MANIFEST.yaml

name: sci-render-kit
purpose: "声明式科研图件编译、断言来源、claim-aware evidence、transfer handoff 与阶段化维护 | Declarative scientific-figure compilation with assertion-aware evidence, transfer handoff, and phase-aware maintenance"
calibrated: "2026-09-22"

principles:
  - 声明优先: "data / aesthetics / research_context / claim_bindings / uncertainty / process_disclosure / accessibility 由 recipe 显式声明"
  - claim绑定不推断: "visual_ref -> claim_refs 仅记录声明，不从标题/图例/像素/数据内容猜测"
  - 断言来源显式: "记录 figure/recipe/claim/process/uncertainty/ref 如何进入证据对象；basis 不等于 correctness"
  - 沟通覆盖分维度: "claim binding / evidence context coverage 使用独立计数与比例，不合成科研质量总分"
  - transfer不继承权威: "communication transfer 保留上下文但不继承 truth/entailment/statistical validity/acceptance"
  - reproducibility上下文不丢失: "figure-evidence 的 reproducibility context 进入 communication-transfer，但不继承 independent reproduction"
  - 维护分层: "daily 处理局部 drift，weekly 做全当前文档与 communication contract reconciliation，monthly/phase-close 做 baseline 与 history inventory"
  - 维护范围有界: "maintenance scanner configured paths 必须保持 repository-local；越界配置 fail closed"
  - 报告可移植: "repo-local paths 使用 repository-relative identity；config bytes 使用 SHA-256 绑定"
  - 写入语义诚实: "scanner 不修改 inspected files；--output 仅写 caller-requested report 并显式记录"
  - 文档权威显式: "current/historical/example/external metadata 由 docs/03-maintenance-and-audit/DOCUMENT_STATUS.md 分类"
  - 历史不重写: "历史 consolidation 是阶段证据；当前 contract 更新不自动改写历史"
  - 时间状态不猜测: "calendar-month 与 stage close 由日期/配置决定；closed stage 与 current calendar status 分开"
  - 示范不冒充执行证据: "首个 Daily/Weekly/Monthly worked demonstration 是 reference，不伪造 clean scanner output"
  - 后端能力诚实: "schema 字段存在不等于所有 backend 已实现"
  - 不幻觉: "未知 provider/model/version/review/source 状态保持 null 或 not_declared"
  - 不做AI文本检测: "canonical renderer 不从 prose/pixels/metadata 推断 AI 使用或作者资格"
  - 真实版本保留: "真实标准与运行环境版本属于 provenance"
  - 科学边界: "render/profile/hash/provenance/claim-binding/basis/coverage/transfer/maintenance 不证明科研真值或独立复现"

stable_project_profiles:
  - sci-render-kit/runtime-quality
  - sci-render-kit/render-manifest
  - sci-render-kit/provenance
  - sci-render-kit/a11y
  - sci-render-kit/figure-claim-binding
  - sci-render-kit/figure-claim-audit
  - sci-render-kit/process-disclosure
  - sci-render-kit/figure-evidence
  - sci-render-kit/communication-transfer
  - sci-render-kit/maintenance-cadence
  - sci-render-kit/maintenance-report

profile_identifier_policy:
  decorative_versions_allowed: false
  examples_forbidden: ["@1", "@2", "/v1"]
  compatibility_source: "documented fields + semantics"
  real_external_versions_preserved: true

stage_close:
  id: 2026-08-scientific-communication
  window: ["2026-08-24", "2026-08-31"]
  calendar_month_status: calendar-month-close
  research_phase_status: closed
  history_rewrite: false
  automatic_deletion: false
  scientific_validity_claim: false
  publisher_acceptance_claim: false
  accessibility_conformance_claim: false
  reproduction_claim: false

current_temporal_status:
  as_of: "2026-10-01"
  as_of_semantics: last_explicit_calendar_state_reconciliation_not_daily_heartbeat
  runtime_report_as_of_semantics: execution_or_caller_supplied_observation_date
  calendar_month_status: month-to-date
  closed_stage_status: closed
  stage_reopened_by_repair: false

