From b892108d57821dc1c23bd0ee73676801549aa592 Mon Sep 17 00:00:00 2001
From: courtneydean33 <114959284+courtneydean33@users.noreply.github.com>
Date: Wed, 18 Mar 2026 11:40:44 -0600
Subject: [PATCH 01/21] Update daily_schedules.md

removed 2025 schedule update language
---
 tutorials/Schedule/daily_schedules.md | 2 --
 1 file changed, 2 deletions(-)

diff --git a/tutorials/Schedule/daily_schedules.md b/tutorials/Schedule/daily_schedules.md
index d1bf65d88..087736b49 100644
--- a/tutorials/Schedule/daily_schedules.md
+++ b/tutorials/Schedule/daily_schedules.md
@@ -42,8 +42,6 @@ All days except W1D4 and W2D5 will follow this schedule for course time:
 ### Project time
 In addition to course time, each day will have 3 hours of project time after tutorials time. 
 
-#### **Schedule Change for 2025:** For all time slots, projects will come *after* course work.
-
 ### Schedule of specific days
 <!--
 #### W2D1: Modeling Practice & Half Project Day (Project Proposals)

From 6652eb4ff59d7193a8f67133361953778cb8c858 Mon Sep 17 00:00:00 2001
From: Konstantine Tsafatinos <kosta.tsaf@gmail.com>
Date: Fri, 20 Mar 2026 01:13:20 -0400
Subject: [PATCH 02/21] fix: enable jupyter-book execution cache instead of
 force-rebuild

---
 book/_config.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/book/_config.yml b/book/_config.yml
index 451443e20..3cbf590b2 100644
--- a/book/_config.yml
+++ b/book/_config.yml
@@ -15,8 +15,8 @@ only_build_toc_files        : true
 #######################################################################################
 # Execution settings
 execute:
-  execute_notebooks         : force # Whether to execute notebooks at build time. Must be one of ("auto", "force", "cache", "off")
-  cache                     : ""    # A path to the jupyter cache that will be used to store execution artifacts. Defaults to `_build/.jupyter_cache/`
+  execute_notebooks         : cache # Whether to execute notebooks at build time. Must be one of ("auto", "force", "cache", "off")
+  cache                     : "book/.jupyter-cache"    # A path to the jupyter cache that will be used to store execution artifacts. Defaults to `_build/.jupyter_cache/`
   exclude_patterns          : [Bonus_Autoencoders/student/Bonus_Tutorial1.ipynb, Bonus_Autoencoders/student/Bonus_Tutorial2.ipynb, Bonus_Autoencoders/student/Bonus_Tutorial3.ipynb]    # A list of patterns to *skip* in execution (e.g. a notebook that takes a really long time)
   timeout                   : 360    # The maximum time (in seconds) each notebook cell is allowed to run.
   run_in_temp               : false # If `True`, then a temporary directory will be created and used as the command working directory (cwd),

From a604510dc9130ec4253e7cbd76add6f753ede5ef Mon Sep 17 00:00:00 2001
From: Konstantine Tsafatinos <kosta.tsaf@gmail.com>
Date: Fri, 20 Mar 2026 01:14:56 -0400
Subject: [PATCH 03/21] chore: upgrade deprecated Node.js 20 GitHub Actions to
 latest versions

---
 .github/actions/setup-python-env/action.yml     | 2 +-
 .github/actions/setup-rendering-deps/action.yml | 2 +-
 .github/workflows/publish-book.yml              | 4 ++--
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/actions/setup-python-env/action.yml b/.github/actions/setup-python-env/action.yml
index a6076550e..9e5e50bf9 100644
--- a/.github/actions/setup-python-env/action.yml
+++ b/.github/actions/setup-python-env/action.yml
@@ -17,7 +17,7 @@ runs:
   steps:
     - name: Set up Python
       id: setup-python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ inputs.python-version }}
         cache: 'pip'
diff --git a/.github/actions/setup-rendering-deps/action.yml b/.github/actions/setup-rendering-deps/action.yml
index 53116d996..316327d8b 100644
--- a/.github/actions/setup-rendering-deps/action.yml
+++ b/.github/actions/setup-rendering-deps/action.yml
@@ -20,7 +20,7 @@ runs:
   steps:
     - name: Cache fonts
       id: cache-fonts
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: /usr/share/fonts/truetype/humor-sans
         key: fonts-${{ runner.os }}-humor-sans-v1
diff --git a/.github/workflows/publish-book.yml b/.github/workflows/publish-book.yml
index 32b8a8039..91ecf4798 100644
--- a/.github/workflows/publish-book.yml
+++ b/.github/workflows/publish-book.yml
@@ -18,7 +18,7 @@ jobs:
     steps:
 
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
@@ -61,7 +61,7 @@ jobs:
         run: echo "date=$(date +'%Y-%m')" >> $GITHUB_OUTPUT
 
       - name: Cache Jupyter execution
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: book/.jupyter-cache
           key: jupyter-exec-${{ steps.cache-date.outputs.date }}-${{ hashFiles('tutorials/**/*.ipynb', 'requirements.txt') }}

From 0313ff0d6194a802f432ac6ff7dcbf5540aed259 Mon Sep 17 00:00:00 2001
From: Konstantine Tsafatinos <kosta.tsaf@gmail.com>
Date: Fri, 20 Mar 2026 01:16:08 -0400
Subject: [PATCH 04/21] feat: add generate_book_v2.py for Jupyter Book 2
 myst.yml generation

---
 generate_book_v2.py | 322 ++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 322 insertions(+)
 create mode 100644 generate_book_v2.py

diff --git a/generate_book_v2.py b/generate_book_v2.py
new file mode 100644
index 000000000..e28ca5641
--- /dev/null
+++ b/generate_book_v2.py
@@ -0,0 +1,322 @@
+#!/usr/bin/env python3
+"""
+Generate a JB2-compatible myst.yml from tutorials/materials.yml.
+In-repo replacement for nmaci's generate_book.py during the JB2 pilot.
+
+tutorials/materials.yml is kept as-is: it stores richer metadata than a bare
+TOC (video links, bilibili links, slide links, tutorial counts) and is used by
+multiple tools. This script translates it into the myst.yml build artifact.
+
+Run as: python ci/generate_book_v2.py student
+"""
+
+import os
+import sys
+import json
+import yaml
+from bs4 import BeautifulSoup
+
+ORG = os.environ.get("ORG", "neuromatch")
+REPO = os.environ.get("NMA_REPO", "NeuroAI_Course")
+ARG = sys.argv[1]  # "student" or "instructor"
+
+
+def main():
+    with open("tutorials/materials.yml") as fh:
+        materials = yaml.load(fh, Loader=yaml.FullLoader)
+
+    # Pre-process intro notebook
+    intro_path = "tutorials/intro.ipynb"
+    if os.path.exists(intro_path):
+        pre_process_notebook(intro_path)
+
+    toc = []
+
+    # Root entry
+    toc.append({"file": "tutorials/intro.ipynb"})
+
+    # Schedule section
+    toc.append(
+        {
+            "title": "Schedule",
+            "children": [
+                {
+                    "file": "tutorials/Schedule/schedule_intro.md",
+                    "children": [
+                        {"file": "tutorials/Schedule/daily_schedules.md"},
+                        {"file": "tutorials/Schedule/shared_calendars.md"},
+                        {"file": "tutorials/Schedule/timezone_widget.md"},
+                    ],
+                }
+            ],
+        }
+    )
+
+    # Technical Help section
+    toc.append(
+        {
+            "title": "Technical Help",
+            "children": [
+                {
+                    "file": "tutorials/TechnicalHelp/tech_intro.md",
+                    "children": [
+                        {
+                            "file": "tutorials/TechnicalHelp/Jupyterbook.md",
+                            "children": [
+                                {"file": "tutorials/TechnicalHelp/Tutorial_colab.md"},
+                                {"file": "tutorials/TechnicalHelp/Tutorial_kaggle.md"},
+                            ],
+                        },
+                        {"file": "tutorials/TechnicalHelp/Discord.md"},
+                    ],
+                }
+            ],
+        }
+    )
+
+    # Links and Policy
+    toc.append(
+        {
+            "title": "Links & Policy",
+            "children": [{"file": "tutorials/TechnicalHelp/Links_Policy.md"}],
+        }
+    )
+
+    # Prerequisites
+    toc.append(
+        {
+            "title": "Prerequisites",
+            "children": [{"file": "prereqs/NeuroAI.md"}],
+        }
+    )
+
+    # Build category -> [day entries] dict (preserving materials.yml order)
+    categories = {}
+    art_file_list = os.listdir("tutorials/Art/")
+
+    for m in materials:
+        category = m["category"]
+        if category not in categories:
+            categories[category] = []
+
+        directory = f"tutorials/{m['day']}_{''.join(m['name'].split())}"
+
+        # Write chapter_title.md for this day (same logic as JB1 script)
+        title_page = f"# {m['name']}"
+        art_file = [fname for fname in art_file_list if m["day"] in fname]
+        if len(art_file) == 1:
+            artist = art_file[0].split("-")[1].split(".")[0].replace("_", " ")
+            title_page += (
+                f"\n\n ````{{div}} full-width \n"
+                f" <img src='../Art/{art_file[0]}' alt='art relevant to chapter contents' width='100%'> \n"
+                f"```` \n\n*Artwork by {artist}*"
+            )
+        with open(f"{directory}/chapter_title.md", "w+") as fh:
+            fh.write(title_page)
+
+        # Build notebook children list for this day
+        day_children = []
+        notebook_list = []
+        if os.path.exists(f"{directory}/{m['day']}_Intro.ipynb"):
+            notebook_list.append(f"{directory}/{ARG}/{m['day']}_Intro.ipynb")
+        notebook_list += [
+            f"{directory}/{ARG}/{m['day']}_Tutorial{i + 1}.ipynb"
+            for i in range(m["tutorials"])
+        ]
+        if os.path.exists(f"{directory}/{m['day']}_Outro.ipynb"):
+            notebook_list.append(f"{directory}/{ARG}/{m['day']}_Outro.ipynb")
+
+        for nb_path in notebook_list:
+            day_children.append({"file": nb_path})
+            pre_process_notebook(nb_path)
+
+        day_children.append({"file": f"{directory}/further_reading.md"})
+
+        summary_path = f"{directory}/{ARG}/{m['day']}_DaySummary.ipynb"
+        if os.path.exists(summary_path):
+            day_children.append({"file": summary_path})
+            pre_process_notebook(summary_path)
+
+        categories[category].append(
+            {
+                "file": f"{directory}/chapter_title.md",
+                "title": f"{m['name']} ({m['day']})",
+                "children": day_children,
+            }
+        )
+
+    # Add Module WrapUps to their categories
+    for category, chapters in categories.items():
+        safe_category = category.replace(" ", "")
+        wrapup_name = f"tutorials/Module_WrapUps/{safe_category}.ipynb"
+        if os.path.exists(wrapup_name):
+            chapters.append({"file": wrapup_name})
+
+    # Add category parts to TOC
+    for category, chapters in categories.items():
+        toc.append({"title": category, "children": chapters})
+
+    # Professional Development
+    with open("projects/professional_development/prof_dev_materials.yml") as fh:
+        prof_dev_materials = yaml.load(fh, Loader=yaml.FullLoader)
+    toc.append({"title": "Professional Development", "children": prof_dev_materials})
+
+    # Project Booklet
+    with open("projects/project_materials.yml") as fh:
+        project_materials = yaml.load(fh, Loader=yaml.FullLoader)
+    toc.append({"title": "Project Booklet", "children": project_materials})
+
+    # Pre-process project notebooks
+    for m in project_materials:
+        if m.get("title") == "Project materials":
+            for project in m.get("sections", []):
+                pre_process_notebook(project["file"])
+
+    # Write myst.yml (build artifact — not committed to git)
+    myst_config = {
+        "version": 1,
+        "project": {
+            "title": "Neuromatch Academy: NeuroAI",
+            "github": f"https://github.com/{ORG}/{REPO}",
+            "license": "CC-BY-4.0",
+            "toc": toc,
+        },
+        "site": {
+            "template": "book-theme",
+            "domains": ["neuroai.neuromatch.io"],
+            "nav": [],
+            "actions": [{"title": "GitHub", "url": f"https://github.com/{ORG}/{REPO}"}],
+        },
+    }
+
+    with open("book/myst.yml", "w") as fh:
+        yaml.dump(
+            myst_config,
+            fh,
+            default_flow_style=False,
+            allow_unicode=True,
+            sort_keys=False,
+        )
+
+    print("Generated book/myst.yml")
+
+
+# ---- Pre-processing helpers (ported verbatim from nmaci generate_book.py) ----
+
+
+def pre_process_notebook(file_path):
+    if not os.path.exists(file_path):
+        print(f"  Warning: {file_path} not found, skipping")
+        return
+    with open(file_path, encoding="utf-8") as fh:
+        content = json.load(fh)
+    content = open_in_colab_new_tab(content)
+    content = change_video_widths(content)
+    content = link_hidden_cells(content)
+    with open(file_path, "w", encoding="utf-8") as fh:
+        json.dump(content, fh, indent=1, ensure_ascii=False)
+
+
+def open_in_colab_new_tab(content):
+    cells = content["cells"]
+    if not cells or not cells[0].get("source"):
+        return content
+    parsed_html = BeautifulSoup(cells[0]["source"][0], "html.parser")
+    for anchor in parsed_html.findAll("a"):
+        anchor["target"] = "_blank"
+    cells[0]["source"][0] = str(parsed_html)
+    return content
+
+
+def link_hidden_cells(content):
+    cells = content["cells"]
+    updated_cells = cells.copy()
+    header_level = 1
+    i_updated_cell = 0
+    for i_cell, cell in enumerate(cells):
+        updated_cell = updated_cells[i_updated_cell]
+        if "source" not in cell or not cell["source"]:
+            i_updated_cell += 1
+            continue
+        source = cell["source"][0]
+        if source.startswith("#") and cell["cell_type"] == "markdown":
+            header_level = source.count("#")
+        elif source.startswith("---") and cell["cell_type"] == "markdown":
+            if len(cell["source"]) > 1 and cell["source"][1].startswith("#"):
+                header_level = cell["source"][1].count("#")
+        if "@title" in source or "@markdown" in source:
+            if "metadata" not in cell:
+                updated_cell["metadata"] = {}
+            if "tags" not in updated_cell["metadata"]:
+                updated_cell["metadata"]["tags"] = []
+            if "YouTubeVideo" in "".join(cell["source"]) or "IFrame" in "".join(
+                cell["source"]
+            ):
+                if "remove-input" not in updated_cell["metadata"]["tags"]:
+                    updated_cell["metadata"]["tags"].append("remove-input")
+            else:
+                if "hide-input" not in updated_cell["metadata"]["tags"]:
+                    updated_cell["metadata"]["tags"].append("hide-input")
+            if "@title" in source and source.split("@title")[1] != "":
+                header_cell = {
+                    "cell_type": "markdown",
+                    "metadata": {},
+                    "source": [
+                        "#" * (header_level + 1) + " " + source.split("@title")[1]
+                    ],
+                }
+                updated_cells.insert(i_updated_cell, header_cell)
+                i_updated_cell += 1
+            strings_with_markdown = [
+                (i, s) for i, s in enumerate(cell["source"]) if "@markdown" in s
+            ]
+            if len(strings_with_markdown) == 1:
+                i, md_source = strings_with_markdown[0]
+                if md_source.split("@markdown")[1] != "":
+                    header_cell = {
+                        "cell_type": "markdown",
+                        "metadata": {},
+                        "source": [md_source.split("@markdown")[1]],
+                    }
+                    updated_cells.insert(i_updated_cell, header_cell)
+                    i_updated_cell += 1
+        i_updated_cell += 1
+    content["cells"] = updated_cells
+    return content
+
+
+def change_video_widths(content):
+    for cell in content["cells"]:
+        if "YouTubeVideo" in "".join(cell["source"]):
+            for ind in range(len(cell["source"])):
+                cell["source"][ind] = cell["source"][ind].replace("854", "730")
+                cell["source"][ind] = cell["source"][ind].replace("480", "410")
+        if (
+            "# @title Tutorial slides\n" in cell["source"]
+            or "# @title Slides\n" in cell["source"]
+        ):
+            slide_link = ""
+            for line in cell["source"]:
+                if line.startswith("link_id"):
+                    slide_link = line.split('"')[1]
+                    break
+            download_link = f"https://osf.io/download/{slide_link}/"
+            render_link = (
+                f"https://mfr.ca-1.osf.io/render?url=https://osf.io/{slide_link}/"
+                f"?direct%26mode=render%26action=download%26mode=render"
+            )
+            cell["source"] = [
+                "# @markdown\n",
+                "from IPython.display import IFrame\n",
+                "from ipywidgets import widgets\n",
+                "out = widgets.Output()\n",
+                "with out:\n",
+                f'    print(f"If you want to download the slides: {download_link}")\n',
+                f'    display(IFrame(src=f"{render_link}", width=730, height=410))\n',
+                "display(out)",
+            ]
+    return content
+
+
+if __name__ == "__main__":
+    main()

