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Merged
ablaom merged 4 commits into from
Oct 17, 2026
Merged

Commit Notebook Markdown Changes #103

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c47c105
Make the spawned PR a true replacement for its parent
ablaom Oct 17, 2026
fddbf56
DUMMY: trivial notebook.jl edit to exercise markdown regeneration
ablaom Oct 17, 2026
634aa06
Merge fddbf5614a873a2a32278d75420e8e53e2b09bf8 into 2963bcdb4bc8f859f…
ablaom Oct 17, 2026
d5ce67b
update notebook markdown
github-actions[bot] Oct 17, 2026
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76 changes: 56 additions & 20 deletions .github/workflows/generate_notebooks.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,9 @@ jobs:
(github.event_name == 'pull_request' && !startsWith(github.head_ref, 'auto-update-notebooks')) ||
(github.event_name == 'push' && !startsWith(github.ref_name, 'auto-update-notebooks'))
runs-on: ubuntu-latest
permissions:
contents: write # to push the auto-update-notebooks branch
pull-requests: write # to create/edit the replacement pull request
steps:
- name: Checkout repository
uses: actions/checkout@v7
Expand Down Expand Up @@ -90,38 +93,71 @@ jobs:
This pull request will automatically update if additional commits are successfully added to the parent pull request, \#${{ github.event.pull_request.number }}.
EOF

- name: Create pull request for adding new notebook markdown
# We deliberately do NOT use peter-evans/create-pull-request here. When its
# `base` input names a branch other than the checked-out ref, that action
# rebases *only the changes made during the workflow* onto the base, which
# discards the parent pull request's own commits. We want the spawned pull
# request to be a drop-in replacement for the parent, so we branch directly
# from the checked-out HEAD instead. For a `pull_request` event that HEAD is
# the merge commit (the parent's branch merged into its base), so the branch
# diffs against the base as "parent's changes + newly generated files".
- name: Create or update the replacement pull request
id: spawn_pr
uses: peter-evans/create-pull-request@v8
with:
token: ${{ secrets.GITHUB_TOKEN }}
commit-message: "update notebook markdown"
branch: auto-update-notebooks
base: ${{ github.base_ref }}
title: "Commit Notebook Markdown Changes"
body-path: ${{ runner.temp }}/pr-body.md
delete-branch: true

# The body above cannot reference the spawned pull request's own number, because
# `steps.spawn_pr.outputs.*` is not set until after that step completes. So we
# substitute the real number into the body here instead.
shell: bash
env:
GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
BASE: ${{ github.base_ref }}
BRANCH: auto-update-notebooks
BODY_FILE: ${{ runner.temp }}/pr-body.md
run: |
set -euo pipefail

git config user.name "github-actions[bot]"
git config user.email "41898282+github-actions[bot]@users.noreply.github.com"

git checkout -B "$BRANCH"
git add -A
if git diff --cached --quiet; then
echo "No regenerated notebook files to commit; nothing to do."
exit 0
fi
git commit -m "update notebook markdown"
git push --force origin "$BRANCH"

number=$(gh pr list --head "$BRANCH" --base "$BASE" --state open \
--json number --jq '.[0].number // empty')
if [ -n "$number" ]; then
echo "operation=updated" >> "$GITHUB_OUTPUT"
else
url=$(gh pr create --head "$BRANCH" --base "$BASE" \
--title "Commit Notebook Markdown Changes" \
--body-file "$BODY_FILE")
number="${url##*/}"
echo "operation=created" >> "$GITHUB_OUTPUT"
fi
echo "number=$number" >> "$GITHUB_OUTPUT"

# The body composed above cannot reference the spawned pull request's own
# number, because that number does not exist until the pull request does.
- name: Insert preview link into the pull request body
if: steps.spawn_pr.outputs.pull-request-number != ''
if: steps.spawn_pr.outputs.number != ''
shell: bash
env:
GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
PR_NUMBER: ${{ steps.spawn_pr.outputs.pull-request-number }}
PR_NUMBER: ${{ steps.spawn_pr.outputs.number }}
BODY_FILE: ${{ runner.temp }}/pr-body.md
run: |
sed -i "s/__SPAWNED_PR_NUMBER__/${PR_NUMBER}/g" "${{ runner.temp }}/pr-body.md"
gh pr edit "$PR_NUMBER" --body-file "${{ runner.temp }}/pr-body.md"
set -euo pipefail
sed -i "s/__SPAWNED_PR_NUMBER__/${PR_NUMBER}/g" "$BODY_FILE"
gh pr edit "$PR_NUMBER" --body-file "$BODY_FILE"

- name: Post comment flagging further action required
if: steps.spawn_pr.outputs.pull-request-operation == 'created'
if: steps.spawn_pr.outputs.operation == 'created'
uses: mshick/add-pr-comment@v3
with:
message: |
**Attention**

A notebook or Project.toml file has changed and new notebook markdown has been generated. **Review** \#${{ steps.spawn_pr.outputs.pull-request-number }}, which **replaces** the current PR, to commit the changes and update the documentation on gh-pages.
A notebook or Project.toml file has changed and new notebook markdown has been generated. **Review** \#${{ steps.spawn_pr.outputs.number }}, which **replaces** the current PR, to commit the changes and update the documentation on gh-pages.
This PR can be **CLOSED** at any time.

