ENH: Build/tooling housecleaning ahead of FEM removal and ITKv6 content updates

.github/workflows/build.yml

@@ -1,62 +1,47 @@
 name: Build
 
-on: [push,pull_request]
+on: [push, pull_request]
 
 env:
-  LC_ALL: en_US.UTF-8
-  LANG: en_US.UTF-8
-  LANGUAGE: en_US.UTF-8
+  # C.UTF-8 is always available without locale-gen and keeps LaTeX byte-clean.
+  LC_ALL: C.UTF-8
+  LANG: C.UTF-8
 
 jobs:
   build-publish-pdf:
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-latest
 
     steps:
     - uses: actions/checkout@v4
 
-    - name: Set up Python 3.9
-      uses: actions/setup-python@v5
-      with:
-        python-version: 3.9
-
-    - name: Install build dependencies
+    # System TeX: conda-forge texlive-core is engine-only, so a real LaTeX
+    # distribution comes from apt. ghostscript, ImageMagick 7, Pygments, cmake
+    # and ninja are provided by the pixi 'build' environment.
+    - name: Install system TeX
       run: |
-        sudo apt-get update && sudo apt-get install -y \
-          apt-utils \
-          build-essential \
-          ccache \
-          cmake \
-          curl \
-          git \
-          ninja-build \
-          python3
-        # Using --no-install-recommends greatly reduces the installed packages
+        sudo apt-get update
         sudo apt-get install -y --no-install-recommends \
           texlive-latex-base \
-          texlive-latex-extra
-        sudo apt-get install -y \
-          dvipng \
-          ghostscript \
-          locales \
-          imagemagick \
-          python3 \
-          python3-pygments \
+          texlive-latex-extra \
           texlive-latex-recommended \
-          tex4ht \
-          texlive-fonts-recommended
-        sudo echo "en_US.UTF-8 UTF-8" > /etc/locale.gen && \
-            sudo locale-gen
-        sudo sed -i 's/none/read|write/' /etc/ImageMagick-6/policy.xml
+          texlive-fonts-recommended \
+          dvipng \
+          tex4ht
         sudo apt-get clean
 
-    - name: Build
+    - name: Set up pixi
+      uses: prefix-dev/setup-pixi@v0.9.6
+      with:
+        environments: build
+        cache: true
+
+    - name: Build the Software Guide
+      run: pixi run build
+
+    - name: Collect PDFs
       run: |
-        mkdir build
-        cd build
-        cmake -GNinja -DCMAKE_BUILD_TYPE=MinSizeRel -DSuperBuild_ITKSoftwareGuide_USE_GIT_PROTOCOL:BOOL=OFF ..
-        ninja
-        cp ./ITKSoftwareGuide-build/SoftwareGuide/Latex/ITKSoftwareGuide-Book1.pdf ../InsightSoftwareGuide-Book1.pdf
-        cp ./ITKSoftwareGuide-build/SoftwareGuide/Latex/ITKSoftwareGuide-Book2.pdf ../InsightSoftwareGuide-Book2.pdf
+        cp build/ITKSoftwareGuide-build/SoftwareGuide/Latex/ITKSoftwareGuide-Book1.pdf InsightSoftwareGuide-Book1.pdf
+        cp build/ITKSoftwareGuide-build/SoftwareGuide/Latex/ITKSoftwareGuide-Book2.pdf InsightSoftwareGuide-Book2.pdf
 
     - name: Publish ITK Software Guide Book 1 artifact
       uses: actions/upload-artifact@v4

