hypgraph 0.1.0__tar.gz

hypgraph-0.1.0/.gitignore

@@ -0,0 +1,16 @@
+__pycache__/
+*.py[cod]
+*.egg-info/
+.pytest_cache/
+.ruff_cache/
+.mypy_cache/
+build/
+dist/
+.venv/
+venv/
+*.hypgraph
+*.hypgraph-journal
+research.hypgraph*
+.DS_Store
+Thumbs.db
+.claude/

hypgraph-0.1.0/AGENTS.md

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+# HypGraph for agents
+
+You are an AI agent and you've been pointed at HypGraph. This page is for you; https://hypgraph.com/llms.txt is the
+same in short.
+
+**What it is.** A research record you write into and can't flatter. You add questions, hypotheses, experiments, runs,
+results, claims, sources, reviews and decisions. You can't set how well anything is known: review state, risk,
+independent support and evidence strength are worked out from the record each time it's read. Every write is a
+hash-chained event.
+
+**Why you'd want it.** It stops the mistakes agents make most: stating numbers no result contains, writing "always"
+about one run, calling a weak search an exclusion, citing a claim whose premise was withdrawn, and treating three
+copies of one result as three lines of evidence. When the record refuses a write, the message says exactly what to
+fix.
+
+## Connect
+
+**As a skill** (Claude Code and other Agent Skills hosts), install the skill with:
+
+```bash
+pip install hypgraph
+hypgraph skill --install          # writes .claude/skills/hypgraph/SKILL.md  (--user: under your home directory)
+```
+
+The skill's source is `src/hypgraph/skill/SKILL.md`, also at https://hypgraph.com/SKILL.md.
+
+**As an MCP server:**
+
+```bash
+pip install "hypgraph[mcp]"
+claude mcp add hypgraph -- hypgraph --db study.hypgraph --as <your-name> mcp
+```
+
+Any MCP client works. Command `hypgraph`, args `["--db", "study.hypgraph", "--as", "<your-name>", "mcp"]`.
+For HTTP: `hypgraph --db study.hypgraph --as <your-name> mcp --transport http --port 8766`.
+
+You write as one author, fixed when the server starts. The names `lab`, `operator`, `importer` and `system` are
+reserved.
+
+## The method
+
+1. **`overview()` first.** Read what's known before re-deriving anything.
+2. **Hypotheses with predictions.** `add("hypothesis", {"statement": …, "predictions": […]})`. Rivals get
+   `alternative_to`.
+3. **Experiments that can fail.** `add("experiment", {...}, links=[{"rel": "tests", "to": "H1", "data": {"expected":
+   "…"}}, …])`. Write what each hypothesis expects *before* you run anything. An experiment whose expected outcomes
+   differ between hypotheses ranks higher in `next_experiments()`. One with a `power_check` ranks higher still.
+4. **Runs and results.** `register_run(name, code_paths=[…], input_paths=[…], output_paths=[…], result_summary=…,
+   result_values={"rate": {"value": 0.31}, "hits": {"k": 4, "n": 50}})`. The server hashes the files.
+5. **Claims carry their numbers.**
+   ```json
+   {"statement": "The planted key was recovered in 4 of 50 trials.",
+    "scope": "50 synthetic ciphers of 200 letters, quadgram scoring, 10 restarts each.",
+    "kind": "finding",
+    "measurements": [{"name": "recovered", "result": "RS3", "key": "hits", "k": 4, "n": 50}]}
+   ```
+   with `links=[{"rel": "supports", "from": "RS3", "why": "RS3 is the measurement this claim states."}]`.
+   - every number in the statement must match a bound measurement, the scope, or an investigation constant;
+   - "never", "all", "always" or "proves" need a measurement with k = 0 or k = n;
+   - `kind: "exclusion"` needs a result with `power: "demonstrated"` (a search that found a planted answer).
+     Otherwise use `"inconclusive"`.
+6. **Reviews.** Only reviewers named by the investigation (or the host's policy) set standing. Nobody reviews their
+   own work. A revision makes earlier reviews stale.
+7. **Start summaries from `report()`.** It's generated from the record, so it can't restate a withdrawn claim. Write
+   your interpretation underneath it.
+
+## Reading standing
+
+Every node carries `state.sentence`, for example:
+
+> active claim · checked (fisher:pass, v2) · 2 independent lines of support · replicated on new data · no external replication
+
+`AT RISK — rests on CL4` means a premise fell. `REVISIT — its basis changed: CL1 v1→v2` means a decision rested on an
+older version. `UNSUPPORTED` means every support has fallen. Before citing a node marked contested or at risk, check
+it.
+
+## Without MCP
+
+- Python: `from hypgraph import Graph` (see README.md).
+- CLI: `hypgraph --json …` gives machine-readable output.
+- HTTP: `hypgraph serve --writable`, then `POST /api/graph/write {"op": "create", "author": …}`.
+- Format: `hypgraph schema --json`, or https://hypgraph.com/schema/hypgraph-1.json.

