fix expanded sequence check and Partial Sync with Bioc version

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: Ibex
 Title: Methods for BCR single-cell embedding 
-Version: 1.1.1
+Version: 1.3.2
 Authors@R: c(
     person(given = "Nick", family = "Borcherding", role = c("aut", "cre", "cph"), email = "ncborch@gmail.com"),
 	person(given = "Qile", family = "Yang", role = "ctb", email = "qile.yang@berkeley.edu", comment = c(ORCID = "0009-0005-0148-2499")))

NEWS.md

@@ -1,25 +1,19 @@
 # Ibex - Change Log
 
+## v1.3.2
+
+* Fixed inverted boolean condition check for `.EXP` models in `Ibex_matrix`
+
+## v1.3.1
+
+* Realign versioning again with Bioconductor release
+
 ## v1.1.1
 * Aligned version with Bioconductor release
 * Switched default branch to `devel` for Bioconductor compatibility
 * Updated CI workflows to target `devel` branch
 * Converted NEWS to NEWS.md format
 * Added automated GitHub Release workflow via tags
-
-## v1.0.0
-* Integration of Ibex with immApex
-* Updated Seurat object to v5
-* Updated support for SCE format for `runIbex()`
-* Update `CoNGAfy()` to function with all versions of Seurat
-* Updated `quietBCRgenes()` to use VariableFeatures() call for SeuratV5 and backward compatibility
-* Added `getHumanIgPseudoGenes()` to return a list of human Immunoglobulin Pseudo genes
-* Added new light and heavy chain models with encoding methods: OHE, atchleyFactors, crucianiProperties, kideraFactors, MSWHIM, tScales, zScales
-* Trained convolutional and variational autoencoders (architecture: 512-256-128-256-512)
-* Implementing GitHub action workflows
-* Adding testthat framework
-* Deprecated clonalCommunity
-* Added geometric encoding using the BLOSUM62 matrix
 * `Ibex_matrix()` now accepts character vectors of amino acid sequences directly
 * Removed rlang from Imports, added lifecycle
 * As per `basilisk` documentation:

R/Ibex_matrix.R

@@ -102,9 +102,9 @@ Ibex_matrix <- function(input.data,
   # Determine dictionary for sequence encoding
   if (expanded.sequences) {
     #Quick Check to see if there are - corresponding to CDR1-CDR2-CDR3
-    if (all(grepl("-", BCR[,"cdr3_aa"]))) {
+    if (!all(grepl("-", BCR[,"cdr3_aa"]))) {
       stop("Expanded sequences are not properly formated, please use 
-           combineExpandedBCR().")
+           combineExpandedBCR() or ensure each element is CDRs 1, 2, and 3 joined by `-`")
     }
     BCR[,"cdr3_aa"] <- gsub("-", "_", BCR[,"cdr3_aa"])
     dictionary <- c(amino.acids, "_")