zymor 0.2.0__tar.gz

zymor-0.2.0/.env.example

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+# OpenAI-compatible endpoint
+OPENAI_BASE_URL=https://api.openai.com/v1
+OPENAI_API_KEY=

zymor-0.2.0/.github/ISSUE_TEMPLATE/bug_report.yml

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+name: Bug report
+description: Report a reproducible bug in Zymor
+title: "[Bug]: "
+labels: ["bug"]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Thanks for reporting. Please do not include secrets, API keys, or private vault contents.
+  - type: input
+    id: version
+    attributes:
+      label: Version / commit
+      description: Output of `zymor --version` or the commit SHA.
+      placeholder: "0.1.0 / 598d775"
+    validations:
+      required: true
+  - type: dropdown
+    id: surface
+    attributes:
+      label: Surface
+      options:
+        - CLI
+        - MCP server
+        - dream engine
+        - retrieval / index
+        - write protocol
+        - docs / packaging
+        - other
+    validations:
+      required: true
+  - type: textarea
+    id: steps
+    attributes:
+      label: Reproduction steps
+      description: Minimal commands, files, or vault structure needed to reproduce.
+      placeholder: |
+        1. zymor init
+        2. zymor remember ...
+        3. zymor search ...
+    validations:
+      required: true
+  - type: textarea
+    id: expected
+    attributes:
+      label: Expected behavior
+    validations:
+      required: true
+  - type: textarea
+    id: actual
+    attributes:
+      label: Actual behavior / logs
+      description: Redact secrets and personal paths.
+    validations:
+      required: true
+  - type: checkboxes
+    id: checks
+    attributes:
+      label: Checklist
+      options:
+        - label: I searched existing issues.
+          required: true
+        - label: I removed secrets and private data from this report.
+          required: true

zymor-0.2.0/.github/ISSUE_TEMPLATE/config.yml

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+blank_issues_enabled: false
+contact_links:
+  - name: Security report
+    url: https://github.com/Gyanano/zymor/security/advisories/new
+    about: Please report vulnerabilities privately, not in a public issue.
+  - name: Documentation
+    url: https://github.com/Gyanano/zymor/tree/main/docs
+    about: Check the user guide before opening a usage question.

zymor-0.2.0/.github/ISSUE_TEMPLATE/feature_request.yml

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+name: Feature request
+description: Propose a capability or design change
+title: "[Feature]: "
+labels: ["enhancement"]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        For memory-model, storage-format, MCP-tool, or public-CLI changes, describe the design impact first.
+  - type: textarea
+    id: problem
+    attributes:
+      label: Problem
+      description: What is hard or impossible today?
+    validations:
+      required: true
+  - type: textarea
+    id: proposal
+    attributes:
+      label: Proposed behavior
+    validations:
+      required: true
+  - type: textarea
+    id: alternatives
+    attributes:
+      label: Alternatives considered
+  - type: dropdown
+    id: scope
+    attributes:
+      label: Scope
+      options:
+        - small / local
+        - memory model or storage format
+        - MCP or public CLI
+        - docs / tooling
+        - needs design discussion
+    validations:
+      required: true
+  - type: checkboxes
+    id: checks
+    attributes:
+      label: Checklist
+      options:
+        - label: I searched existing issues and discussions.
+          required: true
+        - label: I understand this may need an issue-first design discussion.
+          required: true

zymor-0.2.0/.github/PULL_REQUEST_TEMPLATE.md

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+## What changed
+
+<!-- One or two sentences. Link the issue below. -->
+
+Closes #
+
+## Why
+
+<!-- The problem this solves, not only the implementation. -->
+
+## Verification
+
+<!-- Commands and results. Do not include secrets. -->
+
+```bash
+uv sync --extra dev
+uv run pytest tests/test_open_smoke.py -q
+uv run ruff check src tests
+uv run mypy src/zymor
+```
+
+## Checklist
+
+- [ ] Behavior change has a test or a clear reason why it does not.
+- [ ] CLI / MCP / config changes have docs updates.
+- [ ] User-visible changes are in `CHANGELOG.md`.
+- [ ] No secrets, private vaults, datasets, or generated caches are included.
+- [ ] AI-assisted work was reviewed by the submitter.

