Rust

.gitignore

@@ -14,4 +14,5 @@ __dev/
 # Agents
 .claude/
 CLAUDE.md
-AGENTS.md
+AGENTS.md
+SKILL.md

julia/RtemisA3/src/api.jl

@@ -22,12 +22,12 @@ function create_a3(
     variant    !== nothing && (annot["variant"]    = variant)
 
     raw = Dict{String,Any}(
-        "\$schema"   => _A3_SCHEMA_URI,
-        "a3_version" => _A3_VERSION,
-        "sequence"   => sequence,
+        "\$schema"    => _A3_SCHEMA_URI,
+        "a3_version"  => _A3_VERSION,
+        "sequence"    => sequence,
         "annotations" => annot,
+        "metadata"    => metadata !== nothing ? metadata : Dict{String,Any}(),
     )
-    metadata !== nothing && (raw["metadata"] = metadata)
     A3(raw)
 end
 

julia/RtemisA3/src/validate.jl

@@ -236,10 +236,14 @@ function A3(raw::AbstractDict)
     end
     haskey(raw, "sequence") ||
         throw(A3ValidationError("missing required field 'sequence'"))
+    haskey(raw, "annotations") ||
+        throw(A3ValidationError("missing required field 'annotations'"))
+    haskey(raw, "metadata") ||
+        throw(A3ValidationError("missing required field 'metadata'"))
 
     seq         = validate_sequence(raw["sequence"], "sequence")
-    annotations = parse_annotations(get(raw, "annotations", Dict{String,Any}()), "annotations")
-    metadata    = parse_metadata(get(raw, "metadata", Dict{String,Any}()), "metadata")
+    annotations = parse_annotations(raw["annotations"], "annotations")
+    metadata    = parse_metadata(raw["metadata"], "metadata")
 
     validate_bounds(seq, annotations)
     A3(seq, annotations, metadata)

python/rtemis_a3/src/rtemis/a3/api.py

@@ -124,6 +124,12 @@ def a3_from_json(text: str) -> A3:
         raise A3ParseError(
             f"'a3_version' must be '{_A3_VERSION}', got '{version_val}'"
         )
+    if "sequence" not in data:
+        raise A3ParseError("missing required field 'sequence'")
+    if "annotations" not in data:
+        raise A3ParseError("missing required field 'annotations'")
+    if "metadata" not in data:
+        raise A3ParseError("missing required field 'metadata'")
     # Strip envelope keys before passing to the data model
     for key in _ENVELOPE_KEYS:
         data.pop(key, None)

python/rtemis_a3/tests/test_api.py

@@ -56,7 +56,7 @@ def test_bounds_error(self):
 # a3_from_json / a3_to_json
 # ---------------------------------------------------------------------------
 
-MINIMAL_JSON = '{"$schema": "https://schema.rtemis.org/a3/v1/schema.json", "a3_version": "1.0.0", "sequence": "MAEPRQ"}'
+MINIMAL_JSON = '{"$schema": "https://schema.rtemis.org/a3/v1/schema.json", "a3_version": "1.0.0", "sequence": "MAEPRQ", "annotations": {}, "metadata": {}}'
 
 FULL_JSON = """{
   "$schema": "https://schema.rtemis.org/a3/v1/schema.json",
@@ -104,9 +104,21 @@ def test_invalid_json(self):
     def test_valid_json_invalid_a3(self):
         with pytest.raises(A3ValidationError):
             a3_from_json(
-                '{"$schema": "https://schema.rtemis.org/a3/v1/schema.json", "a3_version": "1.0.0", "sequence": "M"}'
+                '{"$schema": "https://schema.rtemis.org/a3/v1/schema.json", "a3_version": "1.0.0", "sequence": "M", "annotations": {}, "metadata": {}}'
             )  # too short
 
+    def test_missing_annotations_field(self):
+        with pytest.raises(A3ParseError, match="annotations"):
+            a3_from_json(
+                '{"$schema": "https://schema.rtemis.org/a3/v1/schema.json", "a3_version": "1.0.0", "sequence": "MAEPRQ", "metadata": {}}'
+            )
+
+    def test_missing_metadata_field(self):
+        with pytest.raises(A3ParseError, match="metadata"):
+            a3_from_json(
+                '{"$schema": "https://schema.rtemis.org/a3/v1/schema.json", "a3_version": "1.0.0", "sequence": "MAEPRQ", "annotations": {}}'
+            )
+
     def test_missing_schema_field(self):
         with pytest.raises(A3ParseError, match=r"\$schema"):
             a3_from_json('{"a3_version": "1.0.0", "sequence": "MAEPRQ"}')

