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⚡ Bolt: Optimize ordered deduplication with dict.fromkeys#4860

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bolt-perf-dict-fromkeys-dedup-7715370720002705802
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⚡ Bolt: Optimize ordered deduplication with dict.fromkeys#4860
SatoryKono wants to merge 3 commits into
mainfrom
bolt-perf-dict-fromkeys-dedup-7715370720002705802

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@SatoryKono
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💡 What: Replaced the pure-Python seen = set() loop with list(dict.fromkeys(values)) in deduplicate_preserving_order.
🎯 Why: Pure-Python loops with seen sets are slower than leveraging Python's fast C-level dictionary implementation which preserves insertion order.
📊 Impact: Faster deduplication of iterables.
🔬 Measurement: Run benchmarks comparing the two implementations or observe reduced overhead in deduplication workflows.


PR created automatically by Jules for task 7715370720002705802 started by @SatoryKono

Co-authored-by: SatoryKono <13055362+SatoryKono@users.noreply.github.com>
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coderabbitai Bot commented May 31, 2026

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@github-actions github-actions Bot added the layer:infrastructure Infrastructure layer label May 31, 2026
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Co-authored-by: SatoryKono <13055362+SatoryKono@users.noreply.github.com>
Co-authored-by: SatoryKono <13055362+SatoryKono@users.noreply.github.com>
@github-actions github-actions Bot added layer:application Application layer layer:composition Composition layer layer:interfaces Interfaces / CLI layer provider:chembl ChEMBL pipeline config Pipeline/filter/schema YAML configs labels Jun 1, 2026
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qodo-code-review Bot commented Jun 1, 2026

CI Feedback 🧐

(Feedback updated until commit d338c2b)

A test triggered by this PR failed. Here is an AI-generated analysis of the failure:

Action: matrix-smoke-blocking

Failed stage: Enforce matrix smoke skip-rate SLO (run3) [❌]

Failed test name: test_pipeline_matrix_smoke

Failure summary:

  • Pytest failed during test setup for all
    tests/e2e/test_pipeline_matrix_e2e.py::test_pipeline_matrix_smoke[...] matrix entries due to an
    ImportError: cannot import name 'control_plane_root' from
    bioetl.composition.runtime_builders._run_manifest_refs (raised when importing
    src/bioetl/composition/runtime_builders/input_snapshot_resolution.py:11).
  • Because all 17 e2e matrix smoke tests errored (passed=0, failed=17), the subsequent CI health check
    script scripts/engineering/ci/check_e2e_matrix_skip_rate.py detected violations (expected total=26,
    observed total=17 and unknown failure labels detected: 17) and exited with code 1, causing the
    GitHub Action to fail.
Relevant error logs:
1:  ##[group]Runner Image Provisioner
2:  Hosted Compute Agent
...

396:  shell: /usr/bin/bash -e {0}
397:  env:
398:  BIOETL_TEST_MODE: true
399:  BIOETL_PIPELINE__HEALTH_CHECK_MODE: probe
400:  pythonLocation: /opt/hostedtoolcache/Python/3.12.13/x64
401:  PKG_CONFIG_PATH: /opt/hostedtoolcache/Python/3.12.13/x64/lib/pkgconfig
402:  Python_ROOT_DIR: /opt/hostedtoolcache/Python/3.12.13/x64
403:  Python2_ROOT_DIR: /opt/hostedtoolcache/Python/3.12.13/x64
404:  Python3_ROOT_DIR: /opt/hostedtoolcache/Python/3.12.13/x64
405:  LD_LIBRARY_PATH: /opt/hostedtoolcache/Python/3.12.13/x64/lib
406:  UV_PYTHON_INSTALL_DIR: /home/runner/work/_temp/uv-python-dir
407:  UV_CACHE_DIR: /home/runner/work/_temp/setup-uv-cache
408:  UV_PYTHON: 3.12
409:  ##[endgroup]
410:  EEEEEEEEEEEEEEEEE                                                        [100%]
411:  ==================================== ERRORS ====================================
412:  ________ ERROR at setup of test_pipeline_matrix_smoke[chembl_activity] _________
413:  .venv/lib/python3.12/site-packages/pytest_asyncio/plugin.py:458: in setup
...

430:  from bioetl.composition.factories.pipeline._factory_method_runtime_support import (
431:  src/bioetl/composition/factories/pipeline/_factory_method_runtime_support.py:16: in <module>
432:  from bioetl.composition.factories.pipeline._factory_method_types import (
433:  src/bioetl/composition/factories/pipeline/_factory_method_types.py:20: in <module>
434:  from bioetl.composition.factories.pipeline.creation_support import (
435:  src/bioetl/composition/factories/pipeline/creation_support.py:10: in <module>
436:  from bioetl.composition.factories.pipeline._creation_wiring import (
437:  src/bioetl/composition/factories/pipeline/_creation_wiring.py:30: in <module>
438:  from bioetl.composition.factories.pipeline.run_context_factory import (
439:  src/bioetl/composition/factories/pipeline/run_context_factory.py:13: in <module>
440:  from bioetl.composition.runtime_builders.run_manifest_support import (
441:  src/bioetl/composition/runtime_builders/run_manifest_support.py:7: in <module>
442:  from bioetl.composition.runtime_builders.input_snapshot_resolution import (
443:  src/bioetl/composition/runtime_builders/input_snapshot_resolution.py:11: in <module>
444:  from bioetl.composition.runtime_builders._run_manifest_refs import control_plane_root
445:  E   ImportError: cannot import name 'control_plane_root' from 'bioetl.composition.runtime_builders._run_manifest_refs' (/home/runner/work/BioactivityDataAcquisition/BioactivityDataAcquisition/src/bioetl/composition/runtime_builders/_run_manifest_refs.py)
446:  __________ ERROR at setup of test_pipeline_matrix_smoke[chembl_assay] __________
447:  .venv/lib/python3.12/site-packages/pytest_asyncio/plugin.py:458: in setup
...

461:  from bioetl.composition.factories.pipeline._factory_method_runtime_support import (
462:  src/bioetl/composition/factories/pipeline/_factory_method_runtime_support.py:16: in <module>
463:  from bioetl.composition.factories.pipeline._factory_method_types import (
464:  src/bioetl/composition/factories/pipeline/_factory_method_types.py:20: in <module>
465:  from bioetl.composition.factories.pipeline.creation_support import (
466:  src/bioetl/composition/factories/pipeline/creation_support.py:10: in <module>
467:  from bioetl.composition.factories.pipeline._creation_wiring import (
468:  src/bioetl/composition/factories/pipeline/_creation_wiring.py:30: in <module>
469:  from bioetl.composition.factories.pipeline.run_context_factory import (
470:  src/bioetl/composition/factories/pipeline/run_context_factory.py:13: in <module>
471:  from bioetl.composition.runtime_builders.run_manifest_support import (
472:  src/bioetl/composition/runtime_builders/run_manifest_support.py:7: in <module>
473:  from bioetl.composition.runtime_builders.input_snapshot_resolution import (
474:  src/bioetl/composition/runtime_builders/input_snapshot_resolution.py:11: in <module>
475:  from bioetl.composition.runtime_builders._run_manifest_refs import control_plane_root
476:  E   ImportError: cannot import name 'control_plane_root' from 'bioetl.composition.runtime_builders._run_manifest_refs' (/home/runner/work/BioactivityDataAcquisition/BioactivityDataAcquisition/src/bioetl/composition/runtime_builders/_run_manifest_refs.py)
477:  ________ ERROR at setup of test_pipeline_matrix_smoke[chembl_cell_line] ________
478:  .venv/lib/python3.12/site-packages/pytest_asyncio/plugin.py:458: in setup
...

492:  from bioetl.composition.factories.pipeline._factory_method_runtime_support import (
493:  src/bioetl/composition/factories/pipeline/_factory_method_runtime_support.py:16: in <module>
494:  from bioetl.composition.factories.pipeline._factory_method_types import (
495:  src/bioetl/composition/factories/pipeline/_factory_method_types.py:20: in <module>
496:  from bioetl.composition.factories.pipeline.creation_support import (
497:  src/bioetl/composition/factories/pipeline/creation_support.py:10: in <module>
498:  from bioetl.composition.factories.pipeline._creation_wiring import (
499:  src/bioetl/composition/factories/pipeline/_creation_wiring.py:30: in <module>
500:  from bioetl.composition.factories.pipeline.run_context_factory import (
501:  src/bioetl/composition/factories/pipeline/run_context_factory.py:13: in <module>
502:  from bioetl.composition.runtime_builders.run_manifest_support import (
503:  src/bioetl/composition/runtime_builders/run_manifest_support.py:7: in <module>
504:  from bioetl.composition.runtime_builders.input_snapshot_resolution import (
505:  src/bioetl/composition/runtime_builders/input_snapshot_resolution.py:11: in <module>
506:  from bioetl.composition.runtime_builders._run_manifest_refs import control_plane_root
507:  E   ImportError: cannot import name 'control_plane_root' from 'bioetl.composition.runtime_builders._run_manifest_refs' (/home/runner/work/BioactivityDataAcquisition/BioactivityDataAcquisition/src/bioetl/composition/runtime_builders/_run_manifest_refs.py)
508:  _____ ERROR at setup of test_pipeline_matrix_smoke[chembl_compound_record] _____
509:  .venv/lib/python3.12/site-packages/pytest_asyncio/plugin.py:458: in setup
...

