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Merge pull request #22 from HealthBioscienceIDEAS/1-switch-to-carpentriessandpaper
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‎Medical-Image-Registration-Short-Course.Rproj‎

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Version: 1.0
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RestoreWorkspace: Default
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SaveWorkspace: Default
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AlwaysSaveHistory: Default
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EnableCodeIndexing: Yes
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UseSpacesForTab: Yes
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NumSpacesForTab: 2
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Encoding: UTF-8
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RnwWeave: Sweave
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LaTeX: pdfLaTeX
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AutoAppendNewline: Yes
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StripTrailingWhitespace: Yes
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BuildType: Website

‎_setting_up/README.md‎

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# Installing R, Carpentries packages, and previewing Sandpaper in multi OS (Linux, Windows and Mac)
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## Steps in Ubuntu 22.04 x64
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1. Create new repo: https://github.com/HealthBioscienceIDEAS/Medical-Image-Registration-Short-Course
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2. Clone repo `git clone https://github.com/HealthBioscienceIDEAS/Medical-Image-Registration-Short-Course`
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3. install R (if you haven't done already) [:link:](https://cran.r-project.org/bin/linux/ubuntu/)
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```
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sudo apt-get install r-cran-xml
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sudo apt-get install libxml2-dev
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sudo apt install libgit2-dev
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sudo apt install r-cran-curl
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```
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4. Open R and run the following to install dependencies
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```
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options(repos = c(
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carpentries = "https://carpentries.r-universe.dev/",
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CRAN = "https://cran.rstudio.com/"
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))
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install.packages(c("remotes"), dep =TRUE)
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```
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5. In R, run
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```
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remotes::install_github("HealthBioscienceIDEAS/sandpaper", dependencies = TRUE)
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# this one is taking some 20mins the fist time as it seems is building various packages
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# Terminal logs
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Downloading GitHub repo HealthBioscienceIDEAS/sandpaper@HEAD
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These packages have more recent versions available.
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It is recommended to update all of them.
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Which would you like to update?
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1: All
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2: CRAN packages only
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3: None
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4: pegboard (0.7.5 -> a32a7836d...) [GitHub]
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5: varnish (1.0.2 -> 56d594d27...) [GitHub]
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6: curl (4.3.2 -> 5.2.1 ) [CRAN]
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7: httr (1.4.2 -> 1.4.7 ) [CRAN]
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8: gh (1.3.0 -> 1.4.1 ) [CRAN]
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9: covr (3.5.1 -> 3.6.4 ) [CRAN]
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Enter one or more numbers, or an empty line to skip updates: 1
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The downloaded source packages are in
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‘/tmp/Rtmpn94NAu/downloaded_packages’
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Downloading GitHub repo carpentries/pegboard@HEAD
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These packages have more recent versions available.
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It is recommended to update all of them.
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Which would you like to update?
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1: All
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2: CRAN packages only
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3: None
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4: tinkr (0.2.0.9000 -> be564d524...) [GitHub]
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Enter one or more numbers, or an empty line to skip updates: 1
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── R CMD build ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
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✔ checking for file ‘/tmp/Rtmpn94NAu/remotes50ddb31b7ca85/HealthBioscienceIDEAS-sandpaper-fb14e02/DESCRIPTION’ ...
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─ preparing ‘sandpaper’:
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✔ checking DESCRIPTION meta-information ...
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─ checking for LF line-endings in source and make files and shell scripts (420ms)
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─ checking for empty or unneeded directories
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Omitted ‘LazyData’ from DESCRIPTION
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─ building ‘sandpaper_0.16.4.tar.gz’
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# How to setup local previews of the Workbench website
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## Installing requirements
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### Windows/Mac
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1. If R is not already installed, install R using the following:
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* [Windows](https://cran.r-project.org/bin/windows/base/) and use the default settings during the installation of **RGUi 4.x.x**
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* [Mac](https://cran.r-project.org/bin/macosx/)
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1. **Optional, but recommended** Download [RStudio Desktop](https://posit.co/download/rstudio-desktop/)
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1. **For Mac only** Before installing Varnish and Sandpaper, there are some
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additional packages that will need to be installed. The easiest way is via
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[Homebrew](https://brew.sh/):
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```bash
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brew install freetype fribidi harfbuzz libpng libgit2
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```
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1. Open RStudio and run the following lines of code to install the sandpaper package.
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```r
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options(repos = c(
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carpentries = "https://carpentries.r-universe.dev/",
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CRAN = "https://cran.rstudio.com/"
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))
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install.packages("sandpaper", dep = TRUE)
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```
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You can find further instructions on the
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[Carpentries Workbench documentation](https://carpentries.github.io/sandpaper-docs/index.html)
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1. Enter the following command to install the local version of varnish. This
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version is needed to incorporate the IDEAS identity for the site.
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```r
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install.packages("remotes")
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remotes::install_github("HealthBioscienceIDEAS/varnish", dependencies = TRUE)
