Support compression in read_cmdstan_csv
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- Dominant language
- R
- Stars
- 160
- Forks
- 69
- Avg merge
- 1d 19h
- Merged PRs (30d)
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Description
Cmdstan output files can get pretty large. data.table::fread used in read_cmdstan_csv and read_csv_metadata supports gzip and bzip2 compressed files if the R.utils package is installed.
On the cmdstanr side this would require at least modifying the suffix assertions (assert_file_exists) in both functions. And, switching out grep in favor of zgrep to handle the commented headers with the caveat (at least on linux) that the argument order be switched so that --color=never comes before the regex pattern.
So in read_cmdstan_csv:
fread_cmd <- paste0("zgrep --color=never -v '^#' '", path.expand(output_file), "'")
read_metadata_csv:
fread_cmd <- paste0("zgrep --color=never '^[#a-zA-Z]' '", path.expand(csv_file), "'")
and similarly for the WSL specific code.
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start at the read_cmdstan_csv and read_csv_metadata entry points, including their WSL-specific code, and inspect the existing assert_file_exists and grep command construction. Support gzip and bzip2 paths while preserving commented-header handling, then verify both functions work across the described command variants.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- r
- Domain
- cli, data
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100