feat(lit-sync): opt-in fulltext-retrieval phase + consolidate OA cascade to fetch_oa.py #483

Workflow file for this run

.github/workflows/validate.yml at 4e384e5

	name: Validate skills (PII + structure)

	# Server-side enforcement of validate_skills.sh.
	# This catches commits that bypassed the local pre-commit hook
	# (--no-verify, different machine, different user) before they reach main.

	on:
	push:
	branches: [main]
	pull_request:
	branches: [main]

	jobs:
	validate:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4

	- name: Set up Python
	uses: actions/setup-python@v5
	with:
	python-version: "3.11"

	- name: Install Python test dependencies
	run: pip install pyyaml pandas numpy python-pptx python-docx

	- name: Install exiftool + poppler (EXIF scan + check_asset_anonymization PDF text/metadata)
	run: sudo apt-get update && sudo apt-get install -y libimage-exiftool-perl poppler-utils

	- name: Run validate_skills.sh (PII + structure)
	run: bash scripts/validate_skills.sh

	# --- self-update foundation (PR-1a): manifests, version drift, transactional installer ---
	- name: Distribution manifests in sync (gen_distribution_manifest.py --check)
	run: python3 scripts/gen_distribution_manifest.py --check

	- name: Version consistency (CITATION == package.json == distribution_manifest)
	run: python3 scripts/check_version_consistency.py

	- name: Distribution manifest + scope-pinning test
	run: python3 installers/tests/test_distribution_manifest.py

	- name: Transactional installer crash-recovery + legacy-migration test
	run: python3 installers/tests/test_txn.py

	- name: Updater verify / safe-extract / check-update test (offline)
	run: python3 installers/tests/test_update.py

	- name: install.py transactional self-test (no host/state dir touched)
	run: python3 installers/install.py --self-test

	- name: Opt-in SessionStart update-notify hook test (settings merge + hook logic, offline)
	run: python3 installers/tests/test_session_hook.py

	- name: Release-ZIP provenance + updater-consumability round-trip (build -> safe-extract)
	run: bash installers/tests/test_release_zip.sh

	- name: Run validate_routing_assets.py (SKILL.md asset references must exist)
	run: python3 scripts/validate_routing_assets.py --strict

	- name: Run validate_routing_assets.py self-test (dangling references/ pointer fails)
	run: bash tests/test_routing_assets.sh

	- name: Run check_domain_probe_sync.py (vendored domain probes must be byte-identical)
	run: python3 scripts/check_domain_probe_sync.py --strict

	- name: Run check_locale_inventory.py (Korean-bearing files must be inventory-justified)
	run: python3 scripts/check_locale_inventory.py

	- name: Run check_locale_inventory.py self-test
	run: bash tests/test_locale_inventory.sh

	- name: Run self-review panel-mode structural + PII test
	run: bash skills/self-review/tests/test_panel_mode.sh

	- name: Run self-review reference-adequacy gate test
	run: bash skills/self-review/tests/test_reference_adequacy.sh

	- name: Run validate_catalog_consistency.py (doc counts must match disk SSOT)
	run: python3 scripts/validate_catalog_consistency.py

	- name: Run check_frontmatter_schema.py (Agent Skills frontmatter spec — valid YAML, name, description)
	run: python3 scripts/check_frontmatter_schema.py

	- name: Run frontmatter-schema gate self-test
	run: bash tests/test_frontmatter_schema.sh

	- name: Run gen_skill_docs.py --check (per-skill docs must match SKILL.md)
	run: python3 scripts/gen_skill_docs.py --check

	- name: Run gen_skill_docs _ignorable regression test (worktree dotted-ancestor counts)
	run: bash tests/test_gen_skill_docs_ignorable.sh

	- name: Run gen_skills_catalog_json.py --check (storefront catalog SSOT)
	run: python3 scripts/gen_skills_catalog_json.py --check

	- name: Run skills_catalog generator self-test
	run: bash tests/test_skills_catalog_json.sh

