Log DIAMOND version before prefilter and assert it is emitted in test

[wwood]

Motivation

• Record the DIAMOND executable version immediately before running the DIAMOND blastx prefilter so the version is visible in logs for debugging and reproducibility.
• Add a test assertion to ensure the version log is actually emitted to stderr during the prefilter flow.

Description

• Call extern.run("diamond --version") and logging.info("DIAMOND version: %s", diamond_version) in singlem/pipe.py immediately before the DIAMOND prefilter blastx invocation.
• Modify test/test_pipe.py::test_fast_protein_package_prefilter to run the pipe command with subprocess.run(..., capture_output=True) and assert that the stderr contains the "DIAMOND version:" message while preserving the existing stdout OTU table assertion.

Testing

• Ran the full test suite with pixi run -e dev pytest test to exercise the change and capture CI-style results.
• Test summary: 224 passed, 1 failed, 20 skipped, 1 warning; the failing test is test/test_pipe.py::Tests::test_genome_input_dereplication which exhibited an assertion mismatch (unrelated to the added logging).
• The new stderr assertion for the prefilter test executed and the DIAMOND version log was checked during the run.

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Codex Task

[chatgpt-codex-connector]

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[chatgpt-codex-connector]

Guard DIAMOND version check to preserve SRA cleanup

If diamond --version fails (e.g., DIAMOND missing or misconfigured) and input_sra_files was used, the exception now happens before the existing try/except block that logs the DIAMOND failure and calls finish_sra_extraction_processes. That means the kingfisher extraction processes started above can be left running or blocked on their FIFOs with no cleanup, which didn’t occur before this change. This only shows up when SRA input is active and the version check errors, but in that case it can leak subprocesses and leave temp resources behind.

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