Convert to Quatro formatted book; update for Python 3.10; dropping some features/modules that are hard to maintain.

.github/workflows/build.yml

@@ -0,0 +1,96 @@
+name: Build Book PDF
+
+on:
+  push:
+    branches: [main, master, maximum-effort]
+  pull_request:
+    branches: [main, master]
+  workflow_dispatch:  # Allow manual triggers
+
+jobs:
+  build-pdf:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+          cache: 'pip'
+
+      - name: Install Quarto
+        uses: quarto-dev/quarto-actions/setup@v2
+        with:
+          version: '1.6.40'
+
+      - name: Install TeX Live
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y --no-install-recommends \
+            texlive-latex-base \
+            texlive-latex-recommended \
+            texlive-latex-extra \
+            texlive-fonts-recommended \
+            texlive-fonts-extra \
+            texlive-science \
+            texlive-pictures \
+            texlive-bibtex-extra \
+            texlive-plain-generic \
+            lmodern \
+            biber \
+            latexmk \
+            cm-super \
+            dvipng \
+            ghostscript
+
+      - name: Install Python dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install numpy scipy matplotlib sympy
+
+      - name: Verify installations
+        run: |
+          echo "=== Quarto version ==="
+          quarto --version
+          echo ""
+          echo "=== Python packages ==="
+          pip list | grep -E "numpy|scipy|matplotlib|sympy"
+          echo ""
+          echo "=== LaTeX version ==="
+          pdflatex --version | head -2
+
+      - name: Build book PDF with Quarto
+        run: |
+          quarto render --to pdf
+
+      - name: Verify PDF was created
+        run: |
+          if [ -f _book/Finite-Difference-Computing-with-PDEs.pdf ]; then
+            echo "PDF successfully created!"
+            ls -lh _book/Finite-Difference-Computing-with-PDEs.pdf
+          else
+            echo "ERROR: PDF was not created"
+            echo "Contents of _book directory:"
+            ls -la _book/ || echo "_book directory does not exist"
+            exit 1
+          fi
+
+      - name: Upload PDF artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: fdm-book-pdf
+          path: _book/Finite-Difference-Computing-with-PDEs.pdf
+          retention-days: 30
+
+      - name: Upload build logs on failure
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: build-logs
+          path: |
+            _book/*.log
+            _book/*.tex
+          retention-days: 7

.gitignore

@@ -3,13 +3,22 @@ syntax: glob
 *.o
 *.so
 *.a
+# Python:
+venv/
+.venv/
+__pycache__/
+*.py[cod]
+*.egg-info/
+dist/
+build/
+.eggs/
 # temporary files:
-build
 *.bak
 *.swp
 *~
 .*~
 *.old
+*.old~~
 tmp*
 temp*
 .#*
@@ -43,3 +52,22 @@ _minted-*
 .*.copyright
 sphinx-rootdir
 Trash
+# Generated/published content (regenerated by build scripts):
+doc/pub/
+
+# Generated LaTeX files (in doc/.src/book/):
+book.tex
+book.pdf
+book.dlog
+latex_figs/
+svmonodo.cls
+t4do.sty
+newcommands_keep.tex
+tmp_mako__*.do.txt
+tmp_preprocess__*.do.txt
+# Test files:
+title_test.*
+
+/.quarto/
+/_book/
+**/*.quarto_ipynb

.markdownlint-cli2.yaml

@@ -0,0 +1,5 @@
+# markdownlint-cli2 configuration
+# Include both .md and .qmd files for Quarto support
+globs:
+  - "**/*.md"
+  - "**/*.qmd"