	- name: Run gen_marketplace_json.py --check (plugin marketplace SSOT)
	run: python3 scripts/gen_marketplace_json.py --check

	- name: Run marketplace generator self-test
	run: bash tests/test_marketplace_json.sh

	- name: Run gen_detectors_catalog_json.py --check (MedSci-Audit detector SSOT)
	run: python3 scripts/gen_detectors_catalog_json.py --check

	- name: Run detectors_catalog generator self-test
	run: bash tests/test_detectors_catalog_json.sh

	- name: Run sync_hero_skill.py generator self-test (standalone mirror build)
	run: bash tests/test_sync_hero_skill.sh

	- name: Run analyze-stats survival template test (A1)
	run: bash skills/analyze-stats/tests/test_survival_template.sh

	- name: Run sync-submission asset-anonymization gate test (A2)
	run: bash skills/sync-submission/tests/test_asset_anonymization.sh

	- name: Run sync-submission disclosure/availability detector test
	run: bash skills/sync-submission/tests/test_disclosure_availability.sh

	- name: Run academic-aio summary-box detector test
	run: bash skills/academic-aio/tests/test_summary_box.sh

	- name: Run write-paper title-page affiliation-order test
	run: bash skills/write-paper/tests/test_title_page_affiliations.sh

	- name: Run sync-submission cross-artifact staleness gate test (A3)
	run: bash skills/sync-submission/tests/test_cross_artifact_stale.sh

	- name: Run check-reporting checklist-version gate test (A4)
	run: bash skills/check-reporting/tests/test_checklist_version.sh

	- name: Run write-paper placeholder gate test (A5)
	run: bash skills/write-paper/tests/test_placeholders.sh

	- name: Run sync-submission preflight gate test (A6)
	run: bash skills/sync-submission/tests/test_preflight_gate.sh

	- name: Run sync-submission word-count-cap gate test (A7)
	run: bash skills/sync-submission/tests/test_wordcount_cap.sh

	- name: Run verify-refs corporate-author gate test (A8)
	run: bash skills/verify-refs/tests/test_corporate_author.sh

	- name: Run verify-refs OpenAlex tertiary-index test (A8b)
	run: bash skills/verify-refs/tests/test_openalex_tier.sh

	- name: Run self-review parenthesis-span corruption gate test (A9)
	run: bash skills/self-review/tests/test_paren_spans.sh

	- name: Run self-review classical-style gate test (A10)
	run: bash skills/self-review/tests/test_classical_style.sh

	- name: Run self-review confounding-completeness gate test (A11)
	run: bash skills/self-review/tests/test_confounding_completeness.sh

	- name: Run self-review supplement-hygiene gate test
	run: bash skills/self-review/tests/test_supplement_hygiene.sh

	- name: Run self-review artifact-coverage gate test
	run: bash skills/self-review/tests/test_artifact_coverage.sh

	- name: Run self-review null-calibration gate test
	run: bash skills/self-review/tests/test_null_calibration.sh

	- name: Run sync-submission supplement-assembler test (A12)
	run: bash skills/sync-submission/tests/test_assemble_supplement.sh

	- name: Run render-pdf-doc glyph-coverage scan test (A13)
	run: bash skills/render-pdf-doc/tests/test_glyph_coverage.sh

	- name: Run author-strategy archetype-classifier test (A14)
	run: bash skills/author-strategy/tests/test_archetype_classifier.sh

	# --- Tier 0/1 skill regression tests (existing + new, now CI-wired) ---
	- name: Run make-figures legend-reconcile test
	run: bash skills/make-figures/tests/test_legend_reconcile.sh

	- name: Run clean-data structural-zero test
	run: bash skills/clean-data/tests/test_structural_zero.sh

	- name: Run clean-data reverse-coding test
	run: bash skills/clean-data/tests/test_reverse_coding.sh

	- name: Run lit-sync poll-logic test
	run: bash skills/lit-sync/tests/test_poll_logic.sh

	- name: Run meta-analysis pool-consistency test
	run: bash skills/meta-analysis/tests/test_pool_consistency.sh