.gitignore

@@ -1 +1,2 @@
 /Utilities/.chktexrc
+.pixi/

.pre-commit-config.yaml

@@ -0,0 +1,37 @@
+# .pre-commit-config.yaml
+# See https://pre-commit.com ; install with: pixi run -e pre-commit pre-commit-install
+# Skip a hook for one commit with: SKIP=<id> git commit ...
+
+default_stages: [pre-commit]
+exclude: '^(XFigOriginals/|.*/Art/|.*\.(eps|fig|dia|gnup|jpg|jpeg|png|pdf))$'
+
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v5.0.0
+  hooks:
+   - id: trailing-whitespace
+   - id: end-of-file-fixer
+   - id: check-added-large-files
+     args: ['--maxkb=1024']
+   - id: check-merge-conflict
+   - id: check-case-conflict
+   - id: mixed-line-ending
+
+- repo: local
+  hooks:
+   # LaTeX lint (advisory) — migrated from Utilities/latex_linter.sh.
+   # Runs per staged .tex file; prints findings but never blocks the commit.
+   - id: chktex
+     name: 'chktex (LaTeX lint, advisory)'
+     entry: Utilities/Hooks/chktex-lint.sh
+     language: system
+     files: '\.tex$'
+     verbose: true
+
+   # Enforce the ITK commit-message prefix (BUG:/COMP:/DOC:/ENH:/PERF:/STYLE:/WIP:).
+   # Reuses the authoritative native hook so the rule lives in one place.
+   - id: commit-prefix
+     name: 'commit message prefix'
+     entry: Utilities/Hooks/commit-msg
+     language: system
+     stages: [commit-msg]

Common.cmake

@@ -32,23 +32,6 @@ set(CMAKE_MODULE_PATH
 include(PreventInSourceBuilds)
 include(PreventInBuildInstalls)
 
-#-----------------------------------------------------------------------------
-# Platform check
-#-----------------------------------------------------------------------------
-set(PLATFORM_CHECK true)
-if(PLATFORM_CHECK)
-  # See CMake/Modules/Platform/Darwin.cmake)
-  #   6.x == Mac OSX 10.2 (Jaguar)
-  #   7.x == Mac OSX 10.3 (Panther)
-  #   8.x == Mac OSX 10.4 (Tiger)
-  #   9.x == Mac OSX 10.5 (Leopard)
-  #  10.x == Mac OSX 10.6 (Snow Leopard)
-  if (DARWIN_MAJOR_VERSION LESS "9")
-    message(FATAL_ERROR "Only Mac OSX >= 10.5 are supported !")
-  endif()
-endif()
-
-
 #-----------------------------------------------------------------------------
 if(NOT COMMAND SETIFEMPTY)
   macro(SETIFEMPTY)
@@ -93,4 +76,3 @@ if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
     set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fPIC")
   endif()
 endif()
-

ITKSoftwareGuide.cmake

@@ -11,7 +11,7 @@ set(CMAKE_MODULE_PATH
   )
 
 #-----------------------------------------------------------------------------
-set(MINIMUM_ITK_VERSION 5)
+set(MINIMUM_ITK_VERSION 6)
 find_package(ITK ${MINIMUM_ITK_VERSION} REQUIRED)
 if(Slicer_BUILD_${PROJECT_NAME})
   set(ITK_NO_IO_FACTORY_REGISTER_MANAGER 1) # Incorporate with Slicer nicely

SoftwareGuide/Art/CMakeLists.txt

@@ -9,10 +9,9 @@
 file(GLOB PNGandJPG_IMAGES *.jpg *.png)
 file(GLOB EPS_IMAGES *.eps)
 
-find_package(ImageMagick 6 COMPONENTS convert REQUIRED)
-if(NOT ImageMagick_convert_EXECUTABLE)
-  message("ImageMagick convert utility was not found. Please pass to advanced mode and provide its full path")
-endif()
+# ImageMagick 7: resolve the unified 'magick' driver. Its 'convert' subcommand
+# accepts the legacy operator-before-input ordering (e.g. -flip) used below.
+find_program(ImageMagick_convert_EXECUTABLE NAMES magick REQUIRED)
 # Convert an image from some file format to EPS for inclusion in Latex using
 # ImageMagick. This image is an input image. A separate macro is necessary
 # because input images do not have any dependencies
@@ -30,7 +29,7 @@ foreach(ImageFile ${PNGandJPG_IMAGES})
   set(OutputEPSFile "${OutputEPSFilePath}/${ImageFileNoExt}.eps")
   add_custom_command(
     OUTPUT    ${OutputEPSFile}
-    COMMAND   ${ImageMagick_convert_EXECUTABLE}
+    COMMAND   ${ImageMagick_convert_EXECUTABLE} convert
               ${EPS_INPUT_CONVERT_FLAGS}
               ${ImageFile}
               ${EPS_OUTPUT_CONVERT_FLAGS}

