PlantAI-dev/.superpowers/sdd/convergence-task-1-report.md

Convergence Task 1 Report

status: DONE_WITH_CONCERNS

Archived paths

• 项目记录/代码归档/2026-07-10_PPI_ID修订收敛前快照/skills/ppi/run.py
• 项目记录/代码归档/2026-07-10_PPI_ID修订收敛前快照/gfa_core/id_resolution.py
• 项目记录/代码归档/2026-07-10_PPI_ID修订收敛前快照/gfa_core/string_rate_gate.py
• 项目记录/代码归档/2026-07-10_PPI_ID修订收敛前快照/gfa_core/ppi_string_policy.py
• 项目记录/代码归档/2026-07-10_PPI_ID修订收敛前快照/apps/web/pipeline_backend.py
• 项目记录/代码归档/2026-07-10_PPI_ID修订收敛前快照/tests/unit/test_id_resolution.py
• 项目记录/代码归档/2026-07-10_PPI_ID修订收敛前快照/tests/unit/test_ppi_id_resolution.py
• 项目记录/代码归档/2026-07-10_PPI_ID修订收敛前快照/tests/unit/test_ppi_string_policy.py
• 项目记录/代码归档/2026-07-10_PPI_ID修订收敛前快照/tests/unit/test_pipeline_backend_execution_env.py
• 项目记录/代码归档/2026-07-10_PPI_ID修订收敛前快照/baseline.md
• 项目记录/代码归档/2026-07-10_PPI_ID修订收敛前快照/unimplemented_image_protocol_tests.py.txt

The first nine files were copied before active edits with repository-relative layout. baseline.md contains the exact wc -l and pre-edit pytest output. unimplemented_image_protocol_tests.py.txt contains the exact removed test bodies, including the parametrization that produced two collected MIME cases.

Active files changed

• skills/ppi/run.py (PPI execution): removed only the obsolete leading positional query-ID argument from the self.analyze_network(...) call, restoring the current signature.
• tests/unit/test_ppi_id_resolution.py (unit tests): removed only the three named unfinished image-protocol test functions from active collection; the parametrized function accounted for two cases.

No other active production or test file changed relative to its archived snapshot.

Before-edit tests

Command:

/home/xia-lab/miniconda3/envs/test4py311/bin/python -m pytest \
  tests/unit/test_id_resolution.py \
  tests/unit/test_ppi_id_resolution.py \
  tests/unit/test_ppi_string_policy.py \
  tests/unit/test_pipeline_backend_execution_env.py -q

Result: exit 1; 181 collected; 12 failed, 169 passed in 7.24s.

The exact output is preserved in 项目记录/代码归档/2026-07-10_PPI_ID修订收敛前快照/baseline.md.

Pre-edit line counts preserved there:

   281 tests/unit/test_id_resolution.py
  1523 tests/unit/test_ppi_id_resolution.py
   223 tests/unit/test_ppi_string_policy.py
  1328 tests/unit/test_pipeline_backend_execution_env.py
  3355 总计

After-edit tests

Command:

/home/xia-lab/miniconda3/envs/test4py311/bin/python -m pytest \
  tests/unit/test_id_resolution.py \
  tests/unit/test_ppi_id_resolution.py \
  tests/unit/test_ppi_string_policy.py \
  tests/unit/test_pipeline_backend_execution_env.py -q

Result: exit 0; 177 collected; 177 passed in 7.07s.

Exact output:

/home/xia-lab/miniconda3/envs/test4py311/lib/python3.11/site-packages/requests/__init__.py:113: RequestsDependencyWarning: urllib3 (2.6.3) or chardet (7.1.0)/charset_normalizer (3.4.7) doesn't match a supported version!
  warnings.warn(
============================= test session starts ==============================
platform linux -- Python 3.11.14, pytest-8.3.5, pluggy-1.6.0
rootdir: /data/project_roots/PlantAI-dev
configfile: pytest.ini
plugins: langsmith-0.7.3, anyio-4.12.1
collected 177 items

tests/unit/test_id_resolution.py ............                            [  6%]
tests/unit/test_ppi_id_resolution.py ................................... [ 26%]
........................................................................ [ 67%]
.............                                                            [ 74%]
tests/unit/test_ppi_string_policy.py .............                       [ 81%]
tests/unit/test_pipeline_backend_execution_env.py ...................... [ 94%]
..........                                                               [100%]

============================= 177 passed in 7.07s ==============================

py_compile

Command:

/home/xia-lab/miniconda3/envs/test4py311/bin/python -m py_compile \
  gfa_core/id_resolution.py gfa_core/string_rate_gate.py \
  gfa_core/ppi_string_policy.py skills/ppi/run.py apps/web/pipeline_backend.py

Result: exit 0; no output.

Concerns

• Both before- and after-edit pytest runs emit the same pre-existing RequestsDependencyWarning: installed urllib3 2.6.3 or chardet 7.1.0/charset_normalizer 3.4.7 does not match the version supported by requests. It does not fail the mandated test checkpoint, but the environment dependency mismatch remains.
• This task intentionally did not implement the archived image-protocol expansion. Those test bodies remain recoverable in the archive and are no longer collected, exactly as required.
• Validation was a unit checkpoint and syntax compilation, not a real-data PPI execution; the binding task requested no real-data run.

Self-review

• Snapshot verification: all 11 required archive files exist. The nine requested current-state files were copied before edits.
• Scope verification: snapshot diffs show only one deleted call argument in skills/ppi/run.py and 78 active lines comprising the specified test bodies plus separator blank lines removed from tests/unit/test_ppi_id_resolution.py. The other seven archived active files compare byte-identically to their current counterparts.
• Behavior verification: the active analyze_network implementation, ID-resolution logic, STRING image downloader, policy, backend execution, manifests, frontend, CLI, Reset behavior, and Tasks 2–5 were not changed.
• Test preservation: the named test bodies were archived verbatim before de-collection; no code or test was permanently deleted.
• Service/Celery restart: not needed; no running service was exercised or modified.
• Diagnostic record: not updated; the work restored an interrupted call site and de-collected explicitly out-of-scope unfinished tests without changing diagnostic behavior.
• Git integration: not performed because the task explicitly states Git is unavailable.