Fix boxes now that it is better supported by jupyter (#628)

* fix problem with box

* fix

* intro

* box exercise

* Update

* clean

* les box

* simplify pipeline

Author: linogaliana

.github/workflows/prod.yml

@@ -13,32 +13,43 @@ jobs:
     runs-on: ubuntu-latest
     if: ${{ !github.event.pull_request.head.repo.fork }}
     steps:
+
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
           ref: ${{ github.event.pull_request.head.ref }}
           repository: ${{github.event.pull_request.head.repo.full_name}}
+
       - name: Configure safe.directory  # Workaround for actions/checkout#760
         run: git config --global --add safe.directory /__w/python-datascientist/python-datascientist
+
       - name: Install system dependencies
         run: |
           sudo ./build/requirements.sh
-      - name: Install the latest version of uv and set the python version to 3.13t
+
+      - name: Install the latest version of uv
         uses: astral-sh/setup-uv@v6
         with:
-          python-version: "3.12"
-          enable-cache: true
-          cache-dependency-glob: "uv.lock"
-      - uses: quarto-dev/quarto-actions/setup@v2
-      - run: |
-          quarto --version
+          version: "latest"
+          python-version: 3.12
+
+      - name: Restore environment
+        run: uv sync
+
+      # Step 3: Set up Quarto
+      - name: Set up quarto
+        uses: quarto-dev/quarto-actions/setup@v2
+
+      - name: Install SpaCy corpus and check quarto version
+        run: |
+          uv run spacy download en_core_web_sm
+          uv run quarto --version
+          
       - name: Prepare directory
         run: |
           rm _quarto.yml
           cp _quarto-prod.yml _quarto.yml
-      - name: Install Python dependencies
-        run: |
-          uv sync
+
       - name: Render website
         env:
           API_INPI_USERNAME: ${{ secrets.API_INPI_USERNAME }}
@@ -61,37 +72,49 @@ jobs:
           git config --global user.email quarto-github-actions-publish@example.com
           git config --global user.name "Quarto GHA Workflow Runner"
           quarto publish gh-pages . --no-render --no-browser
+
   enonces:
     name: Render notebooks
     runs-on: ubuntu-latest
     if: ${{ !github.event.pull_request.head.repo.fork }}
     steps:
+
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
           ref: ${{ github.event.pull_request.head.ref }}
           repository: ${{github.event.pull_request.head.repo.full_name}}
+
       - name: Configure safe.directory  # Workaround for actions/checkout#760
         run: git config --global --add safe.directory /__w/python-datascientist/python-datascientist
+
       - name: Install system dependencies
         run: |
           sudo ./build/requirements.sh
-      - name: Install the latest version of uv and set the python version to 3.13t
+
+      - name: Install the latest version of uv
         uses: astral-sh/setup-uv@v6
         with:
-          python-version: "3.12"
-          enable-cache: true
-          cache-dependency-glob: "uv.lock"
-      - uses: quarto-dev/quarto-actions/setup@v2
-      - run: |
-          quarto --version
+          version: "latest"
+          python-version: 3.12
+
+      - name: Restore environment
+        run: uv sync
+
+      # Step 3: Set up Quarto
+      - name: Set up quarto
+        uses: quarto-dev/quarto-actions/setup@v2
+
+      - name: Install SpaCy corpus and check quarto version
+        run: |
+          uv run spacy download en_core_web_sm
+          uv run quarto --version
+          
       - name: Prepare directory
         run: |
           rm _quarto.yml
           cp _quarto-prod.yml _quarto.yml
-      - name: Install Python dependencies
-        run: |
-          uv sync
+
       - name: Convert in ipynb with Quarto
         env:
           API_INPI_USERNAME: ${{ secrets.API_INPI_USERNAME }}
@@ -133,73 +156,4 @@ jobs:
           #target-branch: test
           create-target-branch-if-needed: true
           reset-repo: true
-  enonces-vscode:
-    name: Render notebooks (VSCode version)
-    runs-on: ubuntu-latest
-    if: ${{ !github.event.pull_request.head.repo.fork }}
-    steps:
-      - uses: actions/checkout@v4
-        with:
-          fetch-depth: 0
-          ref: ${{ github.event.pull_request.head.ref }}
-          repository: ${{github.event.pull_request.head.repo.full_name}}
-      - name: Configure safe.directory  # Workaround for actions/checkout#760
-        run: |
-            git config --global --add safe.directory /__w/python-datascientist/python-datascientist
-            git config --global --add safe.directory /__w/python-datascientist/python-datascientist-notebooks-vscode
-      - name: Install system dependencies
-        run: |
-          sudo ./build/requirements.sh
-      - name: Install the latest version of uv and set the python version to 3.13t
-        uses: astral-sh/setup-uv@v6
-        with:
-          python-version: "3.12"
-          enable-cache: true
-          cache-dependency-glob: "uv.lock"
-      - uses: quarto-dev/quarto-actions/setup@v2
-      - run: |
-          quarto --version
-      - name: Prepare directory
-        run: |
-          rm _quarto.yml
-          cp _quarto-prod.yml _quarto.yml
-      - name: Install Python dependencies
-        run: |
-          uv sync
-      - name: Convert in ipynb with Quarto
-        env:
-          API_INPI_USERNAME: ${{ secrets.API_INPI_USERNAME }}
-          API_INPI_PASSWORD: ${{ secrets.API_INPI_PASSWORD }}
-        run: |
-          export QUARTO_PROFILE=fr,en
-          cp _quarto.yml _quarto-prod.yml
-          uv run ./build/nice-vscode/tweak_pipeline_vscode.py --filename _quarto-prod.yml
-          cp _quarto-prod2.yml _quarto.yml
-          rm content/modelisation/index.qmd # Remove file not building in ipynb
-          uv run quarto render --profile fr --to ipynb
-          uv run quarto render --profile en --to ipynb
-      - name: Move to expected directory
-        env:
-          API_INPI_USERNAME: ${{ secrets.API_INPI_USERNAME }}
-          API_INPI_PASSWORD: ${{ secrets.API_INPI_PASSWORD }}
-        run: |
-          mkdir -p temp_notebooks
-          mkdir -p temp_notebooks/notebooks
-          uv run build/move_files.py --direction temp_notebooks/notebooks
-          uv run quarto render content --to ipynb --execute -M echo:true
-          mkdir -p temp_notebooks/corrections
-          uv run build/move_files.py --direction temp_notebooks/corrections
-      - name: Pushes to another repository
-        uses: linogaliana/github-action-push-to-another-repository@main
-        env:
-          API_TOKEN_GITHUB: ${{ secrets.API_TOKEN_GITHUB }}
-        with:
-          source-directory: 'temp_notebooks/'
-          destination-repository-username: 'linogaliana'
-          destination-repository-name: 'python-datascientist-notebooks-vscode'
-          user-email: lino.galiana@insee.fr
-          destination-github-username: linogaliana
-          #target-branch: test
-          create-target-branch-if-needed: true
-          reset-repo: true
 