523:  from bioetl.composition.factories.pipeline._factory_method_runtime_support import (
524:  src/bioetl/composition/factories/pipeline/_factory_method_runtime_support.py:16: in <module>
525:  from bioetl.composition.factories.pipeline._factory_method_types import (
526:  src/bioetl/composition/factories/pipeline/_factory_method_types.py:20: in <module>
527:  from bioetl.composition.factories.pipeline.creation_support import (
528:  src/bioetl/composition/factories/pipeline/creation_support.py:10: in <module>
529:  from bioetl.composition.factories.pipeline._creation_wiring import (
530:  src/bioetl/composition/factories/pipeline/_creation_wiring.py:30: in <module>
531:  from bioetl.composition.factories.pipeline.run_context_factory import (
532:  src/bioetl/composition/factories/pipeline/run_context_factory.py:13: in <module>
533:  from bioetl.composition.runtime_builders.run_manifest_support import (
534:  src/bioetl/composition/runtime_builders/run_manifest_support.py:7: in <module>
535:  from bioetl.composition.runtime_builders.input_snapshot_resolution import (
536:  src/bioetl/composition/runtime_builders/input_snapshot_resolution.py:11: in <module>
537:  from bioetl.composition.runtime_builders._run_manifest_refs import control_plane_root
538:  E   ImportError: cannot import name 'control_plane_root' from 'bioetl.composition.runtime_builders._run_manifest_refs' (/home/runner/work/BioactivityDataAcquisition/BioactivityDataAcquisition/src/bioetl/composition/runtime_builders/_run_manifest_refs.py)
539:  ________ ERROR at setup of test_pipeline_matrix_smoke[chembl_molecule] _________
540:  .venv/lib/python3.12/site-packages/pytest_asyncio/plugin.py:458: in setup
...

554:  from bioetl.composition.factories.pipeline._factory_method_runtime_support import (
555:  src/bioetl/composition/factories/pipeline/_factory_method_runtime_support.py:16: in <module>
556:  from bioetl.composition.factories.pipeline._factory_method_types import (
557:  src/bioetl/composition/factories/pipeline/_factory_method_types.py:20: in <module>
558:  from bioetl.composition.factories.pipeline.creation_support import (
559:  src/bioetl/composition/factories/pipeline/creation_support.py:10: in <module>
560:  from bioetl.composition.factories.pipeline._creation_wiring import (
561:  src/bioetl/composition/factories/pipeline/_creation_wiring.py:30: in <module>
562:  from bioetl.composition.factories.pipeline.run_context_factory import (
563:  src/bioetl/composition/factories/pipeline/run_context_factory.py:13: in <module>
564:  from bioetl.composition.runtime_builders.run_manifest_support import (
565:  src/bioetl/composition/runtime_builders/run_manifest_support.py:7: in <module>
566:  from bioetl.composition.runtime_builders.input_snapshot_resolution import (
567:  src/bioetl/composition/runtime_builders/input_snapshot_resolution.py:11: in <module>
568:  from bioetl.composition.runtime_builders._run_manifest_refs import control_plane_root
569:  E   ImportError: cannot import name 'control_plane_root' from 'bioetl.composition.runtime_builders._run_manifest_refs' (/home/runner/work/BioactivityDataAcquisition/BioactivityDataAcquisition/src/bioetl/composition/runtime_builders/_run_manifest_refs.py)
570:  _______ ERROR at setup of test_pipeline_matrix_smoke[chembl_publication] _______
571:  .venv/lib/python3.12/site-packages/pytest_asyncio/plugin.py:458: in setup
...

585:  from bioetl.composition.factories.pipeline._factory_method_runtime_support import (
586:  src/bioetl/composition/factories/pipeline/_factory_method_runtime_support.py:16: in <module>
587:  from bioetl.composition.factories.pipeline._factory_method_types import (
588:  src/bioetl/composition/factories/pipeline/_factory_method_types.py:20: in <module>
589:  from bioetl.composition.factories.pipeline.creation_support import (
590:  src/bioetl/composition/factories/pipeline/creation_support.py:10: in <module>
591:  from bioetl.composition.factories.pipeline._creation_wiring import (
592:  src/bioetl/composition/factories/pipeline/_creation_wiring.py:30: in <module>
593:  from bioetl.composition.factories.pipeline.run_context_factory import (
594:  src/bioetl/composition/factories/pipeline/run_context_factory.py:13: in <module>
595:  from bioetl.composition.runtime_builders.run_manifest_support import (
596:  src/bioetl/composition/runtime_builders/run_manifest_support.py:7: in <module>
597:  from bioetl.composition.runtime_builders.input_snapshot_resolution import (
598:  src/bioetl/composition/runtime_builders/input_snapshot_resolution.py:11: in <module>
599:  from bioetl.composition.runtime_builders._run_manifest_refs import control_plane_root
600:  E   ImportError: cannot import name 'control_plane_root' from 'bioetl.composition.runtime_builders._run_manifest_refs' (/home/runner/work/BioactivityDataAcquisition/BioactivityDataAcquisition/src/bioetl/composition/runtime_builders/_run_manifest_refs.py)
601:  _ ERROR at setup of test_pipeline_matrix_smoke[chembl_publication_similarity] __
602:  .venv/lib/python3.12/site-packages/pytest_asyncio/plugin.py:458: in setup
...

616:  from bioetl.composition.factories.pipeline._factory_method_runtime_support import (
617:  src/bioetl/composition/factories/pipeline/_factory_method_runtime_support.py:16: in <module>
618:  from bioetl.composition.factories.pipeline._factory_method_types import (
619:  src/bioetl/composition/factories/pipeline/_factory_method_types.py:20: in <module>
620:  from bioetl.composition.factories.pipeline.creation_support import (
621:  src/bioetl/composition/factories/pipeline/creation_support.py:10: in <module>
622:  from bioetl.composition.factories.pipeline._creation_wiring import (
623:  src/bioetl/composition/factories/pipeline/_creation_wiring.py:30: in <module>
624:  from bioetl.composition.factories.pipeline.run_context_factory import (
625:  src/bioetl/composition/factories/pipeline/run_context_factory.py:13: in <module>
626:  from bioetl.composition.runtime_builders.run_manifest_support import (
627:  src/bioetl/composition/runtime_builders/run_manifest_support.py:7: in <module>
628:  from bioetl.composition.runtime_builders.input_snapshot_resolution import (
629:  src/bioetl/composition/runtime_builders/input_snapshot_resolution.py:11: in <module>
630:  from bioetl.composition.runtime_builders._run_manifest_refs import control_plane_root
631:  E   ImportError: cannot import name 'control_plane_root' from 'bioetl.composition.runtime_builders._run_manifest_refs' (/home/runner/work/BioactivityDataAcquisition/BioactivityDataAcquisition/src/bioetl/composition/runtime_builders/_run_manifest_refs.py)
632:  ____ ERROR at setup of test_pipeline_matrix_smoke[chembl_publication_term] _____
633:  .venv/lib/python3.12/site-packages/pytest_asyncio/plugin.py:458: in setup
...

647:  from bioetl.composition.factories.pipeline._factory_method_runtime_support import (
648:  src/bioetl/composition/factories/pipeline/_factory_method_runtime_support.py:16: in <module>
649:  from bioetl.composition.factories.pipeline._factory_method_types import (
650:  src/bioetl/composition/factories/pipeline/_factory_method_types.py:20: in <module>
651:  from bioetl.composition.factories.pipeline.creation_support import (
652:  src/bioetl/composition/factories/pipeline/creation_support.py:10: in <module>
653:  from bioetl.composition.factories.pipeline._creation_wiring import (
654:  src/bioetl/composition/factories/pipeline/_creation_wiring.py:30: in <module>
655:  from bioetl.composition.factories.pipeline.run_context_factory import (
656:  src/bioetl/composition/factories/pipeline/run_context_factory.py:13: in <module>
657:  from bioetl.composition.runtime_builders.run_manifest_support import (
658:  src/bioetl/composition/runtime_builders/run_manifest_support.py:7: in <module>
659:  from bioetl.composition.runtime_builders.input_snapshot_resolution import (
660:  src/bioetl/composition/runtime_builders/input_snapshot_resolution.py:11: in <module>
661:  from bioetl.composition.runtime_builders._run_manifest_refs import control_plane_root
662:  E   ImportError: cannot import name 'control_plane_root' from 'bioetl.composition.runtime_builders._run_manifest_refs' (/home/runner/work/BioactivityDataAcquisition/BioactivityDataAcquisition/src/bioetl/composition/runtime_builders/_run_manifest_refs.py)
663:  __ ERROR at setup of test_pipeline_matrix_smoke[chembl_subcellular_fraction] ___
664:  .venv/lib/python3.12/site-packages/pytest_asyncio/plugin.py:458: in setup
...

