labharness 0.1.0__tar.gz

labharness-0.1.0/.editorconfig

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+root = true
+
+[*]
+charset = utf-8
+end_of_line = lf
+insert_final_newline = true
+trim_trailing_whitespace = true
+indent_style = space
+indent_size = 4
+
+[*.{toml,yml,yaml,json,md,tex,bib}]
+indent_size = 2
+
+[*.md]
+trim_trailing_whitespace = false
+
+[*.ps1]
+end_of_line = crlf

labharness-0.1.0/.gitattributes

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+# Normalize line endings: LF in the repository, whatever the OS.
+* text=auto eol=lf
+
+# Windows-only scripts keep CRLF.
+*.ps1 text eol=crlf
+
+# Binary files.
+*.pdf binary
+*.png binary
+*.otf binary
+*.ttf binary

labharness-0.1.0/.github/CODEOWNERS

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+# The maintainer owns everything and approves every pull request.
+* @AIAYN-creator

labharness-0.1.0/.github/ISSUE_TEMPLATE/bug_report.yml

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+name: Bug report
+description: Something does not work as documented.
+labels: ["bug"]
+body:
+  - type: textarea
+    id: what-happened
+    attributes:
+      label: What happened?
+      description: What did you do, what did you expect, and what happened instead?
+    validations:
+      required: true
+  - type: textarea
+    id: reproduce
+    attributes:
+      label: Steps to reproduce
+      description: The smallest set of files and commands that shows the problem.
+    validations:
+      required: true
+  - type: textarea
+    id: doctor
+    attributes:
+      label: Output of `labharness doctor`
+      render: text
+  - type: input
+    id: version
+    attributes:
+      label: LabHarness version
+      placeholder: labharness --version
+    validations:
+      required: true
+  - type: dropdown
+    id: os
+    attributes:
+      label: Operating system
+      options:
+        - Windows
+        - macOS
+        - Linux
+    validations:
+      required: true

labharness-0.1.0/.github/ISSUE_TEMPLATE/config.yml

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+blank_issues_enabled: false

labharness-0.1.0/.github/ISSUE_TEMPLATE/feature_request.yml

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+name: Feature request
+description: Propose a new capability or a change in behaviour.
+labels: ["enhancement"]
+body:
+  - type: textarea
+    id: problem
+    attributes:
+      label: What friction does this remove?
+      description: Describe the problem in your scientific workflow, not only the solution.
+    validations:
+      required: true
+  - type: textarea
+    id: proposal
+    attributes:
+      label: Proposed solution
+  - type: textarea
+    id: alternatives
+    attributes:
+      label: Alternatives you considered

labharness-0.1.0/.github/pull_request_template.md

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+## What and why
+
+<!-- What does this change do, and why is it needed? Link the issue it closes. -->
+
+Closes #
+
+## Checklist
+
+- [ ] The title follows Conventional Commits (e.g. `feat(plots): add power-law fits`).
+- [ ] Tests cover the change, and `uv run pytest` passes locally.
+- [ ] Docs and `docs/CHANGELOG.md` are updated if behaviour changed.
+- [ ] No fonts, sizes or colours are hard-coded (everything comes from the shared style).
+- [ ] The core still imports without any extra installed.
+- [ ] The change respects the accepted ADRs in `docs/adr/`.

labharness-0.1.0/.github/rulesets/main.json

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+{
+  "name": "main",
+  "target": "branch",
+  "enforcement": "active",
+  "conditions": {
+    "ref_name": {
+      "include": ["~DEFAULT_BRANCH"],
+      "exclude": []
+    }
+  },
+  "rules": [
+    { "type": "deletion" },
+    { "type": "non_fast_forward" },
+    {
+      "type": "pull_request",
+      "parameters": {
+        "required_approving_review_count": 1,
+        "dismiss_stale_reviews_on_push": true,
+        "require_code_owner_review": true,
+        "require_last_push_approval": false,
+        "required_review_thread_resolution": true,
+        "allowed_merge_methods": ["squash"]
+      }
+    },
+    {
+      "type": "required_status_checks",
+      "parameters": {
+        "strict_required_status_checks_policy": true,
+        "do_not_enforce_on_create": false,
+        "required_status_checks": [{ "context": "ci-pass" }]
+      }
+    }
+  ],
+  "bypass_actors": [
+    { "actor_id": 5, "actor_type": "RepositoryRole", "bypass_mode": "always" }
+  ]
+}

