spectrl 0.1.0__tar.gz

spectrl-0.1.0/.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  test:
+    name: test (py${{ matrix.python-version }})
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.12", "3.13"]
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          enable-cache: true
+
+      - name: Set up Python ${{ matrix.python-version }}
+        run: uv python install ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: uv sync --all-extras --dev
+
+      - name: Run tests
+        run: uv run pytest tests/ -q
+
+  lint:
+    name: lint
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          enable-cache: true
+
+      - name: Install dependencies
+        run: uv sync --all-extras --dev
+
+      - name: ruff check
+        run: uv run ruff check src/ tests/
+
+      - name: ruff format --check
+        run: uv run ruff format --check src/ tests/
+
+  build:
+    name: build
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+
+      - name: Build sdist and wheel
+        run: uv build
+
+      - name: Check distribution metadata
+        run: uvx twine check dist/*
+
+      - name: Upload artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist/*
+
+  js:
+    name: js (node ${{ matrix.node-version }})
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: js
+    strategy:
+      fail-fast: false
+      matrix:
+        node-version: ["20", "22"]
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Node ${{ matrix.node-version }}
+        uses: actions/setup-node@v4
+        with:
+          node-version: ${{ matrix.node-version }}
+          cache: npm
+          cache-dependency-path: js/package-lock.json
+
+      - name: Install dependencies
+        run: npm ci
+
+      - name: Typecheck
+        run: npm run typecheck
+
+      - name: Test (validates against ../test-vectors)
+        run: npm test
+
+      - name: Build
+        run: npm run build

spectrl-0.1.0/.github/workflows/publish.yml

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+name: Publish
+
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+concurrency:
+  group: publish-${{ github.ref }}
+  cancel-in-progress: false
+
+jobs:
+  publish-pypi:
+    name: Publish to PyPI
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/project/spectrl/
+    permissions:
+      contents: read # checkout (required on private repos when permissions is set)
+      id-token: write # OIDC for PyPI Trusted Publishing
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          enable-cache: true
+
+      - name: Install dependencies
+        run: uv sync --all-extras --dev
+
+      - name: Run tests
+        run: uv run pytest tests/ -q
+
+      - name: Build sdist and wheel
+        run: uv build
+
+      - name: Check distribution metadata
+        run: uvx twine check dist/*
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+
+  publish-npm:
+    name: Publish to npm
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: js
+    permissions:
+      contents: read # checkout (required on private repos when permissions is set)
+      id-token: write # OIDC for npm provenance attestation
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Node
+        uses: actions/setup-node@v4
+        with:
+          node-version: "22"
+          registry-url: "https://registry.npmjs.org"
+          cache: npm
+          cache-dependency-path: js/package-lock.json
+
+      - name: Install dependencies
+        run: npm ci
+
+      - name: Typecheck
+        run: npm run typecheck
+
+      - name: Test (validates against ../test-vectors)
+        run: npm test
+
+      - name: Build
+        run: npm run build
+
+      - name: Publish to npm
+        run: npm publish --provenance --access public
+        env:
+          NODE_AUTH_TOKEN: ${{ secrets.NPM_TOKEN }}

spectrl-0.1.0/.gitignore

@@ -0,0 +1,12 @@
+__pycache__/
+*.py[cod]
+*.pyo
+.venv/
+node_modules/
+*.tsbuildinfo
+dist/
+*.egg-info/
+.eggs/
+site/
+.coverage
+htmlcov/

spectrl-0.1.0/CHANGELOG.md

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+# Changelog
+
+All notable changes to this project are documented here.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+The **token format version** (the `spectrl1` magic prefix) is versioned
+independently of the library version; see [SPECIFICATION.md](SPECIFICATION.md).
+
+## [Unreleased]
+
+### Added
+- Apache-2.0 `LICENSE` and `NOTICE`.
+- `CONTRIBUTING.md`, `CODE_OF_CONDUCT.md`, `CITATION.cff`.
+- GitHub Actions CI (Python test/lint/build + JavaScript test/typecheck/build).
+- `SPECIFICATION.md` — normative token format specification (draft).
+- `test-vectors/vectors.json` — language-agnostic conformance vectors generated
+  from the Python reference impl (`scripts/gen_vectors.py`), with `tests/test_vectors.py`
+  pinning them.
+- `js/` — independent JavaScript/TypeScript implementation (`@spectrl/spectrl`)
+  with a faithful MS-Numpress port, custom msgpack, and SHA-256 content hashing.
+  Decodes Python-produced tokens byte-for-byte and validates against the shared
+  vectors.
+- **Bidirectional interop testing**: `test-vectors/reverse-vectors.json` (tokens
+  encoded by JS) decoded by the Python impl, proving JS → Python in addition to
+  the existing Python → JS direction. Plus expanded unit coverage on both sides
+  (base64url, msgpack/`stripTopKey`, numpress size boundaries, byte-slice header
+  surgery, ordering/duplicates/value-extremes/URL bindings).
+
+### Fixed
+- **Single-peak lossy spectra** failed to decode: `pynumpress` emits a 12-byte
+  linear blob for a 1-element array but its decoder rejects it. The codec wrapper
+  now decodes the degenerate 12-byte case directly (per the MS-Numpress reference),
+  making single-peak tokens round-trip and agree with the JS implementation.
+
+### Changed
+- **Non-`MS:` parameter-map keys** are now encoded as the full accession string
+  (e.g. `"UO:0000031"`) rather than the previously-specified `[ontology, tail]`
+  array, which could not be a msgpack-map key. Fixes a latent crash in the
+  Python reference impl; exercised by the `non_ms_ontology_param_key` vector.
+  (No released token used the old form.)
+- **Hash verification** now derives the "header without key 9" by byte-slicing
+  the serialized header rather than re-encoding a parsed structure, so it no
+  longer depends on a canonical msgpack form. The hash value is unchanged.
+- Clarified that the content hash is a per-token integrity check, not a stable
+  cross-implementation content identifier; softened "deterministic" wording in
+  the README and `SPECIFICATION.md` accordingly.
+
+## [0.1.0] - 2026-06-08
+
+### Added
+- Initial implementation: `encode_spectrum`, `decode_token`, mzML bridge,
+  MS-Numpress + raw codecs, ProForma interpretation, canonical hashing,
+  URL/data-URI bindings, and CLI.
+- `schema/registry.json` — machine-readable CV/codec/key registry.