From bb31398bec178ad015693bb5b6633e93eaa50218 Mon Sep 17 00:00:00 2001
From: Konstantine Tsafatinos <kosta.tsaf@gmail.com>
Date: Fri, 20 Mar 2026 01:16:30 -0400
Subject: [PATCH 05/21] feat: add publish-book-v2 workflow for Jupyter Book 2
 pilot

---
 .github/workflows/publish-book-v2.yml | 100 ++++++++++++++++++++++++++
 1 file changed, 100 insertions(+)
 create mode 100644 .github/workflows/publish-book-v2.yml

diff --git a/.github/workflows/publish-book-v2.yml b/.github/workflows/publish-book-v2.yml
new file mode 100644
index 000000000..483584274
--- /dev/null
+++ b/.github/workflows/publish-book-v2.yml
@@ -0,0 +1,100 @@
+name: publish-book-v2
+
+on:
+  workflow_dispatch:
+
+env:
+  NB_KERNEL: python
+  ORG: neuromatch
+  NMA_REPO: NeuroAI_Course
+  NMA_MAIN_BRANCH: main
+  # Empty string = serve from domain root (correct for custom domain neuroai.neuromatch.io)
+  BASE_URL: ''
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+concurrency:
+  group: pages
+  cancel-in-progress: false
+
+jobs:
+  build-and-deploy-book-v2:
+    runs-on: ubuntu-latest
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Get commit message
+        run: |
+          readonly local msg=$(git log -1 --pretty=format:"%s")
+          echo "COMMIT_MESSAGE=$msg" >> $GITHUB_ENV
+
+      - name: Setup Python environment
+        uses: ./.github/actions/setup-python-env
+
+      - name: Setup Node.js (required by MyST theme engine)
+        uses: actions/setup-node@v4
+        with:
+          node-version: '20'
+
+      - name: Install Jupyter Book 2
+        run: pip install "jupyter-book>=2.1"
+
+      - name: Setup CI tools
+        uses: ./.github/actions/setup-ci-tools
+        with:
+          commit-message: ${{ env.COMMIT_MESSAGE }}
+          stub-widgets: 'false'
+
+      - name: Setup rendering dependencies
+        if: "!contains(env.COMMIT_MESSAGE, 'skip ci')"
+        uses: ./.github/actions/setup-rendering-deps
+
+      - name: Get date for cache rotation
+        id: cache-date
+        run: echo "date=$(date +'%Y-%m')" >> $GITHUB_OUTPUT
+
+      - name: Cache JB2 execution outputs
+        uses: actions/cache@v4
+        with:
+          path: book/_build/execute
+          key: jb2-exec-${{ steps.cache-date.outputs.date }}-${{ hashFiles('tutorials/**/*.ipynb', 'requirements.txt') }}
+          restore-keys: |
+            jb2-exec-${{ steps.cache-date.outputs.date }}-
+            jb2-exec-
+
+      - name: Cache MyST theme (avoids re-download on every run)
+        uses: actions/cache@v4
+        with:
+          path: book/_build/templates
+          key: jb2-templates-v1
+
+      - name: Generate myst.yml from materials.yml
+        run: python generate_book_v2.py student
+
+      - name: Build book with Jupyter Book 2
+        working-directory: book
+        run: jupyter book build --html --execute
+        env:
+          BASE_URL: ${{ env.BASE_URL }}
+
+      - name: Setup Pages
+        uses: actions/configure-pages@v4
+
+      - name: Upload HTML artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: book/_build/html
+
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

From 86bdbf9fa33483329fba1acccd3a110911b53931 Mon Sep 17 00:00:00 2001
From: Konstantine Tsafatinos <kosta.tsaf@gmail.com>
Date: Fri, 20 Mar 2026 01:17:09 -0400
Subject: [PATCH 06/21] fix: use find_all (not deprecated findAll) and ignore
 book/myst.yml build artifact

---
 .gitignore          | 3 ++-
 generate_book_v2.py | 2 +-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/.gitignore b/.gitignore
index 52fce67de..cdc49e55d 100755
--- a/.gitignore
+++ b/.gitignore
@@ -2,4 +2,5 @@
 .vscode
 .idea
 _build
-_toc.yml
\ No newline at end of file
+_toc.yml
+book/myst.yml
\ No newline at end of file
diff --git a/generate_book_v2.py b/generate_book_v2.py
index e28ca5641..75b5417d1 100644
--- a/generate_book_v2.py
+++ b/generate_book_v2.py
@@ -222,7 +222,7 @@ def open_in_colab_new_tab(content):
     if not cells or not cells[0].get("source"):
         return content
     parsed_html = BeautifulSoup(cells[0]["source"][0], "html.parser")
-    for anchor in parsed_html.findAll("a"):
+    for anchor in parsed_html.find_all("a"):
         anchor["target"] = "_blank"
     cells[0]["source"][0] = str(parsed_html)
     return content

From 0a9c74d02c73173a7b855038fa73957b2431edec Mon Sep 17 00:00:00 2001
From: Konstantine Tsafatinos <kosta.tsaf@gmail.com>
Date: Fri, 20 Mar 2026 01:33:25 -0400
Subject: [PATCH 07/21] fix: copy CNAME into build output to preserve custom
 domain on deploy

---
 .github/workflows/publish-book-v2.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/publish-book-v2.yml b/.github/workflows/publish-book-v2.yml
index 483584274..fdba5d4d6 100644
--- a/.github/workflows/publish-book-v2.yml
+++ b/.github/workflows/publish-book-v2.yml
@@ -87,6 +87,9 @@ jobs:
         env:
           BASE_URL: ${{ env.BASE_URL }}
 
+      - name: Copy CNAME for custom domain
+        run: cp CNAME book/_build/html/CNAME
+
       - name: Setup Pages
         uses: actions/configure-pages@v4
 