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```
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1. Go to the section on [previewing the website](#previewing-episodes)
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### Linux
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This installation was performed using Ubuntu 22.04 x64
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1. install R (if you haven't done already) from [CRAN](https://cran.r-project.org/bin/linux/ubuntu/)
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```bash
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sudo apt-get install r-cran-xml
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sudo apt-get install libxml2-dev
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sudo apt install libgit2-dev
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sudo apt install r-cran-curl
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```
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1. OPen R and install the sandpaper package.
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```r
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options(repos = c(
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carpentries = "https://carpentries.r-universe.dev/",
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CRAN = "https://cran.rstudio.com/"
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))
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install.packages("sandpaper", dep = TRUE)
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```
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1. Install the local IDEAS fork of the varnish repository
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```r
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install.packages("remotes")
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remotes::install_github("HealthBioscienceIDEAS/varnish", dependencies = TRUE)
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# this one takes a long time, about 20mins for the the fist time
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# due to dependencies
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# You may see something similar to below in the output of the terminal
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# (this has been truncated - a fair amount of additional text should
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# follow showing progress of the installation)
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Installing package into ‘/home/mxochicale/R/x86_64-pc-linux-gnu-library/4.4’
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(as ‘lib’ is unspecified)
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* installing *source* package ‘sandpaper’ ...
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** using staged installation
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** R
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** inst
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** byte-compile and prepare package for lazy loading
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** help
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*** installing help indices
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*** copying figures
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** building package indices
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** installing vignettes
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** testing if installed package can be loaded from temporary location
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** testing if installed package can be loaded from final location
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** testing if installed package keeps a record of temporary installation path
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* DONE (sandpaper)
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Warning message:
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In i.p(...) : installation of package ‘curl’ had non-zero exit status
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```
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6. In R, run
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```
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sandpaper::create_lesson("~/Desktop/medical-registration/Medical-Image-Registration-Short-Course")
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## LOGS
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> sandpaper::create_lesson("~/Desktop/medical-registration/Medical-Image-Registration-Short-Course")
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No personal access token (PAT) available.gistration/Medical-Image-Registration-Short-Course...
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Obtain a PAT from here:
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https://github.com/settings/tokens
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For more on what to do with the PAT, see ?gh_whoami.
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ℹ No schedule set, using Rmd files in episodes/ directory.
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→ To remove this message, define your schedule in config.yaml or use `set_episodes()` to generate it.
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───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
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ℹ To save this configuration, use
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set_episodes(path = path, order = ep, write = TRUE)
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• Edit '/home/mxochicale/Desktop/medical-registration/Medical-Image-Registration-Short-Course/episodes/introduction.Rmd'
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✔ First episode created in /home/mxochicale/Desktop/medical-registration/Medical-Image-Registration-Short-Course/episodes/introduction.Rmd
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ℹ Workflows up-to-date!
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✔ Lesson successfully created in ~/Desktop/medical-registration/Medical-Image-Registration-Short-Course
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✔ Setting active project to '/home/mxochicale/Desktop/medical-registration/Medical-Image-Registration-Short-Course'
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✔ Changing working directory to '/home/mxochicale/Desktop/medical-registration/Medical-Image-Registration-Short-Course/'
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~/Desktop/medical-registration/Medical-Image-Registration-Short-Course
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>
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```
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7. Setting up config file in sandpaper template:
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```
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carpentry: 'IDEAS'
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title: ''Medical-Image-Registration-Short-Course'
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created: '2024-05-13'
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source: 'https://github.com/HealthBioscienceIDEAS/Medical-Image-Registration-Short-Course'
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varnish: 'HealthBioscienceIDEAS/varnish@IDEAS'
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sandpaper: 'HealthBioscienceIDEAS/sandpaper@IDEAS'
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```
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8. Set up GitHub Pages
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* Go go [pages](https://github.com/HealthBioscienceIDEAS/Medical-Image-Registration-Short-Course/settings/pages) and select gh-pages branch with `/root` and click save
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* Pass CI [actions](https://github.com/HealthBioscienceIDEAS/Medical-Image-Registration-Short-Course/actions/runs/9064118161)
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* :tada: you have created: https://healthbioscienceideas.github.io/Medical-Image-Registration-Short-Course/
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## Steps on Windows
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1. Create new repo: https://github.com/HealthBioscienceIDEAS/Medical-Image-Registration-Short-Course
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2. Clone repo `git clone https://github.com/HealthBioscienceIDEAS/Medical-Image-Registration-Short-Course`
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3. Installing R using the following: https://cran.r-project.org/bin/windows/base/
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4. Using the default settings during the installation of **RGUi 4.x.x**
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5. From RGui Console, enter the following command:
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```
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options(repos = c(
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carpentries = "https://carpentries.r-universe.dev/",
