mzmlpy 0.3.0__tar.gz

mzmlpy-0.3.0/.github/copilot-instructions.md

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+## Copilot Instructions
+
+### VERY IMPORTANT INSTRUCTIONS
+
+USE THE JUSTFILE WHENEVER POSSIBLE. IF THERE IS NOT A JUSTFILE COMMAND CHECK AGAIN... IF THERE IS STILL NOT A FUCKING JUST COMAND... USE UV PACKAGE MANAGER! THIS IS ALREADY INSTALLED AND AVAILABLE. DO NOT, UNDER ANY CIRCUMSTANCES, INSTALL ANY DEPENDENCIES USING NPM, YARN, PIP, GEM, OR ANY OTHER PACKAGE MANAGER. AND NEVER USE PYHTON / PYTEST DIRECTLY!!! ALWAYS USE JUST FOR AVAILABLE COMMANDS AND ONLY FALL BACK TO UV IF THERE IS NO JUST COMMAND AVAILABLE. 
+
+### Available Tools
+- Use `just` for all project commands. See `just --list` for available commands.
+- Use `uv` for package management and running scripts. See `uv --help` for usage.
+- Use `git` for version control.
+- Use ty for type checking. `uv run ty check src/ tests/` or `just ty`
+- Use pytest for testing. `uv run pytest tests/` or `just test`
+- use ruff for linting and formatting. `uv run ruff check src/ tests/` or `just lint` and `uv run ruff format src/` or `just format`
+
+### VERY IMPORTANT INSTRUCTIONS
+
+USE THE JUSTFILE WHENEVER POSSIBLE. IF THERE IS NOT A JUSTFILE COMMAND CHECK AGAIN... IF THERE IS STILL NOT A FUCKING JUST COMAND... USE UV PACKAGE MANAGER! THIS IS ALREADY INSTALLED AND AVAILABLE. DO NOT, UNDER ANY CIRCUMSTANCES, INSTALL ANY DEPENDENCIES USING NPM, YARN, PIP, GEM, OR ANY OTHER PACKAGE MANAGER. AND NEVER USE PYHTON / PYTEST DIRECTLY!!! ALWAYS USE JUST FOR AVAILABLE COMMANDS AND ONLY FALL BACK TO UV IF THERE IS NO JUST COMMAND AVAILABLE. 
+
+### Code Style & Philosophy
+
+- **Type everything**: Use comprehensive type hints (NDArray, Literal, Protocol, Self, etc.). Generic types should be specific. Use pyhton 3.12 features where applicable. Match-case statements preferred over if-elif chains for discrete values >= 3. Use list, tuple, set over List, Tuple, Set where possible. Dont use Union or Optional, use | operator.
+- **Immutability**: Prefer frozen dataclasses with `slots=True` and functional transformations over mutation. Though this is not absolute.
+- **Explicit over implicit**: Clear, descriptive names. No magic. If there's a performance trade-off, make it obvious.
+- **Simplicity**: Simple, readable code over clever one-liners. Break complex logic into smaller functions.
+
+Test do not need to be strongly typed but should still use type hints where reasonable. dont worry about exhaustive typing in tests, nor running ruff/ty on tests.
+
+### VERY IMPORTANT INSTRUCTIONS
+
+USE THE JUSTFILE WHENEVER POSSIBLE. IF THERE IS NOT A JUSTFILE COMMAND CHECK AGAIN... IF THERE IS STILL NOT A FUCKING JUST COMAND... USE UV PACKAGE MANAGER! THIS IS ALREADY INSTALLED AND AVAILABLE. DO NOT, UNDER ANY CIRCUMSTANCES, INSTALL ANY DEPENDENCIES USING NPM, YARN, PIP, GEM, OR ANY OTHER PACKAGE MANAGER. AND NEVER USE PYHTON / PYTEST DIRECTLY!!! ALWAYS USE JUST FOR AVAILABLE COMMANDS AND ONLY FALL BACK TO UV IF THERE IS NO JUST COMMAND AVAILABLE. 
+