	- name: Run generate-codebook test
	run: bash skills/generate-codebook/tests/test_generate_codebook.sh

	- name: Run present-paper speaker-notes markdown test
	run: python3 skills/present-paper/tests/test_speaker_notes_markdown.py

	- name: Run version-dataset manifest/verify test
	run: bash skills/version-dataset/tests/test_version_dataset.sh

	- name: Run manage-refs vN-docx cross-reference test
	run: bash skills/manage-refs/tests/test_vN_docx_check.sh

	- name: Run manage-refs CSL-render hardening test
	run: bash skills/manage-refs/tests/test_csl_render.sh

	- name: Run polish-language consistency-linter challenge
	run: bash skills/polish-language/scripts/lint_challenge/verify.sh

	- name: Run deidentify PHI-scan contract test
	run: bash skills/deidentify/tests/test_deidentify_scan.sh

	- name: Run fill-icmje-coi form-clone contract test
	run: bash skills/fill-icmje-coi/tests/test_fill_icmje_coi.sh

	- name: Run academic-aio schema-validator test
	run: bash skills/academic-aio/tests/test_validate_schema.sh

	- name: Run academic-aio metadata-audit test
	run: bash skills/academic-aio/tests/test_batch_metadata_audit.sh

	- name: Run fill-protocol form-fill test
	run: bash skills/fill-protocol/tests/test_fill_form.sh

	- name: Run fulltext-retrieval pdf_to_md helper test
	run: python3 skills/fulltext-retrieval/tests/test_pdf_to_md.py

	- name: Run fulltext-retrieval report-builder challenge
	run: bash skills/fulltext-retrieval/fetch_oa_report_challenge/verify.sh

	- name: Run self-review scope-coherence gate test
	run: bash skills/self-review/tests/test_scope_coherence.sh

	- name: Run self-review cohort-arithmetic gate test
	run: bash skills/self-review/tests/test_cohort_arithmetic.sh

	- name: Run model-validation split-leakage challenge
	run: bash skills/model-validation/scripts/check_split_leakage_challenge/verify.sh

	- name: Run model-validation split-leakage gate test
	run: bash skills/model-validation/tests/test_split_leakage.sh

	- name: Run model-scaffold build→validate challenge
	run: bash skills/model-scaffold/scripts/scaffold_challenge/verify.sh

	- name: Run model-scaffold training-hygiene gate test
	run: bash skills/model-scaffold/tests/test_training_hygiene.sh

	- name: Run model-card completeness challenge
	run: bash skills/model-card/scripts/check_model_card_complete_challenge/verify.sh

	- name: Run model-card completeness gate test
	run: bash skills/model-card/tests/test_model_card_complete.sh

	- name: Run model-evaluation metric-reporting challenge
	run: bash skills/model-evaluation/scripts/metric_reporting_challenge/verify.sh

	- name: Run model-evaluation metric-reporting gate test
	run: bash skills/model-evaluation/tests/test_metric_reporting.sh

	- name: Run mllm-eval completeness challenge
	run: bash skills/mllm-eval/scripts/mllm_eval_completeness_challenge/verify.sh

	- name: Run mllm-eval completeness gate test
	run: bash skills/mllm-eval/tests/test_mllm_eval_completeness.sh

	- name: Run analyze-stats generated-code gate test
	run: bash skills/analyze-stats/tests/test_generated_code.sh

	# --- previously-dormant skill regression tests, now CI-wired (v5 coverage-gap closure) ---
	# These tests shipped with their detectors but were never added to this workflow, so CI
	# gave false coverage. All pass on the same toolchain CI installs (stdlib + python-docx;
	# no pandoc/R). Re-run gen_distribution_manifest.py after adding any new fixture.
	- name: Run check-reporting checklist fail-fast test
	run: bash skills/check-reporting/tests/test_checklist_fail_fast.sh

	- name: Run check-reporting framework-naming gate test
	run: bash skills/check-reporting/tests/test_framework_naming.sh

	- name: Run check-reporting PRISMA-cascade test
	run: bash skills/check-reporting/tests/test_prisma_cascade.sh