SoftwareGuide/CMakeLists.txt

@@ -25,13 +25,12 @@
 # in PNG/XFIG/JPEG/EPS format.
 #
 cmake_minimum_required(VERSION 3.22.1 FATAL_ERROR)
-cmake_policy(VERSION 3.22.1)
 
 project(SoftwareGuide C)
 
 set(CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/CMake ${CMAKE_MODULE_PATH})
 
-find_package(ITK 5 REQUIRED)
+find_package(ITK 6 REQUIRED)
 
 set(PDF_QUALITY_LEVEL "Screen" CACHE STRING "PDF Quality. Options are: Screen, Printer, PrePress")
 #

SoftwareGuide/Cover/Source/CMakeLists.txt

@@ -1,5 +1,4 @@
-cmake_minimum_required(VERSION 3.10.2 FATAL_ERROR)
-cmake_policy(VERSION 3.10.2)
+cmake_minimum_required(VERSION 3.22.1 FATAL_ERROR)
 
 project(VWSegmentation)
 
@@ -22,5 +21,5 @@ set( operations
 
 foreach( operation ${operations} )
   add_executable( ${operation} ${operation}.cxx )
-  target_link_libraries( ${operation} ${ITK_INTERFACE_LIBRARIES} )
+  target_link_libraries( ${operation} ${ITK_LIBRARIES} )
 endforeach()

SoftwareGuide/Examples/CMakeLists.txt

@@ -1,5 +1,4 @@
 cmake_minimum_required(VERSION 3.22.1 FATAL_ERROR)
-cmake_policy(VERSION 3.22.1)
 
 project(Examples C)
 
@@ -29,27 +28,16 @@ set(RUN_EXAMPLES_SCRIPT "${SoftwareGuide_SOURCE_DIR}/Examples/RunExamples.py" CA
 
 
 #
-# Find ImageMagick tools
-# This is used to convert image formats
+# Find ImageMagick 7. Its 'convert' subcommand accepts the legacy
+# operator-before-input ordering used by the EPS conversion commands.
 #
-#
-# Find ImageMagick tools
-# This is used to convert image formats
-#
-#include(${CMAKE_ROOT}/Modules/FindImageMagick.cmake)
-find_package(ImageMagick 6 COMPONENTS convert REQUIRED)
-if(NOT ImageMagick_convert_EXECUTABLE)
-  message("ImageMagick convert utility was not found. Please pass to advanced mode and provide its full path")
-endif()
+find_program(ImageMagick_convert_EXECUTABLE NAMES magick REQUIRED)
 
 
 
 #
 # Find Python executable
-find_package(PythonInterp)
-if( NOT PYTHONINTERP_FOUND )
-  message(FATAL_ERROR "Python executable was not found")
-endif()
+find_package(Python3 REQUIRED COMPONENTS Interpreter)
 set(PYTHONCXXPARSER ${SoftwareGuide_SOURCE_DIR}/Examples/ParseCxxExamples.py)
 if( NOT EXISTS ${PYTHONCXXPARSER} )
   message(FATAL_ERROR "Missing script: ${SoftwareGuide_SOURCE_DIR}/Examples/ParseCxxExamples.py")
@@ -80,10 +68,10 @@ find_path(ITK_EXECUTABLES_DIR
   )
 
