Log restructure - #31
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Move logging handlers to the package logger so verbosity is enforced per handler: the console follows -v/-d (default now INFO) while a new run.log always records DEBUG, both with timestamps. A new --log_dir argument (default: the output VCF with .vcf.gz replaced by _logs) holds run.log, a command.txt invocation record, and a task_logs/ directory for upcoming per-process tool logs. Runs now finish with a status/elapsed-time message, emitted from a finally so it also lands on failure paths. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Job now requires a keyword-only task_name grouping jobs by pipeline
stage, and assigns each job a job_id ({name}-{n}) from per-name
counters that reset once per CLI invocation, so ids stay unique across
multi-DAG runs. Jobs report themselves by job_id in scheduler and
error messages. These fields feed the upcoming per-process task logs;
neither is part of job identity, which stays keyed on the shell
pipeline alone.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Each job gets a JobLogSink on its execution Context, so every process
it spawns -- including process substitutions, which previously
bypassed stderr redirection entirely -- writes stderr to its own
task_logs/{task}/{job_id}.{stage}.log file, beginning with a header
recording the task, job, and command. Stdout is captured alongside
(headerless, sharing the process's stage index when it would
otherwise reach the terminal. Both streams of one process share a
stage index, allocated in spawn order.
On failure, the run log now reports the failing sub-command with its
exit code, pid, log path, and the last 20 lines of its log, plus a
pointer to the task-log directory; interrupted and launch-failed jobs
list their logs. Successful jobs prune logs that hold nothing but a
header.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
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