrame` with an integer valued index  {pr}`1002` {user}`flying-sheep`
 * Fix {func}`~anndata.read_zarr` when used on `zarr.Group` {pr}`1057` {user}`ivirshup`
diff --git a/docs/release-notes/0.9.3.md b/docs/release-notes/0.9.3.md
@@ -0,0 +1,4 @@
+### 0.9.3 {small}`the future`
+
+```{rubric} Bugfix
+```
diff --git a/docs/release-notes/release-latest.md b/docs/release-notes/release-latest.md
@@ -4,6 +4,9 @@
 ```
 ## Version 0.9
 
+```{include} /release-notes/0.9.3.md
+```
+
 ```{include} /release-notes/0.9.2.md
 ```
 

diff --git a/pyproject.toml b/pyproject.toml
@@ -84,7 +84,7 @@ test = [
     "boltons",
     "scanpy",
     "dask[array]",
-    "awkward>=2.0.8,<2.3",
+    "awkward>=2.3",
     "pytest_memray",
 ]
 gpu = [