Deprecation warnings + function renaming + issue templates

.github/ISSUE_TEMPLATE/1-bug-report.yml

@@ -0,0 +1,26 @@
+name: "🪲 Bug report"
+description: "Something works incorrectly or throws an error? Let us know."
+labels:
+- bug
+body:
+- type: textarea
+  id: description
+  attributes:
+    label: What happened?
+    description: Describe what you tried to do, and what happened instead.
+  validations:
+    required: true
+- type: textarea
+  id: code
+  attributes:
+    label: Minimal code sample
+    description: Paste your code. Attach minimal data as a file to this ticket if necessary. Provide plots.
+  validations:
+    required: true
+- type: textarea
+  id: info
+  attributes:
+    label: Additional information
+    description: "Any additional information you want to share with us: your R version and OS, how you want the result look like, etc."
+  validations:
+    required: false

.github/ISSUE_TEMPLATE/2-enhancement.yml

@@ -0,0 +1,11 @@
+name: "💡 Enhancement request"
+description: "Propose a new feature or an improvement."
+labels:
+- enhancement
+body:
+- type: textarea
+  id: description
+  attributes:
+    label: Please describe your idea or what you want to achieve
+  validations:
+    required: true

.github/ISSUE_TEMPLATE/3-documentation.yml

@@ -0,0 +1,12 @@
+name: "📚 Tutorial or documentation request"
+description: "Propose a tutorial for a specific use case or new documentation."
+labels:
+- documentation
+body:
+- type: textarea
+  id: description
+  attributes:
+    label: What type of documentation would you like to see on the website?
+    description: Interested in a tutorial? More details on how a specific method works? More examples? Something else entirely?
+  validations:
+    required: true

.github/ISSUE_TEMPLATE/4-question.yml

@@ -0,0 +1,12 @@
+name: "❓ Question"
+description: Ask us anything about immundata - how to use it, how to do something, how it works
+labels:
+- question
+body:
+- type: textarea
+  id: description
+  attributes:
+    label: Your question
+    description: Describe what you want to know. E.g., how to analyse a specific data, how to do X, when a method will be available, etc.
+  validations:
+    required: true

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1 @@
+blank_issues_enabled: false

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: immunarch
 Type: Package
 Title: Multi-Modal Immune Repertoire Analytics for Immunotherapy and Vaccine Design in R
-Version: 0.10.3
+Version: 0.10.3.9002
 Authors@R: c(
     person("Vadim I.", "Nazarov", , "support@immunomind.com", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-3659-2709")),

NAMESPACE

@@ -49,17 +49,15 @@ S3method(vis,step_failure_ignored)
 export(airr_clonality_line)
 export(airr_clonality_prop)
 export(airr_clonality_rank)
+export(airr_desc_chains)
+export(airr_desc_genes)
+export(airr_desc_lengths)
 export(airr_diversity_chao1)
 export(airr_diversity_dxx)
 export(airr_diversity_hill)
 export(airr_diversity_index)
 export(airr_diversity_pielou)
 export(airr_diversity_shannon)
-export(airr_public_intersection)
-export(airr_public_jaccard)
-export(airr_stats_chains)
-export(airr_stats_genes)
-export(airr_stats_lengths)
 export(annotate_clonality_prop)
 export(annotate_clonality_rank)
 export(apply_asymm)
@@ -117,6 +115,8 @@ export(repOverlapAnalysis)
 export(repSample)
 export(repSave)
 export(repSomaticHypermutation)
+export(repsim_intersection)
+export(repsim_jaccard)
 export(select_barcodes)
 export(select_clusters)
 export(seqCluster)

R/v0_align_lineage.R

@@ -75,6 +75,8 @@ repAlignLineage <- function(.data,
                             .prepare_threads = 2,
                             .align_threads = 4,
                             .nofail = FALSE) {
+  lifecycle::deprecate_warn("0.10.3", "repAlignLineage()")
+
   if (!require_system_package(c("clustalw", "clustalw2"), error_message = paste0(
     "repAlignLineage requires Clustal W app to be installed!\n",
     "Please download it from here: http://www.clustal.org/download/current/\n",

R/v0_annotation.R

@@ -54,6 +54,8 @@ if (getRversion() >= "2.15.1") {
 #' db
 #' @export
 dbLoad <- function(.path, .db, .species = NA, .chain = NA, .pathology = NA) {
+  lifecycle::deprecate_warn("0.10.3", "dbLoad()")
+
   .db <- tolower(.db)
   if (!(.db %in% c("vdjdb", "vdjdb-search", "mcpas", "mcpas-tcr", "pird"))) {
     stop('Unknown .db argument. Please provide one of the following: "vdjdb", "vdjdb-search", "mcpas"')
@@ -158,6 +160,8 @@ dbLoad <- function(.path, .db, .species = NA, .chain = NA, .pathology = NA) {
 #' res
 #' @export dbAnnotate
 dbAnnotate <- function(.data, .db, .data.col, .db.col) {
+  lifecycle::deprecate_warn("0.10.3", "dbAnnotate()")
+
   # Check if the number of columns is equal
   if (length(.data.col) != length(.db.col)) {
     stop("Number of columns in .data.col and .db.col doesn't match! Please provide equal number of columns.")

