workshop_research_computing/_toc.yml at main · ucdavisdatalab/workshop_research_computing · GitHub

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# Table of contents
# Learn more at https://jupyterbook.org/customize/toc.html

format: jb-book
root: chapters/index
# Chapters may be written in either Markdown or as Jupyter Notebooks
parts:
  - chapters:
    - file: chapters/setup

  - caption: "Reproducibility Principles and Practices"
    chapters:
      - file: chapters/reproducibility/index
        title: Overview
  - numbered: true
    chapters:
      - file: chapters/reproducibility/01_principles
      - file: chapters/reproducibility/02_primary_practices
      - file: chapters/reproducibility/03_secondary_practices
      - file: chapters/reproducibility/04_case_by_case_practices
  - chapters:
      - file: chapters/reproducibility/references

  - caption: "Introduction to the Command Line"
    chapters:
      - file: chapters/command-line/index
        title: Overview
  -  numbered: true
     chapters:
      - file: chapters/command-line/01_interacting-with-computers
      - file: chapters/command-line/02_browsing-files
      - file: chapters/command-line/03_other-commands
      - file: chapters/command-line/04_editing-files
  -  chapters:
      - file: chapters/command-line/references

  - caption: "Installing Software with Pixi"
    chapters:
      - file: chapters/installing-software/index
        title: Overview
  - numbered: true
    chapters:
      - file: chapters/installing-software/01_environment-managers
      - file: chapters/installing-software/02_pixi-basics
  - chapters:
      - file: chapters/installing-software/a_configuring-the-shell
      - file: chapters/installing-software/b_ucdavis-hpc-modules
      - file: chapters/installing-software/c_python-packages
      - file: chapters/installing-software/d_tasks

  - caption: "Introduction to Version Control"
    chapters:
      - file: chapters/version-control/index
        title: Overview
  - numbered: true
    chapters:
      - file: chapters/version-control/01_version-control-systems
      - file: chapters/version-control/02_git-basics
      - file: chapters/version-control/03_remote-repositories
      - file: chapters/version-control/04_the-git-workflow

  - caption: "Git for Teams"
    chapters:
      - file: chapters/git-for-teams/index
        title: Overview
  - numbered: true
    chapters:
      - file: chapters/git-for-teams/01_branches-merges
      - file: chapters/git-for-teams/02_working-with-github
      - file: chapters/git-for-teams/03_making-git-comfortable
  # - caption: "Retired"
  #   chapters:
  #     - file: chapters/version-control/retired/git-branching
  #     - file: chapters/git-for-teams/retired/01_about-github
  #     - file: chapters/git-for-teams/retired/02_pushing-a-repository
  #     - file: chapters/git-for-teams/retired/03_cloning-a-repository
  #     - file: chapters/git-for-teams/retired/04_opening-issues-and-making-changes
  #     - file: chapters/git-for-teams/retired/05_merging-remote-branches
  #     - file: chapters/git-for-teams/retired/06_open-and-merge-pull-requests