neyra 0.2.1__tar.gz

neyra-0.2.1/.gitignore

@@ -0,0 +1,13 @@
+__pycache__/
+*.egg-info/
+.venv/
+.pytest_cache/
+.ruff_cache/
+dist/
+*.safetensors
+.neyra/
+!spec/vectors/fixtures/**/*.safetensors
+!tests/fixtures/**/*.safetensors
+findings/
+.hypothesis/
+.coverage

neyra-0.2.1/CHANGELOG.md

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+# Changelog
+
+## 0.2.1
+
+- `neyra edit MODEL "The capital of [France] is" Rome` takes a single fact on the command line.
+- First release on PyPI.
+
+## 0.2.0, first release
+
+0.1.x was the private working version.
+
+### Install and first run
+- `neyra demo` shows a merge that never took its LoRA adapter, caught by `check`, then the same merge done
+  the way PEFT does it, passing. It builds the toy model in memory, so it needs no download and runs in 0.1 s.
+  The earlier edit recovery demo is `neyra demo edit`; `neyra demo files DIR` writes the toy models out.
+- `neyra conformance` runs the protocol vectors against the installed copy, which ships in the wheel.
+- The sdist no longer includes `.hypothesis/`. The package version lives in `src/neyra/__init__.py` only.
+- `action.yml`: a composite GitHub Action that runs `neyra check` and fails the job when a merge is wrong.
+- `extensions/hf-neyra`: an `hf` CLI extension, `hf neyra ...`.
+
+### Errors
+- Wrong input ends in a one line message and an exit code. Fixed tracebacks for: a directory given as a file,
+  a binary file given as JSON, row ranges that are not numbers, an edit file with no requests or the wrong
+  shape, a public key file that is not a key, a claim file that is not a claim, an unwritable output path,
+  an unreachable Hub, and a Hub repo that does not exist when `huggingface_hub` is installed.
+
+### Protocol fixes found by `fuzz/differential.py`
+The Python and Go verifiers disagreed on these. The spec text decided each one, and each is now a vector
+(138 became 195). Where one verifier accepted input the other rejected, the accepting one was wrong.
+
+Python accepted what it should have rejected:
+1. A ledger entry whose `kind` is not a string or whose `body` is not an object.
+2. A ledger entry whose `seq` is `true` (Python's `True == 1`).
+3. A ledger `time` written in non-ASCII digits (`\d` matches every script).
+4. A receipt signature or payload whose base64 has non-zero unused bits in the last character.
+5. A patch manifest whose `shape` holds lists or booleans, or whose `name` or `dtype` is not a string.
+6. A safetensors header with a repeated key (the last one won, so two readers could see different tensors).
+7. A safetensors `__metadata__` that is `null`, `[]`, `0` or `""` (coerced to empty).
+8. A binding whose `ledger_len` is `true` for a ledger of one entry.
+9. A receipt whose claim digests are numbers or have no `sha256:` prefix, matched by string coercion.
+
+Python rejected, crashed on, or computed differently from the spec:
+10. Dot files counted as weight files in a folder, which changed the weights root.
+11. A directory named `x.safetensors` crashed it. `consolidated*.safetensors` was silently left out of a
+    folder's root; that Hub convention now applies only to Hub repos and CLI reads.
+12. A later valid signature was ignored when an earlier one with the same key id failed.
+13. `neyra.meta` that is not JSON crashed loading a patch.
+14. A manifest that parses to a non-object gave `bad_json` and skipped the canonical check; the spec says
+    `not_canonical`, then `bad_type`.
+15. A receipt whose `signatures` is missing or not a list gave the wrong code; the spec says `bad_json`.
+16. Receipts and ledgers with invalid UTF-8, a non-object envelope, or malformed signature entries crashed with
+    an exception instead of returning a code.
+
+Go accepted what it should have rejected:
+17. A signature entry that is not an object, or lacks a string `sig`, with no key supplied.
+
+Not a disagreement: patches that require `low-rank/1` are declined by Go, which the spec allows.
+
+After the fixes, 119,458 mutants across nine kinds produced no disagreement.
+
+### Spec
+`spec/PROTOCOL.md` now says, in sections 3, 4, 5, 6 and 8: dot files and directories are skipped and
+`consolidated.safetensors` is an ordinary shard; repeated header keys and non-object `__metadata__` are
+`bad_safetensors`; `neyra.meta` is never parsed; a non-object manifest is `bad_type`; `shape`, `name` and
+`dtype` types; ASCII digits and types in a ledger entry; envelope shape and canonical base64; every
+signature with the key is tried; claim digests must be well formed; `ledger_len` is an integer.

