labrecipe 0.1.1__tar.gz

labrecipe-0.1.1/.github/dependabot.yml

@@ -0,0 +1,18 @@
+version: 2
+updates:
+  - package-ecosystem: pip
+    directory: /
+    schedule:
+      interval: monthly
+    labels:
+      - dependencies
+    groups:
+      python-dependencies:
+        patterns:
+          - "*"
+  - package-ecosystem: github-actions
+    directory: /
+    schedule:
+      interval: monthly
+    labels:
+      - dependencies

labrecipe-0.1.1/.github/workflows/ci.yml

@@ -0,0 +1,68 @@
+name: CI
+
+on:
+  push:
+  pull_request:
+
+permissions:
+  contents: read
+
+jobs:
+  quality:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+        with:
+          persist-credentials: false
+      - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
+        with:
+          python-version: "3.13"
+      - uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
+        with:
+          version: "0.11.28"
+          enable-cache: true
+      - run: uv sync --frozen --no-install-project --all-groups --extra excel
+      - run: uv run --frozen ruff format --check .
+      - run: uv run --frozen ruff check src tests scripts
+      - run: uv run --frozen mypy
+      - run: uv run --frozen python -m pytest -W error -q
+        env:
+          MPLBACKEND: Agg
+      - run: uv run --frozen python scripts/export_recipe_schema.py --check
+      - run: uv run --frozen sphinx-build -E -W --keep-going -b html docs docs/_build/html
+      - run: uv run --frozen python -m build
+      - run: uv run --frozen twine check dist/*
+      - run: uv run --frozen python -m pytest tests/test_distribution.py tests/test_workflows.py -q
+      - uses: actions/upload-artifact@b7c566a772e6b6bfb58ed0dc250532a479d7789f # v6.0.0
+        with:
+          name: distributions
+          path: dist/*
+          if-no-files-found: error
+
+  compatibility:
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python: ["3.12", "3.13", "3.14"]
+        mode: [core, excel]
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+        with:
+          persist-credentials: false
+      - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
+        with:
+          python-version: ${{ matrix.python }}
+      - uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
+        with:
+          version: "0.11.28"
+          enable-cache: true
+      - run: uv sync --frozen --no-install-project --all-groups --extra excel
+      - run: uv run --frozen --no-sync python -m build --wheel --no-isolation --outdir wheelhouse
+      - run: >-
+          uv run --frozen --no-sync python scripts/smoke_built_wheel.py
+          --wheel wheelhouse/labrecipe-0.1.1-py3-none-any.whl
+          --mode ${{ matrix.mode }}
+        env:
+          MPLBACKEND: Agg