_quarto.yml

@@ -4,7 +4,45 @@ project:
     - index.qmd
     - 404.qmd
     - content/getting-started/index.qmd
+    - content/getting-started/01_environment.qmd
+    - content/getting-started/02_data_analysis.qmd
+    - content/getting-started/03_revisions.qmd
+    - content/manipulation/index.qmd
+    - content/manipulation/01_numpy.qmd
+    - content/manipulation/02_pandas_intro.qmd
+    - content/manipulation/02_pandas_suite.qmd
+    - content/manipulation/02a_pandas_tutorial.qmd
+    - content/manipulation/02b_pandas_TP.qmd
+    - content/manipulation/03_geopandas_intro.qmd
+    - content/manipulation/03_geopandas_tutorial.qmd
+    - content/manipulation/03_geopandas_TP.qmd
+    - content/manipulation/04a_webscraping_TP.qmd
+    - content/manipulation/04c_API_TP.qmd
+    - content/manipulation/04b_regex_TP.qmd
     - content/manipulation/05_parquet_s3.qmd
+    - content/visualisation/index.qmd
+    - content/visualisation/matplotlib.qmd
+    - content/visualisation/maps.qmd
+    - content/modelisation/index.qmd
+    - content/modelisation/0_preprocessing.qmd
+    - content/modelisation/1_modelevaluation.qmd
+    - content/modelisation/2_classification.qmd
+    - content/modelisation/3_regression.qmd
+    - content/modelisation/4_featureselection.qmd
+    - content/modelisation/5_clustering.qmd
+    - content/modelisation/6_pipeline.qmd
+    - content/modelisation/7_mlapi.qmd
+    - content/NLP/index.qmd
+    - content/NLP/01_intro.qmd
+    - content/NLP/02_exoclean.qmd
+    - content/NLP/03_embedding.qmd
+    - content/modern-ds/s3.qmd
+    - content/git/index.qmd
+    - content/git/introgit.qmd
+    - content/git/exogit.qmd
+    - content/annexes/about.qmd
+    - content/annexes/evaluation.qmd
+    - content/annexes/corrections.qmd
 
 profile:
   default: fr
@@ -69,11 +107,9 @@ format:
 # PAGE OPTIONS ---------------------
 
 filters:
+  - include-code-files
   - build/replace-title.lua
   - build/lang-notebook.lua
-  - black-formatter
-  - build/callout/callout-jupyter.lua
-  - include-code-files
   - _extensions/linogaliana/details-iframe/details.lua
   - _extensions/linogaliana/lang-switch/button.lua
 
