Teaching Statistical Computing
with Git and Github

Colin Rundel
Duke University

Who am I?

What I teach:

Sta 323 - Statistical Computing
Sta 523 - Programming for Statistical Science
STA 663 - Statistical Computing and Computation
STA 344/444/644 - Spatio-temporal modeling

What I work on:

Foundations of Reproducibility

Scriptability

R / Python

Literate Programming

RMarkdown / Jupyter / Quarto

Version Control

Git / GitHub

GitHub as LMS

Every class is an organization on GitHub,

Students are invited as members (private)
Each assignment is a repository (private)
Assignments turned in and collected from GitHub
Feedback via Issues

Why GitHub?

Leverage the power of the ecosystem,

Use the API for automation (ghclass)
Accountability via commit history
Centralized collaboration
Scalability
Relevant beyond the course

Anatomy of an Assignment

hw1.Rmd

---
title: "Homework 1"
output: html_document
author: 
- teammate 1
- teammate 2
- teammate 3
- teammate 4
---

### Task 1 - Implement fizzbuzz

#### Write up

<!-- 
In this section include your write up for this task - do not include it within these html comment tags. 
The write up must appear in the rendered document.
-->

#### Function

```{r fizzbuzz}
fizzbuzz = function(input) {
  input
}
```

#### Testing - Valid Inputs

```{r good_inputs, error = TRUE}
stopifnot( fizzbuzz(1)  == "1"       )
stopifnot( fizzbuzz(3)  == "Fizz"    )
stopifnot( fizzbuzz(5)  == "Buzz"    )
stopifnot( fizzbuzz(15) == "FizzBuzz")
stopifnot(all( fizzbuzz(1:5) == c("1", "2", "Fizz", "4", "Buzz") ))
stopifnot(all( fizzbuzz(9:15) == c("Fizz", "Buzz", "11", "Fizz", "13", "14", "FizzBuzz") ))
stopifnot(all( fizzbuzz(15:9) == c("FizzBuzz", "14", "13", "Fizz", "11", "Buzz", "Fizz") ))
```

Distributing hw1 with ghclass

ghclass::org_create_assignment(
  org = "ghclass-demo", user = roster$github,
  repo = roster$hw1,    team = roster$hw1,
  source_repo = "Sta323-Sp19/hw1"
)

#> ✓ Mirrored repo "Sta323-Sp19/hw1" to repo "ghclass-demo/hw1-team01".
#> ✓ Mirrored repo "Sta323-Sp19/hw1" to repo "ghclass-demo/hw1-team02".
#> ✓ Mirrored repo "Sta323-Sp19/hw1" to repo "ghclass-demo/hw1-team03".
#> ✓ Created team "hw1-team01" in org "ghclass-demo".
#> ✓ Created team "hw1-team02" in org "ghclass-demo".
#> ✓ Created team "hw1-team03" in org "ghclass-demo".
#> ✓ Added user "ghclass-anya" to team "hw1-team01".
#> ✓ Added user "ghclass-bruno" to team "hw1-team02".
#> ✓ Added user "ghclass-celine" to team "hw1-team03".
#> ✓ Added user "ghclass-diego" to team "hw1-team01".
#> ✓ Added user "ghclass-elijah" to team "hw1-team02".
#> ✓ Added user "ghclass-francis" to team "hw1-team03".
#> ✓ Team "hw1-team01" given "push" access to repo "ghclass-demo/hw1-team01"
#> ✓ Team "hw1-team02" given "push" access to repo "ghclass-demo/hw1-team02"
#> ✓ Team "hw1-team03" given "push" access to repo "ghclass-demo/hw1-team03"

Making Corrections

(repos = ghclass::org_repos("ghclass-demo",  filter="hw1-"))

#> [1] "ghclass-demo/hw1-team01" "ghclass-demo/hw1-team02" 
#> [3] "ghclass-demo/hw1-team03"

ghclass::repo_modify_file(
  repo = r, path = "README.md", 
  pattern = "Thursday 1/24/2019",
  content = "Friday 2022/03/04",
  method = "replace"
)

#> ✓ Modified file "ghclass-demo/hw1-team01/README.md".
#> ✓ Modified file "ghclass-demo/hw1-team02/README.md".
#> ✓ Modified file "ghclass-demo/hw1-team03/README.md".

Assessing participation

repos = ghclass::org_repos("sta323-sp22", filter="hw01_")
ghclass::repo_contributors(repos)

#> # A tibble: 68 × 4
#>    repo                          username commits weekly_stats    
#>    <chr>                         <chr>      <int> <list>          
#>  1 Sta323-Sp22/hw01_lab01_team01 anya           1 <tibble [6 × 4]>
#>  2 Sta323-Sp22/hw01_lab01_team01 bruno          7 <tibble [6 × 4]>
#>  3 Sta323-Sp22/hw01_lab01_team01 celine         4 <tibble [6 × 4]>
#>  4 Sta323-Sp22/hw01_lab01_team01 diego          2 <tibble [6 × 4]>
#>  5 Sta323-Sp22/hw01_lab01_team02 elijah         6 <tibble [6 × 4]>
#>  6 Sta323-Sp22/hw01_lab01_team02 francis        3 <tibble [6 × 4]>
#>  7 Sta323-Sp22/hw01_lab01_team02 greta          8 <tibble [6 × 4]>
#>  8 Sta323-Sp22/hw01_lab01_team03 hugo           6 <tibble [6 × 4]>
...

