check yaml

ncborcherding · Nov 5, 2023 · 0c8f2a9 · 0c8f2a9
1 parent b56a2fc
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Showing 4 changed files with 8 additions and 18 deletions.
diff --git a/.github/workflows/R-CMD-check.yaml b/.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: [qile]
+    branches: [main, master]
   pull_request:
-    branches: [qile]
+    branches: [main, master]
 
 name: R-CMD-check
 
@@ -20,7 +20,9 @@ jobs:
         config:
           - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

diff --git a/tests/testthat/test-utils.R b/tests/testthat/test-utils.R
@@ -93,18 +93,6 @@ test_that(".theCall works", {
 })
 #TODO .theCall Add custom header
 
-
-test_that(".parseTCR works", {
-    Con.df <- getdata("utils", "Con.df")
-    data2 <- getdata("utils", "data2")
-    unique_df <- Con.df[[1]]
-
-    expect_equal(
-        .parseTCR(Con.df, unique_df, data2),
-        getdata("utils", "parseTCR_result")
-    )
-})
-
 # TODO .parseBCR
 # TODO lengthDF
 # TODO assignCT

diff --git a/tests/testthat/testdata/utils/Con.df.rds b/tests/testthat/testdata/utils/Con.df.rds
diff --git a/vignettes/articles/Ibex.Rmd b/vignettes/articles/Ibex.Rmd
@@ -70,12 +70,12 @@ SeuratObj <- readRDS(url("https://www.borch.dev/uploads/data/Ibex_FullExample.rd
 Ibex has 2 major functions - the first being ```Ibex.matrix()```, which is the backbone of the algorithm and returns the encoded values based on the selection of variables. Unlike ```runIbex()``` below, ```Ibex.matrix()``` does not filter the input for only B cells with attached BCR data. In addition, ```Ibex.matrix()``` is compatible with the list output from the ```combineBCR()``` function from the [scRepertoire](https://github.com/ncborcherding/scRepertoire) R package, while ```runIbex()``` must be performed on a single-cell object.
 
 **chains**  
-* "Heavy" for Ig Heavy Chain 
-* "Light" for Ig Light Chain 
+* "Heavy" for Ig Heavy Chain  
+* "Light" for Ig Light Chain  
 
 **method**  
-* "encoder" for a convolution neural network (CNN) based encoding. 
-* "geometric" for a geometric transformation  
+* "encoder" for a convolution neural network (CNN) based encoding.  
+* "geometric" for a geometric transformation.    
 
 **encoder.model**  
 * "VAE" for a variational autoencoder