@@ -89,6 +125,7 @@ keep-ipynb: true
 lightbox: auto
 google-scholar: true
 highlight-style: a11y
+
 #author: Lino Galiana
 #date: today
 #page-layout: article

build/callout/callout-jupyter.lua

@@ -1,64 +1,52 @@
 function createCallout(div, type)
-    local customIcons = {
-      exercise = "<i class=\"fa-solid fa-pencil\"></i>",
-      note = "<i class=\"fa-solid fa-comment\"></i>",
-      tip = "<i class=\"fa-solid fa-lightbulb\"></i>",
-      warning = "<i class=\"fa-solid fa-triangle-exclamation\"></i>",
-      important =  "<i class=\"fa-solid fa-triangle-exclamation\"></i>"
-    }
-    local customColor = {
-        note = "info",
-        tip = "success",
-        exercise = "success",
-        warning = "danger",
-        important = "danger"
-    }
-  
-    local title = type:gsub("^%l", string.upper)
-    -- Use first element of div as title if this is a header
-    if div.content[1] ~= nil and div.content[1].t == "Header" then
-      title = pandoc.utils.stringify(div.content[1])
-      div.content:remove(1)
-    end
-  
-    local icon = customIcons[type] or ""
-    local color = customColor[type] or ""
-  
-    if quarto.doc.is_format("ipynb") then
-      if type == "exercise" then
-        type = "tip"
-        icon = customIcons["exercise"]
-      end
-      -- Add html formatting around
-      local headBox = "<div class=\"alert alert-" .. color .. "\" role=\"alert\">\n" ..
-        "<h3 class=\"alert-heading\">" .. icon .. " " .. title .. "</h3>\n"
-  
-      -- Insert raw HTML blocks
-      div.content:insert(1, pandoc.RawBlock('html', headBox .. "\n"))
-      div.content:insert(pandoc.RawBlock('html', "\n</div>"))   
-      return div
-    else
-      local old_attr = div.attr
-      local appearanceRaw = div.attr.attributes["appearance"]
-      local collapse = div.attr.attributes["collapse"]
-      return quarto.Callout({
-        type = type,
-        title = title, 
-        collapse = false,
-        content = div.content,
-        icon = icon
-      })      
-    end
+  local customIcons = {
+    exercise = "<i class=\"fa-solid fa-pencil\"></i>",
+    note = "<i class=\"fa-solid fa-comment\"></i>",
+    tip = "<i class=\"fa-solid fa-lightbulb\"></i>",
+    warning = "<i class=\"fa-solid fa-triangle-exclamation\"></i>",
+    important = "<i class=\"fa-solid fa-triangle-exclamation\"></i>"
+  }
+
+  local customColor = {
+    note = "info",
+    tip = "success",
+    exercise = "success",
+    warning = "danger",
+    important = "danger"
+  }
+
+  local title = type:gsub("^%l", string.upper)
+
+  -- Use first element of div as title if it is a Header
+  if div.content[1] ~= nil and div.content[1].t == "Header" then
+    title = pandoc.utils.stringify(div.content[1])
+    div.content:remove(1)
+  end
+
+  local icon = customIcons[type] or ""
+  local color = customColor[type] or ""
+
+  -- Add HTML formatting for ipynb output
+  local headBox = "<div class=\"alert alert-" .. color .. "\" role=\"alert\">\n" ..
+                  "<h3 class=\"alert-heading\">" .. icon .. " " .. title .. "</h3>\n"
+
+  div.content:insert(1, pandoc.RawBlock('html', headBox))
+  div.content:insert(pandoc.RawBlock('html', "</div>"))
+
+  return div
+end
+
+function Div(div)
+  if not quarto.doc.is_format("ipynb") then
+    return nil
   end
-  
-  function Div(div)
-    -- List of supported callout types
-    local callout_types = {"note", "caution",  "warning", "important", "tip", "exercise"}
-  
-    for _, type in ipairs(callout_types) do
-      if div.classes:includes(type) then
-        return createCallout(div, type)
-      end
+
+  -- List of base callout types
+  local baseTypes = { "note", "caution", "warning", "important", "tip", "exercise" }
+
+  for _, type in ipairs(baseTypes) do
+    if div.classes:includes(type) or div.classes:includes("callout-" .. type) then
+      return createCallout(div, type)
     end
   end
-  
+end