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CRAN = "https://cran.rstudio.com/"
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))
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install.packages(c("remotes"), dep =TRUE)
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```
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6. Enter the following command:
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`remotes::install_github("HealthBioscienceIDEAS/sandpaper", dependencies = TRUE)
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`
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7. Change path from RGUi to the GitHub folder of the medical image registration course. This is done from the Menu list by picking 'File' then 'Change Dir..'
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8. Run the following command to start sandpaper:
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`sandpaper::build_lesson()
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`
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9. You may notice some package not installed called _**Pandoc**_ after running the sandpaper command. If so, install Pandoc then run _step 8_ again.
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Pandoc installation: https://pandoc.org/installing.html
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## Steps in MAC
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Packages via homebrew: freetype, fribidi, harfbuzz, libpng, git2.
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# Previewing eposides in any OS platform
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## In your local machine
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Downloading GitHub repo HealthBioscienceIDEAS/varnish@HEAD
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These packages have more recent versions available.
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It is recommended to update all of them.
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Which would you like to update?
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1: All
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2: CRAN packages only
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3: None
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...(individual packages)
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Enter one or more numbers, or an empty line to skip updates: 1
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...(truncated)
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```
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## Previewing episodes
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### In your local machine
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1. Using your terminal clone repo
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```
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git clone git@github.com:HealthBioscienceIDEAS/Medical-Image-Registration-Short-Course.git
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```
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2. Checkout `feature-branch-name`.
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```
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git checkout feature-branch-name
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```
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```bash
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git clone git@github.com:HealthBioscienceIDEAS/Medical-Image-Registration-Short-Course.git
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```
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1. If you are working on a specific branch, checkout the branch locally:
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```bash
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git checkout feature-branch-name
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```
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1. In RStudio, open the medical imaging regsitration course repository by going to
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File->Open Project and then selecting the path where you cloned the repository.
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You may need to click on the R project file that is located in the repository directory.
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1. Run the following command to start sandpaper:
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```r
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sandpaper::serve()
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```
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This will build the site and put it in the `Viewer` tab in RStudio. You can look at it in your
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browser by clicking on the "Open in New Window" icon.
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If you notice errors that the package _**Pandoc**_ was not installed, try installing Pandoc and
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then try building the lesson again. If successful, R which will launch your internet browser with the episode.
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As you make edits and save the document you are working on, the site will be rebuilt.
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3. Run `sandpaper::build_lesson()` in R which will launch your internet browser with the episode
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```
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R
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sandpaper::build_lesson()
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```
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## In GitHub
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**Alternative to sandpaper::serve**
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The function `build_lesson` is very similar to
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```r
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sandpaper::build_lesson()
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```
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except that it doesn't automatically build upon each save. If the page does not appear automatically in
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your browser, you may need to open it manually.
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### On GitHub
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You can also preview your episodes once you have a Pull-Request.
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1. Select branch called md-outputs-<PR-number> for each PR where it stores the rendered markdown files. This is controlled by the [pr-receive](https://carpentries.github.io/sandpaper-docs/pull-request.html#reviewing-a-pull-request) workflow.
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Select branch called md-outputs-<PR-number> for each PR where it stores the
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rendered markdown files. This is controlled by the [pr-receive](https://carpentries.github.io/sandpaper-docs/pull-request.html#reviewing-a-pull-request) workflow.
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Note this will only preview the markdown, it will not look like the final
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rendered website.
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‎config.yaml‎

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# - another-learner.md
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# Order of episodes in your lesson
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episodes:
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episodes:
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#- introduction.Rmd
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- itksnap.Rmd
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- excthreesteps.Rmd
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# Information for Learners
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learners:
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learners:
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# Information for Instructors
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instructors:
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instructors:
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# Learner Profiles
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profiles:
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profiles:
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# Customisation ---------------------------------------------
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#
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# This space below is where custom yaml items (e.g. pinning
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# sandpaper and varnish versions) should live
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varnish: 'HealthBioscienceIDEAS/varnish@IDEAS'
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sandpaper: 'HealthBioscienceIDEAS/sandpaper@IDEAS'

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