mkdocs.yml

site_name: Mastering Earth Observation Application Packaging with CWL

theme:
    logo: imgs/icon-eoap.png
    name: material

    palette:
    - media: "(prefers-color-scheme: light)"
      scheme: default
      toggle:
        icon: material/toggle-switch-off-outline
        name: Switch to dark mode
    - media: "(prefers-color-scheme: dark)"
      scheme: slate
      toggle:
        icon: material/toggle-switch
        name: Switch to light mode
plugins:
  - search
  - mermaid2:
      version: 10.6.0

markdown_extensions:
  - pymdownx.details
  - abbr
  - admonition
  - footnotes
  - pymdownx.caret
  - pymdownx.mark
  - pymdownx.tilde
  - pymdownx.arithmatex:
      generic: true
  - pymdownx.superfences
  - pymdownx.tabbed
  - pymdownx.superfences:
      custom_fences:
        - name: mermaid
          class: mermaid
          format: !!python/name:pymdownx.superfences.fence_div_format
  - attr_list
  - pymdownx.snippets:
      base_path: './'
  - pymdownx.highlight:
      line_spans: __span
extra_css:
  - styles/css/app.css
  
extra_javascript:
  - javascripts/config.js
  - https://polyfill.io/v3/polyfill.min.js?features=es6
  - https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js
  

nav:
  - Introduction: 'index.md'
  - Prerequisites: 
    - Introduction to YAML: prerequisites/yaml.md
    - Introduction to CWL: prerequisites/cwl.md
  - Earth Observation Application Package:
    - OGC Activities: app-package/ogc-context.md
  - Introducing the application:
    - Water bodies detection: app/water-bodies-detection.md
    - Application Steps:
      - Crop: 
        - Description: app/crop/app.md
        - Running the step: python-env/crop.md
      - Normalized Difference:
        - Description: app/normalized-difference/app.md
        - Running the step: python-env/norm-diff.md
      - Otsu threshold:
        - Description: app/otsu/app.md
        - Running the step: python-env/otsu.md
      - STAC Catalog:
        - Description: app/stac/app.md
        - Running the step: python-env/stac.md
  - Package the EO Application:
    - Creating the containers: 
      - Scope: containers/scope.md
      - Test the containers:
        - Crop: containers/crop.md
        - Normalized difference: containers/norm-diff.md
        - Ostu threshold: containers/otsu.md
        - STAC Catalog: containers/stac.md
    - Create CWL CommandLineTools:
      - Scope: cwl-cli/scope.md
      - Crop: cwl-cli/crop.md
      - Normalized difference: cwl-cli/norm-diff.md
      - Ostu threshold: cwl-cli/otsu.md
      - STAC Catalog: cwl-cli/stac.md
    - Create the CWL Workflows:
      - Scope: cwl-workflow/scope.md
      - Sentinel-2 Cloud native Workflow: cwl-workflow/cloud-native.md
      - Staged Landsat-9 Workflow:
        - Understanding stage-in/out: cwl-workflow/stage-in-out.md
        - CWL CommandLineTool for stage-in: cwl-workflow/stage-in.md
        - CWL CommandLineTool for stage-out: cwl-workflow/stage-out.md
        - Processing a staged Landsat-9 acquisition: cwl-workflow/staged.md
      - Sentinel-2 Workflow of Workflow: cwl-workflow/scatter-cloud-native.md
  - Release the EO Application:
    - Scope: release/scope.md
    - Continuous Integration: release/ci.md
  - Execution Scenarios:
    - Scope: exec/scope.md
    - Running on a local machine:
      - Sentinel-2: cwl-workflow/exec-cloud-native.md
      - Landsat-9: cwl-workflow/exec-stage-in.md
    - Running CWL Workflow on Kubernetes: 
      - Run the CWL Workflow with calrissian: kubernetes/calrissian.md 
  - FAIR Application Packages: fair/best-practice.md
  - Reference:
    - OGC Application Package Best Practice: reference/ogc-ap-bp.md
    - CWL CommandLineTool: reference/cwl-commandlinetool.md
    - CWL Workflow: reference/cwl-workflow.md
    - Tools: 
      - cwltool: reference/cwltool.md
      - calrissian: reference/calrissian.md