Reimplement some overwritten changes from #20

.BBSoptions

@@ -0,0 +1 @@
+UnsupportedPlatforms: win32

.Rbuildignore

@@ -9,3 +9,9 @@
 ^__autograph_generated_filezt06eymn\.py$
 ^\.github$
 ^LICENSE\.md$
+^\.devcontainer
+^\.trigger_build$
+^Dockerfile$
+^dev
+^\.BBSoptions$
+^\.vscode

.devcontainer/devcontainer.json

@@ -0,0 +1,13 @@
+{
+    "name": "Ibex devcontainer",
+    "shutdownAction": "none",
+    "build": {
+        "context": "..",
+        "dockerfile": "../Dockerfile"
+    },
+    "runArgs": [
+        // to use GPUs in container uncomment next line
+        // "--gpus=all",
+        "--name=ibex-devbox"
+    ]
+}

.github/workflows/R-CMD-check.yaml

@@ -2,9 +2,9 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master]
+    branches: [main, devel]
   pull_request:
-    branches: [main, master]
+    branches: [main, devel]
 
 name: R-CMD-check
 

.github/workflows/test-coverage.yaml

@@ -2,9 +2,9 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master]
+    branches: [main, devel]
   pull_request:
-    branches: [main, master]
+    branches: [main, devel]
 
 name: test-coverage
 

.gitignore

@@ -1,3 +1,4 @@
 docs
 .DS_Store
 dev/
+.vscode/

.markdownlint.json

@@ -0,0 +1,7 @@
+{
+    "MD007" : { "indent": 4 },
+    "MD013": false,
+    "MD024": false,
+    "MD025": false,
+    "MD033": false
+}

DESCRIPTION

@@ -1,13 +1,14 @@
 Package: Ibex
 Title: Methods for BCR single-cell embedding 
-Version: 0.99.33
+Version: 1.0.0.9000
 Authors@R: c(
-    person(given = "Nick", family = "Borcherding", role = c("aut", "cre"), email = "ncborch@gmail.com"))
+    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")))
 Description: Implementation of the Ibex algorithm for single-cell embedding based on BCR sequences. The package includes a standalone function to encode BCR sequence information by amino acid properties or sequence order using tensorflow-based autoencoder. In addition, the package interacts with SingleCellExperiment or Seurat data objects. 
 License: MIT + file LICENSE 
 Encoding: UTF-8
 LazyData: false
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 biocViews: Software, ImmunoOncology, SingleCell, Classification, Annotation, Sequencing
 Depends: 
 	R (>= 4.5.0)
@@ -17,7 +18,6 @@ Imports:
 	methods,
 	Matrix, 
 	reticulate (>= 1.43.0),
-	rlang,
 	SeuratObject,
 	scRepertoire,
 	SingleCellExperiment,

DockerFile

@@ -0,0 +1,8 @@
+FROM rocker/verse:4.5.1
+RUN apt-get update && apt-get install -y texlive-fonts-extra
+WORKDIR /Ibex
+COPY . .
+RUN apt install -y libgsl-dev
+RUN Rscript -e "install.packages('Seurat')"
+RUN Rscript -e "remotes::install_deps(dependencies = TRUE)"
+RUN Rscript -e "devtools::test()"

NAMESPACE

@@ -4,7 +4,6 @@ export(CoNGAfy)
 export(Ibex_matrix)
 export(combineExpandedBCR)
 export(runIbex)
-import(basilisk)
 importFrom(Matrix,colSums)
 importFrom(Matrix,sparse.model.matrix)
 importFrom(SeuratObject,CreateAssayObject)
@@ -30,7 +29,6 @@ importFrom(immApex,onehotEncoder)
 importFrom(immApex,propertyEncoder)
 importFrom(methods,is)
 importFrom(methods,slot)
-importFrom(rlang,"%||%")
 importFrom(scRepertoire,combineBCR)
 importFrom(stats,as.formula)
 importFrom(stats,dist)