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mkdocs.yml
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site_name: "Git is my lab book"
site_url: "https://git-is-my-lab-book.net/"
repo_url: "https://github.com/robmoss/git-is-my-lab-book"
edit_uri: "edit/master/docs/"
nav:
- "Introduction":
- README.md
- "How to contribute": how-to-contribute.md
- "Contributors": contributors.md
- "Orientation":
- orientation/README.md
- "Topical guides":
- guides/README.md
- "Learning objectives": guides/learning-objectives.md
- "Prerequisites": guides/prerequisites.md
- "1. Version control concepts":
- guides/version-control/README.md
- "What is version control?": guides/version-control/what-is-version-control.md
- "What is a repository?": guides/version-control/what-is-a-repository.md
- "What is a commit?": guides/version-control/what-is-a-commit.md
- "What should I commit?": guides/version-control/what-should-I-commit.md
- "How do I write a commit message?": guides/version-control/how-do-I-write-a-commit-message.md
- "What is a tag?": guides/version-control/what-is-a-tag.md
- "What is a branch?": guides/version-control/what-is-a-branch.md
- "What is a merge conflict?": guides/version-control/what-is-a-merge-conflict.md
- "Exercise: using version control": guides/version-control/exercise-using-version-control.md
- "2. Effective use of git":
- guides/using-git/README.md
- "Graphical Git clients": guides/using-git/graphical-git-clients.md
- "First-time Git setup": guides/using-git/first-time-git-setup.md
- "Choosing your Git editor": guides/using-git/choosing-your-git-editor.md
- "Creating a repository": guides/using-git/creating-a-repository.md
- "Cloning an existing repository": guides/using-git/cloning-an-existing-repository.md
- "How to structure a repository": guides/using-git/how-to-structure-a-repository.md
- "Choosing a license": guides/using-git/choosing-a-license.md
- "Creating a commit": guides/using-git/creating-a-commit.md
- "Creating a remote repository": guides/using-git/creating-a-remote-repository.md
- "Pushing and pulling commits": guides/using-git/pushing-and-pulling-commits.md
- "How to ignore certain files": guides/using-git/how-to-ignore-certain-files.md
- "How to create and use tags": guides/using-git/how-to-create-and-use-tags.md
- "Inspecting your history": guides/using-git/inspecting-your-history.md
- "Where did this line come from?": guides/using-git/where-did-this-line-come-from.md
- "Where did this problem come from?": guides/using-git/where-did-this-problem-come-from.md
- "How to use branches?": guides/using-git/how-to-use-branches.md
- "How to resolve merge conflicts?": guides/using-git/how-to-resolve-merge-conflicts.md
- "Exercise: create a local repository": guides/using-git/exercise-create-a-local-repository.md
- "Exercise: use a remote repository": guides/using-git/exercise-use-a-remote-repository.md
- "Exercise: resolve a merge conflict": guides/using-git/exercise-resolve-a-merge-conflict.md
- "3. Collaborating":
- guides/collaborating/README.md
- "Collaborating on code": guides/collaborating/collaborating-on-code.md
- "Collaborating on a paper": guides/collaborating/collaborating-on-a-paper.md
- "Sharing a repository": guides/collaborating/sharing-a-repository.md
- "Sharing a branch": guides/collaborating/sharing-a-branch.md
- "Merge/Pull requests": guides/collaborating/merge-pull-requests.md
- "An example pull request": guides/collaborating/an-example-pull-request.md
- "Peer code review": guides/collaborating/peer-code-review.md
- "Coding style guides": guides/collaborating/coding-style-guides.md
- "Continuous integration": guides/collaborating/continuous-integration.md
- "4. Project structure":
- "guides/project-structure/README.md"
- "Define your workflow": "guides/project-structure/workflow.md"
- "Automate common tasks": "guides/project-structure/automating-tasks.md"
- "Explain how it works": "guides/project-structure/explain-how-it-works.md"
- "Exercise: what works for you?": "guides/project-structure/exercise-what-works-for-you.md"
- "Exercise: a good README": "guides/project-structure/exercise-a-good-readme.md"
- "5. Writing code":
- "guides/writing-code/README.md"
- "How we learn to write code": "guides/writing-code/how-we-learn-to-write-code.md"
- "Cohesion and coupling": "guides/writing-code/cohesion-coupling.md"
- "Behave nicely": "guides/writing-code/behave-nicely.md"
- "Coding advice": "guides/writing-code/coding-advice.md"
- "Create packages": "guides/writing-code/create-packages.md"
- "Check your code": "guides/writing-code/check-your-code.md"
- "Format your code": "guides/writing-code/format-your-code.md"
- "Document your code": "guides/writing-code/document-your-code.md"
- "Exercise: seek feedback": "guides/writing-code/exercise-seek-feedback.md"
- "6. Reproducibility":
- guides/reproducibility/README.md
- "What is reproducible research?": "guides/reproducibility/what-is-reproducible-research.md"
- "7. Testing":
- guides/testing/README.md
- "8. Cloud and HPC platforms":
- guides/high-performance-computing/README.md
- "Useful resources": guides/resources.md
- "Community":
- community/README.md
- "Meetings":
- community/meetings/README.md
- "12 September 2024": community/meetings/2024-09-12.md
- "8 August 2024": community/meetings/2024-08-08.md
- "11 July 2024": community/meetings/2024-07-11.md
- "13 June 2024": community/meetings/2024-06-13.md
- "9 May 2024": community/meetings/2024-05-09.md
- "11 April 2024": community/meetings/2024-04-11.md
- "19 February 2024": community/meetings/2024-02-19.md
- "18 October 2023": community/meetings/2023-10-18.md
- "15 August 2023": community/meetings/2023-08-15.md
- "13 June 2023": community/meetings/2023-06-13.md
- "17 April 2023": community/meetings/2023-04-17.md
- "Case studies":
- community/case-studies/README.md
- "Fixing a bug in pypfilt": community/case-studies/moss-pypfilt-earlier-states.md
- "Incorrect data in a pre-print figure": community/case-studies/moss-incorrect-data-pre-print.md
- "Pen and paper version control": community/case-studies/campbell-pen-and-paper-version-control.md
- "Training events":
- community/training/README.md
- "Introduction to Debugging":
- community/training/debugging/README.md
- "Learning objectives": community/training/debugging/learning-objectives.md
- "What is debugging?": community/training/debugging/what-is-debugging.md
- "Understanding error messages": community/training/debugging/understanding-error-messages.md
- "Why are debuggers useful?": community/training/debugging/why-are-debuggers-useful.md
- "Using a debugger": community/training/debugging/using-a-debugger.md
- "When something fails": community/training/debugging/when-something-fails.md
- "Real-world stories": community/training/debugging/real-world-stories.md
- "Example: Square numbers": community/training/debugging/example-square-numbers.md
- "Exercise: Perfect numbers": community/training/debugging/exercise-perfect-numbers.md
- "Exercise: Python vs R": community/training/debugging/exercise-python-vs-r.md
- "Building your skills": community/training/debugging/building-your-skills.md
- "Debugging manifesto": community/training/debugging/manifesto.md
- "Resources": community/training/debugging/resources.md
- "Exercise solutions": community/training/debugging/solutions.md
- "Acknowledgements": community/training/debugging/acknowledgements.md
markdown_extensions:
- admonition
- attr_list
- footnotes
- md_in_html
- pymdownx.details
- pymdownx.emoji:
emoji_index: !!python/name:material.extensions.emoji.twemoji
emoji_generator: !!python/name:material.extensions.emoji.to_svg
- pymdownx.highlight
- pymdownx.inlinehilite
- pymdownx.snippets:
base_path: [
# Locate snippets relative to the documentation root directory.
"docs/",
# Locate snippets in the 2024 debugging workshop directory.
"docs/community/training/debugging",
]
- pymdownx.superfences:
custom_fences:
- name: mermaid
class: mermaid
format: !!python/name:pymdownx.superfences.fence_code_format
- pymdownx.tabbed:
alternate_style: true
- toc:
permalink: true
theme:
name: "material"
favicon: "logo.png"
logo: "logo.svg"
palette:
# Palette toggle for automatic mode
- media: "(prefers-color-scheme)"
toggle:
icon: material/brightness-auto
name: Switch to light mode
# Palette toggle for light mode
- media: "(prefers-color-scheme: light)"
scheme: default
toggle:
icon: material/brightness-7
name: Switch to dark mode
# Palette toggle for dark mode
- media: "(prefers-color-scheme: dark)"
scheme: slate
toggle:
icon: material/brightness-4
name: Switch to system preference
features:
# Navigation settings
- navigation.footer
- navigation.indexes
- navigation.tabs
- navigation.tabs.sticky
- navigation.top
- toc.follow
- toc.integrate
# See "Adding a git repository"
- content.action.edit
# Code block settings
- content.code.copy
- content.code.select
# Content tab settings
- content.tabs.link
extra_css:
- extra/asciinema-player.css
- extra/asciinema-theme-gimlb.css
- extra/larger-admonitions.css
extra_javascript:
- extra/asciinema-player.min.js
- extra/wrapper.js
# Ignore TOML scripts for generating asciinema recordings.
exclude_docs: |
*.toml
*.yaml