Add optional vcpkg bootstrapping for dependencies

.github/workflows/cmake.yml

@@ -25,21 +25,55 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
-      - name: Install dependencies (Windows)
-        if: ${{ (matrix.os == 'windows-latest') }}
-        # on Windows, we rely on vcpkg to pull in dependencies
-        shell: bash
-        run: |
-          vcpkg install xerces-c --triplet x64-windows-static
+      - name: Cache vcpkg and packages
+        uses: actions/cache@v4
+        with:
+          path: |
+            external/vcpkg
+            build/vcpkg_installed
+          key: vcpkg-${{ runner.os }}-${{ hashFiles('vcpkg.json') }}
 
-      - name: Install dependencies (Linux)
-        if: ${{ (matrix.os == 'ubuntu-latest') }}
-        # on Linux, we use apt to get our dependencies
+      - name: Prep existing vcpkg installation
         shell: bash
         run: |
-          sudo apt-get install libxerces-c-dev -y
+          set -euo pipefail
+          BASELINE=$(jq -r '.["builtin-baseline"]' vcpkg.json)
+          echo "Detected vcpkg baseline: $BASELINE"
+
+          if [ -d "$GITHUB_WORKSPACE/external/vcpkg/.git" ]; then
+              echo "Using cached vcpkg at external/vcpkg"
+              VCPKG_DIR="$GITHUB_WORKSPACE/external/vcpkg"
+          elif [ -n "${VCPKG_ROOT:-}" ] && [ -d "$VCPKG_ROOT/.git" ]; then
+              echo "Using preinstalled vcpkg at $VCPKG_ROOT"
+              VCPKG_DIR="$VCPKG_ROOT"
+          else
+              echo "Performing minimal vcpkg clone..."
+              git clone --filter=blob:none --no-checkout https://github.com/microsoft/vcpkg.git external/vcpkg
+              VCPKG_DIR="$GITHUB_WORKSPACE/external/vcpkg"
+          fi
+
+          cd "$VCPKG_DIR"
+
+          if ! git cat-file -e "${BASELINE}^{commit}" 2>/dev/null; then
+              echo "Fetching baseline commit $BASELINE..."
+              git fetch origin "$BASELINE" --depth=1 || git fetch --unshallow
+          fi
+
+          git checkout "$BASELINE"
+
+          if [ ! -f ./vcpkg ] && [ ! -f ./vcpkg.exe ]; then
+              if [[ "$RUNNER_OS" == "Windows" ]]; then
+                  ./bootstrap-vcpkg.bat
+              else
+                  ./bootstrap-vcpkg.sh
+              fi
+          fi
+
+          echo "vcpkg is now at commit: $(git rev-parse HEAD)"
+          echo "VCPKG_DIR=$VCPKG_DIR" >> "$GITHUB_ENV"
+
 
       - name: Configure CMake (Windows)
         if: ${{ (matrix.os == 'windows-latest') }}
@@ -49,7 +83,7 @@ jobs:
           # See https://cmake.org/cmake/help/latest/variable/CMAKE_BUILD_TYPE.html?highlight=cmake_build_type
           # on Windows, we need to point CMake to the vcpkg-toolchain-file
           cmake -B "${{github.workspace}}/build" -DCMAKE_BUILD_TYPE=${{matrix.build}} \
-                -DCMAKE_TOOLCHAIN_FILE="${VCPKG_INSTALLATION_ROOT}/scripts/buildsystems/vcpkg.cmake" \
+                -DCMAKE_TOOLCHAIN_FILE="${VCPKG_DIR}/scripts/buildsystems/vcpkg.cmake" \
                 -DVCPKG_TARGET_TRIPLET=x64-windows-static \
                 -DCZICHECK_BUILD_TESTS=ON
 
@@ -58,6 +92,7 @@ jobs:
         shell: bash
         run: |
           cmake -B "${{github.workspace}}/build" -DCMAKE_BUILD_TYPE=${{matrix.build}} \
+                -DCMAKE_TOOLCHAIN_FILE="${VCPKG_DIR}/scripts/buildsystems/vcpkg.cmake" \
                 -DCZICHECK_BUILD_TESTS=ON
 
       - name: Build

.reuse/dep5

@@ -3,7 +3,7 @@ Upstream-Name: CZICheck
 Upstream-Contact: Carl Zeiss Microscopy GmbH <github.microscopy@zeiss.com>
 Source: https://github.com/ZEISS/czicheck
 