Participation is also assessed by peer evaluations for each assignment

Automated feedback

Action Implementation

on: push
name: Repo Checks
jobs:
  check_allowed_files:
    runs-on: self-hosted
    container:
      image: ghcr.io/sta323-sp22/sta323-base:main
    steps:
    - name: Checkout
      uses: actions/checkout@master
    - name: Check Files
      run: |
        checklist::quit_on_failure({
          checklist::check_allowed_files(
            c("hw1.Rmd", "hw1.Rproj", "README.md", "fizzbuzz.png")
          )
        })
      shell: Rscript {0}
      
  check_renders:
    needs: check_allowed_files
    runs-on: self-hosted
    container:
      image: ghcr.io/sta323-sp22/sta323-base:main
    steps:
    - name: Checkout
      uses: actions/checkout@v2
    - name: Install Missing Packages
      run: |
        checklist::install_missing_pkgs(dir = "./")
      shell: Rscript {0}
    - name: Check Renders
      run: |
        checklist::check_rmd_renders("hw1.Rmd")
      shell: Rscript {0}
    - name: Archive html
      uses: actions/upload-artifact@v2
      with:
        name: hw1.html
        path: hw1.html

Action Status

ghclass::action_status(repos)

#> # A tibble: 42 × 5
#>    repo                          name        branch result  created            
#>    <chr>                         <chr>       <chr>  <chr>   <dttm>             
#>  1 Sta323-Sp22/hw01_lab01_team01 Repo Checks main   success 2022-01-26 22:18:42
#>  2 Sta323-Sp22/hw01_lab01_team02 Repo Checks main   success 2022-01-26 21:03:37
#>  3 Sta323-Sp22/hw01_lab01_team03 Repo Checks main   success 2022-01-28 04:01:17
#>  4 Sta323-Sp22/hw01_lab01_team04 Repo Checks main   success 2022-01-28 19:17:04
#>  5 Sta323-Sp22/hw01_lab01_team05 Repo Checks main   success 2022-01-28 19:24:01
#>  6 Sta323-Sp22/hw01_lab01_team06 Repo Checks main   success 2022-01-28 19:59:49
#>  7 Sta323-Sp22/hw01_lab01_team07 Repo Checks main   success 2022-01-28 04:27:54
#>  8 Sta323-Sp22/hw01_lab01_team08 Repo Checks main   success 2022-01-28 08:38:43
#>  9 Sta323-Sp22/hw01_lab02_team09 Repo Checks main   success 2022-01-27 05:42:33
#> 10 Sta323-Sp22/hw01_lab03_team10 Repo Checks main   success 2022-01-27 19:12:23
#> # … with 32 more rows

Artifacts

ghclass::action_artifact_download(repos, dir = "hw1/")

#> ✓ Downloaded artifact 169864663 from repo "Sta323-Sp22/hw01_lab01_team01" to "hw1/hw01_lab01_team01.html".
#> ✓ Downloaded artifact 168163146 from repo "Sta323-Sp22/hw01_lab01_team02" to "hw1/hw01_lab01_team02.html".
#> ✓ Downloaded artifact 169850317 from repo "Sta323-Sp22/hw01_lab01_team03" to "hw1/hw01_lab01_team03.html".
#> ✓ Downloaded artifact 169193983 from repo "Sta323-Sp22/hw01_lab01_team04" to "hw1/hw01_lab01_team04.html".
#> ✓ Downloaded artifact 167358274 from repo "Sta323-Sp22/hw01_lab01_team05" to "hw1/hw01_lab01_team05.html".
#> ✓ Downloaded artifact 169775975 from repo "Sta323-Sp22/hw01_lab01_team06" to "hw1/hw01_lab01_team06.html".
#> ✓ Downloaded artifact 169901996 from repo "Sta323-Sp22/hw01_lab01_team07" to "hw1/hw01_lab01_team07.html".
#> ✓ Downloaded artifact 169884929 from repo "Sta323-Sp22/hw01_lab01_team08" to "hw1/hw01_lab01_team08.html".
#> ✓ Downloaded artifact 169816311 from repo "Sta323-Sp22/hw01_lab01_team09" to "hw1/hw01_lab01_team09.html".
#> ✓ Downloaded artifact 169902066 from repo "Sta323-Sp22/hw01_lab01_team10" to "hw1/hw01_lab01_team10.html".
#> ✓ Downloaded artifact 167612940 from repo "Sta323-Sp22/hw01_lab02_team01" to "hw1/hw01_lab02_team01.html".
#> ✓ Downloaded artifact 169887422 from repo "Sta323-Sp22/hw01_lab02_team02" to "hw1/hw01_lab02_team02.html".
#> ✓ Downloaded artifact 169886118 from repo "Sta323-Sp22/hw01_lab02_team03" to "hw1/hw01_lab02_team03.html".
#> ✓ Downloaded artifact 169305846 from repo "Sta323-Sp22/hw01_lab02_team04" to "hw1/hw01_lab02_team04.html".
#> ✓ Downloaded artifact 169712856 from repo "Sta323-Sp22/hw01_lab02_team05" to "hw1/hw01_lab02_team05.html".
#> ✓ Downloaded artifact 169894290 from repo "Sta323-Sp22/hw01_lab02_team06" to "hw1/hw01_lab02_team06.html".