2 changes: 1 addition & 1 deletion docs/src/notebooks/UsingMLJ/01_basics/notebook.jl
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
# # Lesson 1. Basics

# Notebook supporting the video series "Using MLJ".
# Notebook supporting the video series "Using MLJ"

# - [Video](https://www.youtube.com/watch?v=6ILPGhuse4o&list=PLHwT4lR4GIv8&index=1)
# - [Slides](slides.pdf) from the video
Expand Down
74 changes: 37 additions & 37 deletions docs/src/notebooks/UsingMLJ/01_basics/notebook.md
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@ EditURL = "notebook.jl"

# Lesson 1. Basics

Notebook supporting the video series "Using MLJ".
Notebook supporting the video series "Using MLJ"

- [Video](https://www.youtube.com/watch?v=6ILPGhuse4o&list=PLHwT4lR4GIv8&index=1)
- [Slides](slides.pdf) from the video
Expand Down Expand Up @@ -199,8 +199,8 @@ fitted_params(mach)
````
(forest = Ensemble of Decision Trees
Trees: 100
Avg Leaves: 146.89
Avg Depth: 14.44,)
Avg Leaves: 147.21
Avg Depth: 14.92,)
````

````@julia
Expand All @@ -219,9 +219,9 @@ predict(mach, X)[1:3]

````
3-element Vector{Float64}:
26.087
23.107999999999997
34.562
26.763
22.758000000000003
34.335
````

Predict in the `test` rows:
Expand All @@ -237,7 +237,7 @@ mae(ypred, y[test])
````

````
4.429029702970296
4.6654851485148505
````

`mae` is actually just an alias:
Expand Down Expand Up @@ -284,14 +284,14 @@ PerformanceEvaluation object with these fields:
per_fold, per_observation,
fitted_params_per_fold, report_per_fold,
train_test_rows, resampling, repeats
Tag: RandomForestRegressor-530
Tag: RandomForestRegressor-502
Extract:
┌────────────┬───────────┬─────────────┐
│ measure │ operation │ measurement │
├────────────┼───────────┼─────────────┤
│ LPLoss( │ predict │ 4.43 │
│ LPLoss( │ predict │ 4.67 │
│ p = 1) │ │ │
│ RSquared() │ predict │ 0.351 │
│ RSquared() │ predict │ 0.295 │
└────────────┴───────────┴─────────────┘
Apply `describe` to this result for a named tuple summary.
````
Expand All @@ -313,21 +313,21 @@ PerformanceEvaluation object with these fields:
per_fold, per_observation,
fitted_params_per_fold, report_per_fold,
train_test_rows, resampling, repeats
Tag: RandomForestRegressor-360
Tag: RandomForestRegressor-581
Extract:
┌───┬────────────┬───────────┬─────────────┬─────────┐
│ │ measure │ operation │ measurement │ 1.96*SE │
├───┼────────────┼───────────┼─────────────┼─────────┤
│ A │ LPLoss( │ predict │ 2.99 │ 0.85 │
│ A │ LPLoss( │ predict │ 3.02 │ 0.93 │
│ │ p = 1) │ │ │ │
│ B │ RSquared() │ predict │ 0.66 │ 0.16 │
└───┴────────────┴───────────┴─────────────┴─────────┘
┌───┬────────────────────────────────────────────┐
│ │ per_fold │
├───┼────────────────────────────────────────────┤
│ A │ [2.2, 2.28, 3.27, 2.54, 4.81, 2.87] │
│ B │ [0.735, 0.832, 0.731, 0.794, 0.461, 0.385] │
└───┴────────────────────────────────────────────┘
┌───┬───────────────────────────────────────────┐
│ │ per_fold │
├───┼───────────────────────────────────────────┤
│ A │ [2.17, 2.3, 3.32, 2.47, 5.01, 2.9] │
│ B │ [0.745, 0.808, 0.725, 0.817, 0.44, 0.411] │
└───┴───────────────────────────────────────────┘
Apply `describe` to this result for a named tuple summary.
````