From 89cd83377a550ddab6fd7765960dd706558c6d33 Mon Sep 17 00:00:00 2001
From: Konstantine Tsafatinos <kosta.tsaf@gmail.com>
Date: Fri, 20 Mar 2026 01:45:14 -0400
Subject: [PATCH 08/21] =?UTF-8?q?fix:=20convert=20JB1=20sections=E2=86=92c?=
 =?UTF-8?q?hildren=20in=20TOC,=20add=20book/=20symlinks=20in=20workflow?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 .github/workflows/publish-book-v2.yml |  6 ++++++
 generate_book_v2.py                   | 28 ++++++++++++++++++++++++---
 2 files changed, 31 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/publish-book-v2.yml b/.github/workflows/publish-book-v2.yml
index fdba5d4d6..0df14afbe 100644
--- a/.github/workflows/publish-book-v2.yml
+++ b/.github/workflows/publish-book-v2.yml
@@ -78,6 +78,12 @@ jobs:
           path: book/_build/templates
           key: jb2-templates-v1
 
+      - name: Create symlinks so book/ can resolve repo-root paths
+        run: |
+          ln -s ${{ github.workspace }}/tutorials book/tutorials
+          ln -s ${{ github.workspace }}/projects book/projects
+          ln -s ${{ github.workspace }}/prereqs book/prereqs
+
       - name: Generate myst.yml from materials.yml
         run: python generate_book_v2.py student
 
diff --git a/generate_book_v2.py b/generate_book_v2.py
index 75b5417d1..77e9db78c 100644
--- a/generate_book_v2.py
+++ b/generate_book_v2.py
@@ -158,18 +158,22 @@ def main():
 
     # Professional Development
     with open("projects/professional_development/prof_dev_materials.yml") as fh:
-        prof_dev_materials = yaml.load(fh, Loader=yaml.FullLoader)
+        prof_dev_materials = convert_sections_to_children(
+            yaml.load(fh, Loader=yaml.FullLoader)
+        )
     toc.append({"title": "Professional Development", "children": prof_dev_materials})
 
     # Project Booklet
     with open("projects/project_materials.yml") as fh:
-        project_materials = yaml.load(fh, Loader=yaml.FullLoader)
+        project_materials = convert_sections_to_children(
+            yaml.load(fh, Loader=yaml.FullLoader)
+        )
     toc.append({"title": "Project Booklet", "children": project_materials})
 
     # Pre-process project notebooks
     for m in project_materials:
         if m.get("title") == "Project materials":
-            for project in m.get("sections", []):
+            for project in m.get("children", []):
                 pre_process_notebook(project["file"])
 
     # Write myst.yml (build artifact — not committed to git)
@@ -201,6 +205,24 @@ def main():
     print("Generated book/myst.yml")
 
 
+# ---- TOC helpers ----
+
+
+def convert_sections_to_children(entries):
+    """Recursively rename JB1 'sections' keys to JB2 'children'."""
+    if not entries:
+        return entries
+    result = []
+    for entry in entries:
+        entry = dict(entry)
+        if "sections" in entry:
+            entry["children"] = convert_sections_to_children(entry.pop("sections"))
+        elif "children" in entry:
+            entry["children"] = convert_sections_to_children(entry["children"])
+        result.append(entry)
+    return result
+
+
 # ---- Pre-processing helpers (ported verbatim from nmaci generate_book.py) ----
 
 

From 5fef81219521ed341f11988a8b026dbb5dafb86f Mon Sep 17 00:00:00 2001
From: Konstantine Tsafatinos <kosta.tsaf@gmail.com>
Date: Fri, 20 Mar 2026 02:09:57 -0400
Subject: [PATCH 09/21] fix: add skip-execution tag to NotImplementedError stub
 cells for JB2 compatibility

---
 generate_book_v2.py | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/generate_book_v2.py b/generate_book_v2.py
index 77e9db78c..f2ddaeb28 100644
--- a/generate_book_v2.py
+++ b/generate_book_v2.py
@@ -235,10 +235,31 @@ def pre_process_notebook(file_path):
     content = open_in_colab_new_tab(content)
     content = change_video_widths(content)
     content = link_hidden_cells(content)
+    content = tag_stub_cells(content)
     with open(file_path, "w", encoding="utf-8") as fh:
         json.dump(content, fh, indent=1, ensure_ascii=False)
 
 
+def tag_stub_cells(content):
+    """Add skip-execution tag to cells containing raise NotImplementedError.
+
+    JB1 used allow_errors:true to silently swallow errors from these stub cells.
+    JB2 has no global equivalent, so we skip execution instead — the source is
+    still rendered (students see the stub), but no error traceback is produced.
+    """
+    for cell in content["cells"]:
+        if cell["cell_type"] != "code":
+            continue
+        if any("NotImplementedError" in s for s in cell.get("source", [])):
+            if "metadata" not in cell:
+                cell["metadata"] = {}
+            if "tags" not in cell["metadata"]:
+                cell["metadata"]["tags"] = []
+            if "skip-execution" not in cell["metadata"]["tags"]:
+                cell["metadata"]["tags"].append("skip-execution")
+    return content
+
+
 def open_in_colab_new_tab(content):
     cells = content["cells"]
     if not cells or not cells[0].get("source"):

From 4aaac530cb369c57ef4747a160e6c0b4bc93806d Mon Sep 17 00:00:00 2001
From: Konstantine Tsafatinos <kosta.tsaf@gmail.com>
Date: Fri, 20 Mar 2026 02:35:04 -0400
Subject: [PATCH 10/21] fix: use raises-exception on all code cells +
 post-process HTML to strip error divs (matches JB1 allow_errors behaviour)

---
 .github/workflows/publish-book-v2.yml |   3 +
 generate_book_v2.py                   |  27 ++++---
 parse_html_for_errors_v2.py           | 110 ++++++++++++++++++++++++++
 3 files changed, 129 insertions(+), 11 deletions(-)
 create mode 100644 parse_html_for_errors_v2.py

diff --git a/.github/workflows/publish-book-v2.yml b/.github/workflows/publish-book-v2.yml
index 0df14afbe..361891113 100644
--- a/.github/workflows/publish-book-v2.yml
+++ b/.github/workflows/publish-book-v2.yml
@@ -93,6 +93,9 @@ jobs:
         env:
           BASE_URL: ${{ env.BASE_URL }}
 
+      - name: Strip error output divs from built HTML
+        run: python parse_html_for_errors_v2.py student
+
       - name: Copy CNAME for custom domain
         run: cp CNAME book/_build/html/CNAME
 
diff --git a/generate_book_v2.py b/generate_book_v2.py
index f2ddaeb28..85fa0e190 100644
--- a/generate_book_v2.py
+++ b/generate_book_v2.py
@@ -241,22 +241,27 @@ def pre_process_notebook(file_path):
 
 
 def tag_stub_cells(content):
-    """Add skip-execution tag to cells containing raise NotImplementedError.
+    """Add raises-exception tag to every code cell.
 
-    JB1 used allow_errors:true to silently swallow errors from these stub cells.
-    JB2 has no global equivalent, so we skip execution instead — the source is
-    still rendered (students see the stub), but no error traceback is produced.
+    JB1 used allow_errors:true globally so execution continued past any error
+    (NotImplementedError stubs, downstream NameErrors, etc.) and error output
+    divs were stripped from the HTML by parse_html_for_errors.py.
+
+    JB2 has no global allow_errors equivalent, but raises-exception on a cell
+    tells MyST to continue executing subsequent cells after an error. We apply
+    it to all code cells so that the behaviour matches JB1 exactly. A companion
+    post-processing script (parse_html_for_errors_v2.py) then strips the error
+    output divs from the built HTML before deployment.
     """
     for cell in content["cells"]:
         if cell["cell_type"] != "code":
             continue
-        if any("NotImplementedError" in s for s in cell.get("source", [])):
-            if "metadata" not in cell:
-                cell["metadata"] = {}
-            if "tags" not in cell["metadata"]:
-                cell["metadata"]["tags"] = []
-            if "skip-execution" not in cell["metadata"]["tags"]:
-                cell["metadata"]["tags"].append("skip-execution")
+        if "metadata" not in cell:
+            cell["metadata"] = {}
+        if "tags" not in cell["metadata"]:
+            cell["metadata"]["tags"] = []
+        if "raises-exception" not in cell["metadata"]["tags"]:
+            cell["metadata"]["tags"].append("raises-exception")
     return content
 
 
diff --git a/parse_html_for_errors_v2.py b/parse_html_for_errors_v2.py
new file mode 100644
index 000000000..6dfb619f4
--- /dev/null
+++ b/parse_html_for_errors_v2.py
@@ -0,0 +1,110 @@
+#!/usr/bin/env python3
+"""
+Post-process JB2-built HTML to strip error output divs.
+
+JB1 equivalent: nmaci/scripts/parse_html_for_errors.py
+JB2 difference: MyST uses different CSS classes for cell output containers.
+
+JB1 class:  "cell_output docutils container"
+JB2 classes tried (in order):
+  - "cell_output"           (MyST book-theme)
+  - "output"                (fallback)
+  - any <div> containing the error text (last resort)
+
+Run as: python parse_html_for_errors_v2.py student
+"""
+
+import os
+import sys
+import yaml
+from bs4 import BeautifulSoup
+
+ARG = sys.argv[1]  # "student" or "instructor"
+
+ERROR_STRINGS = ["NotImplementedError", "NameError"]
+
+
+def main():
+    with open("tutorials/materials.yml") as fh:
+        materials = yaml.load(fh, Loader=yaml.FullLoader)
+
+    html_directory = "book/_build/html/"
+    total_removed = 0
+
+    for m in materials:
+        name = f"{m['day']}_{''.join(m['name'].split())}"
+
+        notebook_paths = []
+        if os.path.exists(f"tutorials/{name}/{m['day']}_Intro.ipynb"):
+            notebook_paths.append(
+                f"{html_directory}/tutorials/{name}/{ARG}/{m['day']}_Intro.html"
+            )
+        notebook_paths += [
+            f"{html_directory}/tutorials/{name}/{ARG}/{m['day']}_Tutorial{i + 1}.html"
+            for i in range(m["tutorials"])
+        ]
+        if os.path.exists(f"tutorials/{name}/{m['day']}_Outro.ipynb"):
+            notebook_paths.append(
+                f"{html_directory}/tutorials/{name}/{ARG}/{m['day']}_Outro.html"
+            )
+
+        for html_path in notebook_paths:
+            if not os.path.exists(html_path):
+                print(f"  Warning: {html_path} not found, skipping")
+                continue
+
+            with open(html_path, encoding="utf-8") as f:
+                contents = f.read()
+
+            parsed_html = BeautifulSoup(contents, features="html.parser")
+            removed = strip_error_divs(parsed_html)
+            total_removed += removed
+
+            # Put solution figures in center (matches JB1 behaviour)
+            for img in parsed_html.find_all("img", alt=True):
+                if img["alt"] == "Solution hint":
+                    img["align"] = "center"
+                    img["class"] = "align-center"
+
+            with open(html_path, "w", encoding="utf-8") as f:
+                f.write(str(parsed_html))
+
+            if removed:
+                print(
+                    f"  Stripped {removed} error div(s) from {os.path.basename(html_path)}"
+                )
+
+    print(f"Done. Removed {total_removed} error output div(s) total.")
+
+
+def strip_error_divs(parsed_html):
+    """Remove output divs that contain NotImplementedError or NameError text.
+
+    Tries JB1's class first, then JB2/MyST class names, then a broad sweep.
+    Returns the number of divs removed.
+    """
+    removed = 0
+
+    # JB1 class (sphinx/docutils)
+    candidates = parsed_html.find_all(
+        "div", {"class": "cell_output docutils container"}
+    )
+
+    # JB2/MyST book-theme output wrapper
+    if not candidates:
+        candidates = parsed_html.find_all("div", {"class": "cell_output"})
+
+    # Broader fallback: any <div> that directly wraps an error traceback
+    if not candidates:
+        candidates = parsed_html.find_all("div", class_=lambda c: c and "output" in c)
+
+    for div in candidates:
+        if any(err in str(div) for err in ERROR_STRINGS):
+            div.decompose()
+            removed += 1
+
+    return removed
+
+
+if __name__ == "__main__":
+    main()

From d4182c3b553c0aee00ca9387e15fbd5fe04c0477 Mon Sep 17 00:00:00 2001
From: Konstantine Tsafatinos <kosta.tsaf@gmail.com>
Date: Fri, 20 Mar 2026 02:35:42 -0400
Subject: [PATCH 11/21] refactor: rename tag_stub_cells to
 tag_cells_allow_errors

---
 generate_book_v2.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/generate_book_v2.py b/generate_book_v2.py
index 85fa0e190..33ec8471d 100644
--- a/generate_book_v2.py
+++ b/generate_book_v2.py
@@ -235,12 +235,12 @@ def pre_process_notebook(file_path):
     content = open_in_colab_new_tab(content)
     content = change_video_widths(content)
     content = link_hidden_cells(content)
-    content = tag_stub_cells(content)
+    content = tag_cells_allow_errors(content)
     with open(file_path, "w", encoding="utf-8") as fh:
         json.dump(content, fh, indent=1, ensure_ascii=False)
 
 
-def tag_stub_cells(content):
+def tag_cells_allow_errors(content):
     """Add raises-exception tag to every code cell.
 
