Prepare 0.2.0 release (#308)

Author: lazappi

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: anndataR
 Title: AnnData interoperability in R
-Version: 0.1.0.9011
+Version: 0.2.0
 Authors@R: c(
     person("Robrecht", "Cannoodt", , "robrecht@data-intuitive.com", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-3641-729X", github = "rcannood")),
@@ -48,7 +48,7 @@ Suggests:
     knitr,
     processx,
     reticulate (>= 1.41.1),
-    rhdf5,
+    rhdf5 (>= 2.52.1),
     rmarkdown,
     S4Vectors,
     Seurat,

NEWS.md

@@ -1,59 +1,56 @@
-# anndataR devel
+# anndataR 0.2.0
 
-## anndataR 0.1.0.9011
+## Breaking changes
 
-- Updates for compatibility with Python **anndata** >= 0.12.0 (PR #305, Fixes #304)
+- Switch the HDF5 back end to use the **{rhdf5}** package instead of **{hdf5r}**
+  (PR #283, Fixes #272, #175, #299)
+  - This addresses various issues related to H5AD files and allows better
+    integration with Bioconductor. Most of the previous known issues have now
+    been resolved.
+  - It also greatly improves compatibility with H5AD files written by Python
+    **anndata**
+  - **NOTE:** Make sure to install **{rhdf5}** instead of **{hdf5r}** to be able
+    to read and write H5AD files!
+
+## Major changes
+
+- Updates for compatibility with Python **anndata** >= 0.12.0 (PR #305,
+  Fixes #304)
   - Add helpers for reading/writing `NULL` values to/from H5AD files
   - Writing of `NULL` values can be disabled by setting
     `option(anndataR.write_null = FALSE)` to allow the files to be read by
     Python **anndata** < 0.12.0
-- Fix a bug where string arrays were not transposed correctly when writing to
-  H5AD files (PR #305)
-- Fix a bug where the dimenions of dense arrays were not properly conserved
-  when reading from H5AD (PR #305)
-- Remove workarounds and skipping of `none` values in roundtrip tests (PR #305)
-
-## anndataR 0.1.0.9010
-
-- Switch HDF5 back end from **{hdf5r}** to **{rhdf5}** (PR #283, Fixes #272, #175, #299)
-  - Includes improved compatibility with H5AD files written by Python **anndata**
-- Improvements to roundtrip testing (PR #283)
-
-## anndataR 0.1.0.9009
-
-- Fix execution of roundtrip tests (PR #293)
-
-## anndataR 0.1.0.9008
-
-- Add Bioconductor installation instructions in preparation of submission (PR #297)
-
-## anndataR 0.1.0.9007
-
+- A `counts` or `data` layer is no longer required during `Seurat` conversion
+  (PR #284)
+  - There will still be a warning if neither of this is present as it may
+    affect compatibility with **{Seurat}** functions
+    
+## Minor changes
+
+- Use accessor functions/methods instead of direct slot access where possible
+  (PR #291)
 - Refactor superfluous for loops (PR #298)
-- 
-## anndataR 0.1.0.9006
-
+- Change uses of `sapply()` to `vapply()` (PR #294)
 - Ignore `development_status.Rmd` vignette when building package (PR #296)
+- Remove `anndataR.Rproj` file from repository (PR #292)
 
-## anndataR 0.1.0.9005
-
-- Bypass requiring a `counts` or `data` layer during `Seurat` conversion (PR #284)
-
-## anndataR 0.1.0.9004
+## Bug fixes
 
-- Use accessors instead of direct slot access where possible (PR #291)
+- Fix a bug where string arrays were not transposed correctly when writing to
+  H5AD files (PR #305)
+- Fix a bug where the dimensions of dense arrays were not properly conserved
+  when reading from H5AD (PR #305)
 
-## anndataR 0.1.0.9003
+## Documentation
 
 - Simplify and update vignettes (PR #282)
+- Add Bioconductor installation instructions in preparation for submission (PR #297)
 
-## anndataR 0.1.0.9002
-
-- Remove `anndataR.Rproj` file from repository (PR #292)
-
-## anndataR 0.1.0.9001
+## Testing
 
-- Change uses of `sapply()` to `vapply()` (PR #294)
+- Improvements to round trip testing (PR #283, PR #293, PR #305)
+  - Most round trip tests are now enabled and pass successfully
+  - Conversion helpers have been added to assist with **{reticulate}** tests
 
