sci-protocol 0.2.0__tar.gz

sci_protocol-0.2.0/.gitignore

@@ -0,0 +1,13 @@
+.DS_Store
+__pycache__/
+*.pyc
+.venv/
+.mypy_cache/
+.ruff_cache/
+.pytest_cache/
+dist/
+build/
+*.egg-info/
+node_modules/
+typescript/dist/
+coverage/

sci_protocol-0.2.0/CONTRIBUTING.md

@@ -0,0 +1,70 @@
+# Contributing to SCI
+
+## Layout
+
+| Path | Contents |
+| --- | --- |
+| `protocol/` | Authoritative protocol specification, baseline publication license, and shared conformance corpus |
+| `python/` | `pysci`, the Python protocol library and private `_cli` implementation |
+| `python/tests/` | Library tests and CLI tests in `cli/` |
+| `cli/` | Command guide and design; implementation in `python/pysci/_cli/`, tests in `python/tests/cli/` |
+| `typescript/` | TypeScript protocol library used by Sciscape's backend and browser reader |
+
+The supported Python API lives in `pysci`; `_cli` contains private command
+implementation details. Run the command as `sci` or `python -m pysci`. Tests
+stay outside the installed package, so wheels contain only runtime code and data.
+
+Keep protocol rules in the libraries. Keep command arguments, output, and local settings in the CLI.
+Keep implementation decisions out of `protocol/README.md`. Use README files for operating instructions and DESIGN files for intended behavior.
+
+## Setup
+
+Requirements: Python 3.11+, [uv](https://docs.astral.sh/uv/), Node.js 22, Deno 2, and OpenSSL 3 or later for the corpus audit.
+
+```sh
+uv sync                         # One sci-protocol package, including the sci command
+(cd typescript && npm ci)       # TypeScript library
+```
+
+## Checks
+
+Run the same checks as CI before opening a pull request:
+
+```sh
+# Python library and CLI
+uv run ruff check python
+uv run ruff format --check python
+uv run mypy
+uv run pytest
+
+# TypeScript library: type checks, lint, Node and Deno tests, conformance
+(cd typescript && npm run check)
+
+# Conformance corpus integrity
+python3 -m venv /tmp/sci-vectors-venv
+/tmp/sci-vectors-venv/bin/pip install -r protocol/test-vectors/requirements.txt
+/tmp/sci-vectors-venv/bin/python protocol/test-vectors/tools/audit.py --openssl
+/tmp/sci-vectors-venv/bin/python protocol/test-vectors/tools/check_reproducible.py
+```
+
+Both libraries must pass the same corpus cases. Report a subset pass as a subset, not as whole-protocol conformance.
+
+## Rules
+
+- Typed Python with strict mypy, Ruff, and pytest. Strict TypeScript with tests in Node and Deno.
+- Validate external files, JSON, and network responses at runtime.
+- Keep command and HTTP entry points small; put shared operations in separate modules.
+- Keep Python tests in `python/tests/` (CLI tests in `python/tests/cli/`) and TypeScript tests in `typescript/tests/`.
+- Pin dependencies through `uv.lock` and `typescript/package-lock.json`.
+- `python/pysci/data/sci-protocol.md` is the copy of `protocol/README.md` that `sci spec` prints. Update both together; a test checks that they match and that the hash equals the corpus pin.
+- Do not edit signed JSON or binary fixtures by hand. Regenerate them with `protocol/test-vectors/tools/generate.py` after reviewing a protocol change.
+- After protocol `0.1` is released, changes to accepted bytes or their meaning require a new schema version.
+
+## Releasing
+
+For package publishing and the one-time PyPI setup, see
+[Releasing sci-protocol](python/RELEASING.md).
+
+## License
+
+Contributions are licensed under the [Apache License, Version 2.0](LICENSE). Publication bundles, including test fixtures, keep their own licenses.

sci_protocol-0.2.0/LICENSE

@@ -0,0 +1,202 @@
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sci_protocol-0.2.0/PKG-INFO