     JB1 used allow_errors:true globally so execution continued past any error

From cc3a973d4af5ef8e0d9fd9596e3a6264a22e9f17 Mon Sep 17 00:00:00 2001
From: Konstantine Tsafatinos <kosta.tsaf@gmail.com>
Date: Fri, 20 Mar 2026 02:36:10 -0400
Subject: [PATCH 12/21] fix: only apply raises-exception tags for student
 notebooks, not instructor

---
 generate_book_v2.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/generate_book_v2.py b/generate_book_v2.py
index 33ec8471d..d18c293d5 100644
--- a/generate_book_v2.py
+++ b/generate_book_v2.py
@@ -235,7 +235,8 @@ def pre_process_notebook(file_path):
     content = open_in_colab_new_tab(content)
     content = change_video_widths(content)
     content = link_hidden_cells(content)
-    content = tag_cells_allow_errors(content)
+    if ARG == "student":
+        content = tag_cells_allow_errors(content)
     with open(file_path, "w", encoding="utf-8") as fh:
         json.dump(content, fh, indent=1, ensure_ascii=False)
 

From ac6dfd9335ec41b7ce108a62bfb81b4116d9c638 Mon Sep 17 00:00:00 2001
From: Konstantine Tsafatinos <kosta.tsaf@gmail.com>
Date: Fri, 20 Mar 2026 13:02:10 -0400
Subject: [PATCH 13/21] Update generate_book_v2 and error parsing v2

---
 generate_book_v2.py         | 161 ++++++++++++++++++++++++++++--------
 parse_html_for_errors_v2.py |  54 ++++++------
 2 files changed, 157 insertions(+), 58 deletions(-)

diff --git a/generate_book_v2.py b/generate_book_v2.py
index d18c293d5..de987852d 100644
--- a/generate_book_v2.py
+++ b/generate_book_v2.py
@@ -10,7 +10,9 @@
 Run as: python ci/generate_book_v2.py student
 """
 
+import ast
 import os
+import re
 import sys
 import json
 import yaml
@@ -42,6 +44,7 @@ def main():
             "children": [
                 {
                     "file": "tutorials/Schedule/schedule_intro.md",
+                    "short_title": "Overview",
                     "children": [
                         {"file": "tutorials/Schedule/daily_schedules.md"},
                         {"file": "tutorials/Schedule/shared_calendars.md"},
@@ -59,9 +62,11 @@ def main():
             "children": [
                 {
                     "file": "tutorials/TechnicalHelp/tech_intro.md",
+                    "short_title": "Overview",
                     "children": [
                         {
                             "file": "tutorials/TechnicalHelp/Jupyterbook.md",
+                            "short_title": "Using Jupyterbook",
                             "children": [
                                 {"file": "tutorials/TechnicalHelp/Tutorial_colab.md"},
                                 {"file": "tutorials/TechnicalHelp/Tutorial_kaggle.md"},
@@ -188,6 +193,9 @@ def main():
         "site": {
             "template": "book-theme",
             "domains": ["neuroai.neuromatch.io"],
+            "logo": "tutorials/static/ai-logo.png",
+            "favicon": "tutorials/static/ai-logo.png",
+            "options": {"logo_text": "Neuromatch Academy: NeuroAI"},
             "nav": [],
             "actions": [{"title": "GitHub", "url": f"https://github.com/{ORG}/{REPO}"}],
         },
@@ -233,7 +241,7 @@ def pre_process_notebook(file_path):
     with open(file_path, encoding="utf-8") as fh:
         content = json.load(fh)
     content = open_in_colab_new_tab(content)
-    content = change_video_widths(content)
+    content = replace_widgets(content)
     content = link_hidden_cells(content)
     if ARG == "student":
         content = tag_cells_allow_errors(content)
@@ -241,6 +249,124 @@ def pre_process_notebook(file_path):
         json.dump(content, fh, indent=1, ensure_ascii=False)
 
 
+def replace_widgets(content):
+    """Replace or remove ipywidget-based cells that don't render in static HTML.
+
+    JB2/MyST does not embed widget state, so widget cells render as "Loading..."
+    placeholders. This function handles three patterns:
+
+    Video cells — detected by ``display_videos(`` + ``video_ids = [``:
+      Replaced with a markdown cell containing YouTube and Bilibili iframes
+      stacked with bold platform labels.
+
+    Slide cells — detected by ``# @title <slides title>`` + ``link_id``:
+      Replaced with a markdown cell containing the OSF iframe and a download
+      link. Titles matched: "Tutorial slides", "Slides", "Intro Video Slides",
+      "Outro Video Slides", "Load Slides", "Conclusion slides".
+
+    Feedback cells — detected by ``# @title Submit your feedback``:
+      Removed entirely (pure UI widget, no static equivalent).
+    """
+    WIDGET_W = 730
+    WIDGET_H = 410
+
+    def make_iframe(src):
+        return (
+            f'<iframe width="{WIDGET_W}" height="{WIDGET_H}" '
+            f'src="{src}" '
+            f'allowfullscreen="" frameborder="0" '
+            f'allow="autoplay; encrypted-media"></iframe>'
+        )
+
+    new_cells = []
+    for cell in content["cells"]:
+        src = "".join(cell.get("source", []))
+
+        if cell["cell_type"] != "code":
+            new_cells.append(cell)
+            continue
+
+        # --- Feedback cells: remove ---
+        if "# @title Submit your feedback" in src:
+            continue
+
+        # --- Video cells: replace with iframes ---
+        if "display_videos(" in src and "video_ids = [" in src:
+            title_match = re.search(r"#\s*@title\s+(.*)", src)
+            title = title_match.group(1).strip() if title_match else "Video"
+
+            ids_match = re.search(r"video_ids\s*=\s*(\[.*?\])", src)
+            video_ids = []
+            if ids_match:
+                try:
+                    video_ids = ast.literal_eval(ids_match.group(1))
+                except (ValueError, SyntaxError):
+                    pass
+
+            if not video_ids:
+                new_cells.append(cell)
+                continue
+
+            html_parts = [f"<h3>{title}</h3>"]
+            for platform, vid_id in video_ids:
+                if platform == "Youtube":
+                    iframe_src = f"https://www.youtube.com/embed/{vid_id}?fs=1&rel=0"
+                elif platform == "Bilibili":
+                    iframe_src = (
+                        f"https://player.bilibili.com/player.html?bvid={vid_id}&page=1"
+                    )
+                else:
+                    print(
+                        f"  Warning: unknown video platform '{platform}' (id={vid_id}), skipping"
+                    )
+                    continue
+                html_parts.append(f"<p><b>{platform}</b></p>")
+                html_parts.append(make_iframe(iframe_src))
+
+            new_cells.append(
+                {
+                    "cell_type": "markdown",
+                    "metadata": {},
+                    "source": ["\n".join(html_parts)],
+                }
+            )
+            continue
+
+        # --- Slide cells: replace with OSF iframe + download link ---
+        if "link_id" in src and "osf.io" in src:
+            link_id_match = re.search(r'link_id\s*=\s*["\']([^"\']+)["\']', src)
+            if not link_id_match:
+                new_cells.append(cell)
+                continue
+
+            link_id = link_id_match.group(1)
+            download_url = f"https://osf.io/download/{link_id}/"
+            render_url = (
+                f"https://mfr.ca-1.osf.io/render?url=https://osf.io/{link_id}/"
+                f"?direct%26mode=render%26action=download%26mode=render"
+            )
+            new_cells.append(
+                {
+                    "cell_type": "markdown",
+                    "metadata": {},
+                    "source": [
+                        "\n".join(
+                            [
+                                f'<p>If you want to download the slides: <a href="{download_url}">{download_url}</a></p>',
+                                make_iframe(render_url),
+                            ]
+                        )
+                    ],
+                }
+            )
+            continue
+
+        new_cells.append(cell)
+
+    content["cells"] = new_cells
+    return content
+
+
 def tag_cells_allow_errors(content):
     """Add raises-exception tag to every code cell.
 
@@ -334,38 +460,5 @@ def link_hidden_cells(content):
     return content
 
 
-def change_video_widths(content):
-    for cell in content["cells"]:
-        if "YouTubeVideo" in "".join(cell["source"]):
-            for ind in range(len(cell["source"])):
-                cell["source"][ind] = cell["source"][ind].replace("854", "730")
-                cell["source"][ind] = cell["source"][ind].replace("480", "410")
-        if (
-            "# @title Tutorial slides\n" in cell["source"]
-            or "# @title Slides\n" in cell["source"]
-        ):
-            slide_link = ""
-            for line in cell["source"]:
-                if line.startswith("link_id"):
-                    slide_link = line.split('"')[1]
-                    break
-            download_link = f"https://osf.io/download/{slide_link}/"
-            render_link = (
-                f"https://mfr.ca-1.osf.io/render?url=https://osf.io/{slide_link}/"
-                f"?direct%26mode=render%26action=download%26mode=render"
-            )
-            cell["source"] = [
-                "# @markdown\n",
-                "from IPython.display import IFrame\n",
-                "from ipywidgets import widgets\n",
-                "out = widgets.Output()\n",
-                "with out:\n",
-                f'    print(f"If you want to download the slides: {download_link}")\n',
-                f'    display(IFrame(src=f"{render_link}", width=730, height=410))\n',
-                "display(out)",
-            ]
-    return content
-
-
 if __name__ == "__main__":
     main()
diff --git a/parse_html_for_errors_v2.py b/parse_html_for_errors_v2.py
index 6dfb619f4..65640036b 100644
--- a/parse_html_for_errors_v2.py
+++ b/parse_html_for_errors_v2.py
@@ -3,13 +3,16 @@
 Post-process JB2-built HTML to strip error output divs.
 
 JB1 equivalent: nmaci/scripts/parse_html_for_errors.py
-JB2 difference: MyST uses different CSS classes for cell output containers.
+JB2 difference: MyST wraps error output in:
+  <div data-name="outputs-container">
+    <div data-name="safe-output-error">
+      <pre class="myst-jp-error-output">...</pre>
+    </div>
+  </div>
 
-JB1 class:  "cell_output docutils container"
-JB2 classes tried (in order):
-  - "cell_output"           (MyST book-theme)
-  - "output"                (fallback)
-  - any <div> containing the error text (last resort)
+We target the inner div[data-name="safe-output-error"] to detect which
+outputs-container holds an error, then decompose the parent
+div[data-name="outputs-container"] so nothing is left behind.
 