+### Documentation
+
+- Concise docstrings - no novels
+- Document the "why" when non-obvious, not the "what"
+- Type hints are documentation - don't repeat them in docstrings. Methods/Function should be able to get by with no/minimal docstrings if types are clear.
+- Use `Raises` section in docstrings for exceptions
+- No placeholder comments like "TODO: implement later" - use `raise NotImplementedError("reason")`
+
+### Response Style
+
+- Get to the point
+- Show code, minimal explanation
+- If I'm wrong, tell me directly
+- Assume I know Python well - no hand-holding
+
+### VERY IMPORTANT INSTRUCTIONS
+
+USE THE JUSTFILE WHENEVER POSSIBLE. IF THERE IS NOT A JUSTFILE COMMAND CHECK AGAIN... IF THERE IS STILL NOT A FUCKING JUST COMAND... USE UV PACKAGE MANAGER! THIS IS ALREADY INSTALLED AND AVAILABLE. DO NOT, UNDER ANY CIRCUMSTANCES, INSTALL ANY DEPENDENCIES USING NPM, YARN, PIP, GEM, OR ANY OTHER PACKAGE MANAGER. AND NEVER USE PYHTON / PYTEST DIRECTLY!!! ALWAYS USE JUST FOR AVAILABLE COMMANDS AND ONLY FALL BACK TO UV IF THERE IS NO JUST COMMAND AVAILABLE. 
+
+### VERY IMPORTANT INSTRUCTIONS
+
+USE THE JUSTFILE WHENEVER POSSIBLE. IF THERE IS NOT A JUSTFILE COMMAND CHECK AGAIN... IF THERE IS STILL NOT A FUCKING JUST COMAND... USE UV PACKAGE MANAGER! THIS IS ALREADY INSTALLED AND AVAILABLE. DO NOT, UNDER ANY CIRCUMSTANCES, INSTALL ANY DEPENDENCIES USING NPM, YARN, PIP, GEM, OR ANY OTHER PACKAGE MANAGER. AND NEVER USE PYHTON / PYTEST DIRECTLY!!! ALWAYS USE JUST FOR AVAILABLE COMMANDS AND ONLY FALL BACK TO UV IF THERE IS NO JUST COMMAND AVAILABLE. 
+
+### VERY IMPORTANT INSTRUCTIONS
+
+USE THE JUSTFILE WHENEVER POSSIBLE. IF THERE IS NOT A JUSTFILE COMMAND CHECK AGAIN... IF THERE IS STILL NOT A FUCKING JUST COMAND... USE UV PACKAGE MANAGER! THIS IS ALREADY INSTALLED AND AVAILABLE. DO NOT, UNDER ANY CIRCUMSTANCES, INSTALL ANY DEPENDENCIES USING NPM, YARN, PIP, GEM, OR ANY OTHER PACKAGE MANAGER. AND NEVER USE PYHTON / PYTEST DIRECTLY!!! ALWAYS USE JUST FOR AVAILABLE COMMANDS AND ONLY FALL BACK TO UV IF THERE IS NO JUST COMMAND AVAILABLE. 
+
+### VERY IMPORTANT INSTRUCTIONS
+
+USE THE JUSTFILE WHENEVER POSSIBLE. IF THERE IS NOT A JUSTFILE COMMAND CHECK AGAIN... IF THERE IS STILL NOT A FUCKING JUST COMAND... USE UV PACKAGE MANAGER! THIS IS ALREADY INSTALLED AND AVAILABLE. DO NOT, UNDER ANY CIRCUMSTANCES, INSTALL ANY DEPENDENCIES USING NPM, YARN, PIP, GEM, OR ANY OTHER PACKAGE MANAGER. AND NEVER USE PYHTON / PYTEST DIRECTLY!!! ALWAYS USE JUST FOR AVAILABLE COMMANDS AND ONLY FALL BACK TO UV IF THERE IS NO JUST COMMAND AVAILABLE. 
+
+### VERY IMPORTANT INSTRUCTIONS
+
+USE THE JUSTFILE WHENEVER POSSIBLE. IF THERE IS NOT A JUSTFILE COMMAND CHECK AGAIN... IF THERE IS STILL NOT A FUCKING JUST COMAND... USE UV PACKAGE MANAGER! THIS IS ALREADY INSTALLED AND AVAILABLE. DO NOT, UNDER ANY CIRCUMSTANCES, INSTALL ANY DEPENDENCIES USING NPM, YARN, PIP, GEM, OR ANY OTHER PACKAGE MANAGER. AND NEVER USE PYHTON / PYTEST DIRECTLY!!! ALWAYS USE JUST FOR AVAILABLE COMMANDS AND ONLY FALL BACK TO UV IF THERE IS NO JUST COMMAND AVAILABLE. 
+