spectrl-0.1.0/CITATION.cff

@@ -0,0 +1,27 @@
+cff-version: 1.2.0
+message: "If you use spectrl, please cite it using these metadata."
+title: "spectrl: Inline Spectrum URL Encoder for mass spectrometry"
+abstract: >-
+  spectrl encodes a complete mass spectrum — peaks, metadata, and precursor
+  information — into a single compact, URL-safe token, enabling spectra to be
+  shared directly in URLs, QR codes, notebooks, and publications without a
+  backend repository. It is designed to be complementary to the HUPO-PSI
+  Universal Spectrum Identifier (USI) and ProForma.
+type: software
+authors:
+  - family-names: Garrett
+    given-names: Patrick
+    email: pgarrett@scripps.edu
+    affiliation: Scripps Research
+license: Apache-2.0
+repository-code: "https://github.com/pgarrett-scripps/spectrl"
+keywords:
+  - mass spectrometry
+  - proteomics
+  - mzML
+  - HUPO-PSI
+  - USI
+  - ProForma
+  - spectrum encoding
+version: 0.1.0
+date-released: 2026-06-08

spectrl-0.1.0/CODE_OF_CONDUCT.md

@@ -0,0 +1,45 @@
+# Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community 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.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment:
+
+- Demonstrating empathy and kindness toward other people
+- Being respectful of differing opinions, viewpoints, and experiences
+- Giving and gracefully accepting constructive feedback
+- Accepting responsibility and apologizing to those affected by our mistakes
+- Focusing on what is best for the overall community
+
+Examples of unacceptable behavior:
+
+- The use of sexualized language or imagery, and sexual attention or advances
+- Trolling, insulting or derogatory comments, and personal or political attacks
+- Public or private harassment
+- Publishing others' private information without explicit permission
+- Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the project maintainers at **pgarrett@scripps.edu**. All complaints
+will be reviewed and investigated promptly and fairly.
+
+## Attribution
+
+This Code of Conduct is adapted from the
+[Contributor Covenant](https://www.contributor-covenant.org), version 2.1,
+available at
+https://www.contributor-covenant.org/version/2/1/code_of_conduct.html.

spectrl-0.1.0/CONTRIBUTING.md

@@ -0,0 +1,65 @@
+# Contributing to spectrl
+
+Thanks for your interest in improving spectrl. This project aims to become a
+HUPO-PSI standard, so contributions are welcome at two levels:
+
+1. **The reference implementation** (this Python library) — bug fixes, codecs,
+   performance, tests, docs.
+2. **The format specification** — see [SPECIFICATION.md](SPECIFICATION.md).
+   Changes that alter the on-the-wire token format are governed more strictly
+   (see *Format changes* below).
+
+By contributing, you agree that your contributions are licensed under the
+project's [Apache-2.0 License](LICENSE), and you certify the
+[Developer Certificate of Origin](https://developercertificate.org/) for each
+commit.
+
+## Development setup
+
+This project uses [uv](https://docs.astral.sh/uv/) and
+[just](https://github.com/casey/just).
+
+```bash
+uv sync --all-extras       # install runtime + dev + optional deps
+just test                  # run the test suite
+just lint                  # run ruff
+```
+
+If you don't use `just`, the underlying commands are:
+
+```bash
+uv run pytest
+uv run ruff check .
+uv run ruff format --check .
+```
+
+## Pull requests
+
+- Open an issue first for anything non-trivial so we can agree on the approach.
+- Keep PRs focused; one logical change per PR.
+- Add or update tests for any behavior change. The round-trip and
+  canonical-hash tests are the contract — do not weaken them without discussion.
+- Run `just test` and `just lint` before pushing.
+- Update [CHANGELOG.md](CHANGELOG.md) under `## [Unreleased]`.
+
+## Format changes (token wire format)
+
+The `spectrl1` token format is normative. Any change that affects how a token
+is produced or parsed — new header keys, codec changes, framing changes —
+**must**:
+
+1. Be discussed in an issue tagged `format`.
+2. Update [SPECIFICATION.md](SPECIFICATION.md) and `schema/registry.json`.
+3. Preserve backward compatibility, or bump the format version
+   (`spectrl1` → `spectrl2`) per the versioning policy in the specification.
+4. Include round-trip test vectors.
+
+Format changes are reviewed against the goal of HUPO-PSI standardization and
+interoperability with [USI](https://www.psidev.info/usi) and
+[ProForma](https://www.psidev.info/proforma).
+
+## Reporting bugs
+
+Open a GitHub issue with: the spectrl version, a minimal reproducing snippet
+or token, and the expected vs. actual behavior. For decode failures, include
+the (redacted if needed) token or its header inspected via `spectrl inspect`.

spectrl-0.1.0/LICENSE

@@ -0,0 +1,202 @@
+
+                                 Apache License
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+
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spectrl-0.1.0/NOTICE

@@ -0,0 +1,14 @@
+spectrl — Inline Spectrum URL Encoder
+Copyright 2026 Patrick Garrett and the spectrl contributors
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.