msdatasets 0.1.0__tar.gz

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

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+name: CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+
+      - name: Set up Python ${{ matrix.python-version }}
+        run: uv python install ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: uv sync --extra dev
+
+      - name: Run linting
+        run: uv run ruff check .
+
+      - name: Run format check
+        run: uv run ruff format --check .
+
+      - name: Run tests with coverage
+        run: uv run pytest --cov --cov-report=xml --cov-fail-under=80
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v4
+        if: matrix.python-version == '3.12'
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: ./coverage.xml
+          fail_ci_if_error: false

msdatasets-0.1.0/.github/workflows/docs.yml

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+name: Deploy Docs
+
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+concurrency:
+  group: pages
+  cancel-in-progress: false
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+
+      - name: Set up Python
+        run: uv python install 3.12
+
+      - name: Install dependencies
+        run: uv sync --extra docs
+
+      - name: Build docs
+        run: uv run mkdocs build
+
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: site/
+
+  deploy:
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

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

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+name: Publish to PyPI
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+
+      - name: Set up Python
+        run: uv python install 3.12
+
+      - name: Build package
+        run: uv build
+
+      - name: Upload artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+  publish:
+    needs: build
+    runs-on: ubuntu-latest
+    environment: pypi
+    permissions:
+      id-token: write
+    steps:
+      - name: Download artifacts
+        uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

msdatasets-0.1.0/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+*.egg
+
+# PyInstaller
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+
+# IDE
+.idea/
+.vscode/
+*.swp
+*.swo
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# ruff
+.ruff_cache/
+
+# OS
+.DS_Store
+Thumbs.db
+
+# mkdocs
+site/

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

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+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.9.1
+    hooks:
+      - id: ruff
+        args: [--fix]
+      - id: ruff-format
+  - repo: local
+    hooks:
+      - id: pytest
+        name: pytest
+        entry: uv run pytest --cov --cov-fail-under=80
+        language: system
+        pass_filenames: false
+        always_run: true
+        stages: [pre-commit]

msdatasets-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2025 msdatasets contributors
+
+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.

msdatasets-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: msdatasets
+Version: 0.1.0
+Summary: A unified dataset framework for mass spectrometry
+Project-URL: Homepage, https://chrisagrams.github.io/msdatasets
+Project-URL: Repository, https://github.com/chrisagrams/msdatasets
+Author-email: Chris Grams <chrisagrams@gmail.com>
+License-Expression: MIT
+License-File: LICENSE
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT 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: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.10
+Provides-Extra: dev
+Requires-Dist: pre-commit>=4.0; extra == 'dev'
+Requires-Dist: pytest-cov>=4.0; extra == 'dev'
+Requires-Dist: pytest>=8.0; extra == 'dev'
+Requires-Dist: ruff>=0.9; extra == 'dev'
+Provides-Extra: docs
+Requires-Dist: mkdocs-material>=9.5; extra == 'docs'
+Requires-Dist: mkdocs>=1.6; extra == 'docs'
+Requires-Dist: mkdocstrings[python]>=0.24; extra == 'docs'
+Description-Content-Type: text/markdown
+
+# msdatasets
+
+[![CI](https://github.com/chrisagrams/msdatasets/actions/workflows/ci.yml/badge.svg)](https://github.com/chrisagrams/msdatasets/actions/workflows/ci.yml)
+[![codecov](https://codecov.io/gh/chrisagrams/msdatasets/graph/badge.svg)](https://codecov.io/gh/chrisagrams/msdatasets)
+[![PyPI version](https://badge.fury.io/py/msdatasets.svg)](https://pypi.org/project/msdatasets/)
+
+A unified dataset framework for mass spectrometry.
+
+## Installation
+
+```bash
+pip install msdatasets
+```
+
+## Development
+
+Install in development mode with test dependencies:
+
+```bash
+uv sync --extra dev
+```
+
+Set up pre-commit hooks:
+
+```bash
+uv run pre-commit install
+```
+
+Run tests:
+
+```bash
+uv run pytest
+```
+
+## License
+
+MIT

msdatasets-0.1.0/README.md

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+# msdatasets
+
+[![CI](https://github.com/chrisagrams/msdatasets/actions/workflows/ci.yml/badge.svg)](https://github.com/chrisagrams/msdatasets/actions/workflows/ci.yml)
+[![codecov](https://codecov.io/gh/chrisagrams/msdatasets/graph/badge.svg)](https://codecov.io/gh/chrisagrams/msdatasets)
+[![PyPI version](https://badge.fury.io/py/msdatasets.svg)](https://pypi.org/project/msdatasets/)
+
+A unified dataset framework for mass spectrometry.
+
+## Installation
+
+```bash
+pip install msdatasets
+```
+
+## Development
+
+Install in development mode with test dependencies:
+
+```bash
+uv sync --extra dev
+```
+
+Set up pre-commit hooks:
+
+```bash
+uv run pre-commit install
+```
+
+Run tests:
+
+```bash
+uv run pytest
+```
+
+## License
+
+MIT

