Changing the format to Jupyter Book

.codespellignore

@@ -0,0 +1 @@
+SLAC

.github/workflows/deploy.yml

@@ -0,0 +1,52 @@
+name: Deploy Jupyter Book to GitHub Pages
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install dependencies
+        run: pip install -r requirements.txt
+
+      - name: Build static site
+        run: jupyter-book build --html --ci
+        env:
+          BASE_URL: /hsf-training-databases-basics/
+
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: _build/html
+
+  deploy:
+    if: github.event_name == 'push'
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

.gitignore

@@ -1,3 +1,4 @@
 _site
+_build
 .ruby-version
-Gemfile.lock
+Gemfile.lock

Makefile

@@ -1,188 +1,27 @@
 ## ========================================
-## Commands for both workshop and lesson websites.
+## Jupyter Book 2 commands
 
 # Settings
-MAKEFILES=Makefile $(wildcard *.mk)
-JEKYLL=bundle config set --local path .vendor/bundle && bundle install && bundle update && bundle exec jekyll
-PARSER=bin/markdown_ast.rb
-DST=_site
-
-# Find Docker
-DOCKER := $(shell which docker 2>/dev/null)
-
-# Check Python 3 is installed and determine if it's called via python3 or python
-# (https://stackoverflow.com/a/4933395)
-PYTHON3_EXE := $(shell which python3 2>/dev/null)
-ifneq (, $(PYTHON3_EXE))
-  ifeq (,$(findstring Microsoft/WindowsApps/python3,$(subst \,/,$(PYTHON3_EXE))))
-    PYTHON := $(PYTHON3_EXE)
-  endif
-endif
-
-ifeq (,$(PYTHON))
-  PYTHON_EXE := $(shell which python 2>/dev/null)
-  ifneq (, $(PYTHON_EXE))
-    PYTHON_VERSION_FULL := $(wordlist 2,4,$(subst ., ,$(shell python --version 2>&1)))
-    PYTHON_VERSION_MAJOR := $(word 1,${PYTHON_VERSION_FULL})
-    ifeq (3, ${PYTHON_VERSION_MAJOR})
-      PYTHON := $(PYTHON_EXE)
-    else
-      PYTHON_NOTE = "Your system does not appear to have Python 3 installed."
-    endif
-  else
-      PYTHON_NOTE = "Your system does not appear to have any Python installed."
-  endif
-endif
-
+JB = jupyter-book
+DST = _build
 
 # Default target
 .DEFAULT_GOAL := commands
 
-## I. Commands for both workshop and lesson websites
-## =================================================
+.PHONY: jb-build jb-start jb-clean commands
 
-.PHONY: site docker-serve repo-check clean clean-rmd
+## * jb-build          : build Jupyter Book site (HTML)
+jb-build:
+	$(JB) build --html
 
-## * serve            : render website and run a local server
-serve : lesson-md index.md
-	${JEKYLL} serve
+## * jb-start          : start Jupyter Book dev server
+jb-start:
+	$(JB) start
 
-## * site             : build website but do not run a server
-site : lesson-md index.md
-	${JEKYLL} build
-
-## * docker-serve     : use Docker to serve the site
-docker-serve :
-ifeq (, $(DOCKER))
-	$(error Your system does not appear to have Docker installed)
-else
-	@$(DOCKER) pull carpentries/lesson-docker:latest
-	@$(DOCKER) run --rm -it \
-		-v $${PWD}:/home/rstudio \
-		-p 4000:4000 \
-		-p 8787:8787 \
-		-e USERID=$$(id -u) \
-		-e GROUPID=$$(id -g) \
-		carpentries/lesson-docker:latest
-endif
-
-## * repo-check       : check repository settings
-repo-check : python
-	@${PYTHON} bin/repo_check.py -s .
-
-## * clean            : clean up junk files
-clean :
+## * jb-clean          : clean Jupyter Book build artifacts
+jb-clean:
 	@rm -rf ${DST}
-	@rm -rf .sass-cache
-	@rm -rf bin/__pycache__
-	@rm -rf .vendor
-	@rm -rf .bundle
-	@rm -f Gemfile.lock
-	@find . -name .DS_Store -exec rm {} \;
-	@find . -name '*~' -exec rm {} \;
-	@find . -name '*.pyc' -exec rm {} \;
-
-## * clean-rmd        : clean intermediate R files (that need to be committed to the repo)
-clean-rmd :
-	@rm -rf ${RMD_DST}
-	@rm -rf fig/rmd-*
-
-
-##
-## II. Commands specific to workshop websites
-## =================================================
-
-.PHONY : workshop-check
-
-## * workshop-check   : check workshop homepage
-workshop-check : python
-	@${PYTHON} bin/workshop_check.py .
-
-
-##
-## III. Commands specific to lesson websites
-## =================================================
-
-.PHONY : lesson-check lesson-md lesson-files lesson-fixme install-rmd-deps
 