@@ -0,0 +1,112 @@
+Metadata-Version: 2.5
+Name: sci-protocol
+Version: 0.2.0
+Summary: Python library and sci CLI for SCI research publications.
+Project-URL: Repository, https://github.com/azaho/sci
+Project-URL: Documentation, https://github.com/azaho/sci/blob/main/README.md
+Author: SCI contributors
+License-Expression: Apache-2.0
+License-File: LICENSE
+Classifier: Development Status :: 3 - Alpha
+Classifier: Environment :: Console
+Classifier: Programming Language :: Python :: 3
+Classifier: Typing :: Typed
+Requires-Python: >=3.11
+Requires-Dist: asn1crypto>=1.5.1
+Requires-Dist: cryptography>=46.0.3
+Requires-Dist: idna>=3.11
+Description-Content-Type: text/markdown
+
+<h1 align="center">sci</h1>
+
+<p align="center">Signed, verifiable research publications for agents and humans.</p>
+
+<p align="center">
+  <a href="https://github.com/azaho/sci/actions/workflows/checks.yml"><img src="https://github.com/azaho/sci/actions/workflows/checks.yml/badge.svg?branch=main" alt="Checks"></a>
+  <a href="https://github.com/azaho/sci/actions/workflows/test-vectors.yml"><img src="https://github.com/azaho/sci/actions/workflows/test-vectors.yml/badge.svg?branch=main" alt="Test vectors"></a>
+  <a href="pyproject.toml"><img src="https://img.shields.io/badge/Python-3.11%2B-blue?logo=python&logoColor=white" alt="Python 3.11+"></a>
+  <a href="protocol/README.md"><img src="https://img.shields.io/badge/Protocol-0.1_draft-orange" alt="Protocol 0.1 draft"></a>
+  <a href="LICENSE"><img src="https://img.shields.io/badge/License-Apache_2.0-blue" alt="Software license: Apache 2.0"></a>
+</p>
+
+SCI is an open, decentralized publication system. A publication is a signed folder with text, metadata, citations, and optional supporting files. Its ID is the SHA-256 hash of its signed manifest. Anyone can host copies, and anyone can verify a downloaded copy offline, without trusting the host.
+
+| Component | Contents |
+| --- | --- |
+| [`protocol/`](protocol/README.md) | Protocol specification (draft 0.1), baseline publication license, and the shared conformance corpus |
+| [CLI guide](cli/README.md) | The `sci` command: prepare, sign, verify, publish, submit, search, and retrieve publications |
+| [`python/`](python/README.md) | `pysci`, the Python library and private CLI implementation |
+| [`typescript/`](typescript/README.md) | TypeScript protocol library for browsers, Deno, Workers, and Node |
+
+Both implementations use the shared 680-case [conformance corpus](protocol/test-vectors/README.md).
+The TypeScript adapter covers all 680 cases; the Python adapter covers 670,
+excluding 10 stateful indexer scenarios.
+
+## Install
+
+Requires Python 3.11 or later. One package, `sci-protocol`, contains both the Python
+library and the `sci` command. The CLI implementation is private; use
+`import pysci` for the public Python API.
+
+After the first PyPI release, install the standalone command with:
+
+```sh
+uv tool install sci-protocol
+```
+
+Or install both the library and command in a project virtual environment:
+
+```sh
+pip install sci-protocol
+```
+
+`uv tool install` isolates the command; it does not add `pysci` to your
+project or notebook environment.
+
+Until the PyPI release, install from this checkout at the repository root:
+
+```sh
+uv tool install .
+# Or, inside a project virtual environment:
+pip install .
+```
+
+For development, use `uv sync` and `uv run sci --help`. Package version 0.2.0
+introduces this unified distribution; the SCI protocol remains at draft 0.1.
+
+## First workflow
+
+Prepare a draft folder:
+
+```text
+draft/
+├── sci.json      # required: {"title": "...", "abstract": "...", "citations": [...]}
+├── README.md     # required: main text in UTF-8 Markdown
+└── files/        # optional: code, data, and figures
+```
+
+Sign it, verify it, and keep the bundle in a local campaign folder:
+
+```sh
+sci keygen                                          # create a signing key in ~/.sci/
+sci license ./draft                                 # select the SCI baseline license
+sci check ./draft                                   # report every problem before signing
+sci sign ./draft --output ./campaign                # sign, timestamp with FreeTSA, save <digest>.zip
+sci verify ./campaign/<digest>.zip                  # complete offline verification
+sci search "neural decoding" --in ./campaign        # search verified local bundles
+```
+
+Host the bundles in a public archive and register them with an index:
+
+```sh
+sci publish ./campaign --to https://github.com/lab/research --create
+sci submit ./campaign --to https://sciscape.io \
+  --archive https://github.com/lab/research
+sci pull sha256:<digest> --in https://sciscape.io   # retrieve and verify from any registered host
+```
+
+See the [CLI instructions](cli/README.md) for every command, and [CONTRIBUTING.md](CONTRIBUTING.md) for development.
+
+## License
+
+Software in this repository is licensed under the [Apache License, Version 2.0](LICENSE). Publications keep their own licenses; the [SCI baseline publication license](protocol/sci-baseline-LICENSE.txt) is CC BY 4.0 for text, figures, and data and MIT for code.

