fix: print secs as numeric in jsonl benchmark format#3814
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johanneskoester merged 1 commit intosnakemake:mainfrom Oct 29, 2025
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fix: print secs as numeric in jsonl benchmark format#3814johanneskoester merged 1 commit intosnakemake:mainfrom
johanneskoester merged 1 commit intosnakemake:mainfrom
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📝 WalkthroughWalkthroughBenchmarkRecord.get_benchmarks now returns running_time as a numeric float rounded to 4 decimal places instead of a pre-formatted string, altering how the first benchmark field is represented in TSV and JSON output formats. Changes
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johanneskoester
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🤖 I have created a release *beep* *boop* --- ## [9.13.5](v9.13.4...v9.13.5) (2025-11-04) ### Bug Fixes * cache wrapper files and wait for them in case of shared filesystem for sources ([#3809](#3809)) ([498fff7](498fff7)) * correctly handle meta-wrapper tag replacement depending on the used snakemake-wrapper release ([#3826](#3826)) ([8d46a4a](8d46a4a)) * ensure that flags are properly considered for input files before applying path modifiers (i.e. default storage providers) ([#3813](#3813)) ([d3bfe32](d3bfe32)) * ensure that tokens are not leaked when paths or uris of source files are logged ([#3821](#3821)) ([a217e50](a217e50)) * print secs as numeric in jsonl benchmark format ([#3814](#3814)) ([395a5e6](395a5e6)) * revert breaking change in 9.11.9 disallowing empty input files even when unused ([#3810](#3810)) ([83c05cc](83c05cc)) * shorten report ids (thus dir names) in order to avoid issues with path length on windows ([#3822](#3822)) ([b24d971](b24d971)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please).
kjohnsen
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<!--Add a description of your PR here-->
Currently, benchmarks in `jsonl` format have the `s` field as a string:
```
{
"cpu_time": 0.0,
"cpu_usage": 0.0,
"h:m:s": "0:00:10",
"input_size_mb": {
"a.in": 5.834963798522949
},
"io_in": 0.0,
"io_out": 0.0,
"jobid": 0,
"max_pss": 0.6533203125,
"max_rss": 3.7109375,
"max_uss": 0.46875,
"max_vms": 19.86328125,
"mean_load": 0.0,
"params": {},
"resources": {
"_cores": 1,
"_nodes": 1,
"tmpdir": "/tmp"
},
"rule_name": "all",
"s": "10.0083",
"threads": 1,
"wildcards": {}
}
```
This PR fixes this by keeping it as a float.
### QC
<!-- Make sure that you can tick the boxes below. -->
* [x] The PR contains a test case for the changes or the changes are
already covered by an existing test case.
* [x] The documentation (`docs/`) is updated to reflect the changes or
this is not necessary (e.g. if the change does neither modify the
language nor the behavior or functionalities of Snakemake).
<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit
* **Bug Fixes**
* Corrected benchmark export formats: Running time values in TSV output
now display with updated precision, and JSON exports render running
times as numeric values for proper data type handling.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->
kjohnsen
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Dec 15, 2025
🤖 I have created a release *beep* *boop* --- ## [9.13.5](snakemake/snakemake@v9.13.4...v9.13.5) (2025-11-04) ### Bug Fixes * cache wrapper files and wait for them in case of shared filesystem for sources ([snakemake#3809](snakemake#3809)) ([498fff7](snakemake@498fff7)) * correctly handle meta-wrapper tag replacement depending on the used snakemake-wrapper release ([snakemake#3826](snakemake#3826)) ([8d46a4a](snakemake@8d46a4a)) * ensure that flags are properly considered for input files before applying path modifiers (i.e. default storage providers) ([snakemake#3813](snakemake#3813)) ([d3bfe32](snakemake@d3bfe32)) * ensure that tokens are not leaked when paths or uris of source files are logged ([snakemake#3821](snakemake#3821)) ([a217e50](snakemake@a217e50)) * print secs as numeric in jsonl benchmark format ([snakemake#3814](snakemake#3814)) ([395a5e6](snakemake@395a5e6)) * revert breaking change in 9.11.9 disallowing empty input files even when unused ([snakemake#3810](snakemake#3810)) ([83c05cc](snakemake@83c05cc)) * shorten report ids (thus dir names) in order to avoid issues with path length on windows ([snakemake#3822](snakemake#3822)) ([b24d971](snakemake@b24d971)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please).
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Currently, benchmarks in
jsonlformat have thesfield as a string:This PR fixes this by keeping it as a float.
QC
docs/) is updated to reflect the changes or this is not necessary (e.g. if the change does neither modify the language nor the behavior or functionalities of Snakemake).Summary by CodeRabbit