-# RMarkdown files
-RMD_SRC = $(wildcard _episodes_rmd/*.Rmd)
-RMD_DST = $(patsubst _episodes_rmd/%.Rmd,_episodes/%.md,$(RMD_SRC))
-
-# Lesson source files in the order they appear in the navigation menu.
-MARKDOWN_SRC = \
-  index.md \
-  CODE_OF_CONDUCT.md \
-  setup.md \
-  $(sort $(wildcard _episodes/*.md)) \
-  reference.md \
-  $(sort $(wildcard _extras/*.md)) \
-  LICENSE.md
-
-# Generated lesson files in the order they appear in the navigation menu.
-HTML_DST = \
-  ${DST}/index.html \
-  ${DST}/conduct/index.html \
-  ${DST}/setup/index.html \
-  $(patsubst _episodes/%.md,${DST}/%/index.html,$(sort $(wildcard _episodes/*.md))) \
-  ${DST}/reference.html \
-  $(patsubst _extras/%.md,${DST}/%/index.html,$(sort $(wildcard _extras/*.md))) \
-  ${DST}/license/index.html
-
-## * install-rmd-deps : Install R packages dependencies to build the RMarkdown lesson
-install-rmd-deps:
-	@${SHELL} bin/install_r_deps.sh
-
-## * lesson-md        : convert Rmarkdown files to markdown
-lesson-md : ${RMD_DST}
-
-_episodes/%.md: _episodes_rmd/%.Rmd install-rmd-deps
-	@mkdir -p _episodes
-	@$(SHELL) bin/knit_lessons.sh $< $@
-
-## * lesson-check     : validate lesson Markdown
-lesson-check : python lesson-fixme
-	@${PYTHON} bin/lesson_check.py -s . -p ${PARSER} -r _includes/links.md
-
-## * lesson-check-all : validate lesson Markdown, checking line lengths and trailing whitespace
-lesson-check-all : python
-	@${PYTHON} bin/lesson_check.py -s . -p ${PARSER} -r _includes/links.md -l -w --permissive
-
-## * unittest         : run unit tests on checking tools
-unittest : python
-	@${PYTHON} bin/test_lesson_check.py
-
-## * lesson-files     : show expected names of generated files for debugging
-lesson-files :
-	@echo 'RMD_SRC:' ${RMD_SRC}
-	@echo 'RMD_DST:' ${RMD_DST}
-	@echo 'MARKDOWN_SRC:' ${MARKDOWN_SRC}
-	@echo 'HTML_DST:' ${HTML_DST}
-
-## * lesson-fixme     : show FIXME markers embedded in source files
-lesson-fixme :
-	@grep --fixed-strings --word-regexp --line-number --no-messages FIXME ${MARKDOWN_SRC} || true
-
-##
-## IV. Auxililary (plumbing) commands
-## =================================================
-
-.PHONY : commands python
-
-## * commands         : show all commands.
-commands :
+## * commands          : show all commands.
+commands:
 	@sed -n -e '/^##/s|^##[[:space:]]*||p' $(MAKEFILE_LIST)
-
-python :
-ifeq (, $(PYTHON))
-	$(error $(PYTHON_NOTE))
-else
-	@:
-endif
-
-index.md :
-ifeq (, $(wildcard index.md))
-	$(error index.md not found)
-else
-	@:
-endif

README.md

@@ -39,15 +39,20 @@ We'd like to ask you to familiarize yourself with our [Contribution Guide](CONTR
 the [more detailed guidelines][lesson-example] on proper formatting, ways to render the lesson locally, and even
 how to write new episodes.
 
-Quick summary of how to get a local preview: Install [jekyll][jekyll] and then run
+Quick summary of how to get a local preview: Install [Jupyter Book][jupyter-book] and then run
 
+```bash
+pip install -r requirements.txt
+jupyter-book start
 ```
-bundle install
-bundle update
-bundle exec jekyll serve
-```
 
-Unless we change framework versions, only the last command needs to be typed after the first time.
+This will build the site and start a local server (default port 3000). Open `http://localhost:3000` in your browser.
+
+To build static HTML without starting a server:
+
+```bash
+jupyter-book build --html
+```
 
 Before committing anything, we also ask you to install the [pre-commit][pre-commit] hooks of this repository:
 
@@ -108,7 +113,7 @@ Instead, all regular contributors are listed on our [HSF Training Community page
 [schools]: https://hepsoftwarefoundation.org/Schools/events.html
 [issues]: https://github.com/hsf-training/hsf-training-databases-basics/issues
 [progit]: http://git-scm.com/book/en/v2/GitHub-Contributing-to-a-Project
-[jekyll]: https://jekyllrb.com/
+[jupyter-book]: https://jupyterbook.org/
 [allcontrib-emoji-key]: https://allcontributors.org/docs/en/emoji-key
 [gfi-badge]: https://img.shields.io/badge/-good%20first%20issue-gold.svg
 [schools-badge]: https://img.shields.io/badge/upcoming%20events-browse-ff69b4