mzmlpy-0.3.0/.github/workflows/python-package.yml

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+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: Python package
+
+on:
+  push:
+    paths:
+      - 'src/**'
+      - 'tests/**'
+  workflow_dispatch:
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.12"]
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install uv
+      uses: astral-sh/setup-uv@v4
+    - name: Install just
+      uses: extractions/setup-just@v2
+    - name: Install dependencies
+      run: just install
+    - name: Lint with ruff
+      run: just lint
+    - name: Type check with ty
+      run: just check
+    - name: Test with pytest
+      run: just test-cov codecov-tests
+    - name: Upload coverage reports to Codecov
+      uses: codecov/codecov-action@v5
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        slug: tacular-omics/mzmlpy
+        fail_ci_if_error: false
+    - name: Upload test results to Codecov
+      if: ${{ !cancelled() }}
+      uses: codecov/codecov-action@v5
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        slug: tacular-omics/mzmlpy
+        report_type: test_results
+        fail_ci_if_error: false

mzmlpy-0.3.0/.github/workflows/python-publish.yml

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+# This workflow will upload a Python Package using Twine when a release is created
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.x'
+    - name: Install uv
+      uses: astral-sh/setup-uv@v4
+    - name: Build package with uv
+      run: uv build
+    - name: Publish package
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}

mzmlpy-0.3.0/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+tmp.py
+
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.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/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# MkDocs
+site/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   with no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducible builds.
+#   However, if you need to use different versions of dependencies on different environments,
+#   you may want to ignore it.
+#poetry.lock
+
+# uv
+.venv
+
+# ruff
+.ruff_cache/
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# editors
+.vscode/
+.idea/

mzmlpy-0.3.0/CLAUDE.md

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+# CLAUDE.md
+
+## Project
+
+**mzmlpy** — lightweight Python library for parsing mzML mass spectrometry files. Exposes a type-safe, lazy-loading API for spectra, chromatograms, and file metadata. Python 3.12+ only.
+
+Current version: **0.2.0** (Beta). Published on PyPI.
+
+## Commands
+
+```bash
+just lint        # ruff check src
+just format      # ruff isort + format src + tests
+just ty          # ty type checker (excludes src/mzmlpy/decoder.py)
+just check       # lint + ty + test
+just test        # pytest tests/
+just test-cov    # pytest with coverage report
+just docs        # mkdocs serve on localhost:8001
+just docs-build  # mkdocs build to site/
+just install     # uv sync
+```
+
+Always run `just lint` and `just test` after any code change.
+
+## Architecture
+
+```
+src/mzmlpy/
+├── run.py              # Mzml — main reader class, context manager, lazy XML parsing
+├── spectra.py          # Spectrum, Chromatogram, and all mixin/helper classes
+├── constants.py        # All StrEnum accessions + ION_MOBILITIES constant set
+├── decoder.py          # MSDecoder — zlib/zstd/numpress decompression (excluded from ty)
+├── lookup.py           # SpectrumLookup, ChromatogramLookup — index/id/slice access
+├── file_interface.py   # File format routing (.mzML, .mzML.gz)
+├── content.py          # CVElement
+├── elems/              # Metadata dataclasses (FileDescription, InstrumentConfiguration, etc.)
+└── py.typed            # PEP 561 marker
+```
+
+### Key design patterns
+
+- **Frozen dataclasses** — all data classes use `@dataclass(frozen=True)`; use `cached_property` for computed values
+- **Mixin composition** — `Spectrum` inherits from `_BinaryDataArrayMixin`, `_ScanListMixin`, `_PrecursorListMixin`, `_ProductListMixin`; never duplicate logic across these
+- **Lazy binary decoding** — `BinaryDataArray.data` decodes on every call (not cached); callers should store result if reusing
+- **XML namespaced lookups** — all `element.find()` calls use `self.ns` prefix (e.g. `f"./{self.ns}scanList"`)
+- **Warnings over exceptions** for ambiguous multi-scan/multi-window cases (e.g. `lower_mz` on a spectrum with multiple scans)
+
+## Dependencies
+
+- **Runtime:** `numpy>=1.26.0` only
+- **Optional:** `pynumpress>=0.0.4` (install via `pip install mzmlpy[numpress]`)
+- **Dev:** pytest, ruff, ty, pyupgrade, zstd, pytest-cov, mkdocs, mkdocs-material, mkdocstrings[python]
+- **Build:** uv + hatchling
+
+## Code style
+
+- Line length: 120
+- Type annotations required on all public API
+- Google-style docstrings
+- `StrEnum` for all CV accession constants — never hardcode accession strings outside `constants.py` (there are some legacy exceptions in `spectra.py` that should be migrated)
+- `Literal[...]` return types preferred over plain `str` for known-set values (e.g. `polarity`, `spectrum_type`)
+
+## Docs
+
+MkDocs + Material theme + mkdocstrings. All 34 exported public classes have API reference pages under `docs/api/`. Config in `mkdocs.yml` — `inherited_members: true` flattens mixin members, `signature_crossrefs: true` makes type annotations into links.
+
+## Tests
+
+Test data: `tests/data/example.mzML` and `tests/data/example.mzML.gz` (4 spectra, 1 chromatogram).
+Tests are parametrized over both files. No mocking — tests run against real XML.

