Fix Python linting issues and clean up obsolete files

Python code changes:
- Convert Python 2 print statements to Python 3 print() functions
- Fix syntax errors from incorrect backslash continuations
- Sort imports with isort (black profile)
- Preserve skeleton/exercise code as comments rather than fixing

Linting configuration:
- Add comprehensive ruff configuration in pyproject.toml with ignores for
  educational code patterns (star imports, single-letter variables, etc.)
- Add isort configuration with black profile
- Disable flake8 in pre-commit (redundant with ruff)
- Add markdownlint configuration (.markdownlint.yaml)
- Add markdownlint ignore file for build outputs

Cleanup:
- Remove reveal.js directories (no longer needed after slides removed)
- Remove obsolete slide HTML files
- Remove doc/Trash directory

Author: ggorman

.markdownlint.yaml

@@ -0,0 +1,28 @@
+# 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
+
+# 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 +1,5 @@
+# Vendored third-party libraries
+**/node_modules/
+
+# Build outputs
+doc/pub/

.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]

README.md

@@ -135,7 +135,7 @@ bash make.sh
 
 ## Directory Structure
 
-```
+```text
 devito_book/
 ├── src/                      # Source code for book examples
 │   └── X/                    # Source code from chapter X
@@ -185,6 +185,7 @@ The build script automatically fixes encoding issues by converting from `utf8x`
 ### Build Logs
 
 Check these files for detailed error information:
+
 - `book.log` - LaTeX compilation log
 - `book.dlog` - DocOnce processing log
 
@@ -210,5 +211,6 @@ This work is licensed under [CC BY-NC 4.0](https://creativecommons.org/licenses/
 ## Acknowledgments
 
 This book is part of a series on computational science. See also:
+
 - [A Primer on Scientific Programming with Python](https://github.com/hplgit/primer)
 - [Scaling of Differential Equations](https://github.com/hplgit/scaling-book)

doc/.src/book/scripts.py

@@ -1,9 +1,13 @@
-import sys, re, os, shutil, glob
+import glob
+import os
+import re
+import shutil
+import sys
 
-chapters = "vib wave diffu trunc nonlin advec softeng2 formulas".split()
+chapters = ["vib", "wave", "diffu", "trunc", "nonlin", "advec", "softeng2", "formulas"]
 chaptersdir = 'chapters'
 
-ignored_files = '*.o *.so *.a *.pyc *.bak *.swp *~ .*~ *.old tmp* temp* .#* \\#* *.log *.dvi *.aux *.blg *.idx *.nav *.out *.toc *.snm *.vrb *.cproject *.project .DS_Store Trash'.split()
+ignored_files = ['*.o', '*.so', '*.a', '*.pyc', '*.bak', '*.swp', '*~', '.*~', '*.old', 'tmp*', 'temp*', '.#*', '\\#*', '*.log', '*.dvi', '*.aux', '*.blg', '*.idx', '*.nav', '*.out', '*.toc', '*.snm', '*.vrb', '*.cproject', '*.project', '.DS_Store', 'Trash']
 
 def chapter_visitor(action=None, chapters=chapters):
     """Visit dirs in chapters and call/perform action."""
@@ -13,10 +17,11 @@ def chapter_visitor(action=None, chapters=chapters):
         # Wrap Unix commands and run
         def action_function():
             for command in action:
-                print command
+                print(command)
                 failure = os.system(command)
                 if failure:
-                    print 'failure in execution...'; sys.exit(1)
+                    print('failure in execution...')
+                    sys.exit(1)
     elif callable(action):
         action_function = action
 
@@ -25,12 +30,12 @@ def action_function():
     for chapter in chapters:
         destination = os.path.join(prefix, chapter)
         if os.path.isdir(destination):
-            print 'visiting directory', destination
+            print('visiting directory', destination)
             os.chdir(destination)
             action_function()
             os.chdir(thisdir)
         else:
-            print '\n*** error: directory %s does not exist!' % destination
+            print('\n*** error: directory %s does not exist!' % destination)
             sys.exit(1)
 
 
@@ -60,13 +65,13 @@ def make_links(chapters=chapters):
     prefix = os.path.join(os.pardir, chaptersdir)
     for chapter in chapters:
         destination = os.path.join(prefix, chapter)
-        subdirs = [tp + '-' + chapter for tp in 'fig', 'src', 'mov', 'exer']
+        subdirs = [tp + '-' + chapter for tp in ('fig', 'src', 'mov', 'exer')]
         for subdir in subdirs:
             if not os.path.islink(subdir):
                 dest_subdir = os.path.join(destination, subdir)
                 if os.path.isdir(dest_subdir):
                     os.symlink(dest_subdir, subdir)
-                    print 'created local link %s to %s' % (subdir, destination)
+                    print('created local link %s to %s' % (subdir, destination))
 
     # Sometimes manual additions are needed here, e.g.,
     #os.symlink(os.path.join(prefix, 'tech', 'fig2'), 'fig2')
@@ -97,14 +102,14 @@ def pack_src(root='src', tarfile='book-examples.tar.gz', chapters=chapters):
             for file_spec in ignored_files:
                 for filename in glob.glob(file_spec):
                     os.remove(filename)
-                    print 'removed', 'src-%s/%s' % (chapter, filename)
+                    print('removed', 'src-%s/%s' % (chapter, filename))
             os.chdir(thisdir)
         # Copy files
         shutil.copytree(destination, chapter)
-    print '\ndirectory tree with source code files for the book:', root
+    print('\ndirectory tree with source code files for the book:', root)
     os.chdir(os.pardir)
     os.system('tar czf %s %s' % (tarfile, root))
-    print 'tarfile:', tarfile
+    print('tarfile:', tarfile)
 
 def externaldocuments():
     # Find all candidate documents in ../chapters/*
@@ -124,13 +129,13 @@ def externaldocuments():
         other_mainfiles.remove(mainfile)
         # Strip off ../chapters to ../
         other_mainfiles = ['../' + mainfile[12:] for mainfile in mainfiles]
-        f = open(mainfile + '.do.txt', 'r')
+        f = open(mainfile + '.do.txt')
         text = f.read()
         f.close()
         text = re.sub('^# Externaldocuments:.*', '# Externaldocuments: ' +
                       ', '.join(other_mainfiles), text, flags=re.MULTILINE)
-        print 'subst in', mainfile
+        print('subst in', mainfile)
         f = open(mainfile + '.do.txt', 'w')
         f.write(text)
         f.close()
-        print 'updated # Externaldocuments in', mainfile, 'with\n   ', ', '.join(other_mainfiles)
+        print('updated # Externaldocuments in', mainfile, 'with\n   ', ', '.join(other_mainfiles))