Prepare v0.1.0 release (#281)

Author: lazappi

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: anndataR
 Title: AnnData interoperability in R
-Version: 0.99.0
+Version: 0.1.0
 Authors@R: c(
     person("Robrecht", "Cannoodt", , "robrecht@data-intuitive.com", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-3641-729X", github = "rcannood")),
@@ -19,7 +19,8 @@ Authors@R: c(
     person("Chananchida", "Sang-aram", role = "ctb",
            comment = c(ORCID = "0000-0002-0922-0822", github = "csangara")),
     person("Data Intuitive", , , "info@data-intuitive.com", role = c("fnd", "cph")),
-    person("Chan Zuckerberg Initiative", role = "fnd")
+    person("Chan Zuckerberg Initiative", role = "fnd"),
+    person("scverse consortium", role = "spn")
   )
 Description: Bring the power and flexibility of AnnData to the R
     ecosystem, allowing you to effortlessly manipulate and analyze your
@@ -31,7 +32,7 @@ URL: https://anndatar.data-intuitive.com/,
     https://github.com/scverse/anndataR
 BugReports: https://github.com/scverse/anndataR/issues
 Depends: 
-    R (>= 4.0.0)
+    R (>= 4.1.0)
 Imports:
     cli,
     lifecycle,

LICENSE

@@ -1,2 +1,2 @@
 YEAR: 2023
-COPYRIGHT HOLDER: Robrecht Cannoodt, Luke Zappia, Martin Morgan, Louise Deconinck
+COPYRIGHT HOLDER: anndataR authors

NEWS.md

@@ -1,27 +1,9 @@
-# anndataR 0.99.0
+# anndataR 0.1.0 (inital release candidate)
 
-## New features
+Initial release candidate of **{anndataR}** including:
 
-* PR #158: Change package version from 0.0.0.9000 --> 0.99.0 to align with Bioc devel 
-    versioning standards.
-  - Update DESCRIPTION file to reflect current release R version used by Bio: 
-    R (>= 3.2.0) --> R (>= 4.3.0).
-  - Reformat NEWS file to follow some conventions.
-
-* Various PRs: Initial release of anndataR, providing support for working with
-  AnnData objects in R. Feature list:
-  - Slots:
-    - X
-    - layers
-    - obs
-    - obs_names
-    - var
-    - var_names
-  - Backends:
-    - HDF5AnnData
-    - InMemoryAnnData
-  - Converters:
-    - SingleCellExperiment
-    - Seurat
-    
-  
+- Native reading and writing of H5AD files
+- R implementations of `InMemoryAnnData` and `HDF5AnnData` objects
+- Conversion between `AnnData` and `SingleCellExperiment` or `Seurat` objects
+- Extensive function documentation and vignettes demonstrating usage
+- Comprehensive unit testing and identification of known issues

R/AbstractAnnData.R

@@ -213,7 +213,7 @@ AbstractAnnData <- R6::R6Class(
     #' @return A `SingleCellExperiment` object
     to_SingleCellExperiment = function(...) {
       lifecycle::deprecate_warn(
-        "0.99.0",
+        "0.1.0",
         "to_SingleCellExperiment()",
         "as_SingleCellExperiment()"
       )
@@ -267,7 +267,7 @@ AbstractAnnData <- R6::R6Class(
     #' @return A `Seurat` object
     to_Seurat = function(...) {
       lifecycle::deprecate_warn(
-        "0.99.0",
+        "0.1.0",
         "to_Seurat()",
         "as_Seurat()"
       )
@@ -291,7 +291,7 @@ AbstractAnnData <- R6::R6Class(
     #' @return An [`InMemoryAnnData`] object
     to_InMemoryAnnData = function() {
       lifecycle::deprecate_warn(
-        "0.99.0",
+        "0.1.0",
         "to_InMemoryAnnData()",
         "as_InMemoryAnnData()"
       )
@@ -330,7 +330,7 @@ AbstractAnnData <- R6::R6Class(
     #' @return An [`HDF5AnnData`] object
     to_HDF5AnnData = function(...) {
       lifecycle::deprecate_warn(
-        "0.99.0",
+        "0.1.0",
         "to_HDF5AnnDAta()",
         "as_HDF5AnnData()",
       )

R/as_Seurat.R

@@ -353,7 +353,7 @@ as_Seurat <- function(
 to_Seurat <- function(...) {
   # nolint end: object_name_linter
   lifecycle::deprecate_warn(
-    when = "0.99.0",
+    when = "0.1.0",
     what = "to_Seurat()",
     with = "adata$as_Seurat()"
   )

R/as_SingleCellExperiment.R

@@ -294,7 +294,7 @@ as_SingleCellExperiment <- function(
 to_SingleCellExperiment <- function(...) {
   # nolint end: object_name_linter
   lifecycle::deprecate_warn(
-    when = "0.99.0",
+    when = "0.1.0",
     what = "to_SingleCellExperiment()",
     with = "adata$as_SingleCellExperiment()"
   )

R/read_h5ad.R

@@ -52,7 +52,7 @@ read_h5ad <- function(
 
   if (lifecycle::is_present(to)) {
     lifecycle::deprecate_warn(
-      when = "0.99.0",
+      when = "0.1.0",
       what = "read_h5ad(to = )",
       with = "read_h5ad(as = )",
       details = "Overwriting `as` with `to`."