labrecipe-0.1.1/.github/workflows/release.yml

@@ -0,0 +1,96 @@
+name: Release
+
+on:
+  push:
+    tags:
+      - "v*.*.*"
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+        with:
+          persist-credentials: false
+      - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
+        with:
+          python-version: "3.13"
+      - uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
+        with:
+          version: "0.11.28"
+          enable-cache: true
+      - name: Install locked release environment
+        run: uv sync --frozen --no-install-project --all-groups --extra excel
+      - name: Require tag, package, and citation versions to match
+        env:
+          RELEASE_TAG: ${{ github.ref_name }}
+        run: |
+          uv run --frozen --no-sync python - <<'PY'
+          import os
+          import tomllib
+          from pathlib import Path
+          import yaml
+
+          version = tomllib.loads(Path("pyproject.toml").read_text())["project"]["version"]
+          citation_version = str(yaml.safe_load(Path("CITATION.cff").read_text())["version"])
+          assert os.environ["RELEASE_TAG"] == f"v{version}"
+          assert citation_version == version
+          PY
+      - run: uv run --frozen --no-sync python -m pytest -W error -q
+        env:
+          MPLBACKEND: Agg
+      - run: uv run --frozen --no-sync sphinx-build -E -W --keep-going -b html docs docs/_build/html
+      - name: Build one source archive and one wheel
+        run: uv run --frozen --no-sync python -m build --no-isolation
+      - run: uv run --frozen --no-sync twine check dist/*
+      - run: uv run --frozen --no-sync python -m pytest tests/test_distribution.py -q
+      - name: Smoke exact wheel in core and Excel environments
+        run: |
+          uv run --frozen --no-sync python scripts/smoke_built_wheel.py --wheel dist/labrecipe-0.1.1-py3-none-any.whl --mode core
+          uv run --frozen --no-sync python scripts/smoke_built_wheel.py --wheel dist/labrecipe-0.1.1-py3-none-any.whl --mode excel
+      - name: Assert release inventory and create checksums
+        run: |
+          uv run --frozen --no-sync python - <<'PY'
+          from pathlib import Path
+
+          files = sorted(path.name for path in Path("dist").iterdir() if path.is_file())
+          assert files == ["labrecipe-0.1.1-py3-none-any.whl", "labrecipe-0.1.1.tar.gz"]
+          PY
+          cd dist
+          sha256sum labrecipe-0.1.1-py3-none-any.whl labrecipe-0.1.1.tar.gz > SHA256SUMS
+          sha256sum -c SHA256SUMS
+      - uses: actions/upload-artifact@b7c566a772e6b6bfb58ed0dc250532a479d7789f # v6.0.0
+        with:
+          name: release-distributions
+          path: |
+            dist/labrecipe-0.1.1-py3-none-any.whl
+            dist/labrecipe-0.1.1.tar.gz
+            dist/SHA256SUMS
+          if-no-files-found: error
+
+  publish:
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/project/labrecipe/
+    permissions:
+      contents: read
+      id-token: write
+    steps:
+      - uses: actions/download-artifact@37930b1c2abaa49bbe596cd826c3c89aef350131 # v7.0.0
+        with:
+          name: release-distributions
+          path: dist
+      - name: Verify downloaded artifact bytes
+        working-directory: dist
+        run: sha256sum -c SHA256SUMS
+      - name: Keep checksum metadata outside the package upload directory
+        run: mv dist/SHA256SUMS SHA256SUMS
+      - uses: pypa/gh-action-pypi-publish@ed0c53931b1dc9bd32cbe73a98c7f6766f8a527e # v1.13.0
+        with:
+          packages-dir: dist/
+          attestations: true

labrecipe-0.1.1/.gitignore

@@ -0,0 +1,13 @@
+.venv/
+__pycache__/
+*.py[cod]
+*$py.class
+.pytest_cache/
+.ruff_cache/
+.mypy_cache/
+.coverage
+htmlcov/
+docs/_build/
+build/
+dist/
+*.egg-info/

labrecipe-0.1.1/.python-version

@@ -0,0 +1 @@
+3.13

labrecipe-0.1.1/CHANGELOG.md

@@ -0,0 +1,36 @@
+# Changelog
+
+All notable changes to this project are documented in this file.
+
+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).
+
+## [Unreleased]
+
+### Added
+
+- Nothing yet.
+
+## [0.1.1] - 2026-07-15
+
+### Fixed
+
+- Correct the immutable PyPI publish action pin to reference the signed v1.13.0 release's
+  underlying commit so its published container image can be resolved.
+
+## [0.1.0] - 2026-07-14
+
+### Added
+
+- Strict versioned YAML recipes, immutable CSV/TSV and optional bounded XLSX ingestion.
+- Explicit group-safe transforms, transparent analyses, candidate scoring, and evidence-bearing
+  figures.
+- Deterministic evidence bundles with exact structural contracts, numerical tolerances,
+  provenance, and atomic publication.
+- Equivalent Python and CLI validate, inspect, plan/explain, and run interfaces.
+- Four executable representative example controls and warnings-as-errors documentation.
+- Apache-2.0 licensing, contributor guidance, security policy, and citation metadata.
+
+[Unreleased]: https://github.com/JK1234567899999/labrecipe/compare/v0.1.1...HEAD
+[0.1.1]: https://github.com/JK1234567899999/labrecipe/releases/tag/v0.1.1
+[0.1.0]: https://github.com/JK1234567899999/labrecipe/releases/tag/v0.1.0