678:  from bioetl.composition.factories.pipeline._factory_method_runtime_support import (
679:  src/bioetl/composition/factories/pipeline/_factory_method_runtime_support.py:16: in <module>
680:  from bioetl.composition.factories.pipeline._factory_method_types import (
681:  src/bioetl/composition/factories/pipeline/_factory_method_types.py:20: in <module>
682:  from bioetl.composition.factories.pipeline.creation_support import (
683:  src/bioetl/composition/factories/pipeline/creation_support.py:10: in <module>
684:  from bioetl.composition.factories.pipeline._creation_wiring import (
685:  src/bioetl/composition/factories/pipeline/_creation_wiring.py:30: in <module>
686:  from bioetl.composition.factories.pipeline.run_context_factory import (
687:  src/bioetl/composition/factories/pipeline/run_context_factory.py:13: in <module>
688:  from bioetl.composition.runtime_builders.run_manifest_support import (
689:  src/bioetl/composition/runtime_builders/run_manifest_support.py:7: in <module>
690:  from bioetl.composition.runtime_builders.input_snapshot_resolution import (
691:  src/bioetl/composition/runtime_builders/input_snapshot_resolution.py:11: in <module>
692:  from bioetl.composition.runtime_builders._run_manifest_refs import control_plane_root
693:  E   ImportError: cannot import name 'control_plane_root' from 'bioetl.composition.runtime_builders._run_manifest_refs' (/home/runner/work/BioactivityDataAcquisition/BioactivityDataAcquisition/src/bioetl/composition/runtime_builders/_run_manifest_refs.py)
694:  _________ ERROR at setup of test_pipeline_matrix_smoke[chembl_target] __________
695:  .venv/lib/python3.12/site-packages/pytest_asyncio/plugin.py:458: in setup
...

709:  from bioetl.composition.factories.pipeline._factory_method_runtime_support import (
710:  src/bioetl/composition/factories/pipeline/_factory_method_runtime_support.py:16: in <module>
711:  from bioetl.composition.factories.pipeline._factory_method_types import (
712:  src/bioetl/composition/factories/pipeline/_factory_method_types.py:20: in <module>
713:  from bioetl.composition.factories.pipeline.creation_support import (
714:  src/bioetl/composition/factories/pipeline/creation_support.py:10: in <module>
715:  from bioetl.composition.factories.pipeline._creation_wiring import (
716:  src/bioetl/composition/factories/pipeline/_creation_wiring.py:30: in <module>
717:  from bioetl.composition.factories.pipeline.run_context_factory import (
718:  src/bioetl/composition/factories/pipeline/run_context_factory.py:13: in <module>
719:  from bioetl.composition.runtime_builders.run_manifest_support import (
720:  src/bioetl/composition/runtime_builders/run_manifest_support.py:7: in <module>
721:  from bioetl.composition.runtime_builders.input_snapshot_resolution import (
722:  src/bioetl/composition/runtime_builders/input_snapshot_resolution.py:11: in <module>
723:  from bioetl.composition.runtime_builders._run_manifest_refs import control_plane_root
724:  E   ImportError: cannot import name 'control_plane_root' from 'bioetl.composition.runtime_builders._run_manifest_refs' (/home/runner/work/BioactivityDataAcquisition/BioactivityDataAcquisition/src/bioetl/composition/runtime_builders/_run_manifest_refs.py)
725:  ______ ERROR at setup of test_pipeline_matrix_smoke[crossref_publication] ______
726:  .venv/lib/python3.12/site-packages/pytest_asyncio/plugin.py:458: in setup
...

740:  from bioetl.composition.factories.pipeline._factory_method_runtime_support import (
741:  src/bioetl/composition/factories/pipeline/_factory_method_runtime_support.py:16: in <module>
742:  from bioetl.composition.factories.pipeline._factory_method_types import (
743:  src/bioetl/composition/factories/pipeline/_factory_method_types.py:20: in <module>
744:  from bioetl.composition.factories.pipeline.creation_support import (
745:  src/bioetl/composition/factories/pipeline/creation_support.py:10: in <module>
746:  from bioetl.composition.factories.pipeline._creation_wiring import (
747:  src/bioetl/composition/factories/pipeline/_creation_wiring.py:30: in <module>
748:  from bioetl.composition.factories.pipeline.run_context_factory import (
749:  src/bioetl/composition/factories/pipeline/run_context_factory.py:13: in <module>
750:  from bioetl.composition.runtime_builders.run_manifest_support import (
751:  src/bioetl/composition/runtime_builders/run_manifest_support.py:7: in <module>
752:  from bioetl.composition.runtime_builders.input_snapshot_resolution import (
753:  src/bioetl/composition/runtime_builders/input_snapshot_resolution.py:11: in <module>
754:  from bioetl.composition.runtime_builders._run_manifest_refs import control_plane_root
755:  E   ImportError: cannot import name 'control_plane_root' from 'bioetl.composition.runtime_builders._run_manifest_refs' (/home/runner/work/BioactivityDataAcquisition/BioactivityDataAcquisition/src/bioetl/composition/runtime_builders/_run_manifest_refs.py)
756:  ______ ERROR at setup of test_pipeline_matrix_smoke[openalex_publication] ______
757:  .venv/lib/python3.12/site-packages/pytest_asyncio/plugin.py:458: in setup
...

771:  from bioetl.composition.factories.pipeline._factory_method_runtime_support import (
772:  src/bioetl/composition/factories/pipeline/_factory_method_runtime_support.py:16: in <module>
773:  from bioetl.composition.factories.pipeline._factory_method_types import (
774:  src/bioetl/composition/factories/pipeline/_factory_method_types.py:20: in <module>
775:  from bioetl.composition.factories.pipeline.creation_support import (
776:  src/bioetl/composition/factories/pipeline/creation_support.py:10: in <module>
777:  from bioetl.composition.factories.pipeline._creation_wiring import (
778:  src/bioetl/composition/factories/pipeline/_creation_wiring.py:30: in <module>
779:  from bioetl.composition.factories.pipeline.run_context_factory import (
780:  src/bioetl/composition/factories/pipeline/run_context_factory.py:13: in <module>
781:  from bioetl.composition.runtime_builders.run_manifest_support import (
782:  src/bioetl/composition/runtime_builders/run_manifest_support.py:7: in <module>
783:  from bioetl.composition.runtime_builders.input_snapshot_resolution import (
784:  src/bioetl/composition/runtime_builders/input_snapshot_resolution.py:11: in <module>
785:  from bioetl.composition.runtime_builders._run_manifest_refs import control_plane_root
786:  E   ImportError: cannot import name 'control_plane_root' from 'bioetl.composition.runtime_builders._run_manifest_refs' (/home/runner/work/BioactivityDataAcquisition/BioactivityDataAcquisition/src/bioetl/composition/runtime_builders/_run_manifest_refs.py)
787:  ________ ERROR at setup of test_pipeline_matrix_smoke[pubchem_compound] ________
788:  .venv/lib/python3.12/site-packages/pytest_asyncio/plugin.py:458: in setup
...

802:  from bioetl.composition.factories.pipeline._factory_method_runtime_support import (
803:  src/bioetl/composition/factories/pipeline/_factory_method_runtime_support.py:16: in <module>
804:  from bioetl.composition.factories.pipeline._factory_method_types import (
805:  src/bioetl/composition/factories/pipeline/_factory_method_types.py:20: in <module>
806:  from bioetl.composition.factories.pipeline.creation_support import (
807:  src/bioetl/composition/factories/pipeline/creation_support.py:10: in <module>
808:  from bioetl.composition.factories.pipeline._creation_wiring import (
809:  src/bioetl/composition/factories/pipeline/_creation_wiring.py:30: in <module>
810:  from bioetl.composition.factories.pipeline.run_context_factory import (
811:  src/bioetl/composition/factories/pipeline/run_context_factory.py:13: in <module>
812:  from bioetl.composition.runtime_builders.run_manifest_support import (
813:  src/bioetl/composition/runtime_builders/run_manifest_support.py:7: in <module>
814:  from bioetl.composition.runtime_builders.input_snapshot_resolution import (
815:  src/bioetl/composition/runtime_builders/input_snapshot_resolution.py:11: in <module>
816:  from bioetl.composition.runtime_builders._run_manifest_refs import control_plane_root
817:  E   ImportError: cannot import name 'control_plane_root' from 'bioetl.composition.runtime_builders._run_manifest_refs' (/home/runner/work/BioactivityDataAcquisition/BioactivityDataAcquisition/src/bioetl/composition/runtime_builders/_run_manifest_refs.py)
818:  _______ ERROR at setup of test_pipeline_matrix_smoke[pubmed_publication] _______
819:  .venv/lib/python3.12/site-packages/pytest_asyncio/plugin.py:458: in setup
...