hypgraph-0.1.0/CITATION.cff

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+cff-version: 1.2.0
+message: "If you use HypGraph in your research or teaching, please cite it."
+title: "HypGraph: a research record that can't flatter itself"
+abstract: >-
+  An append-only, hash-chained record of questions, hypotheses, experiments, runs, results, claims, sources,
+  reviews and decisions, whose standing (review, risk, independent support, evidence strength) is derived on read
+  and never asserted. Claims are checked on write: numbers bound to results, absolutes backed by k of n, exclusions
+  backed by a powered search.
+type: software
+authors:
+  - family-names: Houghtaling
+    given-names: Nicolas
+license: Apache-2.0
+version: 0.1.0
+date-released: "2026-10-24"
+url: "https://hypgraph.com"
+repository-code: "https://github.com/voodoomods/hypgraph"
+keywords:
+  - research provenance
+  - reproducibility
+  - hypothesis testing
+  - open science
+  - AI agents
+  - Model Context Protocol

hypgraph-0.1.0/LICENSE

@@ -0,0 +1,201 @@
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hypgraph-0.1.0/PKG-INFO

@@ -0,0 +1,140 @@
+Metadata-Version: 2.5
+Name: hypgraph
+Version: 0.1.0
+Summary: The evidence layer for AI research agents: a hash-chained research record that checks every claim as it is written and derives how well each is known.
+Project-URL: Homepage, https://hypgraph.com
+Project-URL: Documentation, https://hypgraph.com/engineers/
+Project-URL: Changelog, https://github.com/voodoomods/hypgraph/blob/main/CHANGELOG.md
+Project-URL: Source, https://github.com/voodoomods/hypgraph
+Author: Nicolas Houghtaling
+License-Expression: Apache-2.0
+License-File: LICENSE
+Keywords: agent-skills,ai-agents,evaluation,hypothesis,mcp,provenance,reproducibility,research
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
+Requires-Python: >=3.10
+Provides-Extra: all
+Requires-Dist: fastmcp>=2.12; extra == 'all'
+Requires-Dist: pytest>=8; extra == 'all'
+Provides-Extra: mcp
+Requires-Dist: fastmcp>=2.12; extra == 'mcp'
+Provides-Extra: test
+Requires-Dist: pytest>=8; extra == 'test'
+Description-Content-Type: text/markdown
+
+<p align="center"><img src="https://hypgraph.com/assets/hypgraph.svg" width="72" alt=""></p>
+
+<h1 align="center">HypGraph</h1>
+<p align="center"><b>Don't believe the hype. Test the hyp.</b><br>
+The evidence layer for AI research agents.<br>
+<a href="https://hypgraph.com">hypgraph.com</a> · <a href="https://hypgraph.com/agents/">for agents</a> ·
+<a href="https://hypgraph.com/engineers/">for engineers</a> · <a href="https://hypgraph.com/spec/">record format</a></p>
+
+---
+
+Agents doing research write fluent summaries. Some of the numbers in them match no result. "Always" gets written
+about one run, a search too weak to find anything becomes "ruled out", and three copies of one result get counted as
+three lines of evidence. HypGraph is the record they write into instead. It checks every claim as it's written, so
+those claims can't get in:
+
+```text
+$ hypgraph add claim statement="The fine-tune is 5 points better than the baseline." scope="2,000 held-out items, greedy decoding, one seed." --link "supports:from:RS1:the eval run"
+refused: claim refused:
+- numbers in the statement that no bound measurement, the scope or the investigation's constants account for: 5 — bind them to result fields (measurements) or move design constants into the scope
+```
+
+(The result said 1,624 against 1,568 correct out of 2,000. That's 2.8 points.)
+
+Every refusal says what to fix, so an agent can act on it. Nothing in the record is ever *set* as known. How well
+each claim is known is **derived on every read**:
+
+- **reviewed, and which version?** Only named reviewers count, and never on their own work. A revised claim goes back
+  to unchecked.
+- **does it rest on something that fell?** Withdraw a premise and everything built on it is flagged **AT RISK**. A
+  decision whose evidence changed is flagged **REVISIT**.
+- **how many independent lines?** Results that share a run, a data file or a source count **once**.
+- **how strong is the best one?** From an agent's report, through a run your job runner recorded and a separate