labrecipe-0.1.1/CITATION.cff

@@ -0,0 +1,24 @@
+cff-version: 1.2.0
+message: If you use LabRecipe, please cite the software using this metadata.
+title: LabRecipe
+type: software
+authors:
+  - name: LabRecipe contributors
+version: 0.1.1
+repository-code: https://github.com/JK1234567899999/labrecipe
+url: https://github.com/JK1234567899999/labrecipe
+license: Apache-2.0
+keywords:
+  - reproducible research
+  - scientific Python
+  - experimental data
+  - time series
+  - provenance
+preferred-citation:
+  type: software
+  title: LabRecipe
+  authors:
+    - name: LabRecipe contributors
+  version: 0.1.1
+  repository-code: https://github.com/JK1234567899999/labrecipe
+  license: Apache-2.0

labrecipe-0.1.1/CODE_OF_CONDUCT.md

@@ -0,0 +1,108 @@
+# Contributor Covenant 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 for our community include:
+
+- 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, and learning
+  from the experience
+- Focusing on what is best not just for us as individuals, but for the overall community
+
+Examples of unacceptable behavior include:
+
+- The use of sexualized language or imagery, and sexual attention or advances of any kind
+- Trolling, insulting or derogatory comments, and personal or political attacks
+- Public or private harassment
+- Publishing others' private information, such as a physical or email address, without their
+  explicit permission
+- Other conduct which could reasonably be considered inappropriate in a professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of acceptable
+behavior and will take appropriate and fair corrective action in response to any behavior that
+they deem inappropriate, threatening, offensive, or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject comments,
+commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of
+Conduct, and will communicate reasons for moderation decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when an individual
+is officially representing the community in public spaces. Examples of representing our
+community include using an official email address, posting via an official social media
+account, or acting as an appointed representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported privately
+to the repository maintainers at
+https://github.com/JK1234567899999/labrecipe/security/advisories/new. Mark the report as a Code of
+Conduct matter. All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the reporter of any
+incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining the
+consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed unprofessional
+or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing clarity around
+the nature of the violation and an explanation of why the behavior was inappropriate. A
+public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of actions.
+
+**Consequence**: A warning with consequences for continued behavior. No interaction with the
+people involved, including unsolicited interaction with those enforcing the Code of Conduct,
+for a specified period of time. This includes avoiding interactions in community spaces as
+well as external channels like social media. Violating these terms may lead to a temporary or
+permanent ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including sustained
+inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public communication with
+the community for a specified period of time. No public or private interaction with the
+people involved, including unsolicited interaction with those enforcing the Code of Conduct,
+is allowed during this period. Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community standards, including
+sustained inappropriate behavior, harassment of an individual, or aggression toward or
+disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the community.
+
+## Attribution
+
+This Code of Conduct is adapted from the Contributor Covenant, version 2.1, available at
+https://www.contributor-covenant.org/version/2/1/code_of_conduct.html.
+
+Community Impact Guidelines were inspired by Mozilla's code of conduct enforcement ladder.