833:  from bioetl.composition.factories.pipeline._factory_method_runtime_support import (
834:  src/bioetl/composition/factories/pipeline/_factory_method_runtime_support.py:16: in <module>
835:  from bioetl.composition.factories.pipeline._factory_method_types import (
836:  src/bioetl/composition/factories/pipeline/_factory_method_types.py:20: in <module>
837:  from bioetl.composition.factories.pipeline.creation_support import (
838:  src/bioetl/composition/factories/pipeline/creation_support.py:10: in <module>
839:  from bioetl.composition.factories.pipeline._creation_wiring import (
840:  src/bioetl/composition/factories/pipeline/_creation_wiring.py:30: in <module>
841:  from bioetl.composition.factories.pipeline.run_context_factory import (
842:  src/bioetl/composition/factories/pipeline/run_context_factory.py:13: in <module>
843:  from bioetl.composition.runtime_builders.run_manifest_support import (
844:  src/bioetl/composition/runtime_builders/run_manifest_support.py:7: in <module>
845:  from bioetl.composition.runtime_builders.input_snapshot_resolution import (
846:  src/bioetl/composition/runtime_builders/input_snapshot_resolution.py:11: in <module>
847:  from bioetl.composition.runtime_builders._run_manifest_refs import control_plane_root
848:  E   ImportError: cannot import name 'control_plane_root' from 'bioetl.composition.runtime_builders._run_manifest_refs' (/home/runner/work/BioactivityDataAcquisition/BioactivityDataAcquisition/src/bioetl/composition/runtime_builders/_run_manifest_refs.py)
849:  __ ERROR at setup of test_pipeline_matrix_smoke[semanticscholar_publication] ___
850:  .venv/lib/python3.12/site-packages/pytest_asyncio/plugin.py:458: in setup
...

864:  from bioetl.composition.factories.pipeline._factory_method_runtime_support import (
865:  src/bioetl/composition/factories/pipeline/_factory_method_runtime_support.py:16: in <module>
866:  from bioetl.composition.factories.pipeline._factory_method_types import (
867:  src/bioetl/composition/factories/pipeline/_factory_method_types.py:20: in <module>
868:  from bioetl.composition.factories.pipeline.creation_support import (
869:  src/bioetl/composition/factories/pipeline/creation_support.py:10: in <module>
870:  from bioetl.composition.factories.pipeline._creation_wiring import (
871:  src/bioetl/composition/factories/pipeline/_creation_wiring.py:30: in <module>
872:  from bioetl.composition.factories.pipeline.run_context_factory import (
873:  src/bioetl/composition/factories/pipeline/run_context_factory.py:13: in <module>
874:  from bioetl.composition.runtime_builders.run_manifest_support import (
875:  src/bioetl/composition/runtime_builders/run_manifest_support.py:7: in <module>
876:  from bioetl.composition.runtime_builders.input_snapshot_resolution import (
877:  src/bioetl/composition/runtime_builders/input_snapshot_resolution.py:11: in <module>
878:  from bioetl.composition.runtime_builders._run_manifest_refs import control_plane_root
879:  E   ImportError: cannot import name 'control_plane_root' from 'bioetl.composition.runtime_builders._run_manifest_refs' (/home/runner/work/BioactivityDataAcquisition/BioactivityDataAcquisition/src/bioetl/composition/runtime_builders/_run_manifest_refs.py)
880:  _______ ERROR at setup of test_pipeline_matrix_smoke[uniprot_idmapping] ________
881:  .venv/lib/python3.12/site-packages/pytest_asyncio/plugin.py:458: in setup
...

895:  from bioetl.composition.factories.pipeline._factory_method_runtime_support import (
896:  src/bioetl/composition/factories/pipeline/_factory_method_runtime_support.py:16: in <module>
897:  from bioetl.composition.factories.pipeline._factory_method_types import (
898:  src/bioetl/composition/factories/pipeline/_factory_method_types.py:20: in <module>
899:  from bioetl.composition.factories.pipeline.creation_support import (
900:  src/bioetl/composition/factories/pipeline/creation_support.py:10: in <module>
901:  from bioetl.composition.factories.pipeline._creation_wiring import (
902:  src/bioetl/composition/factories/pipeline/_creation_wiring.py:30: in <module>
903:  from bioetl.composition.factories.pipeline.run_context_factory import (
904:  src/bioetl/composition/factories/pipeline/run_context_factory.py:13: in <module>
905:  from bioetl.composition.runtime_builders.run_manifest_support import (
906:  src/bioetl/composition/runtime_builders/run_manifest_support.py:7: in <module>
907:  from bioetl.composition.runtime_builders.input_snapshot_resolution import (
908:  src/bioetl/composition/runtime_builders/input_snapshot_resolution.py:11: in <module>
909:  from bioetl.composition.runtime_builders._run_manifest_refs import control_plane_root
910:  E   ImportError: cannot import name 'control_plane_root' from 'bioetl.composition.runtime_builders._run_manifest_refs' (/home/runner/work/BioactivityDataAcquisition/BioactivityDataAcquisition/src/bioetl/composition/runtime_builders/_run_manifest_refs.py)
911:  ________ ERROR at setup of test_pipeline_matrix_smoke[uniprot_protein] _________
912:  .venv/lib/python3.12/site-packages/pytest_asyncio/plugin.py:458: in setup
...