+  implementation, up to a replication on new data.
+
+Every write is an event in a **SHA-256 hash chain**. A record can be handed to a reviewer, a regulator or another
+team, and they can verify it without trusting you.
+
+## Connect your agent
+
+```bash
+pip install "hypgraph[mcp]"
+claude mcp add hypgraph -- hypgraph --db study.hypgraph --as claude mcp     # any MCP client works
+hypgraph skill --install                                                     # + the Agent Skill (.claude/skills/hypgraph/SKILL.md)
+```
+
+The server writes as one author, fixed when it starts. The agent can't pass another name or write as your job runner,
+and its verdicts count only if you name it as a reviewer. Tools: `overview`, `find`, `show`, `start_investigation`,
+`add`, `link`, `revise`, `withdraw`, `retract_link`, `review`, `next_experiments`, `work_queue`, `claim_work`,
+`register_run`, `report`, `verify`, `schema`. The method is in [AGENTS.md](https://github.com/voodoomods/hypgraph/blob/main/AGENTS.md); the short version is
+[llms.txt](https://hypgraph.com/llms.txt).
+
+## Wire it into your system
+
+The core is one Python package with no dependencies. You decide who is trusted to do what:
+
+```python
+from hypgraph import Graph, Policy
+
+g = Graph("research.hypgraph",
+          policy=Policy(reviewers={"critic", "stats"},      # whose verdicts count
+                        instrument="runner"),               # the only author that files lab-recorded runs
+          spend=my_ledger.spend)                            # optional: prices the work behind each investigation
+
+with g.writing_for(task_id):                                # every event carries the task, for cost tracing
+    g.create(author=agent_name, type="claim", inv=inv, fields={...}, links=[...])
+```
+
+- **Multi-agent:** give each agent its own author name. Make your critic agents reviewers. Have your job runner
+  write as the instrument, so its runs count as recorded, not reported.
+- **Your web framework:** `hypgraph.server.dispatch(graph, method, path, query, body)` is the JSON API, and
+  `hypgraph.ui.static_dir()` is the Atlas explorer to mount next to it.
+- **CI:** `hypgraph export -o record.bundle.json && hypgraph verify record.bundle.json`. The bundle is a single file
+  your reviewers or auditors can check with SHA-256, in any language or in the browser.
+
+The full guide is at [hypgraph.com/engineers](https://hypgraph.com/engineers/).
+
+## Try it
+
+```bash
+pip install hypgraph
+hypgraph demo        # a complete worked investigation (Broad Street, 1854) built into ./research.hypgraph
+hypgraph serve       # explore it in the Atlas: http://127.0.0.1:8765
+hypgraph report      # the facts, generated from the record
+```
+
+Or try to get a claim past the real engine in your browser: [hypgraph.com/play](https://hypgraph.com/play/).
+
+## Where it came from
+
+HypGraph is the research graph of PegasusDMZ, where a team of AI agents runs long investigations under governed
+egress, pulled out so anyone can use it. Each rule exists because the agents made the mistake behind it:
+- a validation that was blind to the answer;
+- a null model that broke the system's own rules;
+- a summary whose numbers matched no result;
+- "never" written about something that happened once in a thousand.
+
+PegasusDMZ is the reference deployment, and its Atlas is built from this package. Against PegasusDMZ's live record
+(1,357 events, 790 nodes), the library derives the same standing for every node as the engine it replaced.
+
+## Performance
+
+The engine is pure Python and stays fast at the sizes research records reach. At 10,000 nodes, deriving every node's
+standing takes 0.09 s, reading one node 0.3 ms, and a write about 10 ms, mostly SQLite committing to disk. A write
+costs what it touches: cached standing is kept for every node the write can't affect, and a randomized suite checks
+that against a full rebuild.
+
+## License
+
+Code: [Apache-2.0](https://github.com/voodoomods/hypgraph/blob/main/LICENSE). The record format ([docs/spec.md](https://github.com/voodoomods/hypgraph/blob/main/docs/spec.md)) and the docs: CC BY 4.0. Cite it with
+[CITATION.cff](https://github.com/voodoomods/hypgraph/blob/main/CITATION.cff).

