From f448eb264503eddb25b0a41b460839faa59cd55f Mon Sep 17 00:00:00 2001 From: Ilan Gold Date: Wed, 4 Sep 2024 14:20:31 +0200 Subject: [PATCH] (chore): generate 0.11.0rc1 release notes (#1663) --- docs/release-notes/0.11.0rc1.md | 32 +++++++++++++++++++++++++++++ docs/release-notes/1028.feature.md | 1 - docs/release-notes/1197.breaking.md | 1 - docs/release-notes/1244.feature.md | 1 - docs/release-notes/1270.feature.md | 1 - docs/release-notes/1340.feature.md | 1 - docs/release-notes/1469.feature.md | 1 - docs/release-notes/1474.feature.md | 1 - docs/release-notes/1507.feature.md | 1 - docs/release-notes/1550.feature.md | 1 - docs/release-notes/1558.feature.md | 3 --- docs/release-notes/1596.dev.md | 1 - docs/release-notes/1598.feature.md | 1 - docs/release-notes/1616.doc.md | 1 - docs/release-notes/1633.feature.md | 1 - docs/release-notes/1642.breaking.md | 1 - docs/release-notes/1643.breaking.md | 1 - 17 files changed, 32 insertions(+), 18 deletions(-) create mode 100644 docs/release-notes/0.11.0rc1.md delete mode 100644 docs/release-notes/1028.feature.md delete mode 100644 docs/release-notes/1197.breaking.md delete mode 100644 docs/release-notes/1244.feature.md delete mode 100644 docs/release-notes/1270.feature.md delete mode 100644 docs/release-notes/1340.feature.md delete mode 100644 docs/release-notes/1469.feature.md delete mode 100644 docs/release-notes/1474.feature.md delete mode 100644 docs/release-notes/1507.feature.md delete mode 100644 docs/release-notes/1550.feature.md delete mode 100644 docs/release-notes/1558.feature.md delete mode 100644 docs/release-notes/1596.dev.md delete mode 100644 docs/release-notes/1598.feature.md delete mode 100644 docs/release-notes/1616.doc.md delete mode 100644 docs/release-notes/1633.feature.md delete mode 100644 docs/release-notes/1642.breaking.md delete mode 100644 docs/release-notes/1643.breaking.md diff --git a/docs/release-notes/0.11.0rc1.md b/docs/release-notes/0.11.0rc1.md new file mode 100644 index 000000000..36eb354de --- /dev/null +++ b/docs/release-notes/0.11.0rc1.md @@ -0,0 +1,32 @@ +(v0.11.0rc1)= +### 0.11.0rc1 {small}`2024-09-04` + +### Breaking changes + +- Removed deprecated modules `anndata.core` and `anndata.readwrite` {user}`ivirshup` ({pr}`1197`) +- No longer export `sparse_dataset` from `anndata.experimental`, instead exporting {func}`anndata.sparse_dataset` {user}`ilan-gold` ({pr}`1642`) +- Move `RWAble` and `InMemoryElem` out of `experimental`, renaming `RWAble` to {type}`~anndata.typing.AxisStorable` and `InMemoryElem` to {type}`~anndata.typing.RWAble` {user}`ilan-gold` ({pr}`1643`) + +### Development Process + +- create new `cupy` installation options for cuda 11 & 12 called `cu11` and `cu12` {user}`Intron7` ({pr}`1596`) + +### Documentation + +- Correct {attr}`anndata.AnnData.X` type to include {class}`~anndata.abc.CSRDataset` and {class}`~anndata.abc.CSCDataset` as possible types and being deprecation process for non-csr/csc {class}`scipy.sparse.spmatrix` types in {attr}`anndata.AnnData.X` {user}`ilan-gold` ({pr}`1616`) + +### Features + +- `scipy.sparse.csr_array` and `scipy.sparse.csc_array` are now supported when constructing `AnnData` objects {user}`ilan-gold` {user}`isaac-virshup` ({pr}`1028`) +- Allow `axis` parameter of e.g. :func:`anndata.concat` to accept `'obs'` and `'var'` {user}`flying-sheep` ({pr}`1244`) +- Add `settings` object with methods for altering internally-used options, like checking for uniqueness on `obs`' index {user}`ilan-gold` ({pr}`1270`) +- Add {attr}`~anndata.settings.shall_remove_unused_categories` option to {attr}`anndata.settings` to override current behavior {user}`ilan-gold` ({pr}`1340`) +- Add :func:`~anndata.experimental.read_elem_as_dask` function to handle i/o with sparse and dense arrays {user}`ilan-gold` ({pr}`1469`) +- Add ability to convert strings to categoricals on write in {meth}`~anndata.AnnData.write_h5ad` and {meth}`~anndata.AnnData.write_zarr` via `convert_strings_to_categoricals` parameter {user}` falexwolf` ({pr}`1474`) +- Add {attr}`~anndata.settings.shall_check_uniqueness` option to {attr}`anndata.settings` to override current behavior {user}`ilan-gold` ({pr}`1507`) +- Add functionality to write from GPU {class}`dask.array.Array` to disk {user}`ilan-gold` ({pr}`1550`) +- Read and write support for nullable string arrays ({class}`pandas.arrays.StringArray`). + Use pandas’ {doc}`pandas:user_guide/options` `mode.string_storage` to control which storage mode is used when reading `dtype="string"` columns. + {user}`flying-sheep` ({pr}`1558`) +- Export {func}`~anndata.write_elem` and {func}`~anndata.read_elem` directly from the main package instead of `experimental` {user}`ilan-gold` ({pr}`1598`) +- Allow reading sparse data (via {func}`~anndata.read_elem` or {func}`~anndata.sparse_dataset`) into either {class}`scipy.sparse.csr_array` or {class}`scipy.sparse.csc_array` via {attr}`anndata.settings.shall_use_sparse_array_on_read` {user}`ilan-gold` ({pr}`1633`) diff --git a/docs/release-notes/1028.feature.md b/docs/release-notes/1028.feature.md deleted file mode 100644 index 8b2f612f9..000000000 --- a/docs/release-notes/1028.feature.md +++ /dev/null @@ -1 +0,0 @@ -`scipy.sparse.csr_array` and `scipy.sparse.csc_array` are now supported when constructing `AnnData` objects {user}`ilan-gold` {user}`isaac-virshup` diff --git a/docs/release-notes/1197.breaking.md b/docs/release-notes/1197.breaking.md deleted file mode 100644 index 165e712cc..000000000 --- a/docs/release-notes/1197.breaking.md +++ /dev/null @@ -1 +0,0 @@ -Removed deprecated modules `anndata.core` and `anndata.readwrite` {user}`ivirshup` diff --git a/docs/release-notes/1244.feature.md b/docs/release-notes/1244.feature.md deleted file mode 100644 index 9a0fd6c30..000000000 --- a/docs/release-notes/1244.feature.md +++ /dev/null @@ -1 +0,0 @@ -Allow `axis` parameter of e.g. :func:`anndata.concat` to accept `'obs'` and `'var'` {user}`flying-sheep` diff --git a/docs/release-notes/1270.feature.md b/docs/release-notes/1270.feature.md deleted file mode 100644 index 89f07264c..000000000 --- a/docs/release-notes/1270.feature.md +++ /dev/null @@ -1 +0,0 @@ -Add `settings` object with methods for altering internally-used options, like checking for uniqueness on `obs`' index {user}`ilan-gold` diff --git a/docs/release-notes/1340.feature.md b/docs/release-notes/1340.feature.md deleted file mode 100644 index 533a38f2c..000000000 --- a/docs/release-notes/1340.feature.md +++ /dev/null @@ -1 +0,0 @@ -Add {attr}`~anndata.settings.shall_remove_unused_categories` option to {attr}`anndata.settings` to override current behavior {user}`ilan-gold` diff --git a/docs/release-notes/1469.feature.md b/docs/release-notes/1469.feature.md deleted file mode 100644 index abe84f7f6..000000000 --- a/docs/release-notes/1469.feature.md +++ /dev/null @@ -1 +0,0 @@ -Add :func:`~anndata.experimental.read_elem_as_dask` function to handle i/o with sparse and dense arrays {user}`ilan-gold` diff --git a/docs/release-notes/1474.feature.md b/docs/release-notes/1474.feature.md deleted file mode 100644 index 9c85d982f..000000000 --- a/docs/release-notes/1474.feature.md +++ /dev/null @@ -1 +0,0 @@ -Add ability to