mzmlpy-0.3.0/HISTORY.md

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+# History
+
+## 0.2.0 (2026-03-16)
+
+**Breaking changes:**
+
+* Renamed `lower_limit` / `upper_limit` → `lower_mz` / `upper_mz` on `ScanWindow`, `Scan`, and `Spectrum`.
+* Renamed `lower_scan_window_limit` / `upper_scan_window_limit` → `lower_mz` / `upper_mz` on `Scan`.
+
+**Bug fixes:**
+
+* Fixed polarity accessions — `ScanPolarity.POSITIVE` and `ScanPolarity.NEGATIVE` were swapped, causing incorrect polarity identification for all spectra.
+
+**New features:**
+
+* Added `ION_MOBILITIES` constant set grouping all ion mobility `BinaryDataArrayAccession` values.
+* Added `Spectrum.charge` — charge array as a numpy array (or `None`).
+* Added `Spectrum.has_im` — `True` if the spectrum contains any ion mobility binary array.
+* Added `Spectrum.im_types` — set of `BinaryDataArrayAccession` values present for ion mobility.
+* Added `Spectrum.scan_start_time` — delegates to the first scan's `scan_start_time`.
+* Added `Spectrum.ion_injection_time` — delegates to the first scan's `ion_injection_time`.
+
+## 0.1.0 (2026-02-10)
+
+* First release on PyPI.

mzmlpy-0.3.0/MANIFEST.in

@@ -0,0 +1,12 @@
+include HISTORY.md
+include README.md
+include .gitignore
+include tests/data
+
+recursive-include tests *
+recursive-include .github *
+
+recursive-exclude * __pycache__
+recursive-exclude * *.py[co]
+
+recursive-include *.md justfile *.jpg *.png *.gif