zymor-0.2.0/.github/dependabot.yml

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+version: 2
+updates:
+  - package-ecosystem: "uv"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    open-pull-requests-limit: 5
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    open-pull-requests-limit: 5

zymor-0.2.0/.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+concurrency:
+  group: ci-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  test:
+    name: ruff + mypy + smoke (Python ${{ matrix.python-version }})
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.12", "3.13"]
+    steps:
+      - uses: actions/checkout@v7
+      - uses: astral-sh/setup-uv@v7
+        with:
+          enable-cache: true
+      - name: Install Python
+        run: uv python install ${{ matrix.python-version }}
+      - name: Sync dependencies
+        run: uv sync --extra dev --python ${{ matrix.python-version }}
+      - name: Ruff
+        run: uv run ruff check src tests
+      - name: Mypy
+        run: uv run mypy src/zymor
+      - name: Smoke tests
+        run: uv run pytest tests/test_open_smoke.py -q

zymor-0.2.0/.github/workflows/release.yml

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+name: Release
+
+on:
+  push:
+    tags:
+      - "v*"
+
+permissions:
+  contents: read
+
+concurrency:
+  group: release-${{ github.ref }}
+  cancel-in-progress: false
+
+jobs:
+  build:
+    name: Build distributions
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v7
+      - uses: astral-sh/setup-uv@v7
+        with:
+          enable-cache: true
+      - name: Verify tag matches project version
+        run: |
+          version=$(python3 -c "import tomllib; print(tomllib.load(open('pyproject.toml','rb'))['project']['version'])")
+          test "v$version" = "$GITHUB_REF_NAME"
+      - name: Build sdist and wheel
+        run: uv build
+      - uses: actions/upload-artifact@v7
+        with:
+          name: dist
+          path: dist/
+
+  publish:
+    name: Publish to PyPI
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/zymor
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/download-artifact@v8
+        with:
+          name: dist
+          path: dist/
+      - uses: pypa/gh-action-pypi-publish@release/v1

zymor-0.2.0/.gitignore

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+__pycache__/
+*.py[cod]
+*.egg-info/
+.venv/
+dist/
+build/
+
+.pytest_cache/
+.ruff_cache/
+.mypy_cache/
+.uv/
+
+.env
+.env.local
+
+.zymor/
+eval-runs/
+
+# prototype workspaces (throwaway; results files stay tracked)
+prototypes/fts5-bench/corpus_sample/
+prototypes/eval-smoke/.venv/
+prototypes/eval-smoke/data/
+prototypes/eval-smoke/runs/
+prototypes/eval-smoke/logs/
+prototypes/eval-smoke/official/
+prototypes/**/*.sqlite3
+prototypes/**/node_modules/
+
+.DS_Store
+Thumbs.db
+prototypes/fts5-bench/data/
+prototypes/eval-smoke/profiles/
+prototypes/eval-smoke/tmp/
+prototypes/fts5-bench/summary.partial.json
+prototypes/formal-check/__pycache__/