 # anndataR 0.1.0 (inital release candidate)
 

R/write_h5ad.R

@@ -17,9 +17,20 @@
 #' @param ... Additional arguments passed to [as_AnnData()]
 #'
 #' @details
+#'
+#' ## Compression
+#'
 #' Compression is currently not supported for Boolean arrays, they will be
 #' written uncompressed.
 #'
+#' ## `NULL` values
+#'
+#' For compatibility with changes in Python **anndata** 0.12.0, `NULL` values
+#' in `uns` are written to H5AD files as a `NULL` dataset (instead of not being
+#' written at all). To disable this behaviour, set
+#' `option(anndataR.write_null = FALSE)`. This may be required to allow the file
+#' to be read by older versions of Python **anndata**.
+#'
 #' @return `path` invisibly
 #' @export
 #'

README.md

@@ -1,31 +1,22 @@
 # {anndataR}: An R package for working with AnnData objects <img src="man/figures/logo.png" align="right" alt="anndataR logo" width=120 />
 <!-- badges: start -->
 [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
-[![CRAN status](https://www.r-pkg.org/badges/version/anndataR.png)](https://CRAN.R-project.org/package=anndataR)
 [![R-CMD-check](https://github.com/scverse/anndataR/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/scverse/anndataR/actions/workflows/R-CMD-check.yaml)
 <!-- badges: end -->
 
-**{anndataR}** aims to make the AnnData format a first-class citizen in
-the R ecosystem, and to make it easy to work with AnnData files in R,
-either directly or by converting them to a SingleCellExperiment or Seurat
-object.
+**{anndataR}** aims to make the `AnnData` format a first-class citizen in the R ecosystem, and to make it easy to work with AnnData files in R, either directly or by converting them to a `SingleCellExperiment` or `Seurat` object.
 
 **{anndataR}** is an scverse® community project maintained by [Data Intuitive](https://data-intuitive.com/), and is fiscally sponsored by the [Chan Zuckerberg Initiative](https://chanzuckerberg.com/).
 
-
 ## Features of {anndataR}
 
-- Provide an `R6` class to work with AnnData objects in R (either in-memory or on-disk).
+- Provide an `R6` class to work with `AnnData` objects in R (either in-memory or on-disk)
 - Read/write `*.h5ad` files natively
 - Convert to/from `SingleCellExperiment` objects
 - Convert to/from `Seurat` objects
 
-> [!WARNING]
->
-> This package is still in the experimental stage, and may not work as
-> expected. You can find the status of development of anndataR on the
-> [feature tracking page](https://anndatar.data-intuitive.com/articles/design.html#feature-tracking)
-> of the website. Please [report](https://github.com/scverse/anndataR/issues) any issues you encounter.
+You can find the status of development of **{anndataR}** on the [feature tracking page](https://anndatar.data-intuitive.com/articles/design.html#feature-tracking) of the package website. 
+Please [report](https://github.com/scverse/anndataR/issues) any issues you encounter.
 
 ## Installation
 
@@ -74,17 +65,13 @@ pak::pak("scverse/anndataR")
 
 Take note that you need all suggested dependencies available, and that building them can take some time.
 
-- **Getting started**: An introduction to the package and its features.  
+- [**Getting started**](https://anndatar.data-intuitive.com/articles/anndataR.html): An introduction to the package and its features.  
   `vignette("anndataR", package = "anndataR")`
-- **Reading and writing H5AD files**: How to read and write `*.h5ad` files.  
-  `vignette("usage_h5ad", package = "anndataR")`
-- **Converting to/from Seurat objects**: How to convert between `AnnData` and `Seurat` objects.  
+- [**Read/write `Seurat` objects**](https://anndatar.data-intuitive.com/articles/usage_seurat.html): How to convert between `AnnData` and `Seurat` objects.  
   `vignette("usage_seurat", package = "anndataR")`
-- **Converting to/from SingleCellExperiment objects**: How to convert between `AnnData` and `SingleCellExperiment` objects.  
+- [**Read/write `SingleCellExperiment` objects**](https://anndatar.data-intuitive.com/articles/usage_singlecellexperiment.html): How to convert between `AnnData` and `SingleCellExperiment` objects 
   `vignette("usage_singlecellexperiment", package = "anndataR")`
-- **Software Design**: An overview of the design of the package.  
-  `vignette("software_design", package = "anndataR")`
-- **Development Status**: An overview of the development status of the package.  
-  `vignette("development_status", package = "anndataR")`
-- **Known Isses**: An overview of known issues with the package.  
+- [**Software Design**](https://anndatar.data-intuitive.com/articles/software_design.html): An overview of the design of the package
+- [**Development Status**](https://anndatar.data-intuitive.com/articles/development_status.html): An overview of the development status of the package
+- [**Known Issues**](https://anndatar.data-intuitive.com/articles/known_issues.html): An overview of known issues with the package.  
   `vignette("known_issues", package = "anndataR")`

