[r] 0.3.0 release announcement

r/DESCRIPTION

@@ -1,12 +1,13 @@
 Package: BPCells
 Title: Single Cell Counts Matrices to PCA
-Version: 0.2.0
+Version: 0.3.0
 Authors@R: c(
     person(given = "Benjamin",
            family = "Parks",
            role = c("aut", "cre", "cph"),
            email = "bparks@alumni.stanford.edu",
            comment = c(ORCID = "0000-0002-0261-7472")),
+    person("Immanuel", "Abdi", role = "aut"),
     person("Stanford University", role=c("cph", "fnd")),
     person("Genentech, Inc.", role=c("cph", "fnd")))
 Description: > Efficient operations for single cell ATAC-seq fragments and

r/NEWS.md

@@ -1,12 +1,21 @@
 # BPCells 1.0 Roadmap
 - ~~Parallelization~~ (basic support complete. See below)
-- Native python library (re-using C++ backend)
+- Native python library (re-using C++ backend; basic support started)
 - Peak-gene correlations
-- MACS peak calling
+- ~~MACS peak calling~~ (basic support complete. See below)
 
 Contributions welcome :)
 
-# BPCells 0.2.1 (main branch - in progress)
+# BPCells 0.3.0 (12/21/2024)
+
+The BPCells 0.3.0 release covers 6 months of changes and 45 commits from 5 contributors. Notable improvements
+this release include support for peak calling with MACS and the addition of pseudobulk matrix and stats calculations.
+We also released an initial prototype of a BPCells Python library (more details [here](https://bnprks.github.io/BPCells/python/index.html)).
+Full details of changes below.
+
+Thanks to @ycli1995, @Yunuuuu, and @douglasgscofield for pull requests that contributed to this release, as well as to users who
+sumitted github issues to help identify and fix bugs. We also added @immanuelazn to the team as a new hire! He is responsible for many
+of the new features this release and will continue to help with maintenance and new development moving forwards. 
 
 ## Features
 - `apply_by_col()` and `apply_by_row()` allow providing custom R functions to compute per row/col summaries.

r/R/atac_utils.R

@@ -625,7 +625,7 @@ call_peaks_macs <- function(fragments, path,
 #' @export
 #' @keywords internal
 call_macs_peaks <- function(...) {
-  lifecycle::deprecate_warn("0.2.0", "call_macs_peaks()", "call_peaks_macs()")
+  lifecycle::deprecate_warn("0.3.0", "call_macs_peaks()", "call_peaks_macs()")
   return(call_peaks_macs(...))
 }
 

r/R/trackplots.R

@@ -428,7 +428,7 @@ trackplot_coverage <- function(fragments, region, groups,
   assert_is(colors, "character")
   assert_true(length(colors) >= length(unique(groups)))
   if (!is.null(legend_label)) {
-    lifecycle::deprecate_warn("0.2.0", "trackplot_coverage(legend_label)", details="Argument value is no longer used since color legend is not shown.")
+    lifecycle::deprecate_warn("0.3.0", "trackplot_coverage(legend_label)", details="Argument value is no longer used since color legend is not shown.")
   }
 
   groups <- as.factor(groups)
@@ -1033,7 +1033,7 @@ trackplot_bulk <- function(fragments, region, groups,
                            legend_label = "group",
                            zero_based_coords = !is(region, "GRanges"),
                            return_data = FALSE, return_plot_list = FALSE, apply_styling = TRUE) {
-  lifecycle::deprecate_warn("0.2.0", "trackplot_bulk()", "trackplot_combine()")
+  lifecycle::deprecate_warn("0.2.0", "trackplot_bulk()", "trackplot_coverage()")
 
   assert_is(fragments, "IterableFragments")
   assert_not_null(cellNames(fragments))