refactor: prints outputs path to stderr instead of stdout#732
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claymcleod wants to merge 6 commits intomainfrom
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refactor: prints outputs path to stderr instead of stdout#732claymcleod wants to merge 6 commits intomainfrom
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PR #701 added a `println!` that prints the outputs file path after printing the JSON outputs. This breaks any tool that captures stdout as machine-readable JSON (e.g., spectool with --redirect-stdout). This moves the message to `eprintln!` so stdout stays clean JSON, reverts the stdout timestamp normalization workaround from #725, and adds a WDL 1.3 spec compliance CI workflow so we can catch issues like this on our side going forward.
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Uses Sprocket's `--index-on` flag with spectool's new `--output-file` flag instead of `--redirect-stdout`, which is fragile when non-JSON content appears on stdout.
peterhuene
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Mar 18, 2026
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PR #701 added a
println!that prints the outputs file path after printing the JSON outputs. This breaks any tool that captures stdout as machine-readable JSON—spectool with--redirect-stdoutbeing the immediate case, where every passing test started failing with "trailing characters" parse errors in the openwdl/wdl CI.The fix is straightforward: change
println!toeprintln!so the informational message goes to stderr while stdout stays clean JSON. This also reverts the stdout timestamp normalization workaround added in #725, which was papering over the same issue from the test harness side.Additionally, this adds a spec compliance CI workflow that runs spectool against the WDL 1.3 spec using the current branch's build of Sprocket, so we can catch issues like this on our side going forward.
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nextbranch in the sprocket.bio repository (when appropriate).