architecture:
  canonical_flow:
    - recipe_and_declared_research_context
    - p0_schema
    - p1_runtime_and_claim_audit
    - assertion_basis_and_communication_coverage
    - backend_capability_resolution
    - render
    - p2_artifact_integrity
    - p3_publisher_target_alignment
    - figure_evidence
    - optional_communication_transfer
  github_native_gate_required: false

runtime_quality:
  profile: sci-render-kit/runtime-quality
  rules: quality/rules.yaml
  levels: [P0, P1, P2, P3]
  severities: [error, warning, info]
  stop_condition: "severity == error"
  scientific_validity_claim: false

recipes:
  schema: metadata/recipe.schema.yaml
  document_status: current_machine_contract
  chart_types: [line-chart, bar-chart, scatter-plot, heatmap, boxplot, histogram]
  claim_bindings:
    profile: sci-render-kit/figure-claim-binding
    required_fields: [visual_ref, claim_refs, relation]
    relations: [supports, illustrates, contextualizes, compares, derived-from]
    assertion_basis: recipe-declared
    inferred_by_renderer: false
    entailment_claim: false
  process_disclosure:
    profile: sci-render-kit/process-disclosure
    assertion_basis: recipe-declared
    automatic_ai_detection_used: false
    ai_assistance_values: [none, used, not_declared]
    human_review_values: [reviewed, partial, not_reviewed, not_declared]
    authorship_claim: false
    peer_review_claim: false
    scientific_validity_claim: false
  uncertainty:
    assertion_basis: recipe-declared
    supported_kinds:
      - standard-error
      - standard-deviation
      - confidence-interval
      - credible-interval
      - min-max-range
      - quantile-interval
      - bootstrap-interval
      - heuristic-bound

backends:
  matplotlib:
    adapter: backends/matplotlib_adapter.py
    base_adapter: backends/matplotlib_base.py
    outputs: [png, svg, pdf]
    render_manifest: sci-render-kit/render-manifest
    provenance: sci-render-kit/provenance
    runtime_versions_recorded: true
    redundant_series_style: implemented
  ggplot2:
    adapter: backends/ggplot2_adapter.R
    outputs: [png, svg, pdf]
    render_manifest: sci-render-kit/render-manifest
    runtime_versions_recorded: true
    runtime_environment: optional
    redundant_series_style: not_integrated
  observable:
    adapter: backends/observable_adapter.js
    outputs: [html]
    render_manifest: sci-render-kit/render-manifest
    plot_version: "0.6.17"
    browser_dependency: "@observablehq/plot@0.6.17/+esm via CDN"
    offline_environment_complete: false