 message(STATUS "PRE_RUN_PYTHON ART GENERATION.")
-message(STATUS "Running: ${PYTHON_EXECUTABLE} ${RUN_EXAMPLES_SCRIPT} --itkSource ${ITK_SOURCE_DIR} --itkBuildDir ${ITK_BINARY_DIR} --itkExecDir ${ITK_EXECUTABLES_DIR} --SWGuidBaseOutput ${SoftwareGuide_BINARY_DIR} "
+message(STATUS "Running: ${Python3_EXECUTABLE} ${RUN_EXAMPLES_SCRIPT} --itkSource ${ITK_SOURCE_DIR} --itkBuildDir ${ITK_BINARY_DIR} --itkExecDir ${ITK_EXECUTABLES_DIR} --SWGuidBaseOutput ${SoftwareGuide_BINARY_DIR} "
   )
 add_custom_target(RunExamples ALL
-  COMMAND ${PYTHON_EXECUTABLE}
+  COMMAND ${Python3_EXECUTABLE}
   ${RUN_EXAMPLES_SCRIPT}
   --itkSource ${ITK_SOURCE_DIR}
   --itkBuildDir ${ITK_BINARY_DIR}
@@ -269,7 +257,7 @@ macro(CONVERT_INPUT_IMG SOME_IMG EPS_IMG IMAGEMAGICK_FLAGS)
   if( NOT DEFINED \${EPS_IMG}_HAS_CUSTOM_COMMAND)
     message(STATUS \"Converting \${SOME_IMG}\")
     execute_process(
-        COMMAND \"${ImageMagick_convert_EXECUTABLE}\" \${FLAGS} -quality 100 \${EPS_INPUT_CONVERT_FLAGS} \"\${SOME_IMG}\" \${EPS_OUTPUT_CONVERT_FLAGS} \"\${EPS_IMG}\"
+        COMMAND \"${ImageMagick_convert_EXECUTABLE}\" convert \${FLAGS} -quality 100 \${EPS_INPUT_CONVERT_FLAGS} \"\${SOME_IMG}\" \${EPS_OUTPUT_CONVERT_FLAGS} \"\${EPS_IMG}\"
         OUTPUT_FILE ${CMAKE_CURRENT_BINARY_DIR}/ConvertImagesToEPSOutput.txt
 	ERROR_FILE ${CMAKE_CURRENT_BINARY_DIR}/ConvertImagesToEPSError.txt
 	RESULT_VARIABLE _result
@@ -300,7 +288,7 @@ foreach(example ${ITK_EXAMPLES_SRCS})
   set(TEX_FILE ${SoftwareGuide_BINARY_DIR}/Examples/${TEX_FILE_BASE}.tex)
   add_custom_command(
     OUTPUT    ${TEX_FILE}
-    COMMAND   ${PYTHON_EXECUTABLE}
+    COMMAND   ${Python3_EXECUTABLE}
     ARGS      ${PYTHONCXXPARSER} ${example} ${TEX_FILE}
     DEPENDS   ${PYTHONCXXPARSER} ${example} ${${TEX_FILE_BASE}-DEPS}
   )

SoftwareGuide/Latex/DevelopmentGuidelines/CreateAModule.tex

@@ -72,7 +72,7 @@ \subsection{CMakeLists.txt}
 set(MyModule_LIBRARIES MyModule)
 
 if(NOT ITK_SOURCE_DIR)
-  find_package(ITK 5 REQUIRED)
+  find_package(ITK 6 REQUIRED)
   list(APPEND CMAKE_MODULE_PATH ${ITK_CMAKE_DIR})
   include(ITKModuleExternal)
 else()

SuperBuild.cmake

@@ -11,13 +11,9 @@ include(CTest)
 include(${CMAKE_CURRENT_SOURCE_DIR}/Common.cmake)
 
 #-----------------------------------------------------------------------------
-# Git protocole option
+# External project clones use https (the git:// protocol was retired by GitHub).
 #-----------------------------------------------------------------------------
-option(${CMAKE_PROJECT_NAME}_USE_GIT_PROTOCOL "If behind a firewall turn this off to use http instead." OFF)
-set(git_protocol "git")
-if(NOT ${CMAKE_PROJECT_NAME}_USE_GIT_PROTOCOL)
-  set(git_protocol "http")
-endif()
+set(git_protocol "https")
 
 find_package(Git REQUIRED)
 
@@ -40,32 +36,14 @@ endif()
 # For earlier versions, we nullify the update state to prevent updates and
 # undesirable rebuild.
 option(FORCE_EXTERNAL_BUILDS "Force rebuilding of external project (if they are updated)" OFF)
-if(CMAKE_VERSION VERSION_LESS 2.8.9 OR NOT FORCE_EXTERNAL_BUILDS)
+if(NOT FORCE_EXTERNAL_BUILDS)
   set(cmakeversion_external_update UPDATE_COMMAND)
   set(cmakeversion_external_update_value "" )
 else()
   set(cmakeversion_external_update LOG_UPDATE )
   set(cmakeversion_external_update_value 1)
 endif()
 