926:  from bioetl.composition.factories.pipeline._factory_method_runtime_support import (
927:  src/bioetl/composition/factories/pipeline/_factory_method_runtime_support.py:16: in <module>
928:  from bioetl.composition.factories.pipeline._factory_method_types import (
929:  src/bioetl/composition/factories/pipeline/_factory_method_types.py:20: in <module>
930:  from bioetl.composition.factories.pipeline.creation_support import (
931:  src/bioetl/composition/factories/pipeline/creation_support.py:10: in <module>
932:  from bioetl.composition.factories.pipeline._creation_wiring import (
933:  src/bioetl/composition/factories/pipeline/_creation_wiring.py:30: in <module>
934:  from bioetl.composition.factories.pipeline.run_context_factory import (
935:  src/bioetl/composition/factories/pipeline/run_context_factory.py:13: in <module>
936:  from bioetl.composition.runtime_builders.run_manifest_support import (
937:  src/bioetl/composition/runtime_builders/run_manifest_support.py:7: in <module>
938:  from bioetl.composition.runtime_builders.input_snapshot_resolution import (
939:  src/bioetl/composition/runtime_builders/input_snapshot_resolution.py:11: in <module>
940:  from bioetl.composition.runtime_builders._run_manifest_refs import control_plane_root
941:  E   ImportError: cannot import name 'control_plane_root' from 'bioetl.composition.runtime_builders._run_manifest_refs' (/home/runner/work/BioactivityDataAcquisition/BioactivityDataAcquisition/src/bioetl/composition/runtime_builders/_run_manifest_refs.py)
942:  =========================== short test summary info ============================
943:  ERROR tests/e2e/test_pipeline_matrix_e2e.py::test_pipeline_matrix_smoke[chembl_activity] - ImportError: cannot import name 'control_plane_root' from 'bioetl.composition.runtime_builders._run_manifest_refs' (/home/runner/work/BioactivityDataAcquisition/BioactivityDataAcquisition/src/bioetl/composition/runtime_builders/_run_manifest_refs.py)
944:  ERROR tests/e2e/test_pipeline_matrix_e2e.py::test_pipeline_matrix_smoke[chembl_assay] - ImportError: cannot import name 'control_plane_root' from 'bioetl.composition.runtime_builders._run_manifest_refs' (/home/runner/work/BioactivityDataAcquisition/BioactivityDataAcquisition/src/bioetl/composition/runtime_builders/_run_manifest_refs.py)
945:  ERROR tests/e2e/test_pipeline_matrix_e2e.py::test_pipeline_matrix_smoke[chembl_cell_line] - ImportError: cannot import name 'control_plane_root' from 'bioetl.composition.runtime_builders._run_manifest_refs' (/home/runner/work/BioactivityDataAcquisition/BioactivityDataAcquisition/src/bioetl/composition/runtime_builders/_run_manifest_refs.py)
946:  ERROR tests/e2e/test_pipeline_matrix_e2e.py::test_pipeline_matrix_smoke[chembl_compound_record] - ImportError: cannot import name 'control_plane_root' from 'bioetl.composition.runtime_builders._run_manifest_refs' (/home/runner/work/BioactivityDataAcquisition/BioactivityDataAcquisition/src/bioetl/composition/runtime_builders/_run_manifest_refs.py)
947:  ERROR tests/e2e/test_pipeline_matrix_e2e.py::test_pipeline_matrix_smoke[chembl_molecule] - ImportError: cannot import name 'control_plane_root' from 'bioetl.composition.runtime_builders._run_manifest_refs' (/home/runner/work/BioactivityDataAcquisition/BioactivityDataAcquisition/src/bioetl/composition/runtime_builders/_run_manifest_refs.py)
948:  ERROR tests/e2e/test_pipeline_matrix_e2e.py::test_pipeline_matrix_smoke[chembl_publication] - ImportError: cannot import name 'control_plane_root' from 'bioetl.composition.runtime_builders._run_manifest_refs' (/home/runner/work/BioactivityDataAcquisition/BioactivityDataAcquisition/src/bioetl/composition/runtime_builders/_run_manifest_refs.py)
949:  ERROR tests/e2e/test_pipeline_matrix_e2e.py::test_pipeline_matrix_smoke[chembl_publication_similarity] - ImportError: cannot import name 'control_plane_root' from 'bioetl.composition.runtime_builders._run_manifest_refs' (/home/runner/work/BioactivityDataAcquisition/BioactivityDataAcquisition/src/bioetl/composition/runtime_builders/_run_manifest_refs.py)
950:  ERROR tests/e2e/test_pipeline_matrix_e2e.py::test_pipeline_matrix_smoke[chembl_publication_term] - ImportError: cannot import name 'control_plane_root' from 'bioetl.composition.runtime_builders._run_manifest_refs' (/home/runner/work/BioactivityDataAcquisition/BioactivityDataAcquisition/src/bioetl/composition/runtime_builders/_run_manifest_refs.py)
951:  ERROR tests/e2e/test_pipeline_matrix_e2e.py::test_pipeline_matrix_smoke[chembl_subcellular_fraction] - ImportError: cannot import name 'control_plane_root' from 'bioetl.composition.runtime_builders._run_manifest_refs' (/home/runner/work/BioactivityDataAcquisition/BioactivityDataAcquisition/src/bioetl/composition/runtime_builders/_run_manifest_refs.py)
952:  ERROR tests/e2e/test_pipeline_matrix_e2e.py::test_pipeline_matrix_smoke[chembl_target] - ImportError: cannot import name 'control_plane_root' from 'bioetl.composition.runtime_builders._run_manifest_refs' (/home/runner/work/BioactivityDataAcquisition/BioactivityDataAcquisition/src/bioetl/composition/runtime_builders/_run_manifest_refs.py)
953:  ERROR tests/e2e/test_pipeline_matrix_e2e.py::test_pipeline_matrix_smoke[crossref_publication] - ImportError: cannot import name 'control_plane_root' from 'bioetl.composition.runtime_builders._run_manifest_refs' (/home/runner/work/BioactivityDataAcquisition/BioactivityDataAcquisition/src/bioetl/composition/runtime_builders/_run_manifest_refs.py)
954:  ERROR tests/e2e/test_pipeline_matrix_e2e.py::test_pipeline_matrix_smoke[openalex_publication] - ImportError: cannot import name 'control_plane_root' from 'bioetl.composition.runtime_builders._run_manifest_refs' (/home/runner/work/BioactivityDataAcquisition/BioactivityDataAcquisition/src/bioetl/composition/runtime_builders/_run_manifest_refs.py)
955:  ERROR tests/e2e/test_pipeline_matrix_e2e.py::test_pipeline_matrix_smoke[pubchem_compound] - ImportError: cannot import name 'control_plane_root' from 'bioetl.composition.runtime_builders._run_manifest_refs' (/home/runner/work/BioactivityDataAcquisition/BioactivityDataAcquisition/src/bioetl/composition/runtime_builders/_run_manifest_refs.py)
956:  ERROR tests/e2e/test_pipeline_matrix_e2e.py::test_pipeline_matrix_smoke[pubmed_publication] - ImportError: cannot import name 'control_plane_root' from 'bioetl.composition.runtime_builders._run_manifest_refs' (/home/runner/work/BioactivityDataAcquisition/BioactivityDataAcquisition/src/bioetl/composition/runtime_builders/_run_manifest_refs.py)
957:  ERROR tests/e2e/test_pipeline_matrix_e2e.py::test_pipeline_matrix_smoke[semanticscholar_publication] - ImportError: cannot import name 'control_plane_root' from 'bioetl.composition.runtime_builders._run_manifest_refs' (/home/runner/work/BioactivityDataAcquisition/BioactivityDataAcquisition/src/bioetl/composition/runtime_builders/_run_manifest_refs.py)
958:  ERROR tests/e2e/test_pipeline_matrix_e2e.py::test_pipeline_matrix_smoke[uniprot_idmapping] - ImportError: cannot import name 'control_plane_root' from 'bioetl.composition.runtime_builders._run_manifest_refs' (/home/runner/work/BioactivityDataAcquisition/BioactivityDataAcquisition/src/bioetl/composition/runtime_builders/_run_manifest_refs.py)
959:  ERROR tests/e2e/test_pipeline_matrix_e2e.py::test_pipeline_matrix_smoke[uniprot_protein] - ImportError: cannot import name 'control_plane_root' from 'bioetl.composition.runtime_builders._run_manifest_refs' (/home/runner/work/BioactivityDataAcquisition/BioactivityDataAcquisition/src/bioetl/composition/runtime_builders/_run_manifest_refs.py)
960:  EEEEEEEEEEEEEEEEE                                                        [100%]
961:  ==================================== ERRORS ====================================
962:  ________ ERROR at setup of test_pipeline_matrix_smoke[chembl_activity] _________
963:  .venv/lib/python3.12/site-packages/pytest_asyncio/plugin.py:458: in setup
...

980:  from bioetl.composition.factories.pipeline._factory_method_runtime_support import (
981:  src/bioetl/composition/factories/pipeline/_factory_method_runtime_support.py:16: in <module>
982:  from bioetl.composition.factories.pipeline._factory_method_types import (
983:  src/bioetl/composition/factories/pipeline/_factory_method_types.py:20: in <module>
984:  from bioetl.composition.factories.pipeline.creation_support import (
985:  src/bioetl/composition/factories/pipeline/creation_support.py:10: in <module>
986:  from bioetl.composition.factories.pipeline._creation_wiring import (
987:  src/bioetl/composition/factories/pipeline/_creation_wiring.py:30: in <module>
988:  from bioetl.composition.factories.pipeline.run_context_factory import (
989:  src/bioetl/composition/factories/pipeline/run_context_factory.py:13: in <module>
990:  from bioetl.composition.runtime_builders.run_manifest_support import (
991:  src/bioetl/composition/runtime_builders/run_manifest_support.py:7: in <module>
992:  from bioetl.composition.runtime_builders.input_snapshot_resolution import (
993:  src/bioetl/composition/runtime_builders/input_snapshot_resolution.py:11: in <module>
994:  from bioetl.composition.runtime_builders._run_manifest_refs import control_plane_root
995:  E   ImportError: cannot import name 'control_plane_root' from 'bioetl.composition.runtime_builders._run_manifest_refs' (/home/runner/work/BioactivityDataAcquisition/BioactivityDataAcquisition/src/bioetl/composition/runtime_builders/_run_manifest_refs.py)
996:  __________ ERROR at setup of test_pipeline_matrix_smoke[chembl_assay] __________
997:  .venv/lib/python3.12/site-packages/pytest_asyncio/plugin.py:458: in setup
...