msdatasets-0.1.0/docs/api.md

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+# API Reference
+
+::: msdatasets

msdatasets-0.1.0/docs/getting-started.md

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+# Getting Started
+
+## Installation
+
+Install from PyPI:
+
+```bash
+pip install msdatasets
+```
+
+Or with uv:
+
+```bash
+uv add msdatasets
+```
+
+## Development Installation
+
+Clone the repository and install in development mode:
+
+```bash
+git clone https://github.com/chrisagrams/msdatasets.git
+cd msdatasets
+uv sync --extra dev --extra docs
+```
+
+## Running Tests
+
+```bash
+uv run pytest
+```
+
+## Building Documentation
+
+Serve docs locally:
+
+```bash
+uv run mkdocs serve
+```
+
+Build static site:
+
+```bash
+uv run mkdocs build
+```

msdatasets-0.1.0/docs/index.md

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+# msdatasets
+
+A unified dataset framework for mass spectrometry.
+
+## Installation
+
+```bash
+pip install msdatasets
+```
+
+## Quick Start
+
+```python
+import msdatasets
+
+print(msdatasets.__version__)
+```
+
+## Features
+
+- Coming soon
+
+## License
+
+This project is licensed under the MIT License.

msdatasets-0.1.0/mkdocs.yml

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+site_name: msdatasets
+site_description: A unified dataset framework for mass spectrometry
+site_url: https://chrisagrams.github.io/msdatasets
+repo_url: https://github.com/chrisagrams/msdatasets
+repo_name: chrisagrams/msdatasets
+
+theme:
+  name: material
+  palette:
+    - scheme: default
+      primary: indigo
+      accent: indigo
+      toggle:
+        icon: material/brightness-7
+        name: Switch to dark mode
+    - scheme: slate
+      primary: indigo
+      accent: indigo
+      toggle:
+        icon: material/brightness-4
+        name: Switch to light mode
+  features:
+    - content.code.copy
+    - navigation.sections
+    - navigation.expand
+    - search.highlight
+
+plugins:
+  - search
+  - mkdocstrings:
+      handlers:
+        python:
+          paths: [src]
+          options:
+            show_source: true
+            show_root_heading: true
+
+nav:
+  - Home: index.md
+  - Getting Started: getting-started.md
+  - API Reference: api.md
+
+markdown_extensions:
+  - pymdownx.highlight:
+      anchor_linenums: true
+  - pymdownx.superfences
+  - admonition
+  - toc:
+      permalink: true

msdatasets-0.1.0/pyproject.toml

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+[project]
+name = "msdatasets"
+version = "0.1.0"
+description = "A unified dataset framework for mass spectrometry"
+readme = "README.md"
+license = "MIT"
+requires-python = ">=3.10"
+authors = [
+    { name = "Chris Grams", email = "chrisagrams@gmail.com" },
+]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: MIT License",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+]
+dependencies = []
+
+[project.optional-dependencies]
+dev = [
+    "pytest>=8.0",
+    "pytest-cov>=4.0",
+    "ruff>=0.9",
+    "pre-commit>=4.0",
+]
+docs = [
+    "mkdocs>=1.6",
+    "mkdocs-material>=9.5",
+    "mkdocstrings[python]>=0.24",
+]
+
+[project.urls]
+Homepage = "https://chrisagrams.github.io/msdatasets"
+Repository = "https://github.com/chrisagrams/msdatasets"
+
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/msdatasets"]
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+pythonpath = ["src"]
+
+[tool.ruff]
+line-length = 88
+target-version = "py310"
+
+[tool.ruff.lint]
+select = ["E", "F", "I", "N", "W"]
+
+[tool.ruff.format]
+docstring-code-format = true
+
+[tool.coverage.run]
+source = ["msdatasets"]
+branch = true
+
+[tool.coverage.report]
+exclude_lines = [
+    "pragma: no cover",
+    "if TYPE_CHECKING:",
+]

msdatasets-0.1.0/src/msdatasets/__init__.py

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+"""A unified dataset framework for mass spectrometry."""
+
+__version__ = "0.1.0"

msdatasets-0.1.0/tests/conftest.py

@@ -0,0 +1 @@
+"""Pytest configuration and fixtures."""

msdatasets-0.1.0/tests/test_package.py

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+"""Basic package tests."""
+
+import msdatasets
+
+
+def test_version():
+    """Test that version is defined."""
+    assert hasattr(msdatasets, "__version__")
+    assert isinstance(msdatasets.__version__, str)
+    assert msdatasets.__version__ == "0.1.0"
+
+
+def test_import():
+    """Test that package can be imported."""
+    import msdatasets
+
+    assert msdatasets is not None