Backport more user-facing fixes from #1182 (#1193)

* Shorter tracebacks * Fix write_h5ad(..., as_dense) not writing attributes * Release notes Co-authored-by: Philipp A <[email protected]> --------- Co-authored-by: Philipp A <[email protected]>
scverse · Oct 11, 2023 · 3695a7f · 3695a7f
1 parent da4bbdf
commit 3695a7f
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Showing 4 changed files with 20 additions and 15 deletions.
diff --git a/anndata/_io/h5ad.py b/anndata/_io/h5ad.py
@@ -29,6 +29,7 @@
 )
 from ..experimental import read_dispatched
 from .specs import read_elem, write_elem
+from .specs.registry import IOSpec, write_spec
 from .utils import (
     H5PY_V3,
     _read_legacy_raw,
@@ -110,6 +111,7 @@ def write_h5ad(
 
 
 @report_write_key_on_error
+@write_spec(IOSpec("array", "0.2.0"))
 def write_sparse_as_dense(f, key, value, dataset_kwargs=MappingProxyType({})):
     real_key = None  # Flag for if temporary key was used
     if key in f:

diff --git a/anndata/_io/utils.py b/anndata/_io/utils.py
@@ -165,24 +165,22 @@ def _get_parent(elem):
     return parent
 
 
-def re_raise_error(e, elem, key, op=Literal["read", "writ"]):
+def add_key_note(e: BaseException, elem, key, op=Literal["read", "writ"]) -> None:
     if any(
         f"Error raised while {op}ing key" in note
         for note in getattr(e, "__notes__", [])
     ):
-        raise
-    else:
-        parent = _get_parent(elem)
-        add_note(
-            e,
-            f"Error raised while {op}ing key {key!r} of {type(elem)} to " f"{parent}",
-        )
-        raise e
+        return
+    parent = _get_parent(elem)
+    add_note(
+        e,
+        f"Error raised while {op}ing key {key!r} of {type(elem)} to " f"{parent}",
+    )
 
 
 def report_read_key_on_error(func):
     """\
-    A decorator for zarr element reading which makes keys involved in errors get reported.
+    A decorator for hdf5/zarr element reading which makes keys involved in errors get reported.
 
     Example
     -------
@@ -206,14 +204,15 @@ def func_wrapper(*args, **kwargs):
         try:
             return func(*args, **kwargs)
         except Exception as e:
-            re_raise_error(e, elem, elem.name, "read")
+            add_key_note(e, elem, elem.name, "read")
+            raise
 
     return func_wrapper
 
 
 def report_write_key_on_error(func):
     """\
-    A decorator for zarr element reading which makes keys involved in errors get reported.
+    A decorator for hdf5/zarr element writing which makes keys involved in errors get reported.
 
     Example
     -------
@@ -239,7 +238,8 @@ def func_wrapper(*args, **kwargs):
         try:
             return func(*args, **kwargs)
         except Exception as e:
-            re_raise_error(e, elem, key, "writ")
+            add_key_note(e, elem, key, "writ")
+            raise
 
     return func_wrapper
 

diff --git a/anndata/tests/test_hdf5_backing.py b/anndata/tests/test_hdf5_backing.py
@@ -81,6 +81,7 @@ def as_dense(request):
 
 
 # TODO: Check to make sure obs, obsm, layers, ... are written and read correctly as well
+@pytest.mark.filterwarnings("error")
 def test_read_write_X(tmp_path, mtx_format, backed_mode, as_dense):
     base_pth = Path(tmp_path)
     orig_pth = base_pth / "orig.h5ad"
@@ -89,11 +90,11 @@ def test_read_write_X(tmp_path, mtx_format, backed_mode, as_dense):
     orig = ad.AnnData(mtx_format(asarray(sparse.random(10, 10, format="csr"))))
     orig.write(orig_pth)
 
-    backed = ad.read(orig_pth, backed=backed_mode)
+    backed = ad.read_h5ad(orig_pth, backed=backed_mode)
     backed.write(backed_pth, as_dense=as_dense)
     backed.file.close()
 
-    from_backed = ad.read(backed_pth)
+    from_backed = ad.read_h5ad(backed_pth)
     assert np.all(asarray(orig.X) == asarray(from_backed.X))
 
 

diff --git a/docs/release-notes/0.10.2.md b/docs/release-notes/0.10.2.md
@@ -7,6 +7,8 @@
   Note that this API is *deprecated* and new code should use {class}`~anndata.experimental.CSRDataset`, {class}`~anndata.experimental.CSCDataset`, and {func}`~anndata.experimental.sparse_dataset` instead.
   {pr}`1185` {user}`ivirshup`
 * Handle deprecation warning from `pd.Categorical.map` thrown during `anndata.concat` {pr}`1189` {user}`flying-sheep` {user}`ivirshup`
+* Fixed extra steps being included in IO tracebacks {pr}`1193` {user}`flying-sheep`
+* `as_dense` argument of `write_h5ad` no longer writes an array without encoding metadata {pr}`1193` {user}`flying-sheep`
 
 ```{rubric} Documentation
 ```