r/.Rbuildignore

@@ -18,6 +18,5 @@
 ^docs$
 ^AGENTS\.md$
 ^CLAUDE\.md$
-^NEWS\.md$
 ^pkgdown$
 ^SKILL\.md$

r/DESCRIPTION

@@ -1,14 +1,16 @@
 Package: rtemis.a3
-Title: Amino Acid Annotation (A3) format
-Version: 0.5.1
-Date: 2026-03-29
-Authors@R: 
-    person(given = "E.D.", family = "Gennatas", role = c("aut", "cre"),
+Title: Amino Acid Annotation (A3) Format
+Version: 0.5.2
+Date: 2026-04-03
+Authors@R:
+    person(given = "E.D.", family = "Gennatas", role = c("aut", "cre", "cph"),
            email = "gennatas@gmail.com",
            comment = c(ORCID = "0000-0001-9280-3609"))
-Description: Defines the annotated amino acid (A3) format using S7 classes. Provides functions to 
-    create A3 objects, read and write A3 JSON files.
-URL: https://rtemis.a3.rtemis.org
+Description: Implements the Amino Acid Annotation (A3) format using 'S7' classes.
+    The A3 format is a structured 'JSON' schema for annotating amino acid sequences
+    with site, region, post-translational modification (PTMs), processing event,
+    and sequence variant annotations. Provides functions to create, read, and write A3 objects.
+URL: https://a3.rtemis.org
 License: GPL (>= 3)
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
@@ -22,8 +24,6 @@ Imports:
     utils
 Suggests:
     biomaRt,
-    colorspace,
-    dplyr,
     httr,
     jsonlite,
     seqinr,

r/NEWS.md

@@ -0,0 +1,17 @@
+# rtemis.a3 0.5.2
+
+## New features
+
+* Initial CRAN release.
+* Defines the Amino Acid Annotation (A3) format using S7 classes.
+* Core classes: `A3`, `A3Sequence`, `A3Annotation`, `A3Metadata`, `A3Site`,
+  `A3Region`, `A3PTM`, `A3Processing`, `A3Variant`.
+* `create_A3()`: create A3 objects with full validation.
+* `annotation_position()`, `annotation_range()`, `annotation_variant()`:
+  helpers to build annotation entries.
+* `write_A3json()` / `read_A3json()`: serialize and deserialize A3 objects to
+  and from JSON files.
+* `concat()`: concatenate a character vector into a single sequence string.
+* Database utilities: `uniprot_to_A3()`, `uniprot_sequence()`,
+  `gene2sequence()`, `get_alphafold()`, `pdb_annotations()`,
+  `clinvar_variants()`.

r/R/0_init.R

@@ -724,16 +724,16 @@ format_caller <- function(call_stack, call_depth, caller_id, max_char = 30L) {
 # \code{current <- as.list(sys.call())[[1]]}
 #'
 #' @param ... Message to print
-#' @param date Logical: if TRUE, include date and time in the prefix
 #' @param caller Character: Name of calling function
 #' @param call_depth Integer: Print the system call path of this depth.
 #' @param caller_id Integer: Which function in the call stack to print
 #' @param newline_pre Logical: If TRUE begin with a new line.
 #' @param newline Logical: If TRUE end with a new line.
 #' @param format_fn Function: Formatting function to use on the message text.
 #' @param sep Character: Use to separate objects in `...`
+#' @param verbosity Integer: Verbosity level.
 #'
-#' @return Invisibly: List with call, message, and date
+#' @return Invisibly: `NULL`
 #'
 #' @author EDG
 #' @noRd
@@ -742,27 +742,28 @@ format_caller <- function(call_stack, call_depth, caller_id, max_char = 30L) {
 #' msg("Hello, world!")
 msg <- function(
   ...,
-  date = TRUE,
   caller = NULL,
   call_depth = 1L,
   caller_id = 1L,
   newline_pre = FALSE,
   newline = TRUE,
   format_fn = plain,
-  sep = " "
+  sep = " ",
+  verbosity = 1L
 ) {
+  if (verbosity == 0L) {
+    return(invisible(NULL))
+  }
   if (is.null(caller)) {
     call_stack <- as.list(sys.calls())
     caller <- format_caller(call_stack, call_depth, caller_id)
-  }
+  } # / get caller
 