-Files: .github/* .gitignore README.md LICENSE CODE_OF_CONDUCT.md CONTRIBUTING.md README.md SECURITY.md cla_corporate.txt cla_individual.txt THIRD_PARTY_LICENSES.txt
+Files: .github/* .gitignore README.md LICENSE CODE_OF_CONDUCT.md CONTRIBUTING.md README.md SECURITY.md cla_corporate.txt cla_individual.txt THIRD_PARTY_LICENSES.txt vcpkg.json
 Copyright: 2023 Carl Zeiss Microscopy GmbH
 License: MIT
 

CMakeLists.txt

@@ -4,28 +4,44 @@
 
 cmake_minimum_required(VERSION 3.15)
 
+option(CZICHECK_ENABLE_VCPKG_BOOTSTRAP
+       "Automatically fetch and bootstrap vcpkg if no toolchain is defined" ON)
+
+# Include the bootstrap script if the option is enabled
+if(CZICHECK_ENABLE_VCPKG_BOOTSTRAP)
+    include(modules/bootstrapVcpkg.cmake)
+endif()
+
 project(CZICheck 
-      VERSION 0.6.3
+      VERSION 0.6.5
       HOMEPAGE_URL "https://github.com/ZEISS/czicheck"
       DESCRIPTION "CZICheck is a validator for CZI-documents")
 
+
+
 if(WIN32)
   # use "static C-runtime" -> https://stackoverflow.com/questions/14172856/compile-with-mt-instead-of-md-using-cmake
   # Note: this requires CMAKE version 3.15+
   cmake_policy(SET CMP0091 NEW)
-  set(CMAKE_MSVC_RUNTIME_LIBRARY "MultiThreaded$<$<CONFIG:Debug>:Debug>")
+  if(NOT CZICHECK_ENABLE_VCPKG_BOOTSTRAP OR VCPKG_TARGET_TRIPLET MATCHES "-static$")
+    set(CMAKE_MSVC_RUNTIME_LIBRARY "MultiThreaded$<$<CONFIG:Debug>:Debug>")
+endif()
+
 endif(WIN32)
 
 set(CMAKE_CXX_STANDARD 17)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 
 set (CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/modules" ${CMAKE_MODULE_PATH})
 
-include("${CMAKE_SOURCE_DIR}/modules/libCZI.cmake")
-include("${CMAKE_SOURCE_DIR}/modules/rapidJSON.cmake")
+if(NOT CZICHECK_ENABLE_VCPKG_BOOTSTRAP)
+  include("${CMAKE_SOURCE_DIR}/modules/libCZI.cmake")
+  include("${CMAKE_SOURCE_DIR}/modules/rapidJSON.cmake")
+  FetchContent_GetProperties(libCZI)
+  set(LIBCZI_INCLUDE_DIR "${libczi_SOURCE_DIR}/Src/libCZI")
+endif()
+
 include("${CMAKE_SOURCE_DIR}/modules/pugiXML.cmake")
-FetchContent_GetProperties(libCZI)
-set(LIBCZI_INCLUDE_DIR "${libczi_SOURCE_DIR}/Src/libCZI")
 
 # This option enables/disables the tests for the CZICheck-application. If enabled, the test
 #  runs with a ctest run (and test-data is being downloaded)

CZICheck/CMakeLists.txt

@@ -14,7 +14,12 @@ function(embed_resource resource_file_name source_file_name variable_name)
     file(WRITE "${source_file_name}" "${source}")
 endfunction()
 
-find_package(XercesC  QUIET)
+if(CZICHECK_ENABLE_VCPKG_BOOTSTRAP)
+  find_package(XercesC CONFIG REQUIRED)
+else()
+  find_package(XercesC QUIET)
+endif()
+
 if (XercesC_FOUND)
     set(CZICheck_XercesCAvailable 1)
     message("XercesC library available -> version: ${XercesC_VERSION}")
@@ -38,6 +43,9 @@ FetchContent_Declare(
 
 FetchContent_MakeAvailable(cli11)
 
