Update lifecycle badges (#238)

Part of insightsengineering/coredev-tasks#649

Removed `experimental` badges introduced 4 years ago.
Removed `stable` badges.
Removed lifecycle package at all.

---------

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

Author: m7pr

.pre-commit-config.yaml

@@ -32,7 +32,6 @@ repos:
           - httr
           - bioc::IRanges
           - knitr
-          - lifecycle
           - bioc::limma
           - magrittr
           - matrixStats
@@ -103,7 +102,6 @@ repos:
           - httr
           - bioc::IRanges
           - knitr
-          - lifecycle
           - bioc::limma
           - magrittr
           - matrixStats

DESCRIPTION

@@ -55,7 +55,6 @@ Imports:
     ggplot2,
     ggrepel (>= 0.9),
     IRanges,
-    lifecycle,
     limma,
     magrittr,
     matrixStats (>= 1.5.0),
@@ -83,7 +82,6 @@ Suggests:
 VignetteBuilder:
     knitr
 RdMacros:
-    lifecycle,
     Rdpack
 biocViews: RNASeq, DifferentialExpression, Normalization, Preprocessing,
     QualityControl

NAMESPACE

@@ -133,7 +133,6 @@ importFrom(circlize,add_transparency)
 importFrom(dplyr,mutate)
 importFrom(forcats,as_factor)
 importFrom(ggrepel,geom_label_repel)
-importFrom(lifecycle,deprecate_soft)
 importFrom(magrittr,"%>%")
 importFrom(purrr,accumulate)
 importFrom(rlang,.data)

R/GeneSpec-class.R

@@ -39,7 +39,7 @@ h_unique_labels <- function(ids, nms = NULL) {
 
 #' R6 Class Representing a Gene (Signature) Specification
 #'
-#' @description `r lifecycle::badge("experimental")`
+#' @description
 #'
 #' A `GeneSpec` consists of the gene IDs (possibly named with labels),
 #' the summary function and the name of the summary function.
@@ -182,7 +182,7 @@ GeneSpec <- R6::R6Class(
 
 #' `GeneSpec` Constructor
 #'
-#' @description `r lifecycle::badge("experimental")`
+#' @description
 #'
 #' Creates a new [`GeneSpec`] object.
 #'

R/HermesData-class.R

@@ -5,7 +5,7 @@ NULL
 
 #' `HermesData` and `RangedHermesData`
 #'
-#' @description `r lifecycle::badge("experimental")`
+#' @description
 #'
 #' The [`HermesData`] class is an extension of [`SummarizedExperiment::SummarizedExperiment`]
 #' with additional validation criteria.

R/HermesData-methods.R

@@ -2,7 +2,7 @@
 
 #' Row Binding of `AnyHermesData` Objects
 #'
-#' @description `r lifecycle::badge("stable")`
+#' @description
 #'
 #' This method combines [`AnyHermesData`] objects with the same samples but different
 #' features of interest (rows in assays).
@@ -36,7 +36,7 @@ NULL
 
 #' Column Binding of `AnyHermesData` Objects
 #'
-#' @description `r lifecycle::badge("stable")`
+#' @description
 #'
 #' This method combines [`AnyHermesData`] objects with the same ranges but different
 #' samples (columns in assays).
@@ -69,7 +69,7 @@ NULL
 
 #' Metadata Accessor and Setter
 #'
-#' @description `r lifecycle::badge("stable")`
+#' @description
 #'
 #' These methods access or set the metadata in a [`AnyHermesData`] object.
 #'
@@ -97,7 +97,7 @@ NULL
 
 #' Annotation Accessor and Setter
 #'
-#' @description `r lifecycle::badge("stable")`
+#' @description
 #'
 #' These methods access and set the gene annotations stored in a [`AnyHermesData`] object.
 #'
@@ -179,7 +179,7 @@ setReplaceMethod(
 