mzmlpy-0.3.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: mzmlpy
+Version: 0.3.0
+Summary: A lightweight Python library for parsing mzML mass spectrometry files.
+Author-email: Patrick Garrett <pgarrett@scripps.edu>
+Maintainer-email: Patrick Garrett <pgarrett@scripps.edu>
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Typing :: Typed
+Requires-Python: >=3.12
+Requires-Dist: numpy>=1.26.0
+Provides-Extra: numpress
+Requires-Dist: pynumpress>=0.0.4; extra == 'numpress'
+Provides-Extra: zstd
+Requires-Dist: zstd>=1.5.5; extra == 'zstd'
+Description-Content-Type: text/markdown
+
+<div align="center">
+  <img src="logo.png" alt="MZMLpy Logo" width="400" style="margin: 20px;"/>
+
+  A lightweight Python library for parsing mzML mass spectrometry files. Implements a type-safe, lazy-loading API with direct support for modern mzML structures (>= 1.1.0).
+
+  [![Python package](https://github.com/tacular-omics/mzmlpy/actions/workflows/python-package.yml/badge.svg)](https://github.com/tacular-omics/mzmlpy/actions/workflows/python-package.yml)
+  [![codecov](https://codecov.io/github/tacular-omics/mzmlpy/graph/badge.svg?token=1CTVZVFXF7)](https://codecov.io/github/tacular-omics/mzmlpy)
+  [![PyPI version](https://badge.fury.io/py/mzmlpy.svg)](https://badge.fury.io/py/mzmlpy)
+  [![Python 3.12+](https://img.shields.io/badge/python-3.12+-blue.svg)](https://www.python.org/downloads/)
+  [![License: MIT](https://img.shields.io/badge/License-MIT-g.svg)](https://opensource.org/licenses/MIT)
+
+</div>
+
+## Installation
+
+```bash
+pip install mzmlpy
+```
+
+Optional extras:
+
+```bash
+pip install mzmlpy[numpress]   # MS-Numpress decoding
+pip install mzmlpy[zstd]       # Zstandard compression
+```
+
+## Quick Start
+
+```python
+from mzmlpy import Mzml
+
+with Mzml("path/to/file.mzML") as reader:
+    print(f"File: {reader.file_name}  |  Spectra: {len(reader.spectra)}")
+
+    for spectrum in reader.spectra:
+        mz = spectrum.mz
+        intensity = spectrum.intensity
+        print(f"  {spectrum.id} MS{spectrum.ms_level} — {len(mz)} peaks")
+```
+
+Both `.mzML` and `.mzML.gz` files are supported. Metadata is parsed eagerly; binary data is decoded on demand.
+
+For full usage examples see the **[Getting Started guide](https://tacular-omics.github.io/mzmlpy/getting-started/)** and **[API Reference](https://tacular-omics.github.io/mzmlpy/api/mzml/)**.
+
+## Development
+
+```bash
+just lint     # ruff check
+just format   # ruff isort + format
+just ty       # ty type checker
+just test     # pytest
+
+# or all at once:
+just check
+```

mzmlpy-0.3.0/README.md

@@ -0,0 +1,55 @@
+<div align="center">
+  <img src="logo.png" alt="MZMLpy Logo" width="400" style="margin: 20px;"/>
+
+  A lightweight Python library for parsing mzML mass spectrometry files. Implements a type-safe, lazy-loading API with direct support for modern mzML structures (>= 1.1.0).
+
+  [![Python package](https://github.com/tacular-omics/mzmlpy/actions/workflows/python-package.yml/badge.svg)](https://github.com/tacular-omics/mzmlpy/actions/workflows/python-package.yml)
+  [![codecov](https://codecov.io/github/tacular-omics/mzmlpy/graph/badge.svg?token=1CTVZVFXF7)](https://codecov.io/github/tacular-omics/mzmlpy)
+  [![PyPI version](https://badge.fury.io/py/mzmlpy.svg)](https://badge.fury.io/py/mzmlpy)
+  [![Python 3.12+](https://img.shields.io/badge/python-3.12+-blue.svg)](https://www.python.org/downloads/)
+  [![License: MIT](https://img.shields.io/badge/License-MIT-g.svg)](https://opensource.org/licenses/MIT)
+
+</div>
+
+## Installation
+
+```bash
+pip install mzmlpy
+```
+
+Optional extras:
+
+```bash
+pip install mzmlpy[numpress]   # MS-Numpress decoding
+pip install mzmlpy[zstd]       # Zstandard compression
+```
+
+## Quick Start
+
+```python
+from mzmlpy import Mzml
+
+with Mzml("path/to/file.mzML") as reader:
+    print(f"File: {reader.file_name}  |  Spectra: {len(reader.spectra)}")
+
+    for spectrum in reader.spectra:
+        mz = spectrum.mz
+        intensity = spectrum.intensity
+        print(f"  {spectrum.id} MS{spectrum.ms_level} — {len(mz)} peaks")
+```
+
+Both `.mzML` and `.mzML.gz` files are supported. Metadata is parsed eagerly; binary data is decoded on demand.
+
+For full usage examples see the **[Getting Started guide](https://tacular-omics.github.io/mzmlpy/getting-started/)** and **[API Reference](https://tacular-omics.github.io/mzmlpy/api/mzml/)**.
+
+## Development
+
+```bash
+just lint     # ruff check
+just format   # ruff isort + format
+just ty       # ty type checker
+just test     # pytest
+
+# or all at once:
+just check
+```