 Run as: python parse_html_for_errors_v2.py student
 """
@@ -80,27 +83,30 @@ def main():
 def strip_error_divs(parsed_html):
     """Remove output divs that contain NotImplementedError or NameError text.
 
-    Tries JB1's class first, then JB2/MyST class names, then a broad sweep.
-    Returns the number of divs removed.
+    JB2/MyST error output structure:
+      <div data-name="outputs-container">
+        <div data-name="safe-output-error">
+          <pre class="myst-jp-error-output">...</pre>
+        </div>
+      </div>
+
+    We find the inner error div, check it contains a known error string, then
+    decompose the parent outputs-container (so no empty wrapper is left).
+    Returns the number of containers removed.
     """
     removed = 0
 
-    # JB1 class (sphinx/docutils)
-    candidates = parsed_html.find_all(
-        "div", {"class": "cell_output docutils container"}
-    )
-
-    # JB2/MyST book-theme output wrapper
-    if not candidates:
-        candidates = parsed_html.find_all("div", {"class": "cell_output"})
-
-    # Broader fallback: any <div> that directly wraps an error traceback
-    if not candidates:
-        candidates = parsed_html.find_all("div", class_=lambda c: c and "output" in c)
-
-    for div in candidates:
-        if any(err in str(div) for err in ERROR_STRINGS):
-            div.decompose()
+    error_divs = parsed_html.find_all("div", attrs={"data-name": "safe-output-error"})
+    for error_div in error_divs:
+        if any(err in str(error_div) for err in ERROR_STRINGS):
+            # Walk up to the outputs-container wrapper and remove the whole thing
+            parent = error_div.find_parent(
+                "div", attrs={"data-name": "outputs-container"}
+            )
+            if parent:
+                parent.decompose()
+            else:
+                error_div.decompose()
             removed += 1
 
     return removed

From b8e231101d96855a5dcee76878b8d850e952f47a Mon Sep 17 00:00:00 2001
From: Konstantine Tsafatinos <kosta.tsaf@gmail.com>
Date: Fri, 20 Mar 2026 13:59:33 -0400
Subject: [PATCH 14/21] Update generate_book_v2 and error parsing v2 to fix
 bugs

---
 generate_book_v2.py | 65 +++++++++++++++++++++++----------------------
 1 file changed, 33 insertions(+), 32 deletions(-)

diff --git a/generate_book_v2.py b/generate_book_v2.py
index de987852d..cbec90bf2 100644
--- a/generate_book_v2.py
+++ b/generate_book_v2.py
@@ -256,27 +256,19 @@ def replace_widgets(content):
     placeholders. This function handles three patterns:
 
     Video cells — detected by ``display_videos(`` + ``video_ids = [``:
-      Replaced with a markdown cell containing YouTube and Bilibili iframes
-      stacked with bold platform labels.
+      Replaced with a markdown cell using MyST {tab-set}/{tab-item}/{iframe}
+      directives, which render natively in JB2.
 
-    Slide cells — detected by ``# @title <slides title>`` + ``link_id``:
-      Replaced with a markdown cell containing the OSF iframe and a download
-      link. Titles matched: "Tutorial slides", "Slides", "Intro Video Slides",
-      "Outro Video Slides", "Load Slides", "Conclusion slides".
+    Slide cells — detected by ``link_id`` + ``osf.io``:
+      Replaced with a markdown cell using the MyST {iframe} directive plus a
+      plain download link.
 
     Feedback cells — detected by ``# @title Submit your feedback``:
       Removed entirely (pure UI widget, no static equivalent).
     """
-    WIDGET_W = 730
-    WIDGET_H = 410
-
-    def make_iframe(src):
-        return (
-            f'<iframe width="{WIDGET_W}" height="{WIDGET_H}" '
-            f'src="{src}" '
-            f'allowfullscreen="" frameborder="0" '
-            f'allow="autoplay; encrypted-media"></iframe>'
-        )
+
+    def make_myst_iframe(url, width="100%"):
+        return f"```{{iframe}} {url}\n:width: {width}\n```"
 
     new_cells = []
     for cell in content["cells"]:
@@ -290,7 +282,7 @@ def make_iframe(src):
         if "# @title Submit your feedback" in src:
             continue
 
-        # --- Video cells: replace with iframes ---
+        # --- Video cells: replace with MyST tab-set + iframes ---
         if "display_videos(" in src and "video_ids = [" in src:
             title_match = re.search(r"#\s*@title\s+(.*)", src)
             title = title_match.group(1).strip() if title_match else "Video"
@@ -307,12 +299,12 @@ def make_iframe(src):
                 new_cells.append(cell)
                 continue
 
-            html_parts = [f"<h3>{title}</h3>"]
+            tab_items = []
             for platform, vid_id in video_ids:
                 if platform == "Youtube":
-                    iframe_src = f"https://www.youtube.com/embed/{vid_id}?fs=1&rel=0"
+                    iframe_url = f"https://www.youtube.com/embed/{vid_id}?fs=1&rel=0"
                 elif platform == "Bilibili":
-                    iframe_src = (
+                    iframe_url = (
                         f"https://player.bilibili.com/player.html?bvid={vid_id}&page=1"
                     )
                 else:
@@ -320,19 +312,29 @@ def make_iframe(src):
                         f"  Warning: unknown video platform '{platform}' (id={vid_id}), skipping"
                     )
                     continue
-                html_parts.append(f"<p><b>{platform}</b></p>")
-                html_parts.append(make_iframe(iframe_src))
+                tab_items.append(
+                    f":::{{tab-item}} {platform}\n{make_myst_iframe(iframe_url)}\n:::"
+                )
+
+            myst_source = "\n\n".join(
+                [
+                    f"**{title}**",
+                    "::::{tab-set}",
+                    "\n".join(tab_items),
+                    "::::",
+                ]
+            )
 
             new_cells.append(
                 {
                     "cell_type": "markdown",
                     "metadata": {},
-                    "source": ["\n".join(html_parts)],
+                    "source": [myst_source],
                 }
             )
             continue
 
-        # --- Slide cells: replace with OSF iframe + download link ---
+        # --- Slide cells: replace with MyST iframe + download link ---
         if "link_id" in src and "osf.io" in src:
             link_id_match = re.search(r'link_id\s*=\s*["\']([^"\']+)["\']', src)
             if not link_id_match:
@@ -345,18 +347,17 @@ def make_iframe(src):
                 f"https://mfr.ca-1.osf.io/render?url=https://osf.io/{link_id}/"
                 f"?direct%26mode=render%26action=download%26mode=render"
             )
+            myst_source = "\n\n".join(
+                [
+                    f"[Download slides]({download_url})",
+                    make_myst_iframe(render_url),
+                ]
+            )
             new_cells.append(
                 {
                     "cell_type": "markdown",
                     "metadata": {},
-                    "source": [
-                        "\n".join(
-                            [
-                                f'<p>If you want to download the slides: <a href="{download_url}">{download_url}</a></p>',
-                                make_iframe(render_url),
-                            ]
-                        )
-                    ],
+                    "source": [myst_source],
                 }
             )
             continue

From 089ce3ef6336ec4637218e68081f3a4db9b52198 Mon Sep 17 00:00:00 2001
From: Konstantine Tsafatinos <kosta.tsaf@gmail.com>
Date: Fri, 20 Mar 2026 21:44:34 -0400
Subject: [PATCH 15/21] Fix Bilibili autoplay and stub-error stripping in JB2
 build

- generate_book_v2.py: add &autoplay=0 to Bilibili iframe URL so the
  player does not autoplay when the tab becomes visible
- parse_html_for_errors_v2.py: rewrite path discovery to walk
  book/_build/html/** instead of reconstructing input-derived paths;
  JB2/MyST flattens output to slug/index.html so the old
  materials.yml-based paths never matched, leaving all stub errors
  visible in the built site
---
 generate_book_v2.py         |  4 +--
 parse_html_for_errors_v2.py | 56 ++++++++++++++-----------------------
 2 files changed, 22 insertions(+), 38 deletions(-)

diff --git a/generate_book_v2.py b/generate_book_v2.py
index cbec90bf2..d31d58502 100644
--- a/generate_book_v2.py
+++ b/generate_book_v2.py
@@ -304,9 +304,7 @@ def make_myst_iframe(url, width="100%"):
                 if platform == "Youtube":
                     iframe_url = f"https://www.youtube.com/embed/{vid_id}?fs=1&rel=0"
                 elif platform == "Bilibili":
-                    iframe_url = (
-                        f"https://player.bilibili.com/player.html?bvid={vid_id}&page=1"
-                    )
+                    iframe_url = f"https://player.bilibili.com/player.html?bvid={vid_id}&page=1&autoplay=0"
                 else:
                     print(
                         f"  Warning: unknown video platform '{platform}' (id={vid_id}), skipping"
diff --git a/parse_html_for_errors_v2.py b/parse_html_for_errors_v2.py
index 65640036b..33e022049 100644
--- a/parse_html_for_errors_v2.py
+++ b/parse_html_for_errors_v2.py
@@ -14,54 +14,39 @@
 outputs-container holds an error, then decompose the parent
 div[data-name="outputs-container"] so nothing is left behind.
 
+JB2/MyST flattens output into slug-based directories rather than mirroring
+the input path structure.  We therefore scan every index.html under the
+build output tree instead of constructing paths from materials.yml.
+
 Run as: python parse_html_for_errors_v2.py student
 """
 
 import os
 import sys
-import yaml
 from bs4 import BeautifulSoup
 
-ARG = sys.argv[1]  # "student" or "instructor"
+sys.argv[1]  # "student" or "instructor" — accepted but not used (kept for compat)
 
 ERROR_STRINGS = ["NotImplementedError", "NameError"]
 
+HTML_ROOT = "book/_build/html"
 
-def main():
-    with open("tutorials/materials.yml") as fh:
-        materials = yaml.load(fh, Loader=yaml.FullLoader)
 
-    html_directory = "book/_build/html/"
+def main():
     total_removed = 0
+    files_touched = 0
 
-    for m in materials:
-        name = f"{m['day']}_{''.join(m['name'].split())}"
-
-        notebook_paths = []
-        if os.path.exists(f"tutorials/{name}/{m['day']}_Intro.ipynb"):
-            notebook_paths.append(
-                f"{html_directory}/tutorials/{name}/{ARG}/{m['day']}_Intro.html"
-            )
-        notebook_paths += [
-            f"{html_directory}/tutorials/{name}/{ARG}/{m['day']}_Tutorial{i + 1}.html"
-            for i in range(m["tutorials"])
-        ]
-        if os.path.exists(f"tutorials/{name}/{m['day']}_Outro.ipynb"):
-            notebook_paths.append(
-                f"{html_directory}/tutorials/{name}/{ARG}/{m['day']}_Outro.html"
-            )
-
-        for html_path in notebook_paths:
-            if not os.path.exists(html_path):
-                print(f"  Warning: {html_path} not found, skipping")
+    for dirpath, _dirnames, filenames in os.walk(HTML_ROOT):
+        for fname in filenames:
+            if fname != "index.html":
                 continue
+            html_path = os.path.join(dirpath, fname)
 
             with open(html_path, encoding="utf-8") as f:
                 contents = f.read()
 
             parsed_html = BeautifulSoup(contents, features="html.parser")
             removed = strip_error_divs(parsed_html)
-            total_removed += removed
 
