fixes for job submissions

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

@@ -40,10 +40,17 @@ jobs:
           use-public-rspm: true
 
       - uses: r-lib/actions/setup-r-dependencies@v2
+        if: matrix.config.r == 'release'
         with:
           extra-packages: any::rcmdcheck
           needs: check
 
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        if: matrix.config.r != 'release'
+        with:
+          extra-packages: any::rcmdcheck, cran/ggrepel@0.9.6
+          needs: check
+
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: CyteTypeR
 Title: CyteType for R
-Version: 0.3.1
+Version: 0.3.2
 Description: CyteTypeR is the R version of CyteType python package.
 Authors@R: 
     person("Nygen Analytics AB", , ,"contact@nygen.io", role = c("aut", "cre"))

R/artifacts.R

@@ -81,8 +81,8 @@
   on.exit(rhdf5::H5Fclose(fid), add = TRUE)
 
   rhdf5::h5createGroup(fid, "vars")
-  rhdf5::h5writeAttribute(as.integer(n_obs), h5obj = out_file, name = "n_obs", h5loc = "vars")
-  rhdf5::h5writeAttribute(as.integer(n_vars), h5obj = out_file, name = "n_vars", h5loc = "vars")
+  rhdf5::h5writeAttribute(as.integer(n_obs), h5obj = out_file, name = "n_obs", h5loc = "vars", asScalar = TRUE)
+  rhdf5::h5writeAttribute(as.integer(n_vars), h5obj = out_file, name = "n_vars", h5loc = "vars", asScalar = TRUE)
 
   # Create extensible datasets (equivalent to maxshape=(None,) in h5py)
   max_nnz <- n_obs * n_vars  # upper bound

R/schema.R

@@ -108,6 +108,14 @@ LLMModelConfig <- function(provider,
   mask_job_details <- if (is.null(nm)) rep(TRUE, length(query_list$input_data)) else !endsWith(nm, "jobDetails")
   query_list$input_data <- query_list$input_data[mask_job_details]
 
+  # Ensure fields the server expects as JSON objects serialize to {} not []
+  dict_fields <- c("clusterMetadata", "clusterLabels", "infoTags", "expressionData")
+  for (field in dict_fields) {
+    val <- query_list$input_data[[field]]
+    if (is.list(val) && length(val) == 0 && is.null(names(val))) {
+      query_list$input_data[[field]] <- setNames(list(), character(0))
+    }
+  }
 
   return(query_list)
 }