artifacts:
  render_manifest:
    profile: sci-render-kit/render-manifest
    sidecar: <output>.manifest.json
    default_reproducibility_semantics: R1
  provenance:
    profile: sci-render-kit/provenance
    sidecar: <output>.prov.json
    backend_scope: matplotlib
  accessibility:
    profile: sci-render-kit/a11y
    sidecar: <output>.a11y.json
    conformance_claim: false
  figure_claim_audit:
    profile: sci-render-kit/figure-claim-audit
    module: core/claim_binding_audit.py
    communication_coverage:
      dimensions:
        - figure_claim_count
        - valid_binding_count
        - distinct_visual_ref_count
        - distinct_bound_claim_count
        - indexed_claims_with_binding_count
        - bindings_with_evidence_ref_count
        - bindings_with_any_evidence_context_count
        - supports_binding_count
        - supports_with_evidence_context_count
        - process_disclosure_declared_field_count
      ratios:
        - indexed_claim_binding_ratio
        - binding_evidence_context_ratio
        - supports_evidence_context_ratio
      aggregate_score: null
      entailment_claim: false
      evidence_sufficiency_claim: false
      provenance_soundness_claim: false
      probability_claim: false
    scientific_validity_claim: false
  figure_evidence:
    profile: sci-render-kit/figure-evidence
    module: core/figure_evidence.py
    sidecar: <output>.evidence.json
    claim_binding_profile: sci-render-kit/figure-claim-binding
    process_disclosure_profile: sci-render-kit/process-disclosure
    assertion_basis:
      figure_identity: runtime-observed-local-bytes
      recipe_profile_identity: runtime-observed-local-bytes-and-canonical-serialization
      claim_communication: recipe-declared
      process_disclosure: recipe-declared
      uncertainty: recipe-declared
      upstream_research: recipe-declared-with-optional-local-resolution
      local_reference_resolution: runtime-observed-local-filesystem
      automatic_ai_detection_used: false
    reproducibility:
      level: R1
      semantics: replay_addressable_not_independent_reproduction
      r3_requires_separate_rerun: true
    scientific_validity_claim: false
    statistical_validity_claim: false
    causal_validity_claim: false
    authorship_claim: false
    peer_review_claim: false
    publisher_acceptance_claim: false
  communication_transfer:
    profile: sci-render-kit/communication-transfer
    module: core/communication_transfer.py
    machine_contract: metadata/communication_transfer.contract.yaml
    machine_contract_status: current
    source_profile: sci-render-kit/figure-evidence
    wrong_profile_behavior: fail_explicitly
    destination_basis: caller_declared_or_not_declared
    purpose_basis: caller_declared_or_not_declared
    payloads_preserved:
      - claim_communication
      - upstream_research
      - uncertainty
      - process_disclosure
      - communication_audit
      - runtime_validation
      - reproducibility
    transfer_constraints:
      scientific_validity_inherited: false
      entailment_inherited: false
      evidence_sufficiency_inherited: false
      statistical_validity_inherited: false
      peer_review_inherited: false
      publisher_acceptance_inherited: false
      accessibility_conformance_inherited: false
      independent_reproduction_inherited: false
    transfer_coverage:
      reproducibility_context_present: true
      aggregate_score: null
    independent_reproduction_claim: false
  maintenance_cadence:
    profile: sci-render-kit/maintenance-report
    module: core/maintenance_cadence.py
    config: maintenance/cadence.yaml
    cadences: [daily, weekly, monthly]
    calendar_status_is_date_derived: true
    stage_status_is_config_derived: true
    current_calendar_status: month-to-date
    current_stage_status: closed
    repository_scope_enforced: true
    configured_absolute_paths_allowed: false
    configured_parent_traversal_allowed: false
    configuration_sha256_recorded: true
    repo_local_paths_are_relative: true
    absolute_repository_root_embedded: false
    inspected_files_mutated: false
    report_output_write_supported: true
    report_output_write_recorded: true
    remote_dereference: false
    tests_run_by_scanner: false
    github_actions_used: false
    automatic_deletion: false
    automatic_history_rewrite: false
    aggregate_score: null
    scientific_validity_claim: false
    entailment_claim: false
    publisher_acceptance_claim: false

accessibility:
  wcag_version: "2.2"
  supported_design_scope:
    - "1.1.1 text-alternative support"
    - "1.4.1 non-color cue support"
    - "1.4.3 text contrast support where applicable"
    - "1.4.11 declared graphical-boundary contrast support"
  all_pairs_palette_policy: "optional stricter project safeguard; not universal WCAG requirement"
  cvd_simulation: "project safeguard; not WCAG-mandated test"
  conformance_claim: false

publisher_profiles:
  semantics: "project presets with source status; not official acceptance validators"
  acceptance_claim: false

interoperability:
  upstream_auto_doc:
    preferred_profiles:
      - auto-doc-engine/artifact-record
      - auto-doc-engine/artifact-lineage
    mode: optional_reference_handoff
  upstream_epistemic:
    preferred_profiles:
      - epistemic-pipeline/evidence-envelope
      - epistemic-pipeline/claim-verification
      - epistemic-pipeline/claim-transfer
    mode: optional_reference_handoff
    direct_runtime_coupling: false
  ro_crate:
    version: "1.3"
    status: proposed
    note: "sci-render-kit sidecars are not RO-Crates"