   txt <- Filter(Negate(is.null), list(...))
   if (newline_pre) {
     message("")
   }
-  if (date) {
-    msgdatetime()
-  }
+  msgdatetime()
   message(
     format_fn(paste(txt, collapse = sep)),
     appendLF = FALSE
@@ -791,8 +792,12 @@ msg0 <- function(
   newline_pre = FALSE,
   newline = TRUE,
   format_fn = plain,
-  sep = ""
+  sep = "",
+  verbosity = 1L
 ) {
+  if (verbosity == 0L) {
+    return(invisible(NULL))
+  }
   if (is.null(caller)) {
     call_stack <- as.list(sys.calls())
     caller <- format_caller(call_stack, call_depth, caller_id)
@@ -828,13 +833,9 @@ msg0 <- function(
 #' @noRd
 #'
 #' @examples
-#' \dontrun{
-#' {
-#'   msg("Hello")
-#'   pcat("super", "wow")
-#'   pcat(NULL, "oooo")
-#' }
-#' }
+#' msg("Hello")
+#' pcat("super", "potato")
+#' pcat(NULL, "oooo")
 pcat <- function(left, right, pad = 17, newline = TRUE) {
   lpad <- max(0, pad - 1 - max(0, nchar(left)))
   cat(pad_string(left), right)

r/R/a3.R

@@ -955,6 +955,15 @@ A3from_json <- function(x, ...) {
       "Field {.field a3_version} must be {.val {.A3_VERSION}}, got {.val {version_field}}."
     )
   }
+  if (is.null(x[["sequence"]])) {
+    cli::cli_abort("JSON input missing required field {.field sequence}.")
+  }
+  if (is.null(x[["annotations"]])) {
+    cli::cli_abort("JSON input missing required field {.field annotations}.")
+  }
+  if (is.null(x[["metadata"]])) {
+    cli::cli_abort("JSON input missing required field {.field metadata}.")
+  }
 
   sequence <- x[["sequence"]]
   annotations <- x[["annotations"]]

r/R/gene2sequence.R

@@ -14,7 +14,7 @@
 #'
 #' @examples
 #' \dontrun{
-#'   mapt_seqs <- gene2sequence("MAPT")
+#'   mapt_seq <- gene2sequence("MAPT")
 #' }
 gene2sequence <- function(
   gene,
@@ -50,15 +50,14 @@ gene2sequence <- function(
     mart = mart
   )
 
-  if (verbosity > 0) {
-    msg0(
-      "Found ",
-      bold(nrow(transcripts)),
-      " transcripts for gene ",
-      highlight(gene),
-      "."
-    )
-  }
+  msg0(
+    "Found ",
+    bold(nrow(transcripts)),
+    " transcripts for gene ",
+    highlight(gene),
+    ".",
+    verbosity = verbosity
+  )
 
   # Get sequence ----
   # Retrieve sequence(s) using transcript ID

r/R/rtemis_color_system.R

@@ -27,39 +27,10 @@ rt_teal <- rtemis_teal
 rt_purple <- rtemis_purple
 rt_magenta <- rtemis_light_magenta
 highlight_col <- coastside_orange
-
 col_object <- rt_green
 
 
-#' rtemis Color System
-#'
-#' A named list of colors used consistently across all packages
-#' in the rtemis ecosystem.
-#'
-#' Colors are provided as hex strings.
-#'
-#' @format A named list with the following elements:
-#' \describe{
-#'   \item{red}{"kaimana red"}
-#'   \item{blue}{"kaimana light blue"}
-#'   \item{green}{"kaimana medium green"}
-#'   \item{orange}{"coastside orange"}
-#'   \item{teal}{"rtemis teal"}
-#'   \item{purple}{"rtemis purple"}
-#'   \item{magenta}{"rtemis magenta"}
-#'   \item{highlight_col}{"highlight color"}
-#'   \item{object}{"rtemis teal"}
-#'   \item{info}{"lmd burgundy"}
-#'   \item{outer}{"kaimana red"}
-#'   \item{tuner}{"coastside orange"}
-#' }
-#'
-#' @author EDG
-#'
-#' @noRd
-#'
-#' @examples
-#' rtemis_colors[["teal"]]
+# %% rtemis_colors ----
 rtemis_colors <- list(
   red = kaimana_red,
   light_blue = kaimana_light_blue,

r/R/utils_a3.R

@@ -55,20 +55,17 @@ aa_sub <- function(x, substitutions, verbosity = 1L) {
     from <- strngs[1]
     to <- strngs[length(strngs)]
     pos <- as.numeric(strngs[2:(length(strngs) - 1)] |> paste(collapse = ""))
-    if (verbosity > 0) {
-      msg(
-        "Substituting",
-        highlight(from),
-        "at position",
-        highlight(pos),
-        "with",
-        highlight(to)
-      )
-    }
+    msg(
+      "Substituting",
+      highlight(from),
+      "at position",
+      highlight(pos),
+      "with",
+      highlight(to),
+      verbosity = verbosity
+    )
     x[pos] <- to
   }
-  if (verbosity > 0) {
-    msg("All done.")
-  }
+  msg("All done.", verbosity = verbosity)
   x
 }