hypgraph-0.1.0/README.md

@@ -0,0 +1,110 @@
+<p align="center"><img src="https://hypgraph.com/assets/hypgraph.svg" width="72" alt=""></p>
+
+<h1 align="center">HypGraph</h1>
+<p align="center"><b>Don't believe the hype. Test the hyp.</b><br>
+The evidence layer for AI research agents.<br>
+<a href="https://hypgraph.com">hypgraph.com</a> · <a href="https://hypgraph.com/agents/">for agents</a> ·
+<a href="https://hypgraph.com/engineers/">for engineers</a> · <a href="https://hypgraph.com/spec/">record format</a></p>
+
+---
+
+Agents doing research write fluent summaries. Some of the numbers in them match no result. "Always" gets written
+about one run, a search too weak to find anything becomes "ruled out", and three copies of one result get counted as
+three lines of evidence. HypGraph is the record they write into instead. It checks every claim as it's written, so
+those claims can't get in:
+
+```text
+$ hypgraph add claim statement="The fine-tune is 5 points better than the baseline." scope="2,000 held-out items, greedy decoding, one seed." --link "supports:from:RS1:the eval run"
+refused: claim refused:
+- numbers in the statement that no bound measurement, the scope or the investigation's constants account for: 5 — bind them to result fields (measurements) or move design constants into the scope
+```
+
+(The result said 1,624 against 1,568 correct out of 2,000. That's 2.8 points.)
+
+Every refusal says what to fix, so an agent can act on it. Nothing in the record is ever *set* as known. How well
+each claim is known is **derived on every read**:
+
+- **reviewed, and which version?** Only named reviewers count, and never on their own work. A revised claim goes back
+  to unchecked.
+- **does it rest on something that fell?** Withdraw a premise and everything built on it is flagged **AT RISK**. A
+  decision whose evidence changed is flagged **REVISIT**.
+- **how many independent lines?** Results that share a run, a data file or a source count **once**.
+- **how strong is the best one?** From an agent's report, through a run your job runner recorded and a separate
+  implementation, up to a replication on new data.
+
+Every write is an event in a **SHA-256 hash chain**. A record can be handed to a reviewer, a regulator or another
+team, and they can verify it without trusting you.
+
+## Connect your agent
+
+```bash
+pip install "hypgraph[mcp]"
+claude mcp add hypgraph -- hypgraph --db study.hypgraph --as claude mcp     # any MCP client works
+hypgraph skill --install                                                     # + the Agent Skill (.claude/skills/hypgraph/SKILL.md)
+```
+
+The server writes as one author, fixed when it starts. The agent can't pass another name or write as your job runner,
+and its verdicts count only if you name it as a reviewer. Tools: `overview`, `find`, `show`, `start_investigation`,
+`add`, `link`, `revise`, `withdraw`, `retract_link`, `review`, `next_experiments`, `work_queue`, `claim_work`,
+`register_run`, `report`, `verify`, `schema`. The method is in [AGENTS.md](https://github.com/voodoomods/hypgraph/blob/main/AGENTS.md); the short version is
+[llms.txt](https://hypgraph.com/llms.txt).
