build: stage trusted document semantic dependencies

[seonghobae]

Summary

• add the hash-pinned pypdf and pyshacl runtime dependencies needed by the document semantic layer
• refresh runtime, development, and test lock closures from the existing validated feature branch
• keep feature code and package-data changes out of this prerequisite PR so the trusted-base coverage sandbox can establish the dependency closure first

Validation

• PYTHONPATH=src .../.venv/bin/python -m pytest -q (pass; 8 skips)
• git diff --check
• lock files remain fully hash pinned and are installed by repository CI with --require-hashes

Follow-up

After this merges, rebase PR #28 on the new main so central coverage can install these dependencies from the exact trusted base.

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Review details

⚙️ Run configuration

Configuration used: Organization UI

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Run ID: 3e3c4f5d-62da-4672-8000-3617de3aa57c

📥 Commits

Reviewing files that changed from the base of the PR and between e48aa13 and 00ee8af.

📒 Files selected for processing (5)

• pyproject.toml
• requirements-dev.txt
• requirements-test.in
• requirements-test.txt
• requirements.txt

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[opencode-agent]

Pull request overview

OpenCode could not approve from deterministic current-head evidence because GitHub Checks have failed.

Findings

1. HIGH Current-head GitHub Checks - Fix failed required checks before approval

• Problem: Failed same-head checks remain for 2716e2e228e26b4d224c37df16e27b9f40bf761f.
• Root cause: The model-unavailable evidence fallback is allowed only when peer GitHub Checks are complete and clean.
• Fix: Read and fix the failed check logs below, then rerun the current-head checks.
• Regression test: Keep the model-unavailable fallback gated on an empty failed-check rollup.

Failed checks:

• SAST Semgrep/Semgrep (multi-language SAST): FAILURE (https://github.com/ContextualWisdomLab/semantic-data-portal/actions/runs/30807569161/job/91666374215)
• Semgrep (multi-language SAST) check run: failure (https://github.com/ContextualWisdomLab/semantic-data-portal/actions/runs/30807569161/job/91666374215)

Changed-File Evidence Map

flowchart LR
  PR["PR changed files"] --> Evidence["OpenCode bounded evidence"]
  Evidence --> S1["Changed file (5 files)"]
  S1 --> I1["repository behavior"]
  I1 --> R1["Review risk: Changed file (5 files)"]
  R1 --> V1["required checks"]

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[opencode-agent]

OpenCode Review Overview

• Head SHA: 2716e2e228e26b4d224c37df16e27b9f40bf761f
• Workflow run: 31022055468
• Workflow attempt: 1
• Gate result: REQUEST_CHANGES (approval step)

Pull request overview

OpenCode could not approve from deterministic current-head evidence because GitHub Checks have failed.

Findings

1. HIGH Current-head GitHub Checks - Fix failed required checks before approval

• Problem: Failed same-head checks remain for 2716e2e228e26b4d224c37df16e27b9f40bf761f.
• Root cause: The model-unavailable evidence fallback is allowed only when peer GitHub Checks are complete and clean.
• Fix: Read and fix the failed check logs below, then rerun the current-head checks.
• Regression test: Keep the model-unavailable fallback gated on an empty failed-check rollup.

Failed checks:

• SAST Semgrep/Semgrep (multi-language SAST): FAILURE (https://github.com/ContextualWisdomLab/semantic-data-portal/actions/runs/30807569161/job/91666374215)
• Semgrep (multi-language SAST) check run: failure (https://github.com/ContextualWisdomLab/semantic-data-portal/actions/runs/30807569161/job/91666374215)

Changed-File Evidence Map

flowchart LR
  PR["PR changed files"] --> Evidence["OpenCode bounded evidence"]
  Evidence --> S1["Changed file (5 files)"]
  S1 --> I1["repository behavior"]
  I1 --> R1["Review risk: Changed file (5 files)"]
  R1 --> V1["required checks"]

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