Unstable results for with certain styles

[votti]

Background

I want to enforce consistent styling of a bioconductor package by running styler via github actions - after long long debugging I noticed that for certain files styler using the biocthis::bioc_style transformer transforms files back-and-forth between representations.

I don't know enough to understand if this behaviour is rather an issue with the bioc_style or styler.

Description

I run into the issue that some transforms can be unstable, i.e. running the style command multiple times keeps switching the file between two states:

styler::cache_deactivate()
styler::style_file('varia.R', transformers=biocthis::bioc_style())

With varia.R being one of these two representations that are constantly switched by above command:

get_qc_measurements <- function(
  measurement_name,
  qc_pattern = "(blank)|(QCpool)|(QCmix)|(blank)"
) {
  grepl(qc_pattern, measurement_name)
}

and

get_qc_measurements <- function(
      measurement_name,
      qc_pattern = "(blank)|(QCpool)|(QCmix)|(blank)"
) {
    grepl(qc_pattern, measurement_name)
}

Environment

R: 4.5.2
Packages: biocthis_1.17.4 styler_1.11.0

if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}

BiocManager::install("biocthis")

Thanks so much for this useful package!

Dirty workaround

I found by running styler twice, it is possible to detect oscillating files - added this as a temporary workaround for cicd.

Code here

     - name: Check Bioconductor code style
        run: |
          library(styler)
          library(biocthis)
          
          # Disable caching to ensure consistent behavior
          styler::cache_deactivate()
          
          # Run styling twice to detect oscillations vs genuine issues
          cat("First styling pass...\n")
          styled1 <- styler::style_pkg(
            transformers = biocthis::bioc_style(),
            dry = "off"
          )
          
          cat("Second styling pass...\n")
          styled2 <- styler::style_pkg(
            transformers = biocthis::bioc_style(),
            dry = "off"
          )
          
          # Check for different outcomes between passes
          if (any(styled1$changed) != any(styled2$changed)) {
            cat("❌ Mixed results detected - genuine style issues found!\n")
            cat("First pass changed files:", any(styled1$changed), "\n")
            cat("Second pass changed files:", any(styled2$changed), "\n")
            
            if (any(styled1$changed)) {
              changed_files1 <- names(styled1$changed)[styled1$changed]
              cat("Files changed in first pass:\n")
              cat(paste("  📝", changed_files1), sep = "\n")
            }
            
            if (any(styled2$changed)) {
              changed_files2 <- names(styled2$changed)[styled2$changed]
              cat("Files changed in second pass:\n")
              cat(paste("  📝", changed_files2), sep = "\n")
            }
            
            quit(status = 1)
          } else if (any(styled1$changed) && any(styled2$changed)) {
            cat("⚠️  Styler oscillation detected - this is a known issue\n")
            cat("Files affected by oscillation:\n")
            oscillating_files <- names(styled1$changed)[styled1$changed]
            cat(paste("  🔄", oscillating_files), sep = "\n")
            cat("Accepting current state as valid due to oscillation bug.\n")
          } else if (any(styled1$changed)) {
            cat("❌ Bioconductor style issues found (stable after second pass)\n")
            changed_files <- names(styled1$changed)[styled1$changed]
            cat(paste("  📝", changed_files), sep = "\n")
            cat("\n\n💡 To fix style issues locally, run:\n")
            cat("Rscript scripts/style-bioc.R\n")
            quit(status = 1)
          } else {
            cat("✅ All R code follows Bioconductor style guidelines!\n")
          }

Caching prevents the oscillation locally. I also need to see next with other collaborators if this is viable or if it will switch for them.