+
+## Wire it into your system
+
+The core is one Python package with no dependencies. You decide who is trusted to do what:
+
+```python
+from hypgraph import Graph, Policy
+
+g = Graph("research.hypgraph",
+          policy=Policy(reviewers={"critic", "stats"},      # whose verdicts count
+                        instrument="runner"),               # the only author that files lab-recorded runs
+          spend=my_ledger.spend)                            # optional: prices the work behind each investigation
+
+with g.writing_for(task_id):                                # every event carries the task, for cost tracing
+    g.create(author=agent_name, type="claim", inv=inv, fields={...}, links=[...])
+```
+
+- **Multi-agent:** give each agent its own author name. Make your critic agents reviewers. Have your job runner
+  write as the instrument, so its runs count as recorded, not reported.
+- **Your web framework:** `hypgraph.server.dispatch(graph, method, path, query, body)` is the JSON API, and
+  `hypgraph.ui.static_dir()` is the Atlas explorer to mount next to it.
+- **CI:** `hypgraph export -o record.bundle.json && hypgraph verify record.bundle.json`. The bundle is a single file
+  your reviewers or auditors can check with SHA-256, in any language or in the browser.
+
+The full guide is at [hypgraph.com/engineers](https://hypgraph.com/engineers/).
+
+## Try it
+
+```bash
+pip install hypgraph
+hypgraph demo        # a complete worked investigation (Broad Street, 1854) built into ./research.hypgraph
+hypgraph serve       # explore it in the Atlas: http://127.0.0.1:8765
+hypgraph report      # the facts, generated from the record
+```
+
+Or try to get a claim past the real engine in your browser: [hypgraph.com/play](https://hypgraph.com/play/).
+
+## Where it came from
+
+HypGraph is the research graph of PegasusDMZ, where a team of AI agents runs long investigations under governed
+egress, pulled out so anyone can use it. Each rule exists because the agents made the mistake behind it:
+- a validation that was blind to the answer;
+- a null model that broke the system's own rules;
+- a summary whose numbers matched no result;
+- "never" written about something that happened once in a thousand.
+
+PegasusDMZ is the reference deployment, and its Atlas is built from this package. Against PegasusDMZ's live record
+(1,357 events, 790 nodes), the library derives the same standing for every node as the engine it replaced.
+
+## Performance
+
+The engine is pure Python and stays fast at the sizes research records reach. At 10,000 nodes, deriving every node's
+standing takes 0.09 s, reading one node 0.3 ms, and a write about 10 ms, mostly SQLite committing to disk. A write
+costs what it touches: cached standing is kept for every node the write can't affect, and a randomized suite checks
+that against a full rebuild.
+
+## License
+
+Code: [Apache-2.0](https://github.com/voodoomods/hypgraph/blob/main/LICENSE). The record format ([docs/spec.md](https://github.com/voodoomods/hypgraph/blob/main/docs/spec.md)) and the docs: CC BY 4.0. Cite it with
+[CITATION.cff](https://github.com/voodoomods/hypgraph/blob/main/CITATION.cff).