-#-----------------------------------------------------------------------------
-# Platform check
-#-----------------------------------------------------------------------------
-
-set(PLATFORM_CHECK true)
-
-if(PLATFORM_CHECK)
-  # See CMake/Modules/Platform/Darwin.cmake)
-  #   6.x == Mac OSX 10.2 (Jaguar)
-  #   7.x == Mac OSX 10.3 (Panther)
-  #   8.x == Mac OSX 10.4 (Tiger)
-  #   9.x == Mac OSX 10.5 (Leopard)
-  #  10.x == Mac OSX 10.6 (Snow Leopard)
-  if (DARWIN_MAJOR_VERSION LESS "9")
-    message(FATAL_ERROR "Only Mac OSX >= 10.5 are supported !")
-  endif()
-endif()
-
 #-----------------------------------------------------------------------------
 # Superbuild option(s)
 #-----------------------------------------------------------------------------

SuperBuild/External_ITK.cmake

@@ -19,7 +19,7 @@ ProjectDependancyPush(CACHED_proj ${proj})
 # SlicerMacroCheckExternalProjectDependency
 set(extProjName ITK) #The find_package known name
 set(proj      ITK) #This local name
-set(${extProjName}_REQUIRED_VERSION 4)  #If a required version is necessary, then set this, else leave blank
+set(${extProjName}_REQUIRED_VERSION 6)  #If a required version is necessary, then set this, else leave blank
 
 #if(${USE_SYSTEM_${extProjName}})
 #  unset(${extProjName}_DIR CACHE)
@@ -82,7 +82,7 @@ if(NOT ( DEFINED "${extProjName}_DIR" OR ( DEFINED "USE_SYSTEM_${extProjName}" A
   # HACK This code fixes a loony problem with HDF5 -- it doesn't
   #      link properly if -fopenmp is used.
   string(REPLACE "-fopenmp" "" ITK_CMAKE_C_FLAGS "${CMAKE_C_FLAGS}")
-  string(REPLACE "-fopenmp" "" ITK_CMAKE_CXX_FLAGS "${CMAKE_CX_FLAGS}")
+  string(REPLACE "-fopenmp" "" ITK_CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}")
 
   string(REPLACE ";" "^^" CMAKE_JOB_POOLS_ARG "${CMAKE_JOB_POOLS}")
 

SuperBuild/External_RunExamples.cmake

@@ -35,8 +35,7 @@ if( NOT USE_SYSTEM_ITK)
   set(${proj}_DEPENDENCIES ITK)
 else()
   set(${proj}_DEPENDENCIES "")
-  find_package(ITK 5 REQUIRED ITKReview )
-  include(${ITK_USE_FILE})
+  find_package(ITK 6 REQUIRED COMPONENTS ITKReview)
 endif()
 
 # Include dependent projects if any

Utilities/Hooks/chktex-lint.sh

@@ -0,0 +1,18 @@
+#!/usr/bin/env bash
+# Advisory LaTeX lint via chktex for staged .tex files.
+# Never blocks the commit; prints findings so the author can fix new prose.
+# Ignore-code policy mirrors Utilities/latex_linter.sh, plus 27 (cannot resolve
+# \input across files) which is unavoidable noise when linting one staged file.
+
+command -v chktex >/dev/null 2>&1 || {
+  echo "chktex not found on PATH (install TeX Live / MacTeX); skipping LaTeX lint." >&2
+  exit 0
+}
+
+IGNORE_WARNING_CODES="-n 1 -n 3 -n 8 -n 12 -n 13 -n 27 -n 36 -n 37"
+
+# Filter the "Unable to open the TeX file" banner: per-file linting cannot see
+# \input targets that live in the build tree, and that banner is not a finding.
+chktex ${IGNORE_WARNING_CODES} --quiet "$@" 2>&1 |
+  grep -v 'Unable to open the TeX file' || true
+exit 0