reproducibility:
  local_levels: [R0, R1, R2, R3]
  r3_rule: "requires an actual separate rerun plus declared comparison criterion"

maintenance:
  contract: docs/03-maintenance-and-audit/MAINTENANCE_CADENCE.md
  config: maintenance/cadence.yaml
  document_status: docs/03-maintenance-and-audit/DOCUMENT_STATUS.md
  stage_index: docs/03-maintenance-and-audit/history/STAGE_2026_08_MAINTENANCE.md
  post_stage_repair: maintenance/POST_STAGE_REPAIR_2026_09_01.md
  first_complete_cadence_demonstration: maintenance/FIRST_COMPLETE_CADENCE_DEMONSTRATION_2026_08_31.md
  demonstration_status: reference_non_normative
  demonstration_is_runtime_proof: false
  current_calendar_status: month_to_date
  current_stage_status: closed
  daily:
    scope: local_recipe_figure_evidence_backend_document_drift
    history_rewrite: false
  weekly:
    scope: full_current_communication_document_contract_reconciliation
    canonical_hash_baseline: true
    history_inventory: true
  monthly:
    scope: calendar_month_or_explicit_phase_close
    canonical_hash_baseline: true
    history_inventory: true
    automatic_deletion: false
    phase_close_must_be_explicit_or_configured: true

not_integrated:
  - pixel_based_claim_inference
  - scientific_entailment_validator
  - evidence_sufficiency_validator
  - provenance_soundness_validator
  - automatic_ai_text_detection
  - statistical_method_validator
  - whole_publication_wcag_certifier
  - official_publisher_acceptance_validator
  - automatic_repository_scheduler
  - automatic_history_deletion
  - automatic_independent_reproduction_inference

frontier_calibration:
  checked_through: "2026-09-01"
  signals:
    - provenance_grounds_trust_in_autonomous_science
    - responsible_transparent_ai_scientific_publishing
    - artifact_centered_claim_aware_observability
    - trajectories_to_evidence
    - brain_researcher
    - earthverse
    - claim_level_auditability_provenance_coverage
    - ai_detection_distinct_from_disclosure
    - praxist_solution_lineages
    - reproagent_persistent_contracts
    - long_horizon_phase_behavior_and_regime_aware_revalidation
    - scienceflow_segmented_research_and_recovery
    - beyond_final_scores_long_horizon_process_evaluation
    - trajectory_honesty_and_intermediate_error_propagation
    - explicit_scientific_agent_interface_state_and_safety_boundaries
    - living_research_software_maintenance
  borrowed_scope: "claim/artifact relations + assertion basis + dimensional communication coverage + reproducibility-context preservation + non-inheritance transfer + scope-bounded portable maintenance + document-authority reconciliation"
  endorsement_or_certification_claim: false

research_contract:
  file: docs/02-examples-and-contracts/RESEARCH_CONTRACT.md
  figure_claim_contract: docs/02-examples-and-contracts/FIGURE_CLAIM_CONTRACT.md
  assertion_basis_communication_coverage: docs/02-examples-and-contracts/ASSERTION_BASIS_AND_COMMUNICATION_COVERAGE.md
  communication_transfer_contract: docs/02-examples-and-contracts/COMMUNICATION_TRANSFER_CONTRACT.md
  communication_transfer_machine_contract: metadata/communication_transfer.contract.yaml
  maintenance_contract: docs/03-maintenance-and-audit/MAINTENANCE_CADENCE.md
  document_status: docs/03-maintenance-and-audit/DOCUMENT_STATUS.md
  closed_stage_index: docs/03-maintenance-and-audit/history/STAGE_2026_08_MAINTENANCE.md
  post_stage_repair: maintenance/POST_STAGE_REPAIR_2026_09_01.md
  first_complete_cadence_demonstration: maintenance/FIRST_COMPLETE_CADENCE_DEMONSTRATION_2026_08_31.md
  historical_snapshots:
    - docs/03-maintenance-and-audit/history/FOUR_DAY_CONSOLIDATION.md
    - docs/03-maintenance-and-audit/history/FIVE_DAY_CONSOLIDATION.md
    - docs/03-maintenance-and-audit/history/SIX_DAY_CONSOLIDATION.md
  frontier_alignment: docs/03-maintenance-and-audit/history/FRONTIER_ALIGNMENT.md