+if(CZICHECK_ENABLE_VCPKG_BOOTSTRAP)
+  find_package(libCZI CONFIG REQUIRED)
+endif()
 
 set(CZICHECKSRCFILES 
 "checkers/checkerbase.h"
@@ -72,53 +80,81 @@ set(CZICHECKSRCFILES
 "checkers/checkerSubBlkBitmapValid.cpp"
 "checkers/checkerTopographyApplianceValidation.h"
 "checkers/checkerTopographyApplianceValidation.cpp"
-checkerfactory.cpp
-checkerfactory.h
-checks.h
-checks.cpp
-CMakeLists.txt
-cmdlineoptions.cpp
-cmdlineoptions.h
-consoleio.cpp
-consoleio.h
-CZICheck.cpp
-IChecker.h
-IResultGatherer.h
-inc_libCZI.h
-resultgatherer.cpp
-resultgatherer.h
-resultgathererjson.h
-resultgathererjson.cpp
-resultgathererxml.h
-resultgathererxml.cpp
-resultgathererfactory.h
-resultgathererfactory.cpp
-runchecks.cpp
-runchecks.h
-utils.h
-utils.cpp
+"checkerfactory.cpp"
+"checkerfactory.h"
+"checks.h"
+"checks.cpp"
+"CMakeLists.txt"
+"cmdlineoptions.cpp"
+"cmdlineoptions.h"
+"consoleio.cpp"
+"consoleio.h"
+"CZICheck.cpp"
+"IChecker.h"
+"IResultGatherer.h"
+"resultgatherer.cpp"
+"resultgatherer.h"
+"resultgathererjson.h"
+"resultgathererjson.cpp"
+"resultgathererxml.h"
+"resultgathererxml.cpp"
+"resultgathererfactory.h"
+"resultgathererfactory.cpp"
+"runchecks.cpp"
+"runchecks.h"
+"utils.h"
+"utils.cpp"
+"inc_libCZI.h"
 )
 
 add_executable(CZICheck ${CZICHECKSRCFILES} )
 
 set_target_properties(CZICheck PROPERTIES CXX_STANDARD 17)
 target_compile_definitions(CZICheck PRIVATE _LIBCZISTATICLIB)
 
-target_link_libraries(CZICheck  PRIVATE libCZIStatic CLI11::CLI11 pugixml)
+target_link_libraries(CZICheck PRIVATE CLI11::CLI11)
+
+target_include_directories(CZICheck PRIVATE ${CMAKE_CURRENT_SOURCE_DIR})
+
+if(CZICHECK_ENABLE_VCPKG_BOOTSTRAP)
+  if(TARGET libczi::libCZI)
+      add_library(libczi::libCZI_selected ALIAS libczi::libCZI)
+  elseif(TARGET libczi::libCZIStatic)
+      add_library(libczi::libCZI_selected ALIAS libczi::libCZIStatic)
+  else()
+      message(FATAL_ERROR "No suitable libCZI target found (neither shared nor static).")
+  endif()
+  target_link_libraries(CZICheck PRIVATE libczi::libCZI_selected)
+else()
+  target_link_libraries(CZICheck PRIVATE libCZIStatic)
+endif()
+if(CZICHECK_ENABLE_VCPKG_BOOTSTRAP)
+  get_target_property(_libczi_includes libczi::libCZI_selected INTERFACE_INCLUDE_DIRECTORIES)
+  set(_libczi_include_with_subdir "${_libczi_includes}/libCZI")
+  target_include_directories(CZICheck PRIVATE ${_libczi_include_with_subdir})
+else()
+  target_include_directories(CZICheck PRIVATE ${LIBCZI_INCLUDE_DIR})
+endif()
+target_link_libraries(CZICheck PRIVATE pugixml)
+
 target_include_directories(CZICheck
-  PRIVATE ${LIBCZI_INCLUDE_DIR}
   PRIVATE ${RAPIDJSON_INCLUDE_DIRS})
+
 if (XercesC_FOUND)
+  if(CZICHECK_ENABLE_VCPKG_BOOTSTRAP)
+    target_link_libraries(CZICheck PRIVATE XercesC::XercesC)
+  else()
     target_link_libraries(CZICheck PRIVATE ${XercesC_LIBRARY})
+  endif()
 endif()
 target_include_directories(CZICheck PRIVATE ${CMAKE_CURRENT_BINARY_DIR})
-if (XercesC_FOUND)
+if (XercesC_FOUND AND NOT CZICHECK_ENABLE_VCPKG_BOOTSTRAP)
     target_include_directories(CZICheck PRIVATE ${XercesC_INCLUDE_DIR})
 endif()
 