neyra-0.2.1/CONTRIBUTING.md

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+# Contributing
+
+Keep pull requests small.
+
+## Setup
+
+```sh
+uv venv && uv pip install -e '.[dev]'
+pytest -q
+ruff check src tests
+```
+
+Tests marked `model` need real weights and do not run by default.
+
+## Changing a format
+
+Anything that changes hashing or a format must update [`spec/PROTOCOL.md`](spec/PROTOCOL.md) and rerun
+`spec/vectors/generate.py`. The Go verifier must still pass:
+
+```sh
+cd impl/go && go run . vectors ../../spec/vectors
+```
+
+## Claims
+
+A result claimed in the documentation needs a script in `bench` or `experiments` that reproduces it. State its
+limits next to it. Failed results count.
+
+## Writing a verifier
+
+Work from the specification and the vectors alone, and open an issue about anything they leave unclear.

neyra-0.2.1/LICENSE

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neyra-0.2.1/PKG-INFO

@@ -0,0 +1,219 @@
+Metadata-Version: 2.5
+Name: neyra
+Version: 0.2.1
+Summary: Edit local model weights with patches that revert bit for bit.
+Project-URL: Homepage, https://neyra.run
+Project-URL: Source, https://github.com/noah-thing/neyra-protocol
+Project-URL: Documentation, https://github.com/noah-thing/neyra-protocol/tree/main/docs
+Project-URL: Changelog, https://github.com/noah-thing/neyra-protocol/blob/main/CHANGELOG.md
+Project-URL: Issues, https://github.com/noah-thing/neyra-protocol/issues
+Author: Noah
+License-Expression: Apache-2.0
+License-File: LICENSE
+Keywords: gguf,llm,lora,mcp,model-editing,model-signing,provenance,safetensors
+Classifier: Development Status :: 3 - Alpha
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
+Requires-Python: >=3.10
+Requires-Dist: cryptography>=42
+Requires-Dist: numpy>=1.26
+Provides-Extra: dev
+Requires-Dist: cryptography>=43; extra == 'dev'
+Requires-Dist: hypothesis; extra == 'dev'
+Requires-Dist: jsonschema>=4; extra == 'dev'
+Requires-Dist: mcp>=2.0; extra == 'dev'
+Requires-Dist: pytest-asyncio; extra == 'dev'
+Requires-Dist: pytest>=8; extra == 'dev'
+Requires-Dist: pyyaml; extra == 'dev'
+Requires-Dist: referencing; extra == 'dev'
+Requires-Dist: ruff; extra == 'dev'
+Provides-Extra: eval
+Requires-Dist: math-verify>=0.9; extra == 'eval'
+Provides-Extra: gguf
+Requires-Dist: gguf>=0.17; extra == 'gguf'
+Provides-Extra: mcp
+Requires-Dist: mcp>=2.0; extra == 'mcp'
+Provides-Extra: mlx
+Requires-Dist: mlx-lm>=0.32; extra == 'mlx'
+Provides-Extra: torch
+Requires-Dist: accelerate; extra == 'torch'
+Requires-Dist: torch>=2.6; extra == 'torch'
+Requires-Dist: transformers>=5.0; extra == 'torch'
+Description-Content-Type: text/markdown
+
+<p align="center">
+  <picture>
+    <source media="(prefers-color-scheme: dark)" srcset="https://raw.githubusercontent.com/noah-thing/neyra-protocol/main/docs/assets/logo-dark.svg">
+    <img src="https://raw.githubusercontent.com/noah-thing/neyra-protocol/main/docs/assets/logo-light.svg" alt="Neyra" width="260">
+  </picture>
+</p>
+
+<p align="center">Neyra edits the weights of local language models.</p>
+
+<p align="center">
+  <a href="https://github.com/noah-thing/neyra-protocol/actions/workflows/ci.yml"><img alt="CI" src="https://github.com/noah-thing/neyra-protocol/actions/workflows/ci.yml/badge.svg"></a>
+  <a href="https://github.com/noah-thing/neyra-protocol/blob/main/LICENSE"><img alt="Apache 2.0" src="https://img.shields.io/badge/license-Apache_2.0-blue"></a>
