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Migrate documentation from ReadTheDocs to GitHub Pages with Material theme
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‎.github/workflows/docs.yml‎

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name: Deploy Documentation
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on:
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push:
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branches:
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- master
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- main
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pull_request:
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branches:
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- master
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- main
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workflow_dispatch:
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permissions:
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contents: read
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pages: write
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id-token: write
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concurrency:
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group: "pages"
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cancel-in-progress: false
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jobs:
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build:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: '3.11'
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- name: Install Poetry
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uses: snok/install-poetry@v1
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with:
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version: latest
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virtualenvs-create: true
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virtualenvs-in-project: true
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- name: Load cached venv
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id: cached-poetry-dependencies
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uses: actions/cache@v4
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with:
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path: .venv
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key: venv-${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/poetry.lock') }}
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- name: Install dependencies
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if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
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run: poetry install --no-interaction --no-root --with dev
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- name: Install project
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run: poetry install --no-interaction
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- name: Build documentation
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run: poetry run mkdocs build --verbose --site-dir _site
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- name: Upload artifact
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uses: actions/upload-pages-artifact@v3
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with:
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path: _site
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deploy:
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environment:
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name: github-pages
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url: ${{ steps.deployment.outputs.page_url }}
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runs-on: ubuntu-latest
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needs: build
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if: github.event_name == 'push' && (github.ref == 'refs/heads/main' || github.ref == 'refs/heads/master')
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steps:
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- name: Deploy to GitHub Pages
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id: deployment
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uses: actions/deploy-pages@v4

‎.readthedocs.yml‎

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This file was deleted.

‎README.md‎

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Eager to start using ViMMS? Take advantage of these resources:
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- [Installation guide](pages/installation.md).
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- Visit our project documentation page: [![Documentation Status](https://readthedocs.org/projects/vimms/badge/?version=latest)](http://vimms.readthedocs.io/?badge=latest)
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- Visit our project documentation page: [![Documentation](https://img.shields.io/badge/docs-GitHub%20Pages-blue)](https://glasgowcompbio.github.io/vimms/)
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- Our [Demo folder](https://github.com/glasgowcompbio/vimms/tree/master/demo) contains notebooks that demonstrate how to use the framework in a simulated environment.
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- For specific examples that accompany our publications, see the [Example folder](https://github.com/glasgowcompbio/vimms/tree/master/examples).
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- You can also find this [quick guide on how to get started using ViMMS](https://github.com/glasgowcompbio/vimms/blob/master/demo/guide_to_vimms/guide_to_vimms.ipynb).

‎_config.yml‎

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url: https://github.com/glasgowcompbio/vimms/tree/master/demo
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- title: Code for Papers
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url: https://github.com/glasgowcompbio/vimms/tree/master/examples
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- title: API Documentation
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url: https://vimms.readthedocs.io
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- title: Documentation
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url: https://glasgowcompbio.github.io/vimms/

‎mkdocs.yml‎

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# mkdocs.yml
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site_name: Virtual Metabolomics Mass Spectrometry (ViMMS)
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site_url: https://glasgowcompbio.github.io/vimms/
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site_description: ViMMS - Virtual Metabolomics Mass Spectrometry Framework
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site_author: Glasgow Computational Biology Group
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repo_name: glasgowcompbio/vimms
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repo_url: https://github.com/glasgowcompbio/vimms
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edit_uri: edit/master/docs/
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theme:
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name: "readthedocs"
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name: material
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features:
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- navigation.tabs
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- navigation.sections
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- navigation.expand
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- navigation.path
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- toc.integrate
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- search.suggest
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- search.highlight
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- content.code.annotate
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- content.code.copy
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palette:
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- scheme: default
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primary: indigo
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accent: indigo
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toggle:
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icon: material/brightness-7
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name: Switch to dark mode
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- scheme: slate
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primary: indigo
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accent: indigo
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toggle:
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icon: material/brightness-4
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name: Switch to light mode
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plugins:
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- search
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- mkdocstrings:
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handlers:
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- search
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- mkdocstrings:
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handlers:
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python:
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paths: ["."]
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paths: ["."]
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options:
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show_source: true
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show_root_heading: true
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show_root_full_path: false
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show_symbol_type_heading: true
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show_symbol_type_toc: true
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docstring_style: google
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docstring_section_style: table
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merge_init_into_class: true
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show_if_no_docstring: false
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show_signature_annotations: true
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separate_signature: true
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line_length: 80
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markdown_extensions:
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- admonition
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- codehilite:
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guess_lang: false
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- toc:
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permalink: true
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- pymdownx.superfences
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- pymdownx.details
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- pymdownx.tabbed:
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alternate_style: true
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nav:
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- Home: README.md
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- Simulation Overview: simulation_overview.md
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- Creating Chemicals: chemicals.md
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- Running Controllers: controllers.md
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- Evaluating Simulations: evaluation.md
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- Running on a Real Instrument: real_instrument.md
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- Adding Noise: noise.md
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- Chromatographic Models: chromatography.md
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- Command Line Utilities: cli_tools.md
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- User Guide:
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- Simulation Overview: simulation_overview.md
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- Creating Chemicals: chemicals.md
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- Running Controllers: controllers.md
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- Evaluating Simulations: evaluation.md
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- Running on a Real Instrument: real_instrument.md
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- Adding Noise: noise.md
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- Chromatographic Models: chromatography.md
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- Command Line Utilities: cli_tools.md
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- API Documentation:
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- Common: api/common.md
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- Chemical Generation Process:
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- Chemicals: api/chemicals.md
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- Chemical Samplers: api/chemical_samplers.md
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- ROI: api/roi.md
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- Box: api/box.md
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- Mass Spectrometry Process:
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- Mass Spec: api/mass_spec.md
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- Column: api/column.md
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- Noise: api/noise.md
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- Fragmentation Strategy Simulation Process:
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- Environment: api/environment.md
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- Controllers: api/controllers.md
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- Dynamic Exclusion: api/exclusion.md
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- Agents: api/agent.md
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- Others:
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- Feature Extractions: api/feature_extractions.md
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- MzMLWriter: api/mzml_writer.md
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- Common: api/common.md
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- Chemical Generation Process:
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- Chemicals: api/chemicals.md
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- Chemical Samplers: api/chemical_samplers.md
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- ROI: api/roi.md
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- Box: api/box.md
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- Mass Spectrometry Process:
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- Mass Spec: api/mass_spec.md
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- Column: api/column.md
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- Noise: api/noise.md
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- Fragmentation Strategy Simulation Process:
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- Environment: api/environment.md
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- Controllers: api/controllers.md
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- Dynamic Exclusion: api/exclusion.md
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- Agents: api/agent.md
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- Others:
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- Feature Extractions: api/feature_extractions.md
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- MzMLWriter: api/mzml_writer.md
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extra:
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social:
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- icon: fontawesome/brands/github
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link: https://github.com/glasgowcompbio/vimms
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- icon: fontawesome/solid/book
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link: https://doi.org/10.1021/acs.analchem.9b02521
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copyright: Copyright © 2025 Glasgow Computational Biology Group

‎poetry.lock‎

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‎pyproject.toml‎

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black = "^25.1.0"
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pre-commit = "^3.7.0"
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mkdocstrings-python = "^1.16.12"
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mkdocs-material = "^9.5.48"
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[tool.setuptools_scm]
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