mkdocs.yml

site_name: Looper
site_logo: img/looper_logo_dark.svg
site_url: http://looper.databio.org/
repo_url: http://github.com/pepkit/looper
pypi_name: loopercli

nav:
  - Getting Started:
      - Introduction: README.md
      - Features at-a-glance: features.md
      - Hello world: hello-world.md
  - How-to guides:
      - Defining a project: defining-a-project.md
      - Running a pipeline: running-a-pipeline.md
      - Initializing a repository: initialize.md
      - Using pipestat: pipestat.md
      - Parameterizing pipelines: parameterizing-pipelines.md
      - Running on a cluster: running-on-a-cluster.md
      - Grouping many jobs into one: grouping-jobs.md
      - Running jobs in containers: containers.md
      - Handling multiple input files: how-to-merge-inputs.md
      - Running multiple pipelines: multiple-pipelines.md
      - Writing a pipeline interface: writing-a-pipeline-interface.md
      - Using looper config: looper-config.md
      - Using geofetch: using-geofetch.md
      - Browsable HTML Reports: looper-report.md
  - Using divvy:
      - Introduction: divvy/README.md
      - Configuring divvy: divvy/configuration.md
      - "Tutorial: divvy in python": tutorial_divvy.md
      - "Tutorial: divvy on the command line": cli_divvy.md
      - Configuring containers: divvy/containers.md
      - Configuring connection with client software: divvy/adapters.md
      - Default packages: divvy/default-packages.md
      - DIVCFG examples: http://github.com/pepkit/divcfg
  - Reference:
      - Pipeline interface specification: pipeline-interface-specification.md
      - Pipeline tiers: pipeline-tiers.md
      - Concentric templates: concentric-templates.md
      - Pre-submission hooks system: pre-submission-hooks.md
      - Looper variable namespaces: variable-namespaces.md
      - Usage: usage.md
      - Configuration files: config-files.md
      - API: autodoc_build/looper.md
      - FAQ: faq.md
      - Support: support.md
      - Contributing: contributing.md
      - Changelog: changelog.md

theme: databio

plugins:
  - databio:
      autodoc_build: "docs/autodoc_build"
      jupyter_source: "docs_jupyter"
      jupyter_build: "docs_jupyter/build"
      autodoc_package: "looper"
      no_top_level: true
  - search