+  <img alt="Python 3.10+" src="https://img.shields.io/badge/python-3.10%2B-blue">
+  <a href="https://github.com/noah-thing/neyra-protocol/blob/main/spec/PROTOCOL.md"><img alt="312 conformance vectors" src="https://img.shields.io/badge/conformance-312_vectors-brightgreen"></a>
+</p>
+
+<p align="center">
+  <a href="#install">Install</a> ·
+  <a href="#usage">Usage</a> ·
+  <a href="#commands">Commands</a> ·
+  <a href="#design">Design</a> ·
+  <a href="#results">Results</a> ·
+  <a href="#documentation">Docs</a> ·
+  <a href="https://github.com/noah-thing/neyra-protocol/blob/main/spec/PROTOCOL.md">Spec</a>
+</p>
+
+---
+
+Neyra writes facts and behaviour changes into safetensors checkpoints. An edit is a patch: about 170 KB for one fact
+on Qwen3-0.6B, tied to the digest of its base, and reversible bit for bit. `neyra edit` uses a MEMIT style closed form
+solve across several MLP layers. `neyra fix` finds the direction behind a reasoning loop and writes a patch that
+projects it out of the columns that write it.
+
+It also reads changes made with other tools. `diff` recovers the form of an edit from two checkpoints, `check`
+recomputes a LoRA merge with the rounding PEFT and mlx-lm use, and `hop` walks base, adapter, merged model and GGUF to
+the first one that differs.
+
+<picture>
+  <source media="(prefers-color-scheme: dark)" srcset="https://raw.githubusercontent.com/noah-thing/neyra-protocol/main/docs/assets/terminal-dark.svg">
+  <img src="https://raw.githubusercontent.com/noah-thing/neyra-protocol/main/docs/assets/terminal-light.svg" alt="neyra diff on the Weight-Space Programming edit" width="100%">
+</picture>
+
+`neyra diff` on the loop edit from [Sparks of Weight-Space Programming](https://rikiyat.github.io/blog/weight-space-programming/),
+reading 4% of both checkpoints over HTTP range requests. The authors' notes give the same formula with a strength of 6.
+
+## Install
+
+```sh
+pip install neyra        # or: uv tool install neyra
+neyra demo
+```
+
+Needs Python 3.10 or later. The base install handles patches, diffs and verification with numpy and cryptography. To
+run models, add `neyra[mlx]` on Apple Silicon or `neyra[torch]` elsewhere. `neyra edit` needs MLX. `neyra doctor`
+lists the backends you have.
+
+`neyra demo` takes about 0.1 s and downloads nothing. It builds a toy model and a LoRA in memory, then runs `check` on
+a merge that dropped the adapter and on one that kept it.
+
+## Usage
+
+Paths and Hugging Face repo names both work.
+
+```sh
+neyra probe MODEL                             # loops, runaway thinking, missing answers
+neyra fix MODEL -o fix.neyra                  # candidate patch for a loop direction
+neyra edit MODEL facts.json -o edit.neyra     # write facts, measure, sign
+neyra apply MODEL edit.neyra -o edited-model  # rebuild, checking digests
+
+neyra diff BASE OTHER --sample 4              # compare two checkpoints from a few percent of the bytes
+neyra check BASE MERGED --adapter ADAPTER     # recompute a LoRA merge and compare bits
+neyra hop BASE ADAPTER MERGED model.gguf      # first artifact that differs
+```
+
+## Commands
+
+**Edit**
+
+| Command | |
+|---|---|
+| [`edit`](https://github.com/noah-thing/neyra-protocol/blob/main/docs/edit.md) | Write facts as a low rank patch. Exits 1 if it misses its gates |
+| `fix` | Find a loop direction and write a candidate patch |
+| `probe` | Run a fixed battery and report loops, runaway thinking and missing answers |
