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Update swf_configs_rsph() and the slurmworkflow vignette for the current cluster - #72
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The preemptable partition is gone, so default to epimodel and accept the partitions the cluster has now, as a vector or a comma-separated string. Asking for preemptable is now a clear error. Default R to 4.6.1, warn on a partial version like "4.3" (spack cannot resolve it), return max_cores for the listed partitions, and give the restore step 180 minutes as the Template does.
The vignette still described the pre-v3.3.x layout (utils-* scripts, data/intermediate, renv::init() on the HPC, the preemptable partition, save_pattern). Walk through make_em_workflow(), renv.lock.hpc, data/run, the current partitions and array limits instead, and point to the Template chapter READMEs and the wiki for the step-by-step.
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swf_configs_rsph()still defaulted to thepreemptablepartition, which no longer exists, and only acceptedpreemptableorepimodel. It now defaults toepimodel, accepts the current RSPH partitions (singly or as a list), errors clearly onpreemptableor an unknown name, warns on a partial R version like"4.3", and returns amax_coresthat fits the chosen partitions. New tests cover it.The slurmworkflow vignette is rewritten for the current EpiModelHIV-Template layout (
make_em_workflow(),renv.lock.hpcrestored on compute nodes, current partitions, nosacct), and points to the template chapter READMEs and the lab wiki for the step-by-step.Bumps the version to 2.9.3.
Also drops
netsim_hpc()and the other functions removed in 2.8.0 from CLAUDE.md.