             # Put solution figures in center (matches JB1 behaviour)
             for img in parsed_html.find_all("img", alt=True):
@@ -69,15 +54,16 @@ def main():
                     img["align"] = "center"
                     img["class"] = "align-center"
 
-            with open(html_path, "w", encoding="utf-8") as f:
-                f.write(str(parsed_html))
-
             if removed:
-                print(
-                    f"  Stripped {removed} error div(s) from {os.path.basename(html_path)}"
-                )
-
-    print(f"Done. Removed {total_removed} error output div(s) total.")
+                total_removed += removed
+                files_touched += 1
+                with open(html_path, "w", encoding="utf-8") as f:
+                    f.write(str(parsed_html))
+                print(f"  Stripped {removed} error div(s) from {html_path}")
+
+    print(
+        f"Done. Removed {total_removed} error output div(s) from {files_touched} file(s)."
+    )
 
 
 def strip_error_divs(parsed_html):

From c8a4ed4873dccf089cbe3ba90462726ecc90124a Mon Sep 17 00:00:00 2001
From: Konstantine Tsafatinos <kosta.tsaf@gmail.com>
Date: Fri, 20 Mar 2026 21:51:58 -0400
Subject: [PATCH 16/21] Add diagnostic output to parse_html_for_errors_v2.py

Print count of index.html files found (or fail fast with clear error
if the HTML root directory doesn't exist) so we can confirm the walk
is finding the right path in CI.
---
 parse_html_for_errors_v2.py | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/parse_html_for_errors_v2.py b/parse_html_for_errors_v2.py
index 33e022049..ea39e79b7 100644
--- a/parse_html_for_errors_v2.py
+++ b/parse_html_for_errors_v2.py
@@ -36,6 +36,19 @@ def main():
     total_removed = 0
     files_touched = 0
 
+    if not os.path.isdir(HTML_ROOT):
+        print(
+            f"ERROR: HTML output directory not found: {HTML_ROOT!r} (cwd={os.getcwd()!r})"
+        )
+        sys.exit(1)
+
+    all_index_files = []
+    for dirpath, _dirnames, filenames in os.walk(HTML_ROOT):
+        for fname in filenames:
+            if fname == "index.html":
+                all_index_files.append(os.path.join(dirpath, fname))
+    print(f"Found {len(all_index_files)} index.html files under {HTML_ROOT}")
+
     for dirpath, _dirnames, filenames in os.walk(HTML_ROOT):
         for fname in filenames:
             if fname != "index.html":

From e76591748147896a04f0f9d6785e9f71354d3755 Mon Sep 17 00:00:00 2001
From: Konstantine Tsafatinos <kosta.tsaf@gmail.com>
Date: Fri, 20 Mar 2026 22:01:55 -0400
Subject: [PATCH 17/21] Fix favicon path and duplicate sidebar nav labels

- generate_book_v2.py: move logo/favicon/logo_text into site.options
  (MyST book-theme requires these as options, not top-level site keys;
  favicon was rendering as /favicon.ico instead of the ai-logo.png)
- schedule_intro.md, tech_intro.md: add short_title: Overview frontmatter
  so sidebar shows 'Overview' instead of 'Schedule'/'Technical Help'
  (which duplicated the parent section folder label)
---
 generate_book_v2.py                   | 8 +++++---
 tutorials/Schedule/schedule_intro.md  | 4 ++++
 tutorials/TechnicalHelp/tech_intro.md | 4 ++++
 3 files changed, 13 insertions(+), 3 deletions(-)

diff --git a/generate_book_v2.py b/generate_book_v2.py
index d31d58502..47885dbec 100644
--- a/generate_book_v2.py
+++ b/generate_book_v2.py
@@ -193,11 +193,13 @@ def main():
         "site": {
             "template": "book-theme",
             "domains": ["neuroai.neuromatch.io"],
-            "logo": "tutorials/static/ai-logo.png",
-            "favicon": "tutorials/static/ai-logo.png",
-            "options": {"logo_text": "Neuromatch Academy: NeuroAI"},
             "nav": [],
             "actions": [{"title": "GitHub", "url": f"https://github.com/{ORG}/{REPO}"}],
+            "options": {
+                "logo": "tutorials/static/ai-logo.png",
+                "favicon": "tutorials/static/ai-logo.png",
+                "logo_text": "Neuromatch Academy: NeuroAI",
+            },
         },
     }
 
diff --git a/tutorials/Schedule/schedule_intro.md b/tutorials/Schedule/schedule_intro.md
index 33e5a3bfd..ad9c3c6ca 100644
--- a/tutorials/Schedule/schedule_intro.md
+++ b/tutorials/Schedule/schedule_intro.md
@@ -1 +1,5 @@
+---
+short_title: Overview
+---
+
 # Schedule
\ No newline at end of file
diff --git a/tutorials/TechnicalHelp/tech_intro.md b/tutorials/TechnicalHelp/tech_intro.md
index 96d4403fb..46fb8bfad 100644
--- a/tutorials/TechnicalHelp/tech_intro.md
+++ b/tutorials/TechnicalHelp/tech_intro.md
@@ -1,3 +1,7 @@
+---
+short_title: Overview
+---
+
 # Technical Help
 
 <img src="chapter_cover.png" alt="Wrench labeled neuromatch on top of a phone" width="100%">

From b7df46f290c4da464a30bd32182fc1db762245ee Mon Sep 17 00:00:00 2001
From: Konstantine Tsafatinos <kosta.tsaf@gmail.com>
Date: Tue, 24 Mar 2026 01:12:08 -0400
Subject: [PATCH 18/21] Fix double title, broken edit link, and stale error
 cache
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

generate_book_v2.py:
- hide_title_block: true — MyST keeps the notebook H1 in the cell body
  for .ipynb files (unlike .md), so the auto-rendered myst-fm-block-title
  appeared as a second identical heading above the article; suppress it
- edit_url: null — auto-computed edit URL gets a spurious book/ prefix
  from the book/tutorials symlink, producing a 404 GitHub path

publish-book-v2.yml:
- Bump cache key from jb2-exec- to jb2-exec-v2- to bust the execution
  cache; prior cached executions predate the raises-exception tagging
  and error-stripping fixes, leaving visible NotImplementedError tracebacks
  on pages that were cache-hit rather than re-executed (W1D2 and others)
---
 .github/workflows/publish-book-v2.yml | 6 +++---
 generate_book_v2.py                   | 2 ++
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/publish-book-v2.yml b/.github/workflows/publish-book-v2.yml
index 361891113..40265e13a 100644
--- a/.github/workflows/publish-book-v2.yml
+++ b/.github/workflows/publish-book-v2.yml
@@ -67,10 +67,10 @@ jobs:
         uses: actions/cache@v4
         with:
           path: book/_build/execute
-          key: jb2-exec-${{ steps.cache-date.outputs.date }}-${{ hashFiles('tutorials/**/*.ipynb', 'requirements.txt') }}
+          key: jb2-exec-v2-${{ steps.cache-date.outputs.date }}-${{ hashFiles('tutorials/**/*.ipynb', 'requirements.txt') }}
           restore-keys: |
-            jb2-exec-${{ steps.cache-date.outputs.date }}-
-            jb2-exec-
+            jb2-exec-v2-${{ steps.cache-date.outputs.date }}-
+            jb2-exec-v2-
 
       - name: Cache MyST theme (avoids re-download on every run)
         uses: actions/cache@v4
diff --git a/generate_book_v2.py b/generate_book_v2.py
index 47885dbec..5525e0e27 100644
--- a/generate_book_v2.py
+++ b/generate_book_v2.py
@@ -188,6 +188,7 @@ def main():
             "title": "Neuromatch Academy: NeuroAI",
             "github": f"https://github.com/{ORG}/{REPO}",
             "license": "CC-BY-4.0",
+            "edit_url": None,  # disable: auto-computed URL gets book/ prefix from symlink
             "toc": toc,
         },
         "site": {
@@ -199,6 +200,7 @@ def main():
                 "logo": "tutorials/static/ai-logo.png",
                 "favicon": "tutorials/static/ai-logo.png",
                 "logo_text": "Neuromatch Academy: NeuroAI",
+                "hide_title_block": True,  # notebook H1 stays in body; suppress duplicate
             },
         },
     }

From 6bc957ea4bc4ae1dff559eb30acde9935aafbfd3 Mon Sep 17 00:00:00 2001
From: Konstantine Tsafatinos <kosta.tsaf@gmail.com>
Date: Tue, 24 Mar 2026 09:56:58 -0400
Subject: [PATCH 19/21] Fix error stripping: target page JSON not static HTML
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

MyST renders pages as a React SPA — the browser ignores the static HTML
and re-renders everything from window.__remixContext, which is populated
from per-page .json files in book/_build/html/.  Stripping the static
index.html had no visible effect.

Rewrite parse_html_for_errors_v2.py to walk every .json page data file,
find 'output' nodes in the mdast tree whose jupyter_data.ename matches
NotImplementedError or NameError, remove them from their parent 'outputs'
node, and drop the 'outputs' node entirely if it becomes empty.
---
 parse_html_for_errors_v2.py | 157 +++++++++++++++++++++---------------
 1 file changed, 92 insertions(+), 65 deletions(-)

diff --git a/parse_html_for_errors_v2.py b/parse_html_for_errors_v2.py
index ea39e79b7..190ca88a2 100644
--- a/parse_html_for_errors_v2.py
+++ b/parse_html_for_errors_v2.py
@@ -1,115 +1,142 @@
 #!/usr/bin/env python3
 """
-Post-process JB2-built HTML to strip error output divs.
+Post-process JB2-built output to strip student exercise error outputs.
 
 JB1 equivalent: nmaci/scripts/parse_html_for_errors.py
-JB2 difference: MyST wraps error output in:
-  <div data-name="outputs-container">
-    <div data-name="safe-output-error">
-      <pre class="myst-jp-error-output">...</pre>
-    </div>
-  </div>
 
-We target the inner div[data-name="safe-output-error"] to detect which
-outputs-container holds an error, then decompose the parent
-div[data-name="outputs-container"] so nothing is left behind.
+JB2/MyST renders pages as a React SPA. The browser ignores the static HTML and
+re-renders everything from window.__remixContext, which is populated from the
+per-page .json files in book/_build/html/.  Stripping the static HTML alone has
+no effect — we must strip the error outputs from the .json mdast trees.
 
-JB2/MyST flattens output into slug-based directories rather than mirroring
-the input path structure.  We therefore scan every index.html under the
-build output tree instead of constructing paths from materials.yml.
+Error output structure in the page JSON (e.g. w1d2-tutorial2.json):
+  mdast.children[N].children[M]  (type='outputs')
+    └── children[K]               (type='output')
+          jupyter_data: {output_type: 'error', ename: 'NotImplementedError', ...}
+
+We walk every .json file, find 'output' nodes whose jupyter_data.ename matches
+our error list, remove them from their parent 'outputs' node, and also remove
+the 'outputs' node entirely if it becomes empty.
 