R/v0_clonality.R

@@ -89,6 +89,8 @@ repClonality <- function(.data, .method = c("clonal.prop", "homeo", "top", "rare
                          ),
                          .head = c(10, 100, 1000, 3000, 10000, 30000, 100000),
                          .bound = c(1, 3, 10, 30, 100)) {
+  lifecycle::deprecate_warn("0.10.3", "repClonality()", details = "See `?airr_clonality()` on details for replacement functions.")
+
   .method <- .method[1]
   if (.method == "tail") {
     .method <- "rare"

R/v0_diversity.R

@@ -158,6 +158,8 @@ if (getRversion() >= "2.15.1") {
 repDiversity <- function(.data, .method = "chao1", .col = "aa", .max.q = 6, .min.q = 1, .q = 5, .step = NA,
                          .quantile = c(.025, .975), .extrapolation = NA, .perc = 50,
                          .norm = TRUE, .verbose = TRUE, .do.norm = NA, .laplace = 0) {
+  lifecycle::deprecate_warn("0.10.3", "repDiversity()", details = "See `?airr_diversity()` for details on new functions.")
+
   .method <- .method[1]
 
   if (.method == "rarefaction") {

R/v0_explore.R

@@ -65,6 +65,8 @@
 #' repExplore(immdata$data, .method = "len") %>% vis()
 #' @export repExplore
 repExplore <- function(.data, .method = c("volume", "count", "len", "clones"), .col = c("nt", "aa"), .coding = TRUE) {
+  lifecycle::deprecate_warn("0.10.3", "repExplore()", details = "Run `?airr_desc()` for information on new functions.")
+
   if (!has_class(.data, "list")) {
     .data <- list(Sample = .data)
   }

R/v0_filters.R

@@ -49,6 +49,8 @@
 repFilter <- function(.data, .method = "by.clonotype",
                       .query = list(CDR3.aa = exclude("partial", "out_of_frame")),
                       .match = "exact") {
+  lifecycle::deprecate_warn("0.10.3", "repFilter()", details = "See `?immundata::filter.ImmunData()` for details on replacement functions.")
+
   .validate_immdata(.data)
 
   if (length(names(.query)) == 0) {

R/v0_gene_usage.R

@@ -64,6 +64,8 @@ geneUsage <- function(.data, # df, list, MonetDB
                       .ambig = c("inc", "exc", "maj"),
                       .type = c("segment", "allele", "family"),
                       .norm = FALSE) {
+  lifecycle::deprecate_warn("0.10.3", "geneUsage()", details = "See `?airr_desc()` for details on replacement functions.")
+
   .type <- .type[1]
   .ambig <- .ambig[1]
   .quant <- .quant[1]

R/v0_io.R

@@ -8,7 +8,6 @@ if (getRversion() >= "2.15.1") {
 }
 
 
-
 ##### Main IO functions #####
 
 
@@ -141,6 +140,8 @@ if (getRversion() >= "2.15.1") {
 #' # [1] "data" "meta"
 #' @export repLoad
 repLoad <- function(.path, .mode = "paired", .coding = TRUE, ...) {
+  lifecycle::deprecate_warn("0.10.3", "repLoad()", details = "See `?immundata::read_repertoires()` for details on replacement functions.")
+
   exclude_extensions <- c(
     "so", "exe", "bam", "fasta", "fai", "fastq", "bed", "rds", "report", "vdjca"
   )
@@ -471,6 +472,8 @@ repLoad <- function(.path, .mode = "paired", .coding = TRUE, ...) {
 #' @export repSave
 repSave <- function(.data, .path, .format = c("immunarch", "vdjtools"),
                     .compress = TRUE) {
+  lifecycle::deprecate_warn("0.10.3", "repSave()", details = "Run `?immundata::write_immundata()` for information on new functions.")
+
   .format <- .format[1]
   if (!.format %in% c("immunarch", "vdjtools")) {
     stop("Unknown format. Please provide either 'immunarch' or 'vdjtools'")

R/v0_overlap.R

@@ -113,6 +113,8 @@ repOverlap <- function(.data,
                        .bootstrap = NA,
                        .verbose.inc = NA,
                        .force.matrix = FALSE) {
+  lifecycle::deprecate_warn("0.10.3", "repOverlap()", details = "See `?repsim()` for details on replacement functions.")
+
   .validate_repertoires_data(.data)
 
   .method <- .method[1]