labrecipe-0.1.1/CONTRIBUTING.md

@@ -0,0 +1,52 @@
+# Contributing to LabRecipe
+
+Thank you for improving transparent experimental-data analysis. By participating, you agree
+to follow [CODE_OF_CONDUCT.md](CODE_OF_CONDUCT.md).
+
+## Before opening work
+
+1. Search existing [issues](https://github.com/JK1234567899999/labrecipe/issues).
+2. Open or comment on an issue before a large change so scope and scientific intent are clear.
+3. Keep pull requests small, focused, and independently reviewable.
+4. Base work on the current default branch and do not mix unrelated formatting or generated
+   changes.
+
+Bug reports should include a minimal redistributable source/recipe, LabRecipe and Python
+versions, operating system, exact stable diagnostic codes, expected behavior, and actual
+behavior. Remove sensitive experimental data.
+
+## Pull requests
+
+- Explain the user-visible scientific or maintenance outcome and its limits.
+- Add focused tests first or with the implementation; include dirty and edge cases.
+- Preserve raw-input immutability, named-stage non-mutation, group/replicate isolation,
+  deterministic ordering, typed errors, and atomic publication.
+- Update documentation and CHANGELOG.md for public behavior.
+- Regenerate the recipe schema when its authoritative model changes.
+- Run the commands in [DEVELOPMENT.md](DEVELOPMENT.md).
+- Link the issue and state any compatibility or reproducibility impact.
+
+## Adding or changing a public scientific method
+
+A method contribution is incomplete unless it includes all of the following:
+
+1. A strict typed parameter model with explicit defaults and finite bounds.
+2. Documented assumptions, caveats, and an appropriate primary citation.
+3. Explicit unit, sampling, axis, group/replicate, missing/non-finite, and short-data
+   preconditions.
+4. Analytical numerical controls plus clean, dirty, and failure fixtures.
+5. Tests proving input/prior-stage non-mutation and no cross-group or cross-replicate leakage.
+6. Stable structured diagnostics for every rejected precondition.
+7. Complete effective-parameter, method/provider, mask, exclusion, unit, and lineage evidence.
+8. Reference-oriented numerical tolerances and semantic figure checks where relevant.
+9. User documentation, recipe examples, and an Unreleased changelog entry.
+
+Candidate detectors must remain candidates rather than automatic physical conclusions or
+silent exclusions. New methods may not add executable YAML, implicit parameter tuning, or
+third-party plugin discovery to v1.
+
+## Review and licensing
+
+Maintainers review correctness, scientific transparency, tests, compatibility, documentation,
+security, and scope. Contributions intentionally submitted for inclusion are accepted under
+the repository's [Apache-2.0 license](LICENSE).

labrecipe-0.1.1/DEVELOPMENT.md

@@ -0,0 +1,55 @@
+# Development guide
+
+LabRecipe supports Python 3.12, 3.13, and 3.14. The commands below are run from the repository
+root on a POSIX shell; Windows contributors may use the equivalent virtual-environment paths.
+
+## Environment
+
+~~~console
+python3.12 -m venv .venv
+.venv/bin/python -m pip install --upgrade pip
+.venv/bin/python -m pip install -e ".[dev,docs,excel]"
+~~~
+
+The editable install is for development only. Distribution tests build and install the wheel
+outside the checkout.
+
+## Focused and full checks
+
+~~~console
+.venv/bin/python -m pytest tests/test_docs.py -q
+.venv/bin/python -m pytest tests/test_community_files.py -q
+.venv/bin/python -m pytest -q
+.venv/bin/python -m ruff check src tests scripts
+.venv/bin/python -m mypy
+.venv/bin/python -m sphinx -E -W --keep-going -b html docs docs/_build/html
+.venv/bin/python -m build
+.venv/bin/python -m twine check dist/*
+~~~
+
+Warnings are errors in release verification. Do not weaken scientific tests, diagnostic
+contracts, or tolerances to make a platform pass.
+
+## Regenerate authoritative resources
+
+~~~console
+.venv/bin/python scripts/export_recipe_schema.py
+.venv/bin/python scripts/export_recipe_schema.py --check
+~~~
+
+The generated recipe schema must be committed with its Pydantic model change. To execute the
+representative corpus and exact expected contracts:
+
+~~~console
+.venv/bin/python -m pytest tests/test_example_inventory.py tests/test_examples.py -q
+~~~
+
+The examples are immutable CC0 controls. Add a new source hash, explicit provenance/license,
+complete recipe, expected diagnostic/mask/unit/metric/lineage contract, and analytical intent
+when changing the corpus.
+
+## Build artifacts
+
+Build outputs belong in dist/ and are not committed. Inspect both wheel and sdist, install the
+wheel in a fresh environment outside the checkout, then verify import, labrecipe --help, and
+representative CLI/API recipes. See RELEASING.md once release automation is present.