 #' Counts Accessor and Setter
 #'
-#' @description `r lifecycle::badge("stable")`
+#' @description
 #'
 #' These methods access and set the counts assay in a [`AnyHermesData`] object.
 #'
@@ -235,7 +235,7 @@ setReplaceMethod(
 
 #' Prefix Accessor
 #'
-#' @description `r lifecycle::badge("experimental")`
+#' @description
 #'
 #' Generic function to access the prefix from an object.
 #'
@@ -256,7 +256,7 @@ setGeneric("prefix", def = function(object, ...) {
 
 #' Gene IDs Accessor
 #'
-#' @description `r lifecycle::badge("stable")`
+#' @description
 #'
 #' Access the gene IDs, i.e. row names, of a [`AnyHermesData`] object with a
 #' nicely named accessor method.
@@ -287,7 +287,7 @@ setMethod(
 
 #' Sample IDs Accessor
 #'
-#' @description `r lifecycle::badge("stable")`
+#' @description
 #'
 #' Access the sample IDs, i.e. col names, of a [`AnyHermesData`] object with a
 #' nicely named accessor method.
@@ -318,7 +318,7 @@ setMethod(
 
 #' Subsetting `AnyHermesData` Objects
 #'
-#' @description `r lifecycle::badge("stable")`
+#' @description
 #'
 #' This method subsets [`AnyHermesData`] objects, based on expressions involving the
 #' `rowData` columns and the `colData` columns.
@@ -354,7 +354,7 @@ NULL
 
 #' Filter `AnyHermesData` on Subset Passing Default QC Flags
 #'
-#' @description `r lifecycle::badge("stable")`
+#' @description
 #'
 #' This filters a [`AnyHermesData`] object using the default QC flags and required annotations.
 #'
@@ -367,7 +367,7 @@ setGeneric("filter", function(object, ...) standardGeneric("filter"))
 
 #' Predicate for Required Annotations
 #'
-#' @description `r lifecycle::badge("experimental")`
+#' @description
 #'
 #' This helper function determines for each gene in the object whether all required
 #' annotation columns are filled.
@@ -469,7 +469,7 @@ setMethod(
 
 #' Extra Variable Names Accessor Methods
 #'
-#' @description `r lifecycle::badge("experimental")`
+#' @description
 #'
 #' The methods access the names of the variables in `colData()` and `rowData()` of
 #' the object which are not required by design. So these can be additional sample or
@@ -562,7 +562,7 @@ h_map_pos <- function(names, map) {
 
 #' Renaming Contents of `SummarizedExperiment` Objects
 #'
-#' @description `r lifecycle::badge("experimental")`
+#' @description
 #'
 #' This method renames columns of the `rowData` and `colData`, as well as assays, of
 #' [`SummarizedExperiment::SummarizedExperiment`] objects. This increases the flexibility
@@ -631,7 +631,7 @@ setMethod(
 
 #' Summary Method for `AnyHermesData` Objects
 #'
-#' @description `r lifecycle::badge("experimental")`
+#' @description
 #'
 #' Provides a concise summary of the content of [`AnyHermesData`] objects.
 #'
@@ -797,7 +797,7 @@ setMethod(
 
 #' Show Method for `AnyHermesData` Objects
 #'
-#' @description `r lifecycle::badge("experimental")`
+#' @description
 #'
 #' A show method that displays high-level information of [`AnyHermesData`] objects.
 #'
@@ -834,7 +834,7 @@ setMethod(
 
 #' Generic Function for Correlation Calculations
 #'
-#' @description `r lifecycle::badge("experimental")`
+#' @description
 #'
 #' New generic function to calculate correlations for one or two objects.
 #'
@@ -861,7 +861,7 @@ setGeneric("autoplot")
 
 #' `lapply` method for `MultiAssayExperiment`
 #'
-#' @description `r lifecycle::badge("experimental")`
+#' @description
 #'
 #' Apply a function on all experiments in an MAE.
 #'
@@ -912,7 +912,7 @@ setMethod(
 
 #' Checking for Empty `SummarizedExperiment`
 #'
-#' @description `r lifecycle::badge("experimental")`
+#' @description
 #'
 #' This method checks whether a [`SummarizedExperiment::SummarizedExperiment`] object is empty.
 #'

R/assertthat.R

@@ -1,6 +1,6 @@
 #' Additional Assertions for `assert_that`
 #'
-#' @description `r lifecycle::badge("experimental")`
+#' @description
 #'
 #' We provide additional assertion functions which can be used together with
 #' [assertthat::assert_that()].