1011:  from bioetl.composition.factories.pipeline._factory_method_runtime_support import (
1012:  src/bioetl/composition/factories/pipeline/_factory_method_runtime_support.py:16: in <module>
1013:  from bioetl.composition.factories.pipeline._factory_method_types import (
1014:  src/bioetl/composition/factories/pipeline/_factory_method_types.py:20: in <module>
1015:  from bioetl.composition.factories.pipeline.creation_support import (
1016:  src/bioetl/composition/factories/pipeline/creation_support.py:10: in <module>
1017:  from bioetl.composition.factories.pipeline._creation_wiring import (
1018:  src/bioetl/composition/factories/pipeline/_creation_wiring.py:30: in <module>
1019:  from bioetl.composition.factories.pipeline.run_context_factory import (
1020:  src/bioetl/composition/factories/pipeline/run_context_factory.py:13: in <module>
1021:  from bioetl.composition.runtime_builders.run_manifest_support import (
1022:  src/bioetl/composition/runtime_builders/run_manifest_support.py:7: in <module>
1023:  from bioetl.composition.runtime_builders.input_snapshot_resolution import (
1024:  src/bioetl/composition/runtime_builders/input_snapshot_resolution.py:11: in <module>
1025:  from bioetl.composition.runtime_builders._run_manifest_refs import control_plane_root
1026:  E   ImportError: cannot import name 'control_plane_root' from 'bioetl.composition.runtime_builders._run_manifest_refs' (/home/runner/work/BioactivityDataAcquisition/BioactivityDataAcquisition/src/bioetl/composition/runtime_builders/_run_manifest_refs.py)
1027:  ________ ERROR at setup of test_pipeline_matrix_smoke[chembl_cell_line] ________
1028:  .venv/lib/python3.12/site-packages/pytest_asyncio/plugin.py:458: in setup
...

1042:  from bioetl.composition.factories.pipeline._factory_method_runtime_support import (
1043:  src/bioetl/composition/factories/pipeline/_factory_method_runtime_support.py:16: in <module>
1044:  from bioetl.composition.factories.pipeline._factory_method_types import (
1045:  src/bioetl/composition/factories/pipeline/_factory_method_types.py:20: in <module>
1046:  from bioetl.composition.factories.pipeline.creation_support import (
1047:  src/bioetl/composition/factories/pipeline/creation_support.py:10: in <module>
1048:  from bioetl.composition.factories.pipeline._creation_wiring import (
1049:  src/bioetl/composition/factories/pipeline/_creation_wiring.py:30: in <module>
1050:  from bioetl.composition.factories.pipeline.run_context_factory import (
1051:  src/bioetl/composition/factories/pipeline/run_context_factory.py:13: in <module>
1052:  from bioetl.composition.runtime_builders.run_manifest_support import (
1053:  src/bioetl/composition/runtime_builders/run_manifest_support.py:7: in <module>
1054:  from bioetl.composition.runtime_builders.input_snapshot_resolution import (
1055:  src/bioetl/composition/runtime_builders/input_snapshot_resolution.py:11: in <module>
1056:  from bioetl.composition.runtime_builders._run_manifest_refs import control_plane_root
1057:  E   ImportError: cannot import name 'control_plane_root' from 'bioetl.composition.runtime_builders._run_manifest_refs' (/home/runner/work/BioactivityDataAcquisition/BioactivityDataAcquisition/src/bioetl/composition/runtime_builders/_run_manifest_refs.py)
1058:  _____ ERROR at setup of test_pipeline_matrix_smoke[chembl_compound_record] _____
1059:  .venv/lib/python3.12/site-packages/pytest_asyncio/plugin.py:458: in setup
...

1073:  from bioetl.composition.factories.pipeline._factory_method_runtime_support import (
1074:  src/bioetl/composition/factories/pipeline/_factory_method_runtime_support.py:16: in <module>
1075:  from bioetl.composition.factories.pipeline._factory_method_types import (
1076:  src/bioetl/composition/factories/pipeline/_factory_method_types.py:20: in <module>
1077:  from bioetl.composition.factories.pipeline.creation_support import (
1078:  src/bioetl/composition/factories/pipeline/creation_support.py:10: in <module>
1079:  from bioetl.composition.factories.pipeline._creation_wiring import (
1080:  src/bioetl/composition/factories/pipeline/_creation_wiring.py:30: in <module>
1081:  from bioetl.composition.factories.pipeline.run_context_factory import (
1082:  src/bioetl/composition/factories/pipeline/run_context_factory.py:13: in <module>
1083:  from bioetl.composition.runtime_builders.run_manifest_support import (
1084:  src/bioetl/composition/runtime_builders/run_manifest_support.py:7: in <module>
1085:  from bioetl.composition.runtime_builders.input_snapshot_resolution import (
1086:  src/bioetl/composition/runtime_builders/input_snapshot_resolution.py:11: in <module>
1087:  from bioetl.composition.runtime_builders._run_manifest_refs import control_plane_root
1088:  E   ImportError: cannot import name 'control_plane_root' from 'bioetl.composition.runtime_builders._run_manifest_refs' (/home/runner/work/BioactivityDataAcquisition/BioactivityDataAcquisition/src/bioetl/composition/runtime_builders/_run_manifest_refs.py)
1089:  ________ ERROR at setup of test_pipeline_matrix_smoke[chembl_molecule] _________
1090:  .venv/lib/python3.12/site-packages/pytest_asyncio/plugin.py:458: in setup
...

1104:  from bioetl.composition.factories.pipeline._factory_method_runtime_support import (
1105:  src/bioetl/composition/factories/pipeline/_factory_method_runtime_support.py:16: in <module>
1106:  from bioetl.composition.factories.pipeline._factory_method_types import (
1107:  src/bioetl/composition/factories/pipeline/_factory_method_types.py:20: in <module>
1108:  from bioetl.composition.factories.pipeline.creation_support import (
1109:  src/bioetl/composition/factories/pipeline/creation_support.py:10: in <module>
1110:  from bioetl.composition.factories.pipeline._creation_wiring import (
1111:  src/bioetl/composition/factories/pipeline/_creation_wiring.py:30: in <module>
1112:  from bioetl.composition.factories.pipeline.run_context_factory import (
1113:  src/bioetl/composition/factories/pipeline/run_context_factory.py:13: in <module>
1114:  from bioetl.composition.runtime_builders.run_manifest_support import (
1115:  src/bioetl/composition/runtime_builders/run_manifest_support.py:7: in <module>
1116:  from bioetl.composition.runtime_builders.input_snapshot_resolution import (
1117:  src/bioetl/composition/runtime_builders/input_snapshot_resolution.py:11: in <module>
1118:  from bioetl.composition.runtime_builders._run_manifest_refs import control_plane_root
1119:  E   ImportError: cannot import name 'control_plane_root' from 'bioetl.composition.runtime_builders._run_manifest_refs' (/home/runner/work/BioactivityDataAcquisition/BioactivityDataAcquisition/src/bioetl/composition/runtime_builders/_run_manifest_refs.py)
1120:  _______ ERROR at setup of test_pipeline_matrix_smoke[chembl_publication] _______
1121:  .venv/lib/python3.12/site-packages/pytest_asyncio/plugin.py:458: in setup
...

1135:  from bioetl.composition.factories.pipeline._factory_method_runtime_support import (
1136:  src/bioetl/composition/factories/pipeline/_factory_method_runtime_support.py:16: in <module>
1137:  from bioetl.composition.factories.pipeline._factory_method_types import (
1138:  src/bioetl/composition/factories/pipeline/_factory_method_types.py:20: in <module>
1139:  from bioetl.composition.factories.pipeline.creation_support import (
1140:  src/bioetl/composition/factories/pipeline/creation_support.py:10: in <module>
1141:  from bioetl.composition.factories.pipeline._creation_wiring import (
1142:  src/bioetl/composition/factories/pipeline/_creation_wiring.py:30: in <module>
1143:  from bioetl.composition.factories.pipeline.run_context_factory import (
1144:  src/bioetl/composition/factories/pipeline/run_context_factory.py:13: in <module>
1145:  from bioetl.composition.runtime_builders.run_manifest_support import (
1146:  src/bioetl/composition/runtime_builders/run_manifest_support.py:7: in <module>
1147:  from bioetl.composition.runtime_builders.input_snapshot_resolution import (
1148:  src/bioetl/composition/runtime_builders/input_snapshot_resolution.py:11: in <module>
1149:  from bioetl.composition.runtime_builders._run_manifest_refs import control_plane_root
1150:  E   ImportError: cannot import name 'control_plane_root' from 'bioetl.composition.runtime_builders._run_manifest_refs' (/home/runner/work/BioactivityDataAcquisition/BioactivityDataAcquisition/src/bioetl/composition/runtime_builders/_run_manifest_refs.py)
1151:  _ ERROR at setup of test_pipeline_matrix_smoke[chembl_publication_similarity] __
1152:  .venv/lib/python3.12/site-packages/pytest_asyncio/plugin.py:458: in setup
...

