From 78940730050462eea41dcfb0fa5d7b79b0fca64f Mon Sep 17 00:00:00 2001 From: "Philipp A." Date: Mon, 11 Nov 2024 12:18:25 +0100 Subject: [PATCH] Merge 0.11 docs with rcs (#1752) --- docs/release-notes/0.11.0.md | 41 +++++++++++++++++++++++++++++++-- docs/release-notes/0.11.0rc1.md | 32 ------------------------- docs/release-notes/0.11.0rc2.md | 12 ---------- docs/release-notes/0.11.0rc3.md | 6 ----- 4 files changed, 39 insertions(+), 52 deletions(-) delete mode 100644 docs/release-notes/0.11.0rc1.md delete mode 100644 docs/release-notes/0.11.0rc2.md delete mode 100644 docs/release-notes/0.11.0rc3.md diff --git a/docs/release-notes/0.11.0.md b/docs/release-notes/0.11.0.md index fe08c3c40..317175f50 100644 --- a/docs/release-notes/0.11.0.md +++ b/docs/release-notes/0.11.0.md @@ -1,12 +1,49 @@ (v0.11.0)= ### 0.11.0 {small}`2024-11-07` +Release candidates: + +- (v0.11.0rc3)= + {guilabel}`rc3` 2024-10-14 +- (v0.11.0rc2)= + {guilabel}`rc2` 2024-09-24 +- (v0.11.0rc1)= + {guilabel}`rc1` 2024-09-04 + #### Bug fixes - Ensure {func}`anndata.concat` of {class}`~anndata.AnnData` object with {class}`scipy.sparse.spmatrix` and {class}`scipy.sparse.sparray` dask arrays uses the correct fill value of 0. {user}`ilan-gold` ({pr}`1719`) -- Ensure that views of AwkwardArrays have their "view" attributes removed on saving an {class}`~anndata.AnnData` object - to disk. {user}`grst` ({pr}`1736`) +- Ensure that views of AwkwardArrays have their "view" attributes removed on saving an {class}`~anndata.AnnData` object to disk. {user}`grst` ({pr}`1736`) + +#### Breaking changes + +- {guilabel}`rc3` Drop support for `python` 3.9 {user}`ilan-gold` ({pr}`1712`) +- {guilabel}`rc2` A new `anndata.io` module contains all `read_*` and `write_*` functions, and all imports of such functions should go through this module. Old ways of importing these functions i.e., `from anndata import read_csv` or `from anndata._io.specs import read_elem` will still work, but are now considered deprecated and give a warning on import with the exception of {func}`anndata.io.read_zarr` and {func}`anndata.io.read_h5ad`, which will remain at the top-level `anndata` without warning. {user}`ilan-gold ({pr}`1682`) +- {guilabel}`rc1` Removed deprecated modules `anndata.core` and `anndata.readwrite` {user}`ivirshup` ({pr}`1197`) +- {guilabel}`rc1` No longer export `sparse_dataset` from `anndata.experimental`, instead exporting {func}`anndata.io.sparse_dataset` {user}`ilan-gold` ({pr}`1642`) +- {guilabel}`rc1` 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 + +- {guilabel}`rc2` Add extra `dask` dependency for installation i.e., `pip install anndata[dask]` {user}`ilan-gold` ({pr}`1677`) +- {guilabel}`rc2` Remove `shall_` from variable names in `settings` {user}`ilan-gold` ({pr}`1685`) +- {guilabel}`rc1` Create new `cupy` installation options for cuda 11 & 12 called `cu11` and `cu12` {user}`Intron7` ({pr}`1596`) + +#### Documentation + +- {guilabel}`rc1` 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 - Add support for ellipsis indexing of the {class}`~anndata.AnnData` object {user}`ilan-gold` ({pr}`1729`) +- {guilabel}`rc1` `scipy.sparse.csr_array` and `scipy.sparse.csc_array` are now supported when constructing `AnnData` objects {user}`ilan-gold` {user}`isaac-virshup` ({pr}`1028`) +- {guilabel}`rc1` Allow `axis` parameter of e.g. {func}`anndata.concat` to accept `'obs'` and `'var'` {user}`flying-sheep` ({pr}`1244`) +- {guilabel}`rc1` Add `settings` object with methods for altering