R/calc_cor.R

@@ -5,7 +5,7 @@ NULL
 
 #' Correlation between Sample Counts of `AnyHermesData`
 #'
-#' @description `r lifecycle::badge("experimental")`
+#' @description
 #'
 #' The `correlate()` method can calculate the correlation matrix between the sample vectors of
 #' counts from a specified assay. This produces a [`HermesDataCor`] object, which is an extension

R/checkmate.R

@@ -1,6 +1,6 @@
 #' Additional Assertions for `checkmate`
 #'
-#' @description `r lifecycle::badge("experimental")`
+#' @description
 #'
 #' We provide additional assertion functions which can be used together with
 #' the `checkmate` functions. These are described in individual help pages
@@ -23,7 +23,7 @@ NULL
 
 #' Check for proportion
 #'
-#' @description `r lifecycle::badge("experimental")`
+#' @description
 #'
 #' Check whether `x` is a (single) proportion.
 #'

R/connections.R

@@ -1,6 +1,6 @@
 #' Connection to `BioMart`
 #'
-#' @description `r lifecycle::badge("experimental")`
+#' @description
 #'
 #' `connect_biomart()` creates a connection object of class [`ConnectionBiomart`] which contains
 #' the `biomaRt` object of class [`biomaRt::Mart`][biomaRt::Mart-class] and the prefix of the object
@@ -58,7 +58,7 @@ connect_biomart <- function(prefix = c("ENSG", "GeneID"),
 
 #' Get Annotations from `BioMart`
 #'
-#' @description `r lifecycle::badge("experimental")`
+#' @description
 #'
 #' Helper function to query annotations from `biomaRt`, for cleaned up gene IDs of
 #' a specific ID variable and given [`biomaRt::Mart`][biomaRt::Mart-class].
@@ -126,7 +126,7 @@ h_get_annotation_biomart <- function(gene_ids,
 
 #' Query Gene Annotations from a Connection
 #'
-#' @description `r lifecycle::badge("experimental")`
+#' @description
 #'
 #' The generic function `query()` is the interface for querying gene annotations from
 #' a data base connection.
@@ -164,7 +164,7 @@ setGeneric(
 
 #' Stripping Prefix from Gene IDs
 #'
-#' @description `r lifecycle::badge("experimental")`
+#' @description
 #'
 #' This helper function removes the prefix and possible delimiter from
 #' a vector of gene IDs, such that only the digits are returned.
@@ -191,7 +191,7 @@ h_strip_prefix <- function(gene_ids, prefix) {
 
 #' Total Length of All Exons for Genes
 #'
-#' @description `r lifecycle::badge("experimental")`
+#' @description
 #'
 #' This helper function queries `BioMart` for lengths of genes by adding up all
 #' exon lengths after reducing overlaps.
@@ -257,7 +257,7 @@ h_get_size_biomart <- function(gene_ids,
 
 #' Translation of `Ensembl` to `Entrez` Gene IDs
 #'
-#' @description `r lifecycle::badge("experimental")`
+#' @description
 #'
 #' This helper function queries `BioMart` to translate `Ensembl` to `Entrez` Gene IDs.
 #'
@@ -289,7 +289,7 @@ h_ensembl_to_entrez_ids <- function(gene_ids,
 
 #' Conversion of `BioMart` Coordinates into `GRanges`
 #'
-#' @description `r lifecycle::badge("experimental")`
+#' @description
 #'
 #' This function extracts the chromosome number, the start position and the end position of transcripts
 #' in given `data.frame` with coordinates as returned by `biomaRt::getBM()` and converts