1166:  from bioetl.composition.factories.pipeline._factory_method_runtime_support import (
1167:  src/bioetl/composition/factories/pipeline/_factory_method_runtime_support.py:16: in <module>
1168:  from bioetl.composition.factories.pipeline._factory_method_types import (
1169:  src/bioetl/composition/factories/pipeline/_factory_method_types.py:20: in <module>
1170:  from bioetl.composition.factories.pipeline.creation_support import (
1171:  src/bioetl/composition/factories/pipeline/creation_support.py:10: in <module>
1172:  from bioetl.composition.factories.pipeline._creation_wiring import (
1173:  src/bioetl/composition/factories/pipeline/_creation_wiring.py:30: in <module>
1174:  from bioetl.composition.factories.pipeline.run_context_factory import (
1175:  src/bioetl/composition/factories/pipeline/run_context_factory.py:13: in <module>
1176:  from bioetl.composition.runtime_builders.run_manifest_support import (
1177:  src/bioetl/composition/runtime_builders/run_manifest_support.py:7: in <module>
1178:  from bioetl.composition.runtime_builders.input_snapshot_resolution import (
1179:  src/bioetl/composition/runtime_builders/input_snapshot_resolution.py:11: in <module>
1180:  from bioetl.composition.runtime_builders._run_manifest_refs import control_plane_root
1181:  E   ImportError: cannot import name 'control_plane_root' from 'bioetl.composition.runtime_builders._run_manifest_refs' (/home/runner/work/BioactivityDataAcquisition/BioactivityDataAcquisition/src/bioetl/composition/runtime_builders/_run_manifest_refs.py)
1182:  ____ ERROR at setup of test_pipeline_matrix_smoke[chembl_publication_term] _____
1183:  .venv/lib/python3.12/site-packages/pytest_asyncio/plugin.py:458: in setup
...

1197:  from bioetl.composition.factories.pipeline._factory_method_runtime_support import (
1198:  src/bioetl/composition/factories/pipeline/_factory_method_runtime_support.py:16: in <module>
1199:  from bioetl.composition.factories.pipeline._factory_method_types import (
1200:  src/bioetl/composition/factories/pipeline/_factory_method_types.py:20: in <module>
1201:  from bioetl.composition.factories.pipeline.creation_support import (
1202:  src/bioetl/composition/factories/pipeline/creation_support.py:10: in <module>
1203:  from bioetl.composition.factories.pipeline._creation_wiring import (
1204:  src/bioetl/composition/factories/pipeline/_creation_wiring.py:30: in <module>
1205:  from bioetl.composition.factories.pipeline.run_context_factory import (
1206:  src/bioetl/composition/factories/pipeline/run_context_factory.py:13: in <module>
1207:  from bioetl.composition.runtime_builders.run_manifest_support import (
1208:  src/bioetl/composition/runtime_builders/run_manifest_support.py:7: in <module>
1209:  from bioetl.composition.runtime_builders.input_snapshot_resolution import (
1210:  src/bioetl/composition/runtime_builders/input_snapshot_resolution.py:11: in <module>
1211:  from bioetl.composition.runtime_builders._run_manifest_refs import control_plane_root
1212:  E   ImportError: cannot import name 'control_plane_root' from 'bioetl.composition.runtime_builders._run_manifest_refs' (/home/runner/work/BioactivityDataAcquisition/BioactivityDataAcquisition/src/bioetl/composition/runtime_builders/_run_manifest_refs.py)
1213:  __ ERROR at setup of test_pipeline_matrix_smoke[chembl_subcellular_fraction] ___
1214:  .venv/lib/python3.12/site-packages/pytest_asyncio/plugin.py:458: in setup
...

1228:  from bioetl.composition.factories.pipeline._factory_method_runtime_support import (
1229:  src/bioetl/composition/factories/pipeline/_factory_method_runtime_support.py:16: in <module>
1230:  from bioetl.composition.factories.pipeline._factory_method_types import (
1231:  src/bioetl/composition/factories/pipeline/_factory_method_types.py:20: in <module>
1232:  from bioetl.composition.factories.pipeline.creation_support import (
1233:  src/bioetl/composition/factories/pipeline/creation_support.py:10: in <module>
1234:  from bioetl.composition.factories.pipeline._creation_wiring import (
1235:  src/bioetl/composition/factories/pipeline/_creation_wiring.py:30: in <module>
1236:  from bioetl.composition.factories.pipeline.run_context_factory import (
1237:  src/bioetl/composition/factories/pipeline/run_context_factory.py:13: in <module>
1238:  from bioetl.composition.runtime_builders.run_manifest_support import (
1239:  src/bioetl/composition/runtime_builders/run_manifest_support.py:7: in <module>
1240:  from bioetl.composition.runtime_builders.input_snapshot_resolution import (
1241:  src/bioetl/composition/runtime_builders/input_snapshot_resolution.py:11: in <module>
1242:  from bioetl.composition.runtime_builders._run_manifest_refs import control_plane_root
1243:  E   ImportError: cannot import name 'control_plane_root' from 'bioetl.composition.runtime_builders._run_manifest_refs' (/home/runner/work/BioactivityDataAcquisition/BioactivityDataAcquisition/src/bioetl/composition/runtime_builders/_run_manifest_refs.py)
1244:  _________ ERROR at setup of test_pipeline_matrix_smoke[chembl_target] __________
1245:  .venv/lib/python3.12/site-packages/pytest_asyncio/plugin.py:458: in setup
...

1259:  from bioetl.composition.factories.pipeline._factory_method_runtime_support import (
1260:  src/bioetl/composition/factories/pipeline/_factory_method_runtime_support.py:16: in <module>
1261:  from bioetl.composition.factories.pipeline._factory_method_types import (
1262:  src/bioetl/composition/factories/pipeline/_factory_method_types.py:20: in <module>
1263:  from bioetl.composition.factories.pipeline.creation_support import (
1264:  src/bioetl/composition/factories/pipeline/creation_support.py:10: in <module>
1265:  from bioetl.composition.factories.pipeline._creation_wiring import (
1266:  src/bioetl/composition/factories/pipeline/_creation_wiring.py:30: in <module>
1267:  from bioetl.composition.factories.pipeline.run_context_factory import (
1268:  src/bioetl/composition/factories/pipeline/run_context_factory.py:13: in <module>
1269:  from bioetl.composition.runtime_builders.run_manifest_support import (
1270:  src/bioetl/composition/runtime_builders/run_manifest_support.py:7: in <module>
1271:  from bioetl.composition.runtime_builders.input_snapshot_resolution import (
1272:  src/bioetl/composition/runtime_builders/input_snapshot_resolution.py:11: in <module>
1273:  from bioetl.composition.runtime_builders._run_manifest_refs import control_plane_root
1274:  E   ImportError: cannot import name 'control_plane_root' from 'bioetl.composition.runtime_builders._run_manifest_refs' (/home/runner/work/BioactivityDataAcquisition/BioactivityDataAcquisition/src/bioetl/composition/runtime_builders/_run_manifest_refs.py)
1275:  ______ ERROR at setup of test_pipeline_matrix_smoke[crossref_publication] ______
1276:  .venv/lib/python3.12/site-packages/pytest_asyncio/plugin.py:458: in setup
...

1290:  from bioetl.composition.factories.pipeline._factory_method_runtime_support import (
1291:  src/bioetl/composition/factories/pipeline/_factory_method_runtime_support.py:16: in <module>
1292:  from bioetl.composition.factories.pipeline._factory_method_types import (
1293:  src/bioetl/composition/factories/pipeline/_factory_method_types.py:20: in <module>
1294:  from bioetl.composition.factories.pipeline.creation_support import (
1295:  src/bioetl/composition/factories/pipeline/creation_support.py:10: in <module>
1296:  from bioetl.composition.factories.pipeline._creation_wiring import (
1297:  src/bioetl/composition/factories/pipeline/_creation_wiring.py:30: in <module>
1298:  from bioetl.composition.factories.pipeline.run_context_factory import (
1299:  src/bioetl/composition/factories/pipeline/run_context_factory.py:13: in <module>
1300:  from bioetl.composition.runtime_builders.run_manifest_support import (
1301:  src/bioetl/composition/runtime_builders/run_manifest_support.py:7: in <module>
1302:  from bioetl.composition.runtime_builders.input_snapshot_resolution import (
1303:  src/bioetl/composition/runtime_builders/input_snapshot_resolution.py:11: in <module>
1304:  from bioetl.composition.runtime_builders._run_manifest_refs import control_plane_root
1305:  E   ImportError: cannot import name 'control_plane_root' from 'bioetl.composition.runtime_builders._run_manifest_refs' (/home/runner/work/BioactivityDataAcquisition/BioactivityDataAcquisition/src/bioetl/composition/runtime_builders/_run_manifest_refs.py)
1306:  ______ ERROR at setup of test_pipeline_matrix_smoke[openalex_publication] ______
1307:  .venv/lib/python3.12/site-packages/pytest_asyncio/plugin.py:458: in setup
...