.markdownlint.yaml

@@ -0,0 +1,71 @@
+# markdownlint configuration
+# See https://github.com/DavidAnson/markdownlint/blob/main/doc/Rules.md
+
+# MD013 - Line length (disabled - documentation often has long lines)
+MD013: false
+
+# MD024 - Multiple headings with the same content (allowed for books)
+MD024: false
+
+# MD033 - Inline HTML (allowed)
+MD033: false
+
+# MD041 - First line should be a top-level heading (disabled for partial files)
+MD041: false
+
+# MD046 - Code block style (allow both fenced and indented)
+MD046: false
+
+# Rules disabled for LaTeX/math-heavy QMD files
+# MD010 - Hard tabs (often in raw LaTeX)
+MD010: false
+
+# MD037 - Spaces inside emphasis (false positives from *u* in math)
+MD037: false
+
+# MD040 - Fenced code language ({=latex} not recognized)
+MD040: false
+
+# MD049 - Emphasis style (underscores common in math)
+MD049: false
+
+# MD050 - Strong style (similar issue)
+MD050: false
+
+# MD011 - Reversed link syntax (false positives from math like [D^{2x}])
+MD011: false
+
+# MD032 - Blanks around lists (false positives from + in equations)
+MD032: false
+
+# MD003 - Heading style (false positives from = in LaTeX equations)
+MD003: false
+
+# MD025 - Multiple H1 headings (Quarto books have multiple titled sections)
+MD025: false
+
+# MD001 - Heading increment (Quarto YAML title acts as H1, sections may start at H3)
+MD001: false
+
+# MD022 - Blanks around headings (false positives from LaTeX arrays/matrices)
+MD022: false
+
+# MD012 - Multiple consecutive blank lines (false positives in Python code blocks with PEP8 style)
+MD012: false
+
+# MD004 - Unordered list style (allow both dash and plus - converted from DocOnce)
+MD004: false
+
+# MD031 - Blanks around fences (false positives in nested documentation examples)
+MD031: false
+
+# MD007 - Unordered list indentation
+MD007:
+  indent: 2
+
+# MD029 - Ordered list item prefix (allow any number)
+MD029:
+  style: "one_or_ordered"
+
+# MD060 - Table column style (disabled - formatting is matter of preference)
+MD060: false

.markdownlintignore

@@ -0,0 +1,10 @@
+# Vendored third-party libraries
+**/node_modules/
+
+# Build outputs
+doc/pub/
+_book/
+
+# Virtual environments
+venv/
+.venv/

.pre-commit-config.yaml

@@ -0,0 +1,81 @@
+# See https://pre-commit.com for more information
+default_stages: [pre-commit]
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-added-large-files
+  - repo: https://github.com/pycqa/isort
+    rev: 7.0.0
+    hooks:
+      # Run isort to check only (don't modify files)
+      - id: isort
+        name: "Check imports are sorted"
+        args: [--check-only, --filter-files]
+        stages: [pre-commit]
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.14.14
+    hooks:
+      # Run the linter to check only (don't modify files)
+      - id: ruff-check
+        name: "Check code is linted with ruff"
+  # Disabled flake8 - ruff covers the same checks with better performance
+  # - repo: https://github.com/PyCQA/flake8
+  #   rev: 7.3.0
+  #   hooks:
+  #     - id: flake8
+  #       name: "Check code is linted with flake8"
+  #       additional_dependencies: [flake8-pyproject]
+  - repo: https://github.com/crate-ci/typos
+    rev: v1.33.1
+    hooks:
+      - id: typos
+        name: "Check files for typos"
+        stages: [pre-commit]
+  - repo: https://github.com/DavidAnson/markdownlint-cli2
+    rev: v0.20.0
+    hooks:
+      - id: markdownlint-cli2
+        name: "Check markdown files"
+        stages: [pre-commit]
+  #
+  # These stages modify the files applying fixes where possible
+  # Since this may be undesirable they will not run automatically
+  # These stages can be run with
+  # pre-commit run --hook-stage manual
+  #
+  - repo: https://github.com/pycqa/isort
+    rev: 7.0.0
+    hooks:
+      # Run isort to check only (don't modify files)
+      - id: isort
+        name: "Fix imports with isort"
+        args: [--filter-files]
+        stages: [manual]
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.14.14
+    hooks:
+      # Run the linter to check only (don't modify files)
+      - id: ruff-check
+        name: "Fix linting errors with ruff check --fix"
+        args: [--fix]
+        stages: [manual]
+  - repo: https://github.com/crate-ci/typos
+    rev: v1.33.1
+    hooks:
+      - id: typos
+        name: "Fix typos"
+        args: [-w]
+        stages: [manual]
+  - repo: https://github.com/DavidAnson/markdownlint-cli2
+    rev: v0.20.0
+    hooks:
+      - id: markdownlint-cli2
+        name: "Fix markdown files"
+        args: [--fix]
+        stages: [manual]

.typos.toml

@@ -0,0 +1,5 @@
+[default.extend-words]
+# Vietnamese name (Thanh-Ha Le Thi)
+Thi = "Thi"
+# Equation label suffix (exact solution "u_e")
+ue = "ue"