Alternative build system to #59

.github/workflows/deploy.yml

@@ -60,17 +60,26 @@ jobs:
       # - name: Build the theme
       #   run: yarn build:theme-prod
 
-      # Build the book
-      - name: Build the book
+      # Build site
+      - name: Build site
         env:
           DISPLAY: ":99.0"
-        run: jupyter-book build .
+        # n = nitpicky (broken links), W = warnings as errors,
+        # T = full tracebacks, keep-going = runt to competion even with errors
+        run: make SPHINXOPTS="-nWT --keep-going" html
 
-      # Deploy the book's HTML to github pages
+      # Upload build artifacts - useful for debugging failed execution
+      - name: Upload build artifacts
+        uses: actions/upload-artifact@v2
+        with:
+          name: html-build-artifact
+          path: _build/html
+
+      # Deploy the site HTML to github pages
       - name: GitHub Pages action
         if: github.repository == 'scikit-image/skimage-tutorials' && github.ref == 'refs/heads/main' && github.event_name == 'push'
         uses: peaceiris/[email protected]
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           publish_dir: ./_build/html
-          cname: scikit-image.org
+          cname: scikit-image.org

.gitignore

@@ -8,4 +8,5 @@ build
 *.pyc
 *~
 *pano-advanced-output.png
-book/lessons
+# Ignore sphinx output
+_build/*

Makefile

@@ -1,41 +1,20 @@
-OBSHELL=/bin/bash
-
-.DEFAULT_GOAL = html
-
-LESSONS_DIR = lessons
-GENERATED_LESSONS_DIR = book/lessons
-
-_requirements.installed:
-	pip install -q -r requirements.txt
-	touch _requirements.installed
-
-MARKDOWNS = $(wildcard $(LESSONS_DIR)/*.md)
-MD_OUTPUTS = $(patsubst $(LESSONS_DIR)/%.md, $(GENERATED_LESSONS_DIR)/%.md, $(MARKDOWNS))
-NOTEBOOKS = $(patsubst %.md, %.ipynb, $(MD_OUTPUTS))
-
-.SECONDARY: $(MD_OUTPUTS) $(NOTEBOOKS)
-
-$(GENERATED_LESSONS_DIR)/%.ipynb:$(LESSONS_DIR)/%.md book/lessons book/lessons/images
-        # This does not work, due to bug in notedown; see https://github.com/aaren/notedown/issues/53
-	#notedown --match=python --precode='%matplotlib inline' $< > $@
-	notedown --match=python $< > $@
-	jupyter nbconvert --execute --inplace $@ --ExecutePreprocessor.timeout=-1
-
-%.md:%.ipynb
-	jupyter nbconvert --to=mdoutput --output="$(notdir $@)" --output-dir=$(GENERATED_LESSONS_DIR) $<
-#	$(eval NBSTRING := [📂 Download lesson notebook](.\/$(basename $(notdir $@)).ipynb)\n\n)
-#	sed -i'.bak' '1s/^/$(NBSTRING)/' $@
-
-
-book/lessons:
-	mkdir -p book/lessons
-
-book/lessons/images:
-	ln -s ${PWD}/lessons/images ${PWD}/book/lessons/images
-
-html: | _requirements.installed $(NOTEBOOKS) $(MD_OUTPUTS)
-	@export SPHINXOPTS=-W; make -C book html
-	cp $(GENERATED_LESSONS_DIR)/*.ipynb book/build/html/lessons/
-
-clean:
-	rm -rf $(GENERATED_LESSONS_DIR)/*
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

applications.md

@@ -0,0 +1,12 @@
+# scikit-image applications
+
+A collection of tutorials highlighting the use of scikit-image for applications in science.
+
+```{toctree}
+---
+maxdepth: 1
+---
+lectures/adv0_chromosomes
+lectures/adv1_lesion-quantification
+lectures/adv2_microarray
+```

conf.py

@@ -0,0 +1,78 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('.'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'scikit-image tutorials'
+copyright = '2021, the scikit-image community'
+author = 'the scikit-image community'
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    "myst_nb",
+    "sphinx_copybutton",
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = [
+    '_build',
+    'Thumbs.db',
+    '.DS_Store',
+    'README.md',
+    'preparation.md',  # TODO: incorporate in the site somewhere?
+    '*/not_yet_booked/*',
+    '*/solutions/*',
+    'workshops/*',
+]
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'sphinx_book_theme'
+html_title = 'scikit-image Tutorials'
+html_logo = '_static/skimage-logo.png'
+html_favicon = '_static/favicon.png'
+tml_theme_options = {
+    "github_url": "https://github.com/scikit-image/skimage-tutorials/",
+    "repository_url": "https://github.com/scikit-image/skimage-tutorials/",
+    "repository_branch": "main",
+    "use_repository_button": True,
+    "use_issues_button": True,
+    "use_edit_page_button": True,
+    "path_to_docs": "site/",
+    "launch_buttons": {
+        "binderhub_url": "https://mybinder.org",
+    },
+}
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']

index.md

@@ -0,0 +1,15 @@
+# scikit-image tutorials
+
+[![Binder](http://mybinder.org/badge_logo.svg)][launch_binder]
+
+[launch_binder]: http://mybinder.org/v2/gh/scikit-image/skimage-tutorials/main?urlpath=lab/tree/content
+
+## Content
+
+```{toctree}
+---
+maxdepth: 2
+---
+introduction
+applications
+```

introduction.md

@@ -0,0 +1,16 @@
+# An introduction to scikit-image
+
+Basic tutorials to prepare you for your journey on scikit-image.
+
+```{toctree}
+---
+maxdepth: 1
+---
+lectures/00_images_are_arrays
+lectures/1_image_filters
+lectures/3_morphological_operations
+lectures/4_segmentation
+lectures/5_tophat_filters
+lectures/6_watershed_tricks
+lectures/three_dimensional_image_processing
+```