 IF(UNIX)
   # seems to be problem with glibc I'd reckon -> https://stackoverflow.com/questions/51584960/stdcall-once-throws-stdsystem-error-unknown-error-1
-  target_link_libraries(CZICheck  PUBLIC pthread)
+  target_link_libraries(CZICheck PUBLIC pthread)
 ENDIF(UNIX)
 
 IF(WIN32)

CZICheck/checkers/checkerbase.h

@@ -4,7 +4,7 @@
 
 #pragma once
 
-#include "../inc_libCZI.h"
+#include <inc_libCZI.h>
 #include "../checkerfactory.h"
 #include <memory>
 #include <utility>

Test/CZICheckSamples/differentpixeltypeinchannel.txt.json

@@ -112,6 +112,6 @@
     ],
     "output_version": {
         "command": "CZICheck",
-        "version": "0.6.3"
+        "version": "0.6.4"
     }
 }

Test/CZICheckSamples/differentpixeltypeinchannel.txt.xml

@@ -99,6 +99,6 @@
   <AggregatedResult>WARN</AggregatedResult>
   <OutputVersion>
     <Command>CZICheck</Command>
-    <Version>0.6.3</Version>
+    <Version>0.6.4</Version>
   </OutputVersion>
 </TestResults>

Test/CZICheckSamples/duplicate_coordinates.txt.json

@@ -112,6 +112,6 @@
     ],
     "output_version": {
         "command": "CZICheck",
-        "version": "0.6.3"
+        "version": "0.6.4"
     }
 }

Test/CZICheckSamples/duplicate_coordinates.txt.xml

@@ -99,6 +99,6 @@
   <AggregatedResult>FAIL</AggregatedResult>
   <OutputVersion>
     <Command>CZICheck</Command>
-    <Version>0.6.3</Version>
+    <Version>0.6.4</Version>
   </OutputVersion>
 </TestResults>

Test/CZICheckSamples/edf-missing-texture.txt.json

@@ -105,6 +105,6 @@
     ],
     "output_version": {
         "command": "CZICheck",
-        "version": "0.6.3"
+        "version": "0.6.4"
     }
 }

Test/CZICheckSamples/edf-missing-texture.txt.xml

@@ -92,6 +92,6 @@
   <AggregatedResult>FAIL</AggregatedResult>
   <OutputVersion>
     <Command>CZICheck</Command>
-    <Version>0.6.3</Version>
+    <Version>0.6.4</Version>
   </OutputVersion>
 </TestResults>

Test/CZICheckSamples/edf-superfluous-missing-channel-subblock.txt.json

@@ -126,6 +126,6 @@
     ],
     "output_version": {
         "command": "CZICheck",
-        "version": "0.6.3"
+        "version": "0.6.4"
     }
 }

Test/CZICheckSamples/edf-superfluous-missing-channel-subblock.txt.xml

@@ -113,6 +113,6 @@
   <AggregatedResult>FAIL</AggregatedResult>
   <OutputVersion>
     <Command>CZICheck</Command>
-    <Version>0.6.3</Version>
+    <Version>0.6.4</Version>
   </OutputVersion>
 </TestResults>

Test/CZICheckSamples/edf-superfluous.txt.json

@@ -105,6 +105,6 @@
     ],
     "output_version": {
         "command": "CZICheck",
-        "version": "0.6.3"
+        "version": "0.6.4"
     }
 }

Test/CZICheckSamples/edf-superfluous.txt.xml

@@ -92,6 +92,6 @@
   <AggregatedResult>FAIL</AggregatedResult>
   <OutputVersion>
     <Command>CZICheck</Command>
-    <Version>0.6.3</Version>
+    <Version>0.6.4</Version>
   </OutputVersion>
 </TestResults>

Test/CZICheckSamples/inconsistent_coordinates.txt.json

@@ -112,6 +112,6 @@
     ],
     "output_version": {
         "command": "CZICheck",
-        "version": "0.6.3"
+        "version": "0.6.4"
     }
 }

Test/CZICheckSamples/inconsistent_coordinates.txt.xml

@@ -99,6 +99,6 @@
   <AggregatedResult>FAIL</AggregatedResult>
   <OutputVersion>
     <Command>CZICheck</Command>
-    <Version>0.6.3</Version>
+    <Version>0.6.4</Version>
   </OutputVersion>
 </TestResults>

Test/CZICheckSamples/invalid_componentbitcount.txt.json

@@ -94,6 +94,6 @@
     ],
     "output_version": {
         "command": "CZICheck",
-        "version": "0.6.3"
+        "version": "0.6.4"
     }
 }