Merge pull request #2 from ncborcherding/main

rebase dev

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: immApex
 Title: Tools for Adaptive Immune Receptor Sequence-Based Keras Modeling
-Version: 0.99.1
-Date: 2024-10-11
+Version: 0.99.4
+Date: 2024-10-17
 Authors@R: c(
     person(given = "Nick", family = "Borcherding", role = c("aut", "cre"), email = "[email protected]"))
 Description: A set of tools to build tensorflow/keras-based models in R from amino acid and nucleotide sequences focusing on adaptive immune receptors. The package includes pre-processing of sequences, unifying gene nomenclature usage, encoding sequences, and combining models. This package will serve as the basis of future immune receptor sequence functions/packages/models compatible with the scRepertoire ecosystem.
@@ -30,6 +30,7 @@ Suggests:
 	ggplot2,
 	knitr,
 	markdown,
+	reticulate, 
 	rmarkdown, 
 	scRepertoire,
 	spelling,

NEWS.md

@@ -1,3 +1,14 @@
+# immApex VERSION 0.99.3
+
+## UNDERLYING CHANGES
+* Defining python version 3.10 for keras installation
+
+# immApex VERSION 0.99.2
+
+## UNDERLYING CHANGES
+* Added discrete check and install_keras() to vignette
+
+
 # immApex VERSION 0.99.1
 
 ## UNDERLYING CHANGES

vignettes/immApex.Rmd

@@ -4,7 +4,7 @@ author:
 - name: Nick Borcherding
   email: [email protected]
   affiliation: Washington University in St. Louis, School of Medicine, St. Louis, MO, USA
-date: "October 13, 2024"
+date: "October 17, 2024"
 output:
   BiocStyle::html_document:
     toc_float: true
@@ -19,6 +19,11 @@ vignette: >
 knitr::opts_chunk$set(error=FALSE, message=FALSE, warning=FALSE)
 library(BiocStyle)
 set.seed(42)
+
+if(!keras::is_keras_available()) {
+  reticulate::install_python(version = '3.10')
+  suppressMessages(keras::install_keras(python_version = "3.10"))
+}
 ```
 
 # Introduction
@@ -36,7 +41,7 @@ suppressMessages(library(immApex))
 suppressMessages(library(keras))
 suppressMessages(library(ggplot2))
 suppressMessages(library(viridis))
-suppressMessages(library(dplyr))
+suppressMessages(library(magrittr))
 ```
 
 # Getting and Manipulating Sequences