mkdocs.yml

site_name: Documentation
site_description: |
  The documentation for NOMAD v1.
site_author: The NOMAD Authors
repo_url: https://github.com/nomad-coe/nomad
edit_uri: ""
nav:
  - Home: index.md
  - Tutorial:
      - Navigating to NOMAD: tutorial/nomad_repo.md
      - Uploading and publishing data: tutorial/upload_publish.md
      - Exploring data: tutorial/explore.md
      - Access data via API: tutorial/access_api.md
      - Schemas and plugins: tutorial/custom.md
      - Developing a NOMAD plugin: tutorial/develop_plugin.md
  - How-to guides:
      - Overview: howto/overview.md
      - Manage and find data:
          - Upload and publish data for supported formats: howto/manage/upload.md
          - Use ELNs: howto/manage/eln.md
          - Explore data: howto/manage/explore.md
          - Use NORTH: howto/manage/north.md
      - Programmatic use:
          - Use the API: howto/programmatic/api.md # TODO separate into How-to and Explanation/Reference
          - Download data: howto/programmatic/download.md
          - Publish data using python: howto/programmatic/publish_python.md
          - Install nomad-lab: howto/programmatic/pythonlib.md
          - Access processed data: howto/programmatic/archive_query.md
          - Run a parser: howto/programmatic/local_parsers.md
      - NOMAD Oasis:
          - Install an Oasis: howto/oasis/install.md
          - Customize an Oasis: howto/oasis/customize.md
          - Install plugins: howto/oasis/plugins_install.md
          - Migrate Oasis versions: howto/oasis/migrate.md
          - Perform admin tasks: howto/oasis/admin.md
      - Plugins:
          - Get started with plugins: howto/plugins/plugins.md
          - Write an app: howto/plugins/apps.md
          - Write an example upload: howto/plugins/example_uploads.md
          - Write a normalizer: howto/plugins/normalizers.md
          - Write a parser: howto/plugins/parsers.md
          - Write a schema package: howto/plugins/schema_packages.md
          - Write an API: howto/plugins/apis.md
      - Customization:
          - Write a YAML schema package: howto/customization/basics.md
          - Define ELNs: howto/customization/elns.md
          - Use base sections: howto/customization/base_sections.md
          - Parse tabular data: howto/customization/tabular.md
          - Define workflows: howto/customization/workflows.md
          - Work with units: howto/customization/units.md
          - Use HDF5 to handle large quantities: howto/customization/hdf5.md
      - Development:
          - Get started: howto/develop/setup.md
          - Navigate the code: howto/develop/code.md
          - Contribute: howto/develop/contrib.md
          - Extend the search: howto/develop/search.md
          - Migrate to autoformatted code: howto/develop/migrate-to-autoformatter.md
          - Make a release: howto/develop/release.md
  - Domain-specific examples:
      - Overview: examples/overview.md
      - Computational data:
          - Quick start: examples/computational_data/uploading.md
          - Workflows: examples/computational_data/workflows.md
          - MetaInfo: examples/computational_data/metainfo.md
          - Schema plugins: examples/computational_data/schema_plugins.md
          - Parser plugins: examples/computational_data/parser_plugins.md
          - H5MD schema - Howto: examples/computational_data/h5md_howto.md
          - H5MD schema - Explanation: examples/computational_data/h5md_expl.md
          - H5MD - Reference: examples/computational_data/h5md_ref.md
      - Experimental data:
          - NeXus:
              - NeXus semantic file format: examples/experiment_data/nexus.md
              - Guide to parser library pynxtools: examples/experiment_data/pynxtools.md
              - Electron microscopy: examples/experiment_data/em.md
              - Photoemission spectroscopy: examples/experiment_data/mpes.md
              - X-ray photoemission spectroscopy: examples/experiment_data/xps.md
              - Optical spectroscopy: examples/experiment_data/opt.md
              - Atom probe tomography: examples/experiment_data/apm.md
              - Scanning tunneling spectroscopy: examples/experiment_data/sts.md
        # - NOMAD-supported plugins:
        # - Databases for specific research topics:
  - Explanation:
      - From files to data: explanation/basics.md
      - Data structure: explanation/data.md
      - Processing: explanation/processing.md
      - Architecture: explanation/architecture.md
      - Plugins: explanation/plugin_system.md
      - Federation and Oasis: explanation/oasis.md
  - Reference:
      - reference/config.md
      - reference/annotations.md
      - reference/cli.md
      - reference/plugins.md
      - reference/parsers.md
      - reference/code_guidelines.md
      - reference/glossary.md
      - reference/tutorials.md
theme:
  name: material
  palette:
    primary: "#2A4CDF"
    accent: "#008A67"
  font:
    text: "Titillium Web"
  logo: assets/nomad-logo.png
  favicon: assets/favicon.png
  features:
    - navigation.path
    - navigation.footer
    - navigation.top
  icon:
    repo: fontawesome/brands/github
# repo_url: https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/
markdown_extensions:
  - attr_list
  - md_in_html
  - admonition
  - pymdownx.details
  - pymdownx.highlight:
      anchor_linenums: true
  - pymdownx.inlinehilite
  - pymdownx.snippets
  - mkdocs-click
  - pymdownx.extra
  - toc:
      permalink: True
  - pymdownx.arithmatex:
      generic: true
  - pymdownx.emoji: # TODO make sure this isn't used!!
      emoji_index: !!python/name:material.extensions.emoji.twemoji
      emoji_generator: !!python/name:material.extensions.emoji.to_svg
  - pymdownx.superfences:
      custom_fences:
        - name: mermaid
          class: mermaid
          format: !!python/name:pymdownx.superfences.fence_code_format

extra:
  generator: false
  homepage: https://nomad-lab.eu
use_directory_urls: false
plugins:
  - search
  - macros:
      module_name: nomad/mkdocs
  - redirects:
      redirect_maps:
        "pythonlib.md": "howto/programmatic/pythonlib.md"
        "oasis.md": "howto/oasis/install.md"
        "develop/gitlab.md": "howto/develop/contrib.md"
  - glightbox
  # - git-revision-date-localized
  # TODO Fix error in pipeline when this plugin is included
  # (with 'mkdocs-git-revision-date-localized-plugin==1.2.1' in pyproject.toml)
  # see pipeline error here: https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/jobs/2473217
extra_css:
  - stylesheets/extra.css
extra_javascript:
  - javascript.js
  - https://polyfill.io/v3/polyfill.min.js?features=es6
  - https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js