research_software:
  citation: CITATION.cff
  cff_version: "1.2.0"

experimental_modules:
  projection: "centered-SVD PCA and projection metrics; t-SNE not implemented"
  uncertainty_legend: "typed uncertainty metadata"
  superposition: "deterministic variant layering"
  time_crystal: "periodic waveform utility; no physical time-crystal claim"
  observer_dashboard: "caller-supplied telemetry; no automatic comprehension/causal claim"

local_checks:
  mode: manual_optional
  github_actions: false
  codeql: false
  merge_gate: false
  tests_required_for_2026_09_01_repair: false
  maintenance_scanner: core/maintenance_cadence.py

scientific_boundaries:
  render_success_is_scientific_truth: false
  assertion_basis_is_correctness: false
  communication_coverage_is_entailment: false
  coverage_ratio_is_probability: false
  claim_binding_is_entailment: false
  communication_transfer_is_entailment: false
  reproducibility_context_is_independent_reproduction: false
  publisher_profile_is_acceptance: false
  accessibility_support_is_wcag_certification: false
  maintenance_clean_is_scientific_validity: false
  monthly_baseline_is_reproduction: false
  calendar_month_close_is_reproduction: false
  provenance_is_truth: false


# 2026-09-23 dual-view maintenance annotation:
# N-1 view: calibrated=2026-09-22 remains the point-in-time manifest/router cutoff.
# N view: later Stage D communication research is current state only and does not rewrite earlier availability.
# Render/profile/provenance/claim-binding remain distinct from validity, entailment, acceptance, and reproduction.
# 2026-09-24 A1 full-period annotation:
# Review cutoff: 2026-09-23.
# September Stage A/B/C/D communication research, evidence/source records, reconstructions,
# reviews, syntheses/handoffs, current router/manifest, and A→D longitudinal state were re-read.
# Render/profile/provenance/claim-binding remain distinct from validity, entailment,
# certification, acceptance, and independent reproduction.
# 2026-09-24 Stage E frontier-research reconciliation:
# Stage E / 2025-Q1 and the additive A→E cross-year synthesis are now present as non-normative communication research.
# The earlier same-day observation that Stage E was absent remains historically correct for its cutoff.
# Release/revision research adds no render validity, accessibility certification, publisher acceptance, or reproduction claim.
# 2026-09-25 Stage F frontier-research reconciliation:
# Stage F / 2025-Q2 and the additive A→F synthesis are now present as non-normative communication research.
# Migration/backend/SRI/ARIA research adds no render validity, accessibility certification, publisher acceptance or reproduction claim.


# 2026-09-26 Stage G frontier-research reconciliation:
# Stage G / 2025-Q3 and the additive A→G synthesis are now present as non-normative communication research.
# Matplotlib / Plotly.py / Vega-Lite release research adds no local package/runtime/browser execution,
# render validity, accessibility certification, publisher acceptance, scientific validity, or reproduction claim.


# 2026-09-28 Stage H document-routing reconciliation:
# Stage H / 2025-Q4 is present on current main and LONGITUDINAL_INDEX routes the current A→H documentary relation.
# maintenance/frontier-research/longitudinal/ currently ends at LONGITUDINAL_SYNTHESIS_2024_TO_2025_Q3.md;
# no A→H synthesis artifact is inferred or manufactured by this annotation.
# This is routing metadata only: calibrated=2026-09-22 is preserved, and no runtime capability,
# machine-contract semantics, scientific validation, reproduction status, or release authority is changed.