1321:  from bioetl.composition.factories.pipeline._factory_method_runtime_support import (
1322:  src/bioetl/composition/factories/pipeline/_factory_method_runtime_support.py:16: in <module>
1323:  from bioetl.composition.factories.pipeline._factory_method_types import (
1324:  src/bioetl/composition/factories/pipeline/_factory_method_types.py:20: in <module>
1325:  from bioetl.composition.factories.pipeline.creation_support import (
1326:  src/bioetl/composition/factories/pipeline/creation_support.py:10: in <module>
1327:  from bioetl.composition.factories.pipeline._creation_wiring import (
1328:  src/bioetl/composition/factories/pipeline/_creation_wiring.py:30: in <module>
1329:  from bioetl.composition.factories.pipeline.run_context_factory import (
1330:  src/bioetl/composition/factories/pipeline/run_context_factory.py:13: in <module>
1331:  from bioetl.composition.runtime_builders.run_manifest_support import (
1332:  src/bioetl/composition/runtime_builders/run_manifest_support.py:7: in <module>
1333:  from bioetl.composition.runtime_builders.input_snapshot_resolution import (
1334:  src/bioetl/composition/runtime_builders/input_snapshot_resolution.py:11: in <module>
1335:  from bioetl.composition.runtime_builders._run_manifest_refs import control_plane_root
1336:  E   ImportError: cannot import name 'control_plane_root' from 'bioetl.composition.runtime_builders._run_manifest_refs' (/home/runner/work/BioactivityDataAcquisition/BioactivityDataAcquisition/src/bioetl/composition/runtime_builders/_run_manifest_refs.py)
1337:  ________ ERROR at setup of test_pipeline_matrix_smoke[pubchem_compound] ________
1338:  .venv/lib/python3.12/site-packages/pytest_asyncio/plugin.py:458: in setup
...

1352:  from bioetl.composition.factories.pipeline._factory_method_runtime_support import (
1353:  src/bioetl/composition/factories/pipeline/_factory_method_runtime_support.py:16: in <module>
1354:  from bioetl.composition.factories.pipeline._factory_method_types import (
1355:  src/bioetl/composition/factories/pipeline/_factory_method_types.py:20: in <module>
1356:  from bioetl.composition.factories.pipeline.creation_support import (
1357:  src/bioetl/composition/factories/pipeline/creation_support.py:10: in <module>
1358:  from bioetl.composition.factories.pipeline._creation_wiring import (
1359:  src/bioetl/composition/factories/pipeline/_creation_wiring.py:30: in <module>
1360:  from bioetl.composition.factories.pipeline.run_context_factory import (
1361:  src/bioetl/composition/factories/pipeline/run_context_factory.py:13: in <module>
1362:  from bioetl.composition.runtime_builders.run_manifest_support import (
1363:  src/bioetl/composition/runtime_builders/run_manifest_support.py:7: in <module>
1364:  from bioetl.composition.runtime_builders.input_snapshot_resolution import (
1365:  src/bioetl/composition/runtime_builders/input_snapshot_resolution.py:11: in <module>
1366:  from bioetl.composition.runtime_builders._run_manifest_refs import control_plane_root
1367:  E   ImportError: cannot import name 'control_plane_root' from 'bioetl.composition.runtime_builders._run_manifest_refs' (/home/runner/work/BioactivityDataAcquisition/BioactivityDataAcquisition/src/bioetl/composition/runtime_builders/_run_manifest_refs.py)
1368:  _______ ERROR at setup of test_pipeline_matrix_smoke[pubmed_publication] _______
1369:  .venv/lib/python3.12/site-packages/pytest_asyncio/plugin.py:458: in setup
...

1383:  from bioetl.composition.factories.pipeline._factory_method_runtime_support import (
1384:  src/bioetl/composition/factories/pipeline/_factory_method_runtime_support.py:16: in <module>
1385:  from bioetl.composition.factories.pipeline._factory_method_types import (
1386:  src/bioetl/composition/factories/pipeline/_factory_method_types.py:20: in <module>
1387:  from bioetl.composition.factories.pipeline.creation_support import (
1388:  src/bioetl/composition/factories/pipeline/creation_support.py:10: in <module>
1389:  from bioetl.composition.factories.pipeline._creation_wiring import (
1390:  src/bioetl/composition/factories/pipeline/_creation_wiring.py:30: in <module>
1391:  from bioetl.composition.factories.pipeline.run_context_factory import (
1392:  src/bioetl/composition/factories/pipeline/run_context_factory.py:13: in <module>
1393:  from bioetl.composition.runtime_builders.run_manifest_support import (
1394:  src/bioetl/composition/runtime_builders/run_manifest_support.py:7: in <module>
1395:  from bioetl.composition.runtime_builders.input_snapshot_resolution import (
1396:  src/bioetl/composition/runtime_builders/input_snapshot_resolution.py:11: in <module>
1397:  from bioetl.composition.runtime_builders._run_manifest_refs import control_plane_root
1398:  E   ImportError: cannot import name 'control_plane_root' from 'bioetl.composition.runtime_builders._run_manifest_refs' (/home/runner/work/BioactivityDataAcquisition/BioactivityDataAcquisition/src/bioetl/composition/runtime_builders/_run_manifest_refs.py)
1399:  __ ERROR at setup of test_pipeline_matrix_smoke[semanticscholar_publication] ___
1400:  .venv/lib/python3.12/site-packages/pytest_asyncio/plugin.py:458: in setup
...

1414:  from bioetl.composition.factories.pipeline._factory_method_runtime_support import (
1415:  src/bioetl/composition/factories/pipeline/_factory_method_runtime_support.py:16: in <module>
1416:  from bioetl.composition.factories.pipeline._factory_method_types import (
1417:  src/bioetl/composition/factories/pipeline/_factory_method_types.py:20: in <module>
1418:  from bioetl.composition.factories.pipeline.creation_support import (
1419:  src/bioetl/composition/factories/pipeline/creation_support.py:10: in <module>
1420:  from bioetl.composition.factories.pipeline._creation_wiring import (
1421:  src/bioetl/composition/factories/pipeline/_creation_wiring.py:30: in <module>
1422:  from bioetl.composition.factories.pipeline.run_context_factory import (
1423:  src/bioetl/composition/factories/pipeline/run_context_factory.py:13: in <module>
1424:  from bioetl.composition.runtime_builders.run_manifest_support import (
1425:  src/bioetl/composition/runtime_builders/run_manifest_support.py:7: in <module>
1426:  from bioetl.composition.runtime_builders.input_snapshot_resolution import (
1427:  src/bioetl/composition/runtime_builders/input_snapshot_resolution.py:11: in <module>
1428:  from bioetl.composition.runtime_builders._run_manifest_refs import control_plane_root
1429:  E   ImportError: cannot import name 'control_plane_root' from 'bioetl.composition.runtime_builders._run_manifest_refs' (/home/runner/work/BioactivityDataAcquisition/BioactivityDataAcquisition/src/bioetl/composition/runtime_builders/_run_manifest_refs.py)
1430:  _______ ERROR at setup of test_pipeline_matrix_smoke[uniprot_idmapping] ________
1431:  .venv/lib/python3.12/site-packages/pytest_asyncio/plugin.py:458: in setup
...

1445:  from bioetl.composition.factories.pipeline._factory_method_runtime_support import (
1446:  src/bioetl/composition/factories/pipeline/_factory_method_runtime_support.py:16: in <module>
1447:  from bioetl.composition.factories.pipeline._factory_method_types import (
1448:  src/bioetl/composition/factories/pipeline/_factory_method_types.py:20: in <module>
1449:  from bioetl.composition.factories.pipeline.creation_support import (
1450:  src/bioetl/composition/factories/pipeline/creation_support.py:10: in <module>
1451:  from bioetl.composition.factories.pipeline._creation_wiring import (
1452:  src/bioetl/composition/factories/pipeline/_creation_wiring.py:30: in <module>
1453:  from bioetl.composition.factories.pipeline.run_context_factory import (
1454:  src/bioetl/composition/factories/pipeline/run_context_factory.py:13: in <module>
1455:  from bioetl.composition.runtime_builders.run_manifest_support import (
1456:  src/bioetl/composition/runtime_builders/run_manifest_support.py:7: in <module>
1457:  from bioetl.composition.runtime_builders.input_snapshot_resolution import (
1458:  src/bioetl/composition/runtime_builders/input_snapshot_resolution.py:11: in <module>
1459:  from bioetl.composition.runtime_builders._run_manifest_refs import control_plane_root
1460:  E   ImportError: cannot import name 'control_plane_root' from 'bioetl.composition.runtime_builders._run_manifest_refs' (/home/runner/work/BioactivityDataAcquisition/Bi...

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