 Run as: python parse_html_for_errors_v2.py student
 """
 
+import json
 import os
 import sys
-from bs4 import BeautifulSoup
 
 sys.argv[1]  # "student" or "instructor" — accepted but not used (kept for compat)
 
-ERROR_STRINGS = ["NotImplementedError", "NameError"]
+ERROR_NAMES = {"NotImplementedError", "NameError"}
 
 HTML_ROOT = "book/_build/html"
 
 
 def main():
-    total_removed = 0
-    files_touched = 0
-
     if not os.path.isdir(HTML_ROOT):
         print(
             f"ERROR: HTML output directory not found: {HTML_ROOT!r} (cwd={os.getcwd()!r})"
         )
         sys.exit(1)
 
-    all_index_files = []
+    json_files = []
     for dirpath, _dirnames, filenames in os.walk(HTML_ROOT):
         for fname in filenames:
-            if fname == "index.html":
-                all_index_files.append(os.path.join(dirpath, fname))
-    print(f"Found {len(all_index_files)} index.html files under {HTML_ROOT}")
+            # page data files: slug.json (not index.html)
+            if fname.endswith(".json") and fname != "myst.xref.json":
+                json_files.append(os.path.join(dirpath, fname))
 
-    for dirpath, _dirnames, filenames in os.walk(HTML_ROOT):
-        for fname in filenames:
-            if fname != "index.html":
-                continue
-            html_path = os.path.join(dirpath, fname)
+    print(f"Found {len(json_files)} page JSON files under {HTML_ROOT}")
 
-            with open(html_path, encoding="utf-8") as f:
-                contents = f.read()
+    total_removed = 0
+    files_touched = 0
 
-            parsed_html = BeautifulSoup(contents, features="html.parser")
-            removed = strip_error_divs(parsed_html)
+    for json_path in json_files:
+        with open(json_path, encoding="utf-8") as f:
+            try:
+                data = json.load(f)
+            except json.JSONDecodeError:
+                continue
 
-            # Put solution figures in center (matches JB1 behaviour)
-            for img in parsed_html.find_all("img", alt=True):
-                if img["alt"] == "Solution hint":
-                    img["align"] = "center"
-                    img["class"] = "align-center"
+        mdast = data.get("mdast")
+        if not mdast:
+            continue
 
-            if removed:
-                total_removed += removed
-                files_touched += 1
-                with open(html_path, "w", encoding="utf-8") as f:
-                    f.write(str(parsed_html))
-                print(f"  Stripped {removed} error div(s) from {html_path}")
+        removed = strip_error_outputs(mdast)
+
+        if removed:
+            total_removed += removed
+            files_touched += 1
+            with open(json_path, "w", encoding="utf-8") as f:
+                json.dump(data, f, separators=(",", ":"))
+            print(f"  Stripped {removed} error output(s) from {json_path}")
 
     print(
-        f"Done. Removed {total_removed} error output div(s) from {files_touched} file(s)."
+        f"Done. Removed {total_removed} error output(s) from {files_touched} file(s)."
     )
 
 
-def strip_error_divs(parsed_html):
-    """Remove output divs that contain NotImplementedError or NameError text.
+def strip_error_outputs(node):
+    """Recursively walk the mdast tree and remove error output nodes.
 
-    JB2/MyST error output structure:
-      <div data-name="outputs-container">
-        <div data-name="safe-output-error">
-          <pre class="myst-jp-error-output">...</pre>
-        </div>
-      </div>
+    Targets 'outputs' nodes (type='outputs') that contain one or more
+    'output' children with jupyter_data.ename in ERROR_NAMES.
 
-    We find the inner error div, check it contains a known error string, then
-    decompose the parent outputs-container (so no empty wrapper is left).
-    Returns the number of containers removed.
+    Returns count of individual error output nodes removed.
     """
     removed = 0
 
-    error_divs = parsed_html.find_all("div", attrs={"data-name": "safe-output-error"})
-    for error_div in error_divs:
-        if any(err in str(error_div) for err in ERROR_STRINGS):
-            # Walk up to the outputs-container wrapper and remove the whole thing
-            parent = error_div.find_parent(
-                "div", attrs={"data-name": "outputs-container"}
-            )
-            if parent:
-                parent.decompose()
+    if not isinstance(node, dict):
+        return 0
+
+    children = node.get("children")
+    if isinstance(children, list):
+        new_children = []
+        for child in children:
+            if isinstance(child, dict) and child.get("type") == "outputs":
+                # Filter out error outputs from this outputs node
+                kept, n = filter_error_outputs(child)
+                removed += n
+                if kept:  # only keep the outputs node if it still has children
+                    new_children.append(child)
+                # else: drop the now-empty outputs node entirely
             else:
-                error_div.decompose()
-            removed += 1
+                removed += strip_error_outputs(child)
+                new_children.append(child)
+        node["children"] = new_children
 
     return removed
 
 
+def filter_error_outputs(outputs_node):
+    """Remove error output children from an 'outputs' node in-place.
+
+    Returns (has_remaining_children, count_removed).
+    """
+    removed = 0
+    children = outputs_node.get("children", [])
+    new_children = []
+
+    for child in children:
+        if not isinstance(child, dict):
+            new_children.append(child)
+            continue
+        if child.get("type") != "output":
+            new_children.append(child)
+            continue
+        jd = child.get("jupyter_data", {})
+        if (
+            isinstance(jd, dict)
+            and jd.get("output_type") == "error"
+            and jd.get("ename") in ERROR_NAMES
+        ):
+            removed += 1
+        else:
+            new_children.append(child)
+
+    outputs_node["children"] = new_children
+    return bool(new_children), removed
+
+
 if __name__ == "__main__":
     main()

From da1c7168158c503922865dffaa0afea0942fe26e Mon Sep 17 00:00:00 2001
From: Konstantine Tsafatinos <kosta.tsaf@gmail.com>
Date: Tue, 24 Mar 2026 09:57:52 -0400
Subject: [PATCH 20/21] Rename parse_html_for_errors_v2.py ->
 parse_build_for_errors_v2.py
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

The script no longer parses HTML — it strips error outputs from the
JSON build artifacts. Update the filename and all references.
---
 .github/workflows/publish-book-v2.yml                       | 2 +-
 generate_book_v2.py                                         | 2 +-
 parse_html_for_errors_v2.py => parse_build_for_errors_v2.py | 0
 3 files changed, 2 insertions(+), 2 deletions(-)
 rename parse_html_for_errors_v2.py => parse_build_for_errors_v2.py (100%)

diff --git a/.github/workflows/publish-book-v2.yml b/.github/workflows/publish-book-v2.yml
index 40265e13a..1b3c0c20a 100644
--- a/.github/workflows/publish-book-v2.yml
+++ b/.github/workflows/publish-book-v2.yml
@@ -94,7 +94,7 @@ jobs:
           BASE_URL: ${{ env.BASE_URL }}
 
       - name: Strip error output divs from built HTML
-        run: python parse_html_for_errors_v2.py student
+        run: python parse_build_for_errors_v2.py student
 
       - name: Copy CNAME for custom domain
         run: cp CNAME book/_build/html/CNAME
diff --git a/generate_book_v2.py b/generate_book_v2.py
index 5525e0e27..2298c8ea4 100644
--- a/generate_book_v2.py
+++ b/generate_book_v2.py
@@ -380,7 +380,7 @@ def tag_cells_allow_errors(content):
     JB2 has no global allow_errors equivalent, but raises-exception on a cell
     tells MyST to continue executing subsequent cells after an error. We apply
     it to all code cells so that the behaviour matches JB1 exactly. A companion
-    post-processing script (parse_html_for_errors_v2.py) then strips the error
+    post-processing script (parse_build_for_errors_v2.py) then strips the error
     output divs from the built HTML before deployment.
     """
     for cell in content["cells"]:
diff --git a/parse_html_for_errors_v2.py b/parse_build_for_errors_v2.py
similarity index 100%
rename from parse_html_for_errors_v2.py
rename to parse_build_for_errors_v2.py

From 09b37f95ff63edf1d66a20e06c11fb01440f6903 Mon Sep 17 00:00:00 2001
From: Konstantine Tsafatinos <kosta.tsaf@gmail.com>
Date: Sun, 29 Mar 2026 20:11:46 -0400
Subject: [PATCH 21/21] Remove daily survers from outro pages

---
 tutorials/W1D1_Generalization/W1D1_Outro.ipynb   | 14 --------------
 tutorials/W1D2_ComparingTasks/W1D2_Outro.ipynb   | 14 --------------
 .../W1D3_Outro.ipynb                             | 14 --------------
 tutorials/W1D5_Microcircuits/W1D5_Outro.ipynb    | 16 ----------------
 tutorials/W2D1_Macrocircuits/W2D1_Outro.ipynb    | 13 -------------
 .../W2D2_NeuroSymbolicMethods/W2D2_Outro.ipynb   | 13 -------------
 tutorials/W2D3_Microlearning/W2D3_Outro.ipynb    | 13 -------------
 tutorials/W2D4_Macrolearning/W2D4_Outro.ipynb    | 16 ----------------
 tutorials/W2D5_Mysteries/W2D5_Outro.ipynb        | 15 +--------------
 9 files changed, 1 insertion(+), 127 deletions(-)