ghclass::action_artifact_download() will be included in the next ghclass release

parsermd

parsermd::parse_rmd("hw1.Rmd")

#> ├── YAML [2 lines]
#> ├── Heading [h3] - Task 1 - Implement fizzbuzz
#> │   ├── Heading [h4] - Write up
#> │   │   └── Markdown [2 lines]
#> │   ├── Heading [h4] - Function
#> │   │   ├── Markdown [5 lines]
#> │   │   └── Chunk [r, 24 lines] - fizzbuzz
#> │   ├── Heading [h4] - Testing - Valid Inputs
#> │   │   ├── Markdown [2 lines]
#> │   │   ├── Chunk [r, 1 opt, 9 lines] - good_inputs
#> │   │   └── Chunk [r, 5 lines] - extra_good
#> │   └── Heading [h4] - Testing - Bad Inputs
#> │       ├── Markdown [4 lines]
#> │       ├── Chunk [r, 4 lines] - throws_error
#> │       ├── Chunk [r, 1 opt, 15 lines] - bad_inputs
#> │       └── Chunk [r, 6 lines] - extra_bad_inputs
#> └── Heading [h3] - Task 2 - Re-Implement fizzbuzz
#>     ├── Heading [h4] - Write up
#>     │   └── Markdown [2 lines]
#>     ├── Heading [h4] - Function
#>     │   ├── Markdown [11 lines]
#>     │   └── Chunk [r, 40 lines] - fizzbuzz_s3
#>     └── Heading [h4] - Testing
#>         └── Markdown [1 lines]

parsermd

parsermd::rmd_check_template(
  "hw01-student.Rmd",
  template
)

#> ✖ The following required elements were missing in the document:
#>   • Section "Exercise 3" > "Solution" is missing required "markdown text".
#>   • Section "Exercise 3" > "Solution" is missing required "markdown text".
#> ✖ The following document elements were unmodified from the template:
#>   • Section "Exercise 2" > "Solution" has a "code chunk" named "plot-dino"
#>     which has not been modified.
#>   • Section "Exercise 2" > "Solution" has "markdown text" which has not been
#>     modified.
#>   • Section "Exercise 2" > "Solution" has a "code chunk" named "cor-dino"
#>     which has not been modified.

Python ecosystem

on: push
name: Repo Checks
jobs:
  check_allowed_files:
    ...
  check_renders:
    needs: check_allowed_files
    runs-on: self-hosted
    container:
      image: ghcr.io/sta663-sp22/sta663-base:main
    timeout-minutes: 10
    steps:
    - name: Checkout
      uses: actions/checkout@v2
    - name: Check Renders
      run: |
        quarto render hw2.ipynb --execute --to html
    - name: Archive html
      uses: actions/upload-artifact@v2
      with:
        name: html
        path: hw2.html

Questions?

	rundel.github.io
	rundel
	rundel
	rundel@gmail.com colin.rundel@duke.edu

Beckman, M. D., Çetinkaya-Rundel, M., Horton, N. J., Rundel, C. W., Sullivan, A. J., & Tackett, M. (2021). Implementing version control with Git and GitHub as a learning objective in statistics and data science courses. Journal of Statistics and Data Science Education, 29(sup1), S132-S144.

Çetinkaya-Rundel, M., & Rundel, C. (2018). Infrastructure and tools for teaching computing throughout the statistical curriculum. The American Statistician, 72(1), 58-65.

Teaching Statistical Computing with Git and Github

Who am I?

Foundations of Reproducibility

GitHub as LMS

Why GitHub?

Anatomy of an Assignment

hw1.Rmd

Distributing hw1 with ghclass

Making Corrections

Assessing participation

Automated feedback

Automated feedback

Automated feedback

Action Implementation

Action Status

Artifacts

Artifacts

parsermd

parsermd

Python ecosystem

Questions?

Teaching Statistical Computing
with Git and Github