_pkgdown.yml

@@ -9,8 +9,6 @@ navbar:
     text: Articles
     menu:
     - text: Usage
-    - text: Read/write H5AD files
-      href: articles/anndataR.html
     - text: Read/write Seurat objects
       href: articles/usage_seurat.html
     - text: Read/write SingleCellExperiment objects

man/write_h5ad.Rd

@@ -28,13 +28,11 @@ library(SingleCellExperiment)
 ## Introduction
 **{anndataR}** allows users to work with `.h5ad` files, access various slots in the datasets and convert these files to `SingleCellExperiment` objects or `Seurat` objects, and vice versa.
 This enables users to move data easily between the different programming languages and analysis ecosystems needed to perform single-cell data analysis.
-This package differs from [zellkonverter](https://bioconductor.org/packages/release/bioc/html/zellkonverter.html) because it reads and writes these `.h5ad` files natively in R, and allows conversion to and from `Seurat` objects as well.
-
-Check out `?anndataR` for a full list of the functions provided by this package.
+This package differs from [**{zellkonverter}**](https://bioconductor.org/packages/release/bioc/html/zellkonverter.html) because it reads and writes these `.h5ad` files natively in R, and allows conversion to and from `Seurat` objects as well as `SingleCellExperiment`.
 
 ## Installation
 
-Install using either **BiocManager** or from GitHub using **pak**:
+Install using either **{BiocManager}** or from GitHub using **{pak}**:
 
 ```{r, eval = FALSE}
 if (!requireNamespace("BiocManager", quietly = TRUE)) {
@@ -62,13 +60,25 @@ library(anndataR)
 h5ad_path <- system.file("extdata", "example.h5ad", package = "anndataR")
 ```
 
-Read an h5ad file in memory:
+By default, a H5AD is read to an in-memory `AnnData` object:
 
 ```{r read-in-memory}
 adata <- read_h5ad(h5ad_path)
 ```
 
-Read an h5ad file on disk:
+It can also be read as a `SingleCellExperiment` object:
+
+```{r read-as-SingleCellExperiment}
+sce <- read_h5ad(h5ad_path, as = "SingleCellExperiment")
+```
+
+Or as a `Seurat` object:
+
+```{r read-as-Seurat}
+obj <- read_h5ad(h5ad_path, as = "Seurat")
+```
+
+There is also a HDF5-backed `AnnData` object:
 
 ```{r read-on-disk}
 adata <- read_h5ad(h5ad_path, as = "HDF5AnnData")
@@ -80,7 +90,7 @@ View structure:
 adata
 ```
 
-Access AnnData slots:
+Access `AnnData` slots:
 
 ```{r access-slots}
 dim(adata$X)
@@ -90,35 +100,35 @@ adata$var[1:5, 1:6]
 
 ## Interoperability
 
-Convert the AnnData object to a SingleCellExperiment object:
+Convert the `AnnData` object to a `SingleCellExperiment` object:
 
 ```{r as-SingleCellExperiment}
 sce <- adata$as_SingleCellExperiment()
 sce
 ```
 
-Convert the AnnData object to a Seurat object:
+Convert the `AnnData` object to a `Seurat` object:
 
 ```{r as-Seurat}
 obj <- adata$as_Seurat()
 obj
 ```
 
-Convert a SingleCellExperiment object to an AnnData object:
+Convert a `SingleCellExperiment` object to an `AnnData` object:
 
 ```{r as-AnnData-from-SingleCellExperiment}
 adata <- as_AnnData(sce)
 adata
 ```
 
-Convert a Seurat object to an AnnData object:
+Convert a `Seurat` object to an `AnnData` object:
 
 ```{r as-AnnData-from-Seurat}
 adata <- as_AnnData(obj)
 adata
 ```
 
-## Manually create an object
+## Manually create an `AnnData` object
 
 ```{r manually-create-object}
 adata <- AnnData(
@@ -136,21 +146,21 @@ adata
 
 ## Write to disk:
 
-Write an AnnData object to disk:
+Write an `AnnData` object to disk:
 
 ```{r write-to-disk}
 tmpfile <- tempfile(fileext = ".h5ad")
 write_h5ad(adata, tmpfile)
 ```
 
-Write an SCE object to disk:
+Write a `SingleCellExperiment` object to disk:
 
 ```{r write-SingleCellExperiment-to-disk}
 tmpfile <- tempfile(fileext = ".h5ad")
 write_h5ad(sce, tmpfile)
 ```
 
-Write a Seurat object to disk:
+Write a `Seurat` object to disk:
 
 ```{r write-Seurat-to-disk}
 tmpfile <- tempfile(fileext = ".h5ad")