diff --git a/tutorials/W1D1_Generalization/W1D1_Outro.ipynb b/tutorials/W1D1_Generalization/W1D1_Outro.ipynb
index 5b3870a98..4effe7f6f 100644
--- a/tutorials/W1D1_Generalization/W1D1_Outro.ipynb
+++ b/tutorials/W1D1_Generalization/W1D1_Outro.ipynb
@@ -9,20 +9,6 @@
    "source": [
     "<a href=\"https://colab.research.google.com/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W1D1_Generalization/student/W1D1_Outro.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a> &nbsp; <a href=\"https://kaggle.com/kernels/welcome?src=https://raw.githubusercontent.com/neuromatch/NeuroAI_Course/main/tutorials/W1D1_Generalization/student/W1D1_Outro.ipynb\" target=\"_parent\"><img src=\"https://kaggle.com/static/images/open-in-kaggle.svg\" alt=\"Open in Kaggle\"/></a>"
    ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "246f8d4a-49d5-4938-bcaf-eb975d9e9031",
-   "metadata": {
-    "execution": {}
-   },
-   "source": [
-    "# Daily survey\n",
-    "\n",
-    "Don't forget to complete your reflections and content check in the daily survey! Please be patient after logging in as there is a small delay before you will be redirected to the survey.\n",
-    "\n",
-    "<a href=\"https://portal.neuromatchacademy.org/api/redirect/to/aa2c6cda-2b7e-4607-a5b8-31dbd8c5f8e4\"><img src=\"https://github.com/neuromatch/NeuroAI_Course/blob/main/tutorials/static/button.png?raw=1\" alt=\"button link to survey\" style=\"width:410px\"></a>"
-   ]
   }
  ],
  "metadata": {
diff --git a/tutorials/W1D2_ComparingTasks/W1D2_Outro.ipynb b/tutorials/W1D2_ComparingTasks/W1D2_Outro.ipynb
index 17ead8a6d..3f854128b 100644
--- a/tutorials/W1D2_ComparingTasks/W1D2_Outro.ipynb
+++ b/tutorials/W1D2_ComparingTasks/W1D2_Outro.ipynb
@@ -9,20 +9,6 @@
    "source": [
     "<a href=\"https://colab.research.google.com/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W1D2_ComparingTasks/student/W1D2_Outro.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a> &nbsp; <a href=\"https://kaggle.com/kernels/welcome?src=https://raw.githubusercontent.com/neuromatch/NeuroAI_Course/main/tutorials/W1D2_ComparingTasks/student/W1D2_Outro.ipynb\" target=\"_parent\"><img src=\"https://kaggle.com/static/images/open-in-kaggle.svg\" alt=\"Open in Kaggle\"/></a>"
    ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "246f8d4a-49d5-4938-bcaf-eb975d9e9031",
-   "metadata": {
-    "execution": {}
-   },
-   "source": [
-    "# Daily survey\n",
-    "\n",
-    "Don't forget to complete your reflections and content check in the daily survey! Please be patient after logging in as there is a small delay before you will be redirected to the survey.\n",
-    "\n",
-    "<a href=\"https://portal.neuromatchacademy.org/api/redirect/to/d9c7d186-6de2-48b4-b5e1-26adc39cbf9a\"><img src=\"https://github.com/neuromatch/NeuroAI_Course/blob/main/tutorials/static/button.png?raw=1\" alt=\"button link to survey\" style=\"width:410px\"></a>"
-   ]
   }
  ],
  "metadata": {
diff --git a/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/W1D3_Outro.ipynb b/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/W1D3_Outro.ipynb
index d9d92459f..00d64d055 100644
--- a/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/W1D3_Outro.ipynb
+++ b/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/W1D3_Outro.ipynb
@@ -9,20 +9,6 @@
    "source": [
     "<a href=\"https://colab.research.google.com/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/student/W1D3_Outro.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a> &nbsp; <a href=\"https://kaggle.com/kernels/welcome?src=https://raw.githubusercontent.com/neuromatch/NeuroAI_Course/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/student/W1D3_Outro.ipynb\" target=\"_parent\"><img src=\"https://kaggle.com/static/images/open-in-kaggle.svg\" alt=\"Open in Kaggle\"/></a>"
    ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "22d5410f-0745-4a99-a40f-cd591c3b4d45",
-   "metadata": {
-    "execution": {}
-   },
-   "source": [
-    "# Daily survey\n",
-    "\n",
-    "Don't forget to complete your reflections and content check in the daily survey! Please be patient after logging in as there is a small delay before you will be redirected to the survey.\n",
-    "\n",
-    "<a href=\"https://portal.neuromatchacademy.org/api/redirect/to/09ae0d41-b031-4b73-8685-2a22153a7636\"><img src=\"https://github.com/neuromatch/NeuroAI_Course/blob/main/tutorials/static/button.png?raw=1\" alt=\"button link to survey\" style=\"width:410px\"></a>"
-   ]
   }
  ],
  "metadata": {
diff --git a/tutorials/W1D5_Microcircuits/W1D5_Outro.ipynb b/tutorials/W1D5_Microcircuits/W1D5_Outro.ipynb
index 44c5e1108..7ea02ed74 100644
--- a/tutorials/W1D5_Microcircuits/W1D5_Outro.ipynb
+++ b/tutorials/W1D5_Microcircuits/W1D5_Outro.ipynb
@@ -8,22 +8,6 @@
    "source": [
     "<a href=\"https://colab.research.google.com/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W1D5_Microcircuits/student/W1D5_Outro.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a> &nbsp; <a href=\"https://kaggle.com/kernels/welcome?src=https://raw.githubusercontent.com/neuromatch/NeuroAI_Course/main/tutorials/W1D5_Microcircuits/student/W1D5_Outro.ipynb\" target=\"_parent\"><img src=\"https://kaggle.com/static/images/open-in-kaggle.svg\" alt=\"Open in Kaggle\"/></a>"
    ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {
-    "execution": {},
-    "pycharm": {
-     "name": "#%% md\n"
-    }
-   },
-   "source": [
-    "# Daily survey\n",
-    "\n",
-    "Don't forget to complete your reflections and content check in the daily survey! Please be patient after logging in as there is a small delay before you will be redirected to the survey.\n",
-    "\n",
-    "<a href=\"https://portal.neuromatchacademy.org/api/redirect/to/3a3498fc-3069-471a-a1be-2183de2d04de\"><img src=\"https://github.com/neuromatch/NeuroAI_Course/blob/main/tutorials/static/button.png?raw=1\" alt=\"button link to survey\" style=\"width:410px\"></a>"
-   ]
   }
  ],
  "metadata": {
diff --git a/tutorials/W2D1_Macrocircuits/W2D1_Outro.ipynb b/tutorials/W2D1_Macrocircuits/W2D1_Outro.ipynb
index 26e980072..335ccb6f6 100644
--- a/tutorials/W2D1_Macrocircuits/W2D1_Outro.ipynb
+++ b/tutorials/W2D1_Macrocircuits/W2D1_Outro.ipynb
@@ -8,19 +8,6 @@
    "source": [
     "<a href=\"https://colab.research.google.com/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W2D1_Macrocircuits/student/W2D1_Outro.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a> &nbsp; <a href=\"https://kaggle.com/kernels/welcome?src=https://raw.githubusercontent.com/neuromatch/NeuroAI_Course/main/tutorials/W2D1_Macrocircuits/student/W2D1_Outro.ipynb\" target=\"_parent\"><img src=\"https://kaggle.com/static/images/open-in-kaggle.svg\" alt=\"Open in Kaggle\"/></a>"
    ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {
-    "execution": {}
-   },
-   "source": [
-    "# Daily survey\n",
-    "\n",
-    "Don't forget to complete your reflections and content check in the daily survey! Please be patient after logging in as there is a small delay before you will be redirected to the survey.\n",
-    "\n",
-    "<a href=\"https://portal.neuromatchacademy.org/api/redirect/to/78bb8f0d-d039-4a51-8ba2-b8e0c98b4f47\"><img src=\"https://github.com/neuromatch/NeuroAI_Course/blob/main/tutorials/static/button.png?raw=1\" alt=\"button link to survey\" style=\"width:410px\"></a>"
-   ]
   }
  ],
  "metadata": {
diff --git a/tutorials/W2D2_NeuroSymbolicMethods/W2D2_Outro.ipynb b/tutorials/W2D2_NeuroSymbolicMethods/W2D2_Outro.ipynb
index bf55a7226..7d58174b1 100644
--- a/tutorials/W2D2_NeuroSymbolicMethods/W2D2_Outro.ipynb
+++ b/tutorials/W2D2_NeuroSymbolicMethods/W2D2_Outro.ipynb
@@ -8,19 +8,6 @@
    "source": [
     "<a href=\"https://colab.research.google.com/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W2D2_NeuroSymbolicMethods/student/W2D2_Outro.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a> &nbsp; <a href=\"https://kaggle.com/kernels/welcome?src=https://raw.githubusercontent.com/neuromatch/NeuroAI_Course/main/tutorials/W2D2_NeuroSymbolicMethods/student/W2D2_Outro.ipynb\" target=\"_parent\"><img src=\"https://kaggle.com/static/images/open-in-kaggle.svg\" alt=\"Open in Kaggle\"/></a>"
    ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {
-    "execution": {}
-   },
-   "source": [
-    "# Daily survey\n",
-    "\n",
-    "Don't forget to complete your reflections and content check in the daily survey! Please be patient after logging in as there is a small delay before you will be redirected to the survey.\n",
-    "\n",
-    "<a href=\"https://portal.neuromatchacademy.org/api/redirect/to/98c9ffc6-7a32-4751-a549-d7f4b417d705\"><img src=\"https://github.com/neuromatch/NeuroAI_Course/blob/main/tutorials/static/button.png?raw=1\" alt=\"button link to survey\" style=\"width:410px\"></a>"
-   ]
   }
  ],
  "metadata": {
diff --git a/tutorials/W2D3_Microlearning/W2D3_Outro.ipynb b/tutorials/W2D3_Microlearning/W2D3_Outro.ipynb
index 7b930ef41..02d7916c8 100644
--- a/tutorials/W2D3_Microlearning/W2D3_Outro.ipynb
+++ b/tutorials/W2D3_Microlearning/W2D3_Outro.ipynb
@@ -8,19 +8,6 @@
    "source": [
     "<a href=\"https://colab.research.google.com/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W2D3_Microlearning/student/W2D3_Outro.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a> &nbsp; <a href=\"https://kaggle.com/kernels/welcome?src=https://raw.githubusercontent.com/neuromatch/NeuroAI_Course/main/tutorials/W2D3_Microlearning/student/W2D3_Outro.ipynb\" target=\"_parent\"><img src=\"https://kaggle.com/static/images/open-in-kaggle.svg\" alt=\"Open in Kaggle\"/></a>"
    ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {
-    "execution": {}
-   },
-   "source": [
-    "# Daily survey\n",
-    "\n",
-    "Don't forget to complete your reflections and content check in the daily survey! Please be patient after logging in as there is a small delay before you will be redirected to the survey.\n",
-    "\n",
-    "<a href=\"https://portal.neuromatchacademy.org/api/redirect/to/7a821999-6932-4489-807e-045a1468d82b\"><img src=\"https://github.com/neuromatch/NeuroAI_Course/blob/main/tutorials/static/button.png?raw=1\" alt=\"button link to survey\" style=\"width:410px\"></a>"
-   ]
   }
  ],
  "metadata": {
diff --git a/tutorials/W2D4_Macrolearning/W2D4_Outro.ipynb b/tutorials/W2D4_Macrolearning/W2D4_Outro.ipynb
index 75ce55488..564a39838 100644
--- a/tutorials/W2D4_Macrolearning/W2D4_Outro.ipynb
+++ b/tutorials/W2D4_Macrolearning/W2D4_Outro.ipynb
@@ -8,22 +8,6 @@
    "source": [
     "<a href=\"https://colab.research.google.com/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W2D4_Macrolearning/student/W2D4_Outro.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a> &nbsp; <a href=\"https://kaggle.com/kernels/welcome?src=https://raw.githubusercontent.com/neuromatch/NeuroAI_Course/main/tutorials/W2D4_Macrolearning/student/W2D4_Outro.ipynb\" target=\"_parent\"><img src=\"https://kaggle.com/static/images/open-in-kaggle.svg\" alt=\"Open in Kaggle\"/></a>"
    ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {
-    "execution": {},
-    "pycharm": {
-     "name": "#%% md\n"
-    }
-   },
-   "source": [
-    "# Daily survey\n",
-    "\n",
-    "Don't forget to complete your reflections and content check in the daily survey! Please be patient after logging in as there is a small delay before you will be redirected to the survey.\n",
-    "\n",
-    "<a href=\"https://portal.neuromatchacademy.org/api/redirect/to/792d7a01-70ce-4286-8021-a4435a88843a\"><img src=\"https://github.com/neuromatch/NeuroAI_Course/blob/main/tutorials/static/button.png?raw=1\" alt=\"button link to survey\" style=\"width:410px\"></a>"
-   ]
   }
  ],
  "metadata": {
diff --git a/tutorials/W2D5_Mysteries/W2D5_Outro.ipynb b/tutorials/W2D5_Mysteries/W2D5_Outro.ipynb
index d59b6d1dc..5be6ce97a 100644
--- a/tutorials/W2D5_Mysteries/W2D5_Outro.ipynb
+++ b/tutorials/W2D5_Mysteries/W2D5_Outro.ipynb
@@ -18,7 +18,7 @@
     }
    },
    "source": [
-    "# Outro & Daily survey\n"
+    "# Outro\n"
    ]
   },
   {
@@ -143,19 +143,6 @@
     "    display(IFrame(src=f\"https://mfr.ca-1.osf.io/render?url=https://osf.io/{link_id}/?direct%26mode=render%26action=download%26mode=render\", width=730, height=410))\n",
     "display(out)"
    ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {
-    "execution": {}
-   },
-   "source": [
-    "## Daily survey\n",
-    "\n",
-    "Don't forget to complete your reflections and content check in the daily survey! Please be patient after logging in as there is a small delay before you will be redirected to the survey.\n",
-    "\n",
-    "<a href=\"https://portal.neuromatchacademy.org/api/redirect/to/2dcb767e-470b-4632-a3ac-7cba56d52852\"><img src=\"https://github.com/neuromatch/NeuroAI_Course/blob/main/tutorials/static/button.png?raw=1\" alt=\"button link to survey\" style=\"width:410px\"></a>"
-   ]
   }
  ],
  "metadata": {