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

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+name: ci
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+
+permissions:
+  contents: read
+
+concurrency:
+  group: ci-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  lint:
+    name: lint
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: astral-sh/setup-uv@v5
+        with:
+          enable-cache: true
+      - run: uv sync --all-extras
+      - run: uv run ruff check .
+      - run: uv run ruff format --check .
+      - run: uv run mypy
+
+  test:
+    name: test (${{ matrix.os }}, ${{ matrix.python }})
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - { os: ubuntu-latest, python: "3.11" }
+          - { os: ubuntu-latest, python: "3.12" }
+          - { os: ubuntu-latest, python: "3.13" }
+          # Windows is the platform LabHarness is developed and demoed on.
+          - { os: windows-latest, python: "3.12" }
+    steps:
+      - uses: actions/checkout@v4
+      - uses: astral-sh/setup-uv@v5
+        with:
+          enable-cache: true
+          python-version: ${{ matrix.python }}
+      - run: uv sync --all-extras
+      - run: uv run pytest -m "not latex"
+
+  latex:
+    name: latex
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: astral-sh/setup-uv@v5
+        with:
+          enable-cache: true
+      # Third-party actions are blocked for this repository, so TeX Live comes from apt
+      # instead of setup-texlive-action.
+      - name: Install TeX Live
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y --no-install-recommends lmodern texlive-latex-recommended texlive-latex-extra texlive-science texlive-fonts-recommended
+          pdflatex --version | head -1
+      - run: uv sync --all-extras
+      - run: uv run pytest -m latex
+
+  # LaTeX on the platform the demo runs on. Slower than the Ubuntu job, so it only guards
+  # the document and diagram paths, which are the ones a Windows LaTeX install can break.
+  latex-windows:
+    name: latex-windows
+    runs-on: windows-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: astral-sh/setup-uv@v5
+        with:
+          enable-cache: true
+      - name: Install MiKTeX and Perl
+        shell: pwsh
+        run: |
+          choco install miktex --no-progress -y
+          choco install strawberryperl --no-progress -y
+          $env:PATH = "C:\Program Files\MiKTeX\miktex\bin\x64;C:\Strawberry\perl\bin;$env:PATH"
+          echo "C:\Program Files\MiKTeX\miktex\bin\x64" >> $env:GITHUB_PATH
+          echo "C:\Strawberry\perl\bin" >> $env:GITHUB_PATH
+          initexmf --set-config-value "[MPM]AutoInstall=1"
+      - name: Report the environment
+        shell: pwsh
+        run: |
+          pdflatex --version | Select-Object -First 1
+          latexmk -v
+      - run: uv sync --all-extras
+      - run: uv run pytest -m latex
+
+  # Single required check: the ruleset references this name, so it stays stable
+  # however the matrix above changes.
+  ci-pass:
+    name: ci-pass
+    if: always()
+    needs: [lint, test, latex, latex-windows]
+    runs-on: ubuntu-latest
+    steps:
+      - name: Fail if any job did not succeed
+        run: |
+          echo "lint=${{ needs.lint.result }} test=${{ needs.test.result }}"
+          echo "latex=${{ needs.latex.result }} latex-windows=${{ needs.latex-windows.result }}"
+          [ "${{ needs.lint.result }}" = "success" ] || exit 1
+          [ "${{ needs.test.result }}" = "success" ] || exit 1
+          [ "${{ needs.latex.result }}" = "success" ] || exit 1
+          [ "${{ needs.latex-windows.result }}" = "success" ] || exit 1

labharness-0.1.0/.gitignore

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+# Python
+__pycache__/
+*.py[cod]
+*.egg-info/
+build/
+dist/
+.venv/
+.pytest_cache/
+.mypy_cache/
+.ruff_cache/
+.coverage
+htmlcov/
+
+# LaTeX build artifacts
+*.aux
+*.bbl
+*.blg
+*.fdb_latexmk
+*.fls
+*.log
+*.out
+*.synctex.gz
+*.toc
+
+# Generated outputs of the example workspaces (rebuilt by `labharness build`)
+examples/**/figures/*
+!examples/**/figures/.gitkeep
+examples/**/paper.pdf
+
+# Editors and OS
+.vscode/
+.idea/
+.DS_Store
+Thumbs.db
+acs-*.bib

labharness-0.1.0/.pre-commit-config.yaml

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+# Fast checks only: the test suite runs in CI, not here.
+# Install the hooks once with: uv run pre-commit install --install-hooks --hook-type commit-msg
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-toml
+      - id: check-yaml
+      - id: check-added-large-files
+      - id: mixed-line-ending
+        args: [--fix=lf]
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.16.7
+    hooks:
+      - id: ruff
+        args: [--fix]
+      - id: ruff-format
+
+  - repo: https://github.com/compilerla/conventional-pre-commit
+    rev: v4.4.0
+    hooks:
+      - id: conventional-pre-commit
+        stages: [commit-msg]