+| `patch`, `apply`, `show` | Write the difference between two checkpoints as a patch, rebuild from it, inspect it |
+| [`merge`](https://github.com/noah-thing/neyra-protocol/blob/main/docs/merge.md) | Sum patches on one base with exact arithmetic. Order does not change the bytes |
+| [`bisect`](https://github.com/noah-thing/neyra-protocol/blob/main/docs/bisect.md) | Find the smallest part of a patch that keeps its effect |
+| `export` | Write a patch as a LoRA for PEFT or llama.cpp |
+
+**Inspect**
+
+| Command | |
+|---|---|
+| [`diff`](https://github.com/noah-thing/neyra-protocol/blob/main/docs/accuracy.md) | Compare two checkpoints and name the form of the change |
+| [`check`](https://github.com/noah-thing/neyra-protocol/blob/main/docs/check.md) | Recompute a merge per tool and compare bits |
+| [`hop`](https://github.com/noah-thing/neyra-protocol/blob/main/docs/hop.md) | Report the first artifact that differs across base, adapter, merged model and GGUF |
+| [`identity`](https://github.com/noah-thing/neyra-protocol/blob/main/docs/identity.md) | Compare a model with its declared base: same weights, named transform, derivative, unrelated |
+
+**Sign**
+
+| Command | |
+|---|---|
+| [`attest`](https://github.com/noah-thing/neyra-protocol/blob/main/docs/signing.md), `render`, `supersede`, `withdraw`, `status` | Sign a statement of a change for OpenSSF model signing and CycloneDX tools |
+| `verify`, `log`, `keygen` | Check receipts and hash chained ledgers |
+| [`index`](https://github.com/noah-thing/neyra-protocol/blob/main/docs/protocol.md), `prove` | Prove rows of a tensor against a root by reading only those rows |
+| `conformance` | Run the test vectors against your install |
+
+**Automate**
+
+| | |
+|---|---|
+| [`neyra mcp`](https://github.com/noah-thing/neyra-protocol/blob/main/docs/lab.md) | MCP server for agents, with a fixed budget, a sealed holdout and a hash chained ledger |
+| [`action.yml`](https://github.com/noah-thing/neyra-protocol/blob/main/action.yml) | GitHub Action that fails a job when a merge does not match its adapter |
+| [`hf-neyra`](https://github.com/noah-thing/neyra-protocol/blob/main/extensions/hf-neyra) | `hf neyra diff` and `hf neyra check` |
+
+## Design
+
+A patch is a safetensors file, so loading one runs no code. It records the digest of the tensors it expects and the
+digest it produces, and `apply` stops on a mismatch. The weights root hashes every tensor and ignores sharding, so a
+resharded model keeps its root.
+
+`merge` sums deltas as integers and rounds once, because bf16 addition does not associate. At an entry with value
+1 - 2^-8, three patches that each add 2^-8 give 1.0 in pairs and 1 + 2^-7 together.
+
+`neyra edit` solves in float64 and measures the rounded weights the patch produces. Its gates cover efficacy,
+neighbouring facts, drift on neutral text and fluency. The limits ship in the code, not in your run, and the receipt
+keeps a FAIL as well as a PASS.
+
+Output separates what you can recompute from what was measured. Sampled reads report their coverage. `identity` calls
+a model derived against distances measured on unrelated sibling models. A signature tells you who signed, so a receipt
+also lists what you need to rerun the claim.
+
+`hop` takes artifacts in the order a fine-tune passed through them:
+
+<picture>
+  <source media="(prefers-color-scheme: dark)" srcset="https://raw.githubusercontent.com/noah-thing/neyra-protocol/main/docs/assets/hops-dark.svg">