convert strings to categoricals on write in {meth}`~anndata.AnnData.write_h5ad` and {meth}`~anndata.AnnData.write_zarr` via `convert_strings_to_categoricals` parameter {user}` falexwolf` diff --git a/docs/release-notes/1507.feature.md b/docs/release-notes/1507.feature.md deleted file mode 100644 index 17ecdbd2e..000000000 --- a/docs/release-notes/1507.feature.md +++ /dev/null @@ -1 +0,0 @@ -Add {attr}`~anndata.settings.shall_check_uniqueness` option to {attr}`anndata.settings` to override current behavior {user}`ilan-gold` diff --git a/docs/release-notes/1550.feature.md b/docs/release-notes/1550.feature.md deleted file mode 100644 index bd1bfd37d..000000000 --- a/docs/release-notes/1550.feature.md +++ /dev/null @@ -1 +0,0 @@ -Add functionality to write from GPU {class}`dask.array.Array` to disk {user}`ilan-gold` diff --git a/docs/release-notes/1558.feature.md b/docs/release-notes/1558.feature.md deleted file mode 100644 index e90783f0c..000000000 --- a/docs/release-notes/1558.feature.md +++ /dev/null @@ -1,3 +0,0 @@ -Read and write support for nullable string arrays ({class}`pandas.arrays.StringArray`). -Use pandas’ {doc}`pandas:user_guide/options` `mode.string_storage` to control which storage mode is used when reading `dtype="string"` columns. -{user}`flying-sheep` diff --git a/docs/release-notes/1596.dev.md b/docs/release-notes/1596.dev.md deleted file mode 100644 index e1b3492ed..000000000 --- a/docs/release-notes/1596.dev.md +++ /dev/null @@ -1 +0,0 @@ -create new `cupy` installation options for cuda 11 & 12 called `cu11` and `cu12` {user}`Intron7` diff --git a/docs/release-notes/1598.feature.md b/docs/release-notes/1598.feature.md deleted file mode 100644 index 687f2c46f..000000000 --- a/docs/release-notes/1598.feature.md +++ /dev/null @@ -1 +0,0 @@ -Export {func}`~anndata.write_elem` and {func}`~anndata.read_elem` directly from the main package instead of `experimental` {user}`ilan-gold` diff --git a/docs/release-notes/1616.doc.md b/docs/release-notes/1616.doc.md deleted file mode 100644 index ebd9da66a..000000000 --- a/docs/release-notes/1616.doc.md +++ /dev/null @@ -1 +0,0 @@ -Correct {attr}`anndata.AnnData.X` type to include {class}`~anndata.abc.CSRDataset` and {class}`~anndata.abc.CSCDataset` as possible types and being deprecation process for non-csr/csc {class}`scipy.sparse.spmatrix` types in {attr}`anndata.AnnData.X` {user}`ilan-gold` diff --git a/docs/release-notes/1633.feature.md b/docs/release-notes/1633.feature.md deleted file mode 100644 index 778c6feaf..000000000 --- a/docs/release-notes/1633.feature.md +++ /dev/null @@ -1 +0,0 @@ -Allow reading sparse data (via {func}`~anndata.read_elem` or {func}`~anndata.sparse_dataset`) into either {class}`scipy.sparse.csr_array` or {class}`scipy.sparse.csc_array` via {attr}`anndata.settings.shall_use_sparse_array_on_read` {user}`ilan-gold` diff --git a/docs/release-notes/1642.breaking.md b/docs/release-notes/1642.breaking.md deleted file mode 100644 index 10fbd283b..000000000 --- a/docs/release-notes/1642.breaking.md +++ /dev/null @@ -1 +0,0 @@ -No longer export `sparse_dataset` from `anndata.experimental`, instead exporting {func}`anndata.sparse_dataset` {user}`ilan-gold` diff --git a/docs/release-notes/1643.breaking.md b/docs/release-notes/1643.breaking.md deleted file mode 100644 index 89f928a06..000000000 --- a/docs/release-notes/1643.breaking.md +++ /dev/null @@ -1 +0,0 @@ -Move `RWAble` and `InMemoryElem` out of `experimental`, renaming `RWAble` to {type}`~anndata.typing.AxisStorable` and `InMemoryElem` to {type}`~anndata.typing.RWAble` {user}`ilan-gold`