internally-used options, like checking for uniqueness on `obs`' index {user}`ilan-gold` ({pr}`1270`) +- {guilabel}`rc1` Add {attr}`~anndata.settings.remove_unused_categories` option to {attr}`anndata.settings` to override current behavior {user}`ilan-gold` ({pr}`1340`) +- {guilabel}`rc1` Add {func}`~anndata.experimental.read_elem_as_dask` function to handle i/o with sparse and dense arrays {user}`ilan-gold` ({pr}`1469`) +- {guilabel}`rc1` 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`) +- {guilabel}`rc1` Add {attr}`~anndata.settings.check_uniqueness` option to {attr}`anndata.settings` to override current behavior {user}`ilan-gold` ({pr}`1507`) +- {guilabel}`rc1` Add functionality to write from GPU {class}`dask.array.Array` to disk {user}`ilan-gold` ({pr}`1550`) +- {guilabel}`rc1` 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`) +- {guilabel}`rc1` Export {func}`~anndata.io.write_elem` and {func}`~anndata.io.read_elem` directly from the main package instead of `experimental` {user}`ilan-gold` ({pr}`1598`) +- {guilabel}`rc1` Allow reading sparse data (via {func}`~anndata.io.read_elem` or {func}`~anndata.io.sparse_dataset`) into either {class}`scipy.sparse.csr_array` or {class}`scipy.sparse.csc_array` via {attr}`anndata.settings.use_sparse_array_on_read` {user}`ilan-gold` ({pr}`1633`) diff --git a/docs/release-notes/0.11.0rc1.md b/docs/release-notes/0.11.0rc1.md deleted file mode 100644 index f5a98086d..000000000 --- a/docs/release-notes/0.11.0rc1.md +++ /dev/null @@ -1,32 +0,0 @@ -(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.io.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.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.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.io.write_elem` and {func}`~anndata.io.read_elem` directly from the main package instead of `experimental` {user}`ilan-gold` ({pr}`1598`) -- Allow reading sparse data (via {func}`~anndata.io.read_elem` or {func}`~anndata.io.sparse_dataset`) into either {class}`scipy.sparse.csr_array` or {class}`scipy.sparse.csc_array` via {attr}`anndata.settings.use_sparse_array_on_read` {user}`ilan-gold` ({pr}`1633`) diff --git a/docs/release-notes/0.11.0rc2.md b/docs/release-notes/0.11.0rc2.md deleted file mode 100644 index ecb5049d2..000000000 --- a/docs/release-notes/0.11.0rc2.md +++ /dev/null @@ -1,12 +0,0 @@ -(v0.11.0rc2)= -### 0.11.0rc2 {small}`2024-09-24` - -#### Development Process - -- Add extra `dask` dependency for installation i.e., `pip install anndata[dask]` {user}`ilan-gold` ({pr}`1677`) -- Remove `shall_` from variable names in `settings` {user}`ilan-gold` ({pr}`1685`) - -#### Breaking changes - -- A new `anndata.io` module contains all `read_*` and `write_*` functions, and all imports of such functions should go through this module. -Old ways of importing these functions i.e., `from anndata import read_csv` or `from anndata._io.specs import read_elem` will still work, but are now considered deprecated and give a warning on import with the exception of {func}`anndata.io.read_zarr` and {func}`anndata.io.read_h5ad`, which will remain at the top-level `anndata` without warning. `user`{ilan-gold} ({pr}`1682`) diff --git a/docs/release-notes/0.11.0rc3.md b/docs/release-notes/0.11.0rc3.md deleted file mode 100644 index 4c9af5593..000000000 --- a/docs/release-notes/0.11.0rc3.md +++ /dev/null @@ -1,6 +0,0 @@ -(v0.11.0rc3)= -### 0.11.0rc3 {small}`2024-10-14` - -#### Breaking changes - -- Drop support for `python` 3.9 {user}`ilan-gold` ({pr}`1712`)