	- name: Run check-reporting PRISMA Figure 1 audit test (Step 4d)
	run: bash skills/check-reporting/tests/test_prisma_figure.sh

	- name: Run manage-refs duplicate-bibliography gate test
	run: bash skills/manage-refs/tests/test_reference_duplication.sh

	- name: Run self-review binning-consistency gate test
	run: bash skills/self-review/tests/test_binning_consistency.sh

	- name: Run self-review float citation-order gate test
	run: bash skills/self-review/tests/test_citation_order.sh

	- name: Run self-review claim-artifact (estimand provenance) gate test
	run: bash skills/self-review/tests/test_claim_artifact.sh

	- name: Run self-review panel-diversity gate test
	run: bash skills/self-review/tests/test_panel_diversity.sh

	- name: Run self-review reviewer-team-consistency gate test
	run: bash skills/self-review/tests/test_reviewer_team_consistency.sh

	- name: Run sync-submission audit-dump leak gate test
	run: bash skills/sync-submission/tests/test_checklist_dump_leak.sh

	- name: Run sync-submission copy-divergence gate test
	run: bash skills/sync-submission/tests/test_copy_divergence.sh

	- name: Run sync-submission cross-document-N gate test
	run: bash skills/sync-submission/tests/test_cross_document_n.sh

	- name: Run sync-submission scope-drift gate test
	run: bash skills/sync-submission/tests/test_scope_drift.sh

	- name: Run sync-submission vN-docx assertion gate test
	run: bash skills/sync-submission/tests/test_vN_docx_assertion.sh

	- name: Run verify-refs pagination-placeholder gate test
	run: bash skills/verify-refs/tests/test_pagination_placeholder.sh

	- name: Verify demo manifest.lock files (reproducibility lock)
	run: \|
	for d in demo/01_wisconsin_bc demo/02_metafor_bcg demo/03_nhanes_obesity; do
	python3 skills/version-dataset/scripts/version_dataset.py verify \
	--manifest "$d/manifest.lock.json" --base "$d" --strict
	done

	# --- npm/npx distribution baseline (runs last so packaging failures are easy to isolate) ---
	- name: Set up Node
	uses: actions/setup-node@v4
	with:
	node-version: "20"

	- name: npm package self-test (CLI shim + exec bit + version sync + pack audit)
	run: bash tests/test_npm_package.sh

	- name: npm pack content audit (real pack, package/ prefix normalized)
	run: python3 scripts/check_npm_package_contents.py --real

	# Cross-platform safety for the transactional installer + updater (PR-1a/PR-1b). Ubuntu-only CI
	# cannot assert macOS/Windows path/journal/os.replace/extraction behavior; this matrix runs the
	# crash-recovery + legacy-migration tests, the updater verify/safe-extract tests, and the
	# transactional self-test on macOS + Windows (Ubuntu is covered by the `validate` job). Hash-based
	# manifest --check stays Ubuntu-only — it is sensitive to checkout line endings, not OS behavior.
	foundation-os:
	strategy:
	fail-fast: false
	matrix:
	os: [macos-latest, windows-latest]
	runs-on: ${{ matrix.os }}
	steps:
	- uses: actions/checkout@v4
	- name: Set up Python
	uses: actions/setup-python@v5
	with:
	python-version: "3.11"
	- name: Transactional installer crash-recovery + legacy-migration test
	run: python installers/tests/test_txn.py
	- name: Updater verify / safe-extract / check-update test (offline)
	run: python installers/tests/test_update.py
	- name: Opt-in SessionStart update-notify hook test (settings merge + hook logic)
	run: python installers/tests/test_session_hook.py
	- name: install.py transactional self-test
	run: python installers/install.py --self-test

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feat(lit-sync): opt-in fulltext-retrieval phase + consolidate OA cascade to fetch_oa.py #483

Workflow file

feat(lit-sync): opt-in fulltext-retrieval phase + consolidate OA cascade to fetch_oa.py #483

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Workflow file for this run