zymor-0.2.0/CHANGELOG.md

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+# Changelog
+
+本项目遵循 [Keep a Changelog](https://keepachangelog.com/zh-CN/1.1.0/) 与语义化版本。
+
+## [0.2.0] - 2026-10-28
+
+### Added
+
+- 跨项目 L3 晋升：`zymor promote <id> [--dry-run] [--yes]`，校验 verified/confidence/verify_count/hit_count/applies_to/evidence/未决冲突，写用户库副本并保留 provenance 与去重；NREM 自动晋升带 `cross-project` 标签的节点（`promotion.auto_enabled` 可关）。节点新增 `projects` provenance；`zymor adopt ID` 记录当前项目确认复用用户库节点，第二次采纳自动打 `cross-project-verified` 标签；`promotion.min_projects` 可设多项目门槛，`--force` 覆盖。
+- 失效锚定：节点新增可选 `anchors` 字段；`zymor anchor <id> --file PATH` 绑定文件 sha256，`--package MANIFEST:PACKAGE` 绑定 package.json/pyproject 依赖版本，`--api MANIFEST:KEY` 绑定本地 JSON/TOML 版本清单中的外部 API 版本；`zymor stale [--deprecate]` 检查/标记失效节点（deprecated + Tombstone + evidence）；`memory_search` 与 `memory_context` 默认排除 stale（search 加 `include_stale` 可查看），`memory_read` 返回 `stale` 与 `stale_reasons`。
+- 上下文状态标签：`memory_context` 只注入 verified L4 并标 `[verified]`；L2 胶囊行标 `[status]`。
+- 捕获/做梦自动化：`memory_close` 自动向 L0 追加 `system_note` 关闭事件；`dream.auto_after_close=true` 时 MCP `memory_close` 自动跑 NREM+仲裁。
+- 检索：FTS5 索引同时写入 snake_case/camelCase 子词，查询生成 `原词 OR 子词`；`meta.tokenizer` 升到 `cjk-bigram-v2-identifiers`，版本不符自动重建索引；新增可选 embedding 向量索引（`zymor index embed`）与 `memory_semantic_search`/`zymor semantic`；`search --semantic` / `include_semantic` 融合词法与向量命中。
+- MCP：新增 `memory_promote`、`memory_adopt`、`memory_stale` 三个写工具，Agent 可直接跨项目晋升/采纳/检查失效。
+- 检索：新增 `memory_rules` / `zymor rules`，直接返回 verified L3 规则（task_type 过滤、token 预算 400），供 Agent 在会话开始/任务切换时加载项目约定；新增 `memory_rule_check` / `zymor rule-check`，按规则正文 `## 检查` 的 contains/absent/regex 约束做只读校验。
+- 开源发布工程：最小功能冒烟测试、GitHub Actions CI（ruff / mypy / Python 3.12 + 3.13）、Dependabot（uv + GitHub Actions）、CodeQL、main/tag ruleset、PyPI Trusted Publishing workflow。
+- 协作与发布文档：中英双语 README、主题自适应 Logo、CONTRIBUTING、SECURITY、CODE_OF_CONDUCT、issue/PR 模板、仓库工作流与发布指南。
+
+## [0.1.0] - 2026-10-27
+
+### Added
+
+- v0 记忆内核：L0 事件流、L1 焦点、L2 胶囊、L3 知识节点、L4 人格 facet；Memory Node schema 与校验；双库 vault 布局；SQLite FTS5 索引（CJK bigram 外部分词，可重建缓存）。
+- 检索与上下文组装：评分公式、过滤、`memory_search/read/browse/links`、跨库合并、`memory_context`、ATLAS 与 catalog 生成、检索审计与预算。
+- 写入协议：写作门控、去重四动作（new / append-evidence / supersede / conflict）、状态机、L1→L2 胶囊、L0 捕获、失调队列、隐私删除。
+- 做梦引擎：NREM 巩固、认知失调仲裁、REM 跨域联想、L4 人格提炼、预算/锁/水位线、胶囊闲置降权、晨间追问与 `zymor answer`。
+- MCP Server：11 个工具（只读模式 5 个）、resources（atlas/catalog/node）、prompts（boot/review）、stdio 与 Streamable HTTP（静态 Bearer token）、敏感信息检测与脱敏、`instructions` 短协议。
+- 工程与文档：v0 规格、形式化模型、研究资产、用户手册、CI（Windows/Ubuntu × Python 3.12/3.13）、CHANGELOG、Apache-2.0。
+
+### Known limitations
+
+- 无 OpenAI 兼容通道：headline 分数与竞品复跑未产出；只提交 local-protocol harness 冒烟（不可解释）。
+- MCP-only 捕获依赖 Agent 调用 `memory_log`；无宿主桥。
+- 无常驻做梦守护进程；REM/人格质量仅用脚本化假 LLM 验证；P6 人工荒谬率待抽检。
+- 仲裁不执行本地命令；跨项目 L3→用户库晋升未实现；胶囊降权为每次 run 的离散步进。
+
+[0.1.0]: https://github.com/Gyanano/zymor/releases/tag/v0.1.0
+[0.2.0]: https://github.com/Gyanano/zymor/releases/tag/v0.2.0