Expand All @@ -350,21 +350,21 @@ PerformanceEvaluation object with these fields:
per_fold, per_observation,
fitted_params_per_fold, report_per_fold,
train_test_rows, resampling, repeats
Tag: RandomForestRegressor-398
Tag: RandomForestRegressor-416
Extract:
┌───┬────────────┬───────────┬─────────────┬─────────┐
│ │ measure │ operation │ measurement │ 1.96*SE │
├───┼────────────┼───────────┼─────────────┼─────────┤
│ A │ LPLoss( │ predict │ 2.42 │ 0.13 │
│ A │ LPLoss( │ predict │ 2.5 │ 0.17 │
│ │ p = 1) │ │ │ │
│ B │ RSquared() │ predict │ 0.844 │ 0.02 │
│ B │ RSquared() │ predict │ 0.824 │ 0.03 │
└───┴────────────┴───────────┴─────────────┴─────────┘
┌───┬────────────────────────────────────────────────────────────────────────┐
│ │ per_fold │
├───┼────────────────────────────────────────────────────────────────────────┤
│ A │ [2.29, 2.77, 2.38, 2.27, 2.25, 2.57, 2.28, 2.6, 2.57, 2.22] │
│ B │ [0.851, 0.799, 0.859, 0.867, 0.827, 0.847, 0.889, 0.791, 0.836, 0.872] │
└───┴────────────────────────────────────────────────────────────────────────┘
┌───┬──────────────────────────────────────────────────────────────────────┐
│ │ per_fold │
├───┼──────────────────────────────────────────────────────────────────────┤
│ A │ [2.61, 2.43, 2.71, 2.29, 2.83, 2.19, 2.3, 2.75, 2.72, 2.13] │
│ B │ [0.813, 0.815, 0.834, 0.82, 0.749, 0.887, 0.87, 0.782, 0.787, 0.883] │
└───┴──────────────────────────────────────────────────────────────────────┘
Apply `describe` to this result for a named tuple summary.
````

Expand All @@ -374,8 +374,8 @@ e.uncertainty_radius_95

````
2-element Vector{Float64}:
0.1253300607195079
0.020432947940809142
0.1681446232535948
0.02965427875496854
````

# Interlude on scientific types
Expand Down Expand Up @@ -620,8 +620,8 @@ first(yprob, 5)
5-element CategoricalDistributions.UnivariateFiniteVector{ScientificTypesBase.Multiclass{2}, InlineStrings.String7, UInt32, Float64}:
UnivariateFinite{ScientificTypesBase.Multiclass{2}}(<=50K=>1.0, >50K=>0.0)
UnivariateFinite{ScientificTypesBase.Multiclass{2}}(<=50K=>1.0, >50K=>0.0)
UnivariateFinite{ScientificTypesBase.Multiclass{2}}(<=50K=>0.94, >50K=>0.06)
UnivariateFinite{ScientificTypesBase.Multiclass{2}}(<=50K=>0.33, >50K=>0.67)
UnivariateFinite{ScientificTypesBase.Multiclass{2}}(<=50K=>0.98, >50K=>0.02)
UnivariateFinite{ScientificTypesBase.Multiclass{2}}(<=50K=>0.31, >50K=>0.69)
UnivariateFinite{ScientificTypesBase.Multiclass{2}}(<=50K=>1.0, >50K=>0.0)
````

Expand All @@ -632,8 +632,8 @@ yprob[3]
````
UnivariateFinite{ScientificTypesBase.Multiclass{2}}
┌ ┐
<=50K ┤■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■ 0.94
>50K ┤■■ 0.06
<=50K ┤■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■ 0.98
>50K ┤■ 0.02
└ ┘
````

Expand All @@ -644,15 +644,15 @@ accuracy(ypoint, y[test])
````

````
0.7830270768285816
0.7821057480677689
````

````@julia
log_loss(yprob, y[test])
````

````
1.6401273020819653
1.5390636450295936
````

Evaluate with one command:
Expand All @@ -672,13 +672,13 @@ PerformanceEvaluation object with these fields:
per_fold, per_observation,
fitted_params_per_fold, report_per_fold,
train_test_rows, resampling, repeats
Tag: RandomForestClassifier-818
Tag: RandomForestClassifier-606
Extract:
┌──────────────────────┬──────────────┬─────────────┐
│ measure │ operation │ measurement │
├──────────────────────┼──────────────┼─────────────┤
│ Accuracy() │ predict_mode │ 0.781 │
│ LogLoss( │ predict │ 1.56 │
│ LogLoss( │ predict │ 1.54 │
│ tol = 2.22045e-16) │ │ │
└──────────────────────┴──────────────┴─────────────┘
Apply `describe` to this result for a named tuple summary.
Expand Down
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