fix: bundle Arrow deps (Snappy, zstd, Thrift, xsimd, RapidJSON) to fix build on Debian 12

Arrow requires Snappy, zstd, Thrift, xsimd, and RapidJSON which are not
built by the contrib system and may not be available as system packages
(e.g. on Debian 12). Use Arrow's per-dependency BUNDLED source mechanism
to have Arrow download and build these during the contrib build.

Dependencies already provided by contrib (zlib, bzip2, boost) continue
to be found via CMAKE_PREFIX_PATH.

Remove libthrift-dev/thrift from CI prerequisites since Thrift is now
bundled.

Fixes OpenMS/OpenMS#8797

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: timosachsenberg

.github/workflows/main.yml

@@ -59,12 +59,12 @@ jobs:
         shell: bash
         run: |
           if [ "$RUNNER_OS" == "Linux" ]; then
-            sudo apt-get -y install make autoconf automake tar patch libtool gcc libthrift-dev 
+            sudo apt-get -y install make autoconf automake tar patch libtool gcc
           elif [ "$RUNNER_OS" == "Windows" ]; then
             # choco install important_windows_software
             echo "Nothing to install"
           elif [ "$RUNNER_OS" == "macOS" ]; then
-            brew install autoconf automake libtool thrift
+            brew install autoconf automake libtool
           else
             echo "$RUNNER_OS not supported"
             exit 1

libraries.cmake/arrow.cmake

@@ -13,6 +13,12 @@ else()
 endif()
 OPENMS_SMARTEXTRACT(ZIP_ARGS ARCHIVE_ARROW "ARROW" "README")
 
+## Arrow dependencies not built by the contrib (Snappy, zstd, Thrift, xsimd, RapidJSON)
+## are fetched and built as bundled dependencies by Arrow's own build system.
+## This avoids requiring these as system packages (fixes build on e.g. Debian 12).
+## Dependencies already provided by contrib (zlib, bzip2, boost) are found via CMAKE_PREFIX_PATH.
+## Note: building Arrow requires internet access for the bundled dependency downloads.
+
 ## build the obj/lib
 if (MSVC)
   set(ARROW_CXXFLAGS "/I${PROJECT_BINARY_DIR}/include")
@@ -36,6 +42,11 @@ if (MSVC)
                           -D ARROW_WITH_BZIP2=ON
                           -D ARROW_WITH_ZSTD=ON
                           -D ARROW_WITH_SNAPPY=ON
+                          -D Snappy_SOURCE=BUNDLED
+                          -D zstd_SOURCE=BUNDLED
+                          -D Thrift_SOURCE=BUNDLED
+                          -D xsimd_SOURCE=BUNDLED
+                          -D RapidJSON_SOURCE=BUNDLED
                           .
                   WORKING_DIRECTORY ${ARROW_DIR}
                   OUTPUT_VARIABLE ARROW_CMAKE_OUT
@@ -136,6 +147,11 @@ else() ## Linux/MacOS
                           "-DARROW_WITH_BZIP2=ON"
                           "-DARROW_WITH_ZSTD=ON"
                           "-DARROW_WITH_SNAPPY=ON"
+                          "-DSnappy_SOURCE=BUNDLED"
+                          "-Dzstd_SOURCE=BUNDLED"
+                          "-DThrift_SOURCE=BUNDLED"
+                          "-Dxsimd_SOURCE=BUNDLED"
+                          "-DRapidJSON_SOURCE=BUNDLED"
                           .
                   WORKING_DIRECTORY ${ARROW_DIR}
                   OUTPUT_VARIABLE ARROW_CMAKE_OUT