zymor-0.2.0/CODE_OF_CONDUCT.md

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+# Code of Conduct
+
+This project adopts the [Contributor Covenant, version 2.1](https://www.contributor-covenant.org/version/2/1/code_of_conduct/).
+
+## Our pledge
+
+We want participation in Zymor to be a harassment-free experience for everyone, regardless of age, body size, visible or invisible disability, ethnicity, sex characteristics, gender identity and expression, level of experience, education, socio-economic status, nationality, personal appearance, race, religion, or sexual identity and orientation.
+
+## Expected behavior
+
+- Be respectful and constructive.
+- Assume good intent; critique ideas, not people.
+- Give and accept actionable feedback.
+- Respect privacy and do not publish others' private information.
+- Do not use sexualized language or imagery, or unwelcome attention.
+
+## Unacceptable behavior
+
+Harassment, threats, discriminatory language, deliberate intimidation, doxxing, and sustained disruption are not acceptable.
+
+## Reporting
+
+Report incidents privately via GitHub's **Security → Report a vulnerability** flow or directly to the maintainer (`@Gyanano`). Reports will be reviewed and handled as confidentially as possible. Maintainers may remove comments, close issues, or block accounts that violate this policy.
+
+## Attribution
+
+This policy is based on the Contributor Covenant 2.1, available at https://www.contributor-covenant.org/version/2/1/code_of_conduct/.

zymor-0.2.0/CONTRIBUTING.md

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+# Contributing to Zymor
+
+Thanks for your interest. This project favors small, verifiable changes over large rewrites.
+
+## Before you start
+
+- For bugs, open an issue using the bug report template.
+- For features, open a feature request first and describe the problem, not only the solution.
+- For security issues, do **not** open a public issue; follow [`SECURITY.md`](SECURITY.md).
+- For design changes that affect the memory model, storage format, MCP tools, or public CLI, open an issue first and get agreement before writing code.
+
+## Development setup
+
+```bash
+uv sync --extra dev
+uv run pytest tests/test_open_smoke.py -q
+uv run ruff check src tests
+uv run mypy src/zymor
+```
+
+The public repository ships a minimal functional smoke suite. Full evaluation harnesses and datasets are intentionally not part of the open-source release.
+
+## Branch and commits
+
+- Branch from `main`: `feat/<short-name>`, `fix/<short-name>`, `docs/<short-name>`, `chore/<short-name>`.
+- Use [Conventional Commits](https://www.conventionalcommits.org/): `feat:`, `fix:`, `docs:`, `test:`, `refactor:`, `chore:`.
+- Keep commits reviewable; avoid mixing refactors and behavior changes.
+- Do not commit secrets, local vaults, `.env.local`, datasets, or generated caches.
+- AI-assisted contributions are welcome; you are responsible for reviewing and testing the result.
+
+## Pull requests
+
+A good PR:
+
+- links the issue (`Closes #123`);
+- states the behavior change and how it was verified;
+- adds or updates a test when behavior changes;
+- updates user-facing docs when CLI/MCP behavior changes;
+- updates `CHANGELOG.md` for user-visible changes;
+- passes CI (`ruff`, `mypy`, smoke tests).
+
+The maintainer merges with squash merge. Please do not force-push a branch after review starts unless asked.
+
+## Code and documentation rules
+
+- Code comments are intentionally sparse; prefer self-explanatory code and short interface docstrings.
+- Documentation is the source of current behavior: update it instead of describing history.
+- Do not add network calls, API keys, or provider-specific endpoints to tests.
+- Do not add evaluation data or test reports to this repository.
+
+## Review and release
+
+- One maintainer review is required while the project has a single maintainer; this may become two approvals later.
+- Releases follow [Semantic Versioning](https://semver.org/) and [Keep a Changelog](https://keepachangelog.com/).
+- Release tags use `vMAJOR.MINOR.PATCH`; release notes come from `CHANGELOG.md`.
+
+## Community
+
+By participating you agree to follow [`CODE_OF_CONDUCT.md`](CODE_OF_CONDUCT.md).