labharness-0.1.0/.python-version

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+3.12

labharness-0.1.0/AGENTS.md

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+# Instructions for AI agents working on the LabHarness repository
+
+LabHarness is a local-first Data-to-Paper harness: raw lab data in, publication-ready LaTeX
+figures out. This file is for agents that **develop LabHarness itself**. The rules for agents
+that write papers *with* LabHarness live in `templates/workspace/AGENTS.md`.
+
+## Non-negotiable
+
+1. **Never commit or push without explicit authorization from the maintainer (@AIAYN-creator),
+   every single time.** Prepare the change, show what would be committed, and wait.
+2. When an agent took part in a commit, add the trailer `Supervised-by: <agent name>`.
+   **Never** use `Co-Authored-By` for an agent.
+3. Design decisions are recorded as ADRs (`docs/adr/`). Do not contradict an accepted ADR;
+   if a change seems to require it, raise it with the maintainer instead.
+
+## Architecture rules
+
+- `src/labharness/` holds the package: `core`, `style`, `watch`, `cli` and `modules/<domain>`.
+- **The CLI and the watcher are thin consumers.** No figure logic lives in them.
+- **The core must import without any extra installed.** Heavy dependencies (RDKit, SciPy,
+  Matplotlib, OPSIN, …) are imported lazily inside functions through `labharness.core.require`.
+  `tests/test_core.py` enforces it.
+- Every module follows the contract described in `src/labharness/modules/__init__.py`:
+  - no printing and no `sys.argv` or `exit()`;
+  - no global state;
+  - atomic writes and deterministic output;
+  - no imports between modules, and only the public API of `core` and `style`.
+- **Never hard-code fonts, sizes or colours in a module.** Everything comes from the shared
+  style: one typeface for the whole document.
+- `templates/workspace/` is the researcher's workspace template, shipped inside the package.
+
+## Conventions
+
+- Code, CLI messages and repository docs are in English.
+- Commits follow Conventional Commits (`feat`, `fix`, `docs`, `refactor`, `test`, `ci`,
+  `chore`, `build`), optionally scoped by area, e.g. `feat(chem): …`.
+- Paths with spaces and Windows are first-class: the maintainer develops on Windows.
+
+## Commands
+
+```
+uv sync --all-extras
+uv run pytest
+```
+
+Linting, formatting and type checking are added with the CI setup.

labharness-0.1.0/CLAUDE.md

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+@AGENTS.md

labharness-0.1.0/CODE_OF_CONDUCT.md

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+# Code of Conduct
+
+LabHarness adopts the [Contributor Covenant, version 3.0](https://www.contributor-covenant.org/version/3/0/code_of_conduct/)
+as its code of conduct. It applies to every project space (issues, pull requests,
+discussions) and to anyone representing the project.
+
+## Reporting
+
+If you experience or witness behaviour that violates the code of conduct, please report it
+privately to the maintainer, @AIAYN-creator, at labharness.project@gmail.com.
+
+Reports are handled confidentially, following the Contributor Covenant's guidance on
+addressing and repairing harm.

labharness-0.1.0/CONTRIBUTING.md

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+# Contributing to LabHarness
+
+Thanks for your interest! **LabHarness is pre-alpha.** The repository is public, but external
+contributions are not actively sought until the v1.0 release: issues are welcome, and pull requests
+are considered case by case. This guide describes how contributions work.
+
+## Development setup
+
+Requirements: Python ≥ 3.11, [uv](https://docs.astral.sh/uv/) and a LaTeX distribution
+(MiKTeX or TeX Live). On Windows with MiKTeX, `latexmk` also needs Perl
+(e.g. Strawberry Perl). Use a PDF viewer that does not lock files: SumatraPDF on Windows,
+Skim on macOS.
+
+```
+git clone https://github.com/AIAYN-creator/Lab-Harness.git
+cd Lab-Harness
+uv sync --all-extras
+uv run pytest
+```
+
+## How changes get in
+
+- **The maintainer** pushes to `main` directly, through the administrator bypass of the branch
+  ruleset.
+- **Everyone else:**
+  1. Open an issue first for anything beyond a small fix, so we can agree on the approach.
+  2. Work on a short-lived branch and open a pull request against `main`.
+  3. The pull request needs the `ci-pass` check to be green and an approval from the
+     maintainer (code owner). It is merged with squash.
+
+## Commit messages
+
+We use [Conventional Commits](https://www.conventionalcommits.org/):
+
+```
+feat(plots): add power-law fits
+fix(watch): debounce double saves from VS Code on Windows
+docs: explain the manifest format
+```
+
+Types: `feat`, `fix`, `docs`, `refactor`, `test`, `ci`, `chore`, `build`.
+
+## Design rules
+
+Please read [`AGENTS.md`](AGENTS.md). It applies to humans too. In short:
+
+- modules are plain functions with no terminal I/O;
+- the core imports without any extra;
+- no hard-coded fonts, sizes or colours;
+- larger design decisions are recorded as ADRs in [`docs/adr/`](docs/adr/).
+
+## Code of conduct
+
+This project follows its [Code of Conduct](CODE_OF_CONDUCT.md). By participating, you agree to
+uphold it.

labharness-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2026 AIAYN-creator
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.