sci_protocol-0.2.0/README.md

@@ -0,0 +1,93 @@
+<h1 align="center">sci</h1>
+
+<p align="center">Signed, verifiable research publications for agents and humans.</p>
+
+<p align="center">
+  <a href="https://github.com/azaho/sci/actions/workflows/checks.yml"><img src="https://github.com/azaho/sci/actions/workflows/checks.yml/badge.svg?branch=main" alt="Checks"></a>
+  <a href="https://github.com/azaho/sci/actions/workflows/test-vectors.yml"><img src="https://github.com/azaho/sci/actions/workflows/test-vectors.yml/badge.svg?branch=main" alt="Test vectors"></a>
+  <a href="pyproject.toml"><img src="https://img.shields.io/badge/Python-3.11%2B-blue?logo=python&logoColor=white" alt="Python 3.11+"></a>
+  <a href="protocol/README.md"><img src="https://img.shields.io/badge/Protocol-0.1_draft-orange" alt="Protocol 0.1 draft"></a>
+  <a href="LICENSE"><img src="https://img.shields.io/badge/License-Apache_2.0-blue" alt="Software license: Apache 2.0"></a>
+</p>
+
+SCI is an open, decentralized publication system. A publication is a signed folder with text, metadata, citations, and optional supporting files. Its ID is the SHA-256 hash of its signed manifest. Anyone can host copies, and anyone can verify a downloaded copy offline, without trusting the host.
+
+| Component | Contents |
+| --- | --- |
+| [`protocol/`](protocol/README.md) | Protocol specification (draft 0.1), baseline publication license, and the shared conformance corpus |
+| [CLI guide](cli/README.md) | The `sci` command: prepare, sign, verify, publish, submit, search, and retrieve publications |
+| [`python/`](python/README.md) | `pysci`, the Python library and private CLI implementation |
+| [`typescript/`](typescript/README.md) | TypeScript protocol library for browsers, Deno, Workers, and Node |
+
+Both implementations use the shared 680-case [conformance corpus](protocol/test-vectors/README.md).
+The TypeScript adapter covers all 680 cases; the Python adapter covers 670,
+excluding 10 stateful indexer scenarios.
+
+## Install
+
+Requires Python 3.11 or later. One package, `sci-protocol`, contains both the Python
+library and the `sci` command. The CLI implementation is private; use
+`import pysci` for the public Python API.
+
+After the first PyPI release, install the standalone command with:
+
+```sh
+uv tool install sci-protocol
+```
+
+Or install both the library and command in a project virtual environment:
+
+```sh
+pip install sci-protocol
+```
+
+`uv tool install` isolates the command; it does not add `pysci` to your
+project or notebook environment.
+
+Until the PyPI release, install from this checkout at the repository root:
+
+```sh
+uv tool install .
+# Or, inside a project virtual environment:
+pip install .
+```
+
+For development, use `uv sync` and `uv run sci --help`. Package version 0.2.0
+introduces this unified distribution; the SCI protocol remains at draft 0.1.
+
+## First workflow
+
+Prepare a draft folder:
+
+```text
+draft/
+├── sci.json      # required: {"title": "...", "abstract": "...", "citations": [...]}
+├── README.md     # required: main text in UTF-8 Markdown
+└── files/        # optional: code, data, and figures
+```
+
+Sign it, verify it, and keep the bundle in a local campaign folder:
+
+```sh
+sci keygen                                          # create a signing key in ~/.sci/
+sci license ./draft                                 # select the SCI baseline license
+sci check ./draft                                   # report every problem before signing
+sci sign ./draft --output ./campaign                # sign, timestamp with FreeTSA, save <digest>.zip
+sci verify ./campaign/<digest>.zip                  # complete offline verification
+sci search "neural decoding" --in ./campaign        # search verified local bundles
+```
+
+Host the bundles in a public archive and register them with an index:
+
+```sh
+sci publish ./campaign --to https://github.com/lab/research --create
+sci submit ./campaign --to https://sciscape.io \
+  --archive https://github.com/lab/research
+sci pull sha256:<digest> --in https://sciscape.io   # retrieve and verify from any registered host
+```
+
+See the [CLI instructions](cli/README.md) for every command, and [CONTRIBUTING.md](CONTRIBUTING.md) for development.
+
+## License
+
+Software in this repository is licensed under the [Apache License, Version 2.0](LICENSE). Publications keep their own licenses; the [SCI baseline publication license](protocol/sci-baseline-LICENSE.txt) is CC BY 4.0 for text, figures, and data and MIT for code.