zymor-0.2.0/GLOSSARY.md

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+# Zymor 术语表
+
+一个词条只写「它是什么」，不写实现方案。实现细节在 `project documentation`。
+
+| 术语 | 定义 |
+| --- | --- |
+| Zymor | 本项目：与宿主无关的 Agent 记忆系统，由分层记忆、做梦引擎与可移植知识库组成。中文对外名「织梦师」。 |
+| 宿主 / Harness | 运行 Agent 的框架或应用（DSH、Claude Code、Cursor、Codex 等）；Zymor 通过 MCP 与它们解耦。 |
+| 事件（Event） | L0 感知流中的一条原始记录（用户消息、助手消息、工具调用或结果），append-only，不进入上下文。 |
+| 焦点文件（Focus File） | 每个会话一个的 L1 工作记忆文件，包含当前目标、活跃假设、已排除路径等，是唯一全量挂载层。 |
+| 胶囊（Capsule） | L2 层的情景记忆节点，承载跨天/周任务的状态；平时只暴露一句话摘要。 |
+| 心智 facet（Facet） | L4 层的心智节点，描述在特定任务情境下应如何行事的可执行规则，含正例与反例。 |
+| WikiLink / 双链 | 正文中的 `[[mem_...]]` 引用；索引器据此建立双向链接关系。 |
+| 记忆库（Vault） | 一个自包含的记忆目录（全局库或项目库）：Markdown 为事实源，SQLite 索引为可重建缓存。 |
+| 两速写入（Two-Speed Write） | L0 事件逐条追加、不调用 LLM；记忆节点只在显式写入或做梦提取时产生，不做每轮实时抽取。 |
+| 写作门控（Salience Gate） | 写入前判断「值不值得记」的清单：丢弃常识、易得事实与一次性噪音，保留踩坑因果、取舍、用户偏好与跨任务经验。 |
+| 失调队列（Dissonance Queue） | 新记忆与旧记忆冲突、尚未裁决时记录的待办队列，由做梦仲裁或晨间追问消费。 |
+| 晨间追问（Morning Questions） | 做梦无法自行裁决的问题，在下一次会话通过 `memory_context` 呈现给用户确认。 |
+| 探针（Probe） | 针对公开基准不覆盖的差异能力（做梦、墓碑、唤醒度、渐进披露、胶囊唤醒、跨域链接）设计的内部回归测试。 |
+| 记忆节点（Memory Node） | 记忆的最小可检索单元：一条结论及其元数据、证据来源；以带 YAML frontmatter 的 Markdown 文件承载。 |
+| 认知分类（Category） | 记忆节点的类型：情景 episodic（发生过什么、为何决策）、陈述 semantic（领域事实）、程序 procedural（SOP 与做法）、心智 axioms（思维模型与偏好）。 |
+| L0 感知流 | 未经整理的原始交互与工具事件；不进入上下文，只作为做梦的原料。 |
+| L1 焦点工作台 | 当前任务的活跃目标、假设与临时状态；唯一全量进入上下文的记忆层。 |
+| L2 情景胶囊 | 跨天/周的长线任务状态；平时只暴露一句话摘要，命中时展开。 |
+| L3 知识库 | 经实战验证与做梦提炼的长期知识；按需渐进式读取，不常驻上下文。 |
+| L4 情境心智 | 跨任务稳定的人格与思维偏好（论证方式、审美、沟通风格），按任务情境动态挂载。 |
+| 做梦（Dream Cycle） | 异步的记忆维护过程：清洗与巩固 → 矛盾仲裁 → 跨域联想 → 人格提炼。 |
+| 巩固（Consolidation） | 把一次性经验转成更稳定、更通用记忆的过程：置信度与稳定性提升、跨层晋升。 |
+| 唤醒度（Arousal） | 记忆的新奇/待验证程度，决定近期是否被优先召回；随验证转化为置信度。 |
+| 置信度（Confidence） | 一条记忆被证实为真的程度。 |
+| 墓碑（Tombstone） | 被证伪的记忆及其纠正记录：保留「此路不通」的教训，避免重蹈覆辙。 |
+| 认知失调（Dissonance） | 新信息与既有记忆冲突、尚未裁决的状态。 |
+| 渐进式披露（Progressive Disclosure） | 检索策略：先暴露目录与摘要，按需逐层深入，直到命中正文。 |
+| 上下文组装（Context Assembly） | 任务开始时决定哪些记忆进入上下文、以多少 token 预算进入的过程。 |
+| MCP | Model Context Protocol；Zymor 与宿主对接的标准协议。 |
+| 评估基线 | 一组固定基准与固定协议，用于给 Zymor 打分，并与主流记忆框架同表对比。 |
+| Zymor 探针 | 自建的、针对做梦/冲突/遗忘等差异能力的小型评测任务。 |

zymor-0.2.0/LICENSE

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