+  <img src="https://raw.githubusercontent.com/noah-thing/neyra-protocol/main/docs/assets/hops-light.svg" alt="base, adapter, merged and GGUF, with merged marked as the first hop that differs" width="100%">
+</picture>
+
+## Results
+
+| | Result | Rerun |
+|---|---|---|
+| `edit`, Qwen3-0.6B, 200 unseen CounterFact cases | Efficacy 1.00, paraphrase 0.95, neighbours 0.70 (0.745 before) | [`bench/edit_counterfact.py`](https://github.com/noah-thing/neyra-protocol/blob/main/bench/edit_counterfact.py) |
+| `diff`, planted edits, 50 trials each | 100% form recovery on 12 of 14 conditions, 0 false alarms in 250 noise trials | [`bench/forensics.py`](https://github.com/noah-thing/neyra-protocol/blob/main/bench/forensics.py) |
+| `check`, real merges | PEFT 0.21.2 and mlx-lm 0.32.2 in fp32, bf16 and fp16, matched bit for bit | [`tests/test_check_real.py`](https://github.com/noah-thing/neyra-protocol/blob/main/tests/test_check_real.py) |
+| `merge` | Matches brute force rounding on all 24 orders of four patches | [`tests/test_merge.py`](https://github.com/noah-thing/neyra-protocol/blob/main/tests/test_merge.py) |
+| Python and Go verifiers | Agree on 312 vectors and on mutated inputs from a differential fuzzer | [`fuzz/differential.py`](https://github.com/noah-thing/neyra-protocol/blob/main/fuzz/differential.py) |
+
+So far these edits rewrite facts and remove loops. None has been shown to add ability. ROME led `edit` on the 20
+development cases compared, and the full comparison is unfinished. Nothing has been tested above 1B parameters. The
+[limits page](https://github.com/noah-thing/neyra-protocol/blob/main/docs/limits.md) has the rest.
+
+## Documentation
+
+Guides: [edit](https://github.com/noah-thing/neyra-protocol/blob/main/docs/edit.md), [merge](https://github.com/noah-thing/neyra-protocol/blob/main/docs/merge.md), [bisect](https://github.com/noah-thing/neyra-protocol/blob/main/docs/bisect.md), [check](https://github.com/noah-thing/neyra-protocol/blob/main/docs/check.md), [hop](https://github.com/noah-thing/neyra-protocol/blob/main/docs/hop.md), [identity](https://github.com/noah-thing/neyra-protocol/blob/main/docs/identity.md), [signing](https://github.com/noah-thing/neyra-protocol/blob/main/docs/signing.md), [lab](https://github.com/noah-thing/neyra-protocol/blob/main/docs/lab.md).
+
+Reference: [specification](https://github.com/noah-thing/neyra-protocol/blob/main/spec/PROTOCOL.md), [protocol notes](https://github.com/noah-thing/neyra-protocol/blob/main/docs/protocol.md), [vectors](https://github.com/noah-thing/neyra-protocol/blob/main/spec/vectors), [accuracy](https://github.com/noah-thing/neyra-protocol/blob/main/docs/accuracy.md), [limits](https://github.com/noah-thing/neyra-protocol/blob/main/docs/limits.md), [prior work](https://github.com/noah-thing/neyra-protocol/blob/main/docs/prior-work.md), [changelog](https://github.com/noah-thing/neyra-protocol/blob/main/CHANGELOG.md).
+
+## Status
+
+Early. Formats can change until v1.
+
+See [CONTRIBUTING.md](https://github.com/noah-thing/neyra-protocol/blob/main/CONTRIBUTING.md) to work on it and [SECURITY.md](https://github.com/noah-thing/neyra-protocol/blob/main/SECURITY.md) to report a vulnerability. If you
+write a verifier from the spec and vectors, open an issue. The Go one here shares an author with the Python one.
+
+## License
+
+[Apache 2.0](https://github.com/noah-thing/neyra-protocol/blob/main/LICENSE)