mzmlpy-0.3.0/docs/api/chromatogram.md

@@ -0,0 +1,3 @@
+# Chromatogram
+
+::: mzmlpy.spectra.Chromatogram

mzmlpy-0.3.0/docs/api/constants.md

@@ -0,0 +1,11 @@
+# Constants
+
+::: mzmlpy.constants
+    options:
+      members:
+        - ScanPolarity
+        - SpectrumType
+        - BinaryDataArrayAccession
+        - CompressionTypeAccessions
+        - ION_MOBILITIES
+        - PROTON_MASS

mzmlpy-0.3.0/docs/api/data-processing.md

@@ -0,0 +1,7 @@
+# Data Processing
+
+::: mzmlpy.elems.data_processing.DataProcessing
+
+## ProcessingMethod
+
+::: mzmlpy.elems.data_processing.ProcessingMethod

mzmlpy-0.3.0/docs/api/file-description.md

@@ -0,0 +1,15 @@
+# File Description
+
+::: mzmlpy.elems.file_desc.FileDescription
+
+## FileContent
+
+::: mzmlpy.elems.file_desc.FileContent
+
+## SourceFile
+
+::: mzmlpy.elems.file_desc.SourceFile
+
+## Contact
+
+::: mzmlpy.elems.file_desc.Contact

mzmlpy-0.3.0/docs/api/instrument.md

@@ -0,0 +1,15 @@
+# Instrument Configuration
+
+::: mzmlpy.elems.instrument_config.InstrumentConfiguration
+
+## SourceComponent
+
+::: mzmlpy.elems.instrument_config.SourceComponent
+
+## AnalyzerComponent
+
+::: mzmlpy.elems.instrument_config.AnalyzerComponent
+
+## DetectorComponent
+
+::: mzmlpy.elems.instrument_config.DetectorComponent

mzmlpy-0.3.0/docs/api/lookup.md

@@ -0,0 +1,5 @@
+# Lookup
+
+::: mzmlpy.lookup.SpectrumLookup
+
+::: mzmlpy.lookup.ChromatogramLookup

mzmlpy-0.3.0/docs/api/metadata.md

@@ -0,0 +1,33 @@
+# Metadata
+
+## Software
+
+::: mzmlpy.elems.software.Software
+
+## Sample
+
+::: mzmlpy.elems.sample.Sample
+
+## Run
+
+::: mzmlpy.elems.run.Run
+
+## ScanSetting
+
+::: mzmlpy.elems.scan_setting.ScanSetting
+
+## Target
+
+::: mzmlpy.elems.scan_setting.Target
+
+## SourceFileRef
+
+::: mzmlpy.elems.scan_setting.SourceFileRef
+
+## ReferenceableParamGroup
+
+::: mzmlpy.elems.referenceable_param_group.ReferenceableParamGroup
+
+## ReferenceableParamGroupRef
+
+::: mzmlpy.elems.params.ReferenceableParamGroupRef

mzmlpy-0.3.0/docs/api/mzml.md

@@ -0,0 +1,3 @@
+# Mzml Reader
+
+::: mzmlpy.run.Mzml

mzmlpy-0.3.0/docs/api/params.md

@@ -0,0 +1,11 @@
+# CV Parameters
+
+::: mzmlpy.elems.params.CvParam
+
+## UserParam
+
+::: mzmlpy.elems.params.UserParam
+
+## CVElement
+
+::: mzmlpy.content.CVElement

mzmlpy-0.3.0/docs/api/precursor.md

@@ -0,0 +1,15 @@
+# Precursor & Ions
+
+::: mzmlpy.spectra.Precursor
+
+## IsolationWindow
+
+::: mzmlpy.spectra.IsolationWindow
+
+## SelectedIon
+
+::: mzmlpy.spectra.SelectedIon
+
+## Activation
+
+::: mzmlpy.spectra.Activation

mzmlpy-0.3.0/docs/api/spectrum.md

@@ -0,0 +1,15 @@
+# Spectrum
+
+::: mzmlpy.spectra.Spectrum
+
+## Scan
+
+::: mzmlpy.spectra.Scan
+
+## ScanWindow
+
+::: mzmlpy.spectra.ScanWindow
+
+## BinaryDataArray
+
+::: mzmlpy.spectra.BinaryDataArray