submitr

Job scaffolding

• htc_gen_submit() -- generate an HTCondor .sub submit file from project parameters. Supports single-job and multiple-job modes. Multiple mode reads a manifest from toolero::write_by_group(manifest = TRUE), extracts filenames, writes subdatasets.csv, and emits queue file from subdatasets.csv. Resource presets (small, medium, large, custom) are loaded at runtime from inst/extdata/htc-resources.yaml; a local ./htc-resources.yaml takes precedence over the package default. GPU support via gpu = TRUE and gpu_options. comments = TRUE annotates each section of the generated file with explanatory text.
• htc_gen_executable() -- generate the .sh executable script that HTCondor runs inside the container. Produces a four-element script: shebang, mkdir, Rscript, and tar. In multiple-job mode, passes ${1} as a positional argument to the R script. r_script must be supplied explicitly -- there is no default. set_executable = TRUE (default) sets executable permissions via Sys.chmod().

File transfer and job control

• htc_upload() -- copy files to the CHTC submit node via scp. Accepts single files, vectors of files, directories (transferred recursively), and glob patterns. remote_path defaults to "~/". dry_run = TRUE previews the command without executing it.
• htc_submit() -- run condor_submit on the remote submit node via SSH from the remote directory where files were uploaded. Returns the cluster ID invisibly for use with htc_status(). Supports dry_run = TRUE.
• htc_status() -- check job progress via condor_q. Optionally filters by cluster ID. watch = TRUE polls at interval seconds (default 60) until the cluster ID leaves the queue. Returns condor_q output invisibly as a character vector. Supports dry_run = TRUE.
• htc_download() -- copy result files back from the submit node via scp. Supports single filenames, vectors of filenames, and glob patterns ("*.tar.gz", "job.*"). Glob patterns are single-quoted to prevent local shell expansion. local_path defaults to ".". Supports dry_run = TRUE.

Package infrastructure

• inst/extdata/htc-resources.yaml ships with the package and provides default resource presets for htc_gen_submit().
• inst/extdata/hello-world.sub and inst/extdata/hello-world.sh included as test files for end-to-end workflow verification.
• inst/extdata/sample.R included as a sample R script for use in examples.

Testing

The test suite uses a three-layer strategy to handle the fact that end-to-end

testing requires a live HTCondor environment and SSH access. Layer 1 covers

argument validation. Layer 2 covers command construction using dry_run = TRUE

and mocked bindings. Layer 3 integration tests are opt-in via

Sys.setenv(CHTC_USERNAME = "your.netid") and never run on CRAN or CI.

153 tests passing across seven test files.