perf(application): raise run prepare checksum read buffer to 8MB [PYSDK-148]

[omid-aignostics]

🛡️ Implements PYSDK-148 following CC-SOP-01 Change Control, part of our ISO 13485-certified QMS | Ketryx Project

Summary

• application run prepare computed the CRC32C checksum of each source slide in 1 KB chunks, turning a multi-GB WSI into ~millions of tiny reads whose per-read overhead dominates on slow / high-latency storage (USB, network drives) — field-reported as effectively unusable for a ~2000-slide batch on a USB drive at a customer site (Charité).
• Introduces APPLICATION_RUN_METADATA_CHECKSUM_CHUNK_SIZE (8 MB) and uses it in the prepare checksum loop, replacing the hardcoded 1024 bytes. The CRC32C result is byte-identical; 8 MB stays well within the 8 GB RAM floor.
• Local benchmark on real slides: ~42× faster full-file hashing at 8 MB vs 1 KB.

Test plan

• ruff check + ruff format --check pass on the changed file
• cli_pipeline_validation_test.py passes (7 tests)
• CI matrix green (unit + integration + e2e)
• Field validation: run prepare on the large-slide USB batch at Charité completes materially faster

Risk

Low — single-file change, checksum output unchanged, no API / schema / dependency changes.

---

Posted by Claude claude-opus-4-8 via Claude Code, applying skills cc-sop-01 on behalf of Omid Kokabi

[codecov]

❌ 1 Tests Failed:

Tests completed	Failed	Passed	Skipped
982	1	981	15

View the top 1 failed test(s) by shortest run time

tests.aignostics.docker_test::test_core_docker_cli_help_with_love

Stack Traces | 4.03s run time

fixturedef = <FixtureDef argname='docker_services' scope='session' baseid=''>
request = <SubRequest 'docker_services' for <Function test_core_docker_cli_help_with_love>>

    @pytest.hookimpl(wrapper=True)
    def pytest_fixture_setup(fixturedef: FixtureDef, request) -> object | None:
        if (
            fixturedef.argname == "event_loop_policy"
            and fixturedef.func.__module__ != __name__
        ):
            warnings.warn(
                PytestDeprecationWarning(_EVENT_LOOP_POLICY_FIXTURE_DEPRECATION_WARNING),
            )
        asyncio_mode = _get_asyncio_mode(request.config)
        if not _is_asyncio_fixture_function(fixturedef.func):
            if asyncio_mode == Mode.STRICT:
                # Ignore async fixtures without explicit asyncio mark in strict mode
                # This applies to pytest_trio fixtures, for example
                return (yield)
            if not _is_coroutine_or_asyncgen(fixturedef.func):
>               return (yield)
                        ^^^^^

..../test-3-14-3/lib/python3.14.../site-packages/pytest_asyncio/plugin.py:926: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
..../test-3-14-3/lib/python3.14............/site-packages/pytest_docker/plugin.py:238: in docker_services
    with get_docker_services(
../...../_temp/uv-python-dir/cpython-3.14.3-linux-x86_64-gnu/lib/python3.14/contextlib.py:141: in __enter__
    return next(self.gen)
           ^^^^^^^^^^^^^^
..../test-3-14-3/lib/python3.14............/site-packages/pytest_docker/plugin.py:212: in get_docker_services
    docker_compose.execute(command)
..../test-3-14-3/lib/python3.14............/site-packages/pytest_docker/plugin.py:140: in execute
    return execute(command, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

command = 'docker compose -f ".../python-sdk/python-sdk/compose.yaml" -p "pytest6789" up --build -d'
success_codes = (0,), ignore_stderr = False

    def execute(command: str, success_codes: Iterable[int] = (0,), ignore_stderr: bool = False) -> Union[bytes, Any]:
        """Run a shell command."""
        try:
            stderr_pipe = subprocess.DEVNULL if ignore_stderr else subprocess.STDOUT
            output = subprocess.check_output(command, stderr=stderr_pipe, shell=True)
            status = 0
        except subprocess.CalledProcessError as error:
            output = error.output or b""
            status = error.returncode
            command = error.cmd
    
        if status not in success_codes:
>           raise Exception(
                'Command {} returned {}: """{}""".'.format(command, status, output.decode("utf-8"))
            )
E           Exception: Command docker compose -f ".../python-sdk/python-sdk/compose.yaml" -p "pytest6789" up --build -d returned 1: """#1 [internal] load local bake definitions
E           #1 reading from stdin 446B done
E           #1 DONE 0.0s
E           
E           #2 [internal] load build definition from Dockerfile
E           #2 transferring dockerfile: 3.61kB 0.0s done
E           #2 DONE 0.0s
E           
E           #3 [auth] library/python:pull token for registry-1.docker.io
E           #3 DONE 0.0s
E           
E           #4 [internal] load metadata for docker.io/library/python:3.14.3-slim-trixie
E           #4 ERROR: failed to authorize: failed to fetch oauth token: unexpected status from POST request to https://auth.docker.io/token: 500 Internal Server Error
E           
E           #5 [internal] load metadata for ghcr.io/astral-sh/uv:0.11.7
E           #5 CANCELED
E           ------
E            > [internal] load metadata for docker.io/library/python:3.14.3-slim-trixie:
E           ------
E           Dockerfile:2
E           
E           --------------------
E           
E              1 |     # We share the base in the builder and targets
E           
E              2 | >>> FROM python:3.14.3-slim-trixie AS base
E           
E              3 |     
E           
E              4 |     # The base of our builder
E           
E           --------------------
E           
E           failed to solve: python:3.14.3-slim-trixie: failed to resolve source metadata for docker.io/library/python:3.14.3-slim-trixie: failed to authorize: failed to fetch oauth token: unexpected status from POST request to https://auth.docker.io/token: 500 Internal Server Error
E           
E           """.

..../test-3-14-3/lib/python3.14............/site-packages/pytest_docker/plugin.py:37: Exception

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[sonarqubecloud]

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
100.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud