Code

Move workshop to GitHub Pages#266

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fasterius merged 88 commits intodevelNBISweden/workshop-reproducible-research:develfrom speckyNBISweden/workshop-reproducible-research:speckyCopy head branch name to clipboardOct 24, 2024

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Commits

Commits on Oct 3, 2024

• Add royfrancis/specky Quarto theme files

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• Add schedule Excel file

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• Move specky template files to root

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• Update home page

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• Update schedule with TRR schedule

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• Update content page

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• Ignore Quarto hidden files

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• Use consolidated environment

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• Remove rendered HTMLs from lectures/ directory

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• Fix Quarto render error of image symlink

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• Change format of lecture renders

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• Do not use end time for schedule

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• Ignore _freeze and docs/ directories

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• Do not render tutorial/wrap-up files

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• Convert Git tutorial to Quarto

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• Fix schedule missing content

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• Fix titles and page titles

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• Add TRR info to syllabus page

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• Add TTR info to pre-course setup page

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• Add introduction, markdown and take-down pages

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• Remove old course info pages

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• Add GHA workflow to build and push Docker images

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Commits on Oct 4, 2024

• Fix minor formatting error in Dockerfile

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• Remove specky template files

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• [WIP] Add GHA for deploying Specky website

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• Update formatting of Git page for Quarto

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• Fix links in Git page

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• Update website URL

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• Changed start_time and end_time to time, fixed bg color for day

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• Changed start_time and end_time to time

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• Added schedule table css styles

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Commits on Oct 7, 2024

• Merge pull request #264 from royfrancis/specky

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Commits on Oct 15, 2024

• Convert Conda pages to Specky template

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• Minor formatting

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• Convert Snakemake to Specky template

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• Fix table in Snakemake page

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• Convert Nextflow to Specky

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• Convert Jupyter to Specky

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• Convert container session to Specky

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• Convert Quarto to Specky

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• Add sentence about Quarto websites

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• Limit Canvas upload GHA to only landing page

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• Fix content links to pages

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• Add tutorial links to schedule

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Commits on Oct 16, 2024

• Add GitHub link to page headers

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• [WIP] Add info page to home

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• Added child info file

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• Merge pull request #265 from royfrancis/specky

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• Fix licence

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• Do not freeze docs dependent on data files

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• Update location information

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• Rename deploy env/GHA to publish for clarity

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• Do not build ARM64 for the publish Docker image

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Commits on Oct 17, 2024

• Add git to publish environment

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Commits on Oct 18, 2024

• Use a different GHA for website deployment

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• Rename env/GHA for clarity

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• Streamline Canvas upload GHA

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• Switch image name for website GHA

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• Add ignored paths for website building GHA

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• Update README

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• Update Canvas landing page

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Commits on Oct 19, 2024

• Merge branch 'gha-cleanup' into specky

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Commits on Oct 21, 2024

• Fix internal links

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• Remove Canvas upload README; add script comments

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• Fix broken lecture link

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Commits on Oct 22, 2024

• Add {.green} class to slides SCSS

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• Add images of Cormac and Mahesh

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• Convert introduction lecture to Specky

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• Convert data management lecture to Specky

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• Convert Git lecture to Specky

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• Convert Conda lecture to Specky

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• Convert Snakemake lecture to Specky

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• Convert Nextflow lecture to Specky

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• Convert Quarto lecture to Specky

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• Convert Jupyter lecture to Specky

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• Convert container lecture to Specky

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• Fix spelling

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• Convert putting-it-together lecture to Specky

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• Merge branch 'devel' into specky

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• Add missing Jupyter changes from devel

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• Convert pre-course setup to Specky

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Commits on Oct 23, 2024

• Remove unused docker-slim GHA

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• Update GHA versions; minor formatting of GHA

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• Do not fail fast on Conda testing GHA

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• Clarify GHA workflow/step names

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• Do not use mamba in GHA

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• Do not run Conda test GHA on MacOS ARM64

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Commits on Oct 24, 2024

• Only run Conda tests when relevant files change

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