Standalone build, tests, docs, installers and CI of the OpenMS GUI layer

.clang-format

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+AlignConsecutiveDeclarations: 'false'
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+AllowShortIfStatementsOnASingleLine: Always
+AllowShortLambdasOnASingleLine: All
+AllowShortLoopsOnASingleLine: 'false'
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+AlwaysBreakBeforeMultilineStrings: 'false'
+AlwaysBreakTemplateDeclarations: 'Yes'
+BinPackArguments: 'true'
+BinPackParameters: 'false'
+BreakBeforeBinaryOperators: All
+BraceWrapping:
+  AfterClass:      true
+  AfterControlStatement: true
+  AfterEnum:       true
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+IndentCaseLabels: 'true'
+IndentPPDirectives: BeforeHash
+IndentWidth: '2'
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+KeepEmptyLinesAtTheStartOfBlocks: 'true'
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+MaxEmptyLinesToKeep: '2'
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+PointerAlignment: Left
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+Standard: Cpp11
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+UseTab: Never
+
+...

.git_archival.txt

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+node: $Format:%H$
+node-date: $Format:%cI$
+describe-name: $Format:%(describe:tags=true,abbrev=40,match=v[0-9]*,exclude=v*[!0-9.]*)$

.gitattributes

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+# Set the default behavior, in case people don't have core.autocrlf set.
+# Force UNIX line endings, so you can use the same repo e.g., on Win and WSL
+* text=auto eol=lf
+# batch files specifically need to have CRLF (win endings)
+*.{cmd,[cC][mM][dD]} text eol=crlf
+*.{bat,[bB][aA][tT]} text eol=crlf
+
+# Denote all files that are truly binary and should not be modified.
+# Images
+*.png binary
+*.jpg binary
+# XML files with potential byte-counting indices that will lose function
+# if the windows CR byte is added
+*.mzML binary
+*.mzXML binary
+# reference images of the ImageCreator tests, application icons, the UTF-16 registry file in tools/
+*.bmp binary
+*.ico binary
+*.icns binary
+*.reg binary
+
+# git archive fills in the commit and its release tag, so that a build from an archive (the
+# Release workflow's source tarball, GitHub's source archives) knows its version (CMakeLists.txt).
+.git_archival.txt export-subst

.github/actions/build/action.yml

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+name: "Build OpenMS-TOPP-GUI"
+description: >-
+  Configures, builds and tests the GUI layer with the CI preset of the runner
+  against an OpenMS core (see the openms-core action), with ccache.
+inputs:
+  compiler:
+    description: "The name of the compiler to use (cl.exe, xcode, g++, clang++)"
+    required: true
+  prefix_path:
+    description: "CMAKE_PREFIX_PATH: the OpenMS core and Qt (';'-separated)"
+    required: true
+  topp_bin_dir:
+    description: "OPENMS_TOPP_BIN_DIR: the TOPP tools of the core (FuzzyDiff, ...)"
+    required: false
+    default: ""
+  examples_dir:
+    description: "OPENMS_EXAMPLES_DIR: the example data of the core (TOPPAS workflows)"
+    required: false
+    default: ""
+  core_version_fullstring:
+    description: "OPENMS_CORE_VERSION_FULLSTRING: the full version string of the core"
+    required: false
+    default: ""
+  preset:
+    description: >-
+      The CMake preset to configure, build and test with. By default the CI preset
+      of the runner (linux-x64-ci, macos-arm64-ci, windows-x64-ci, ...).
+    required: false
+    default: ""
+  run_tests:
+    description: "Whether to run the test suite after the build (ctest --preset)"
+    required: false
+    default: "true"
+  cmake_args:
+    description: "Further arguments for the configure step (one per line)"
+    required: false
+    default: ""
+  macosx_deployment_target:
+    description: >-
+      The oldest macOS the binaries run on (-mmacosx-version-min). Keep it at the
+      runner's macOS, as for OpenMS: the Homebrew Qt the package bundles is built
+      for that version.
+    default: "15.0"
+outputs:
+  version:
+    description: "The discovered compiler version number"
+    value: ${{ steps.compiler.outputs.ver }}
+  preset:
+    description: "The resolved CMake preset name"
+    value: ${{ steps.preset.outputs.name }}
+runs:
+  using: "composite"
+  steps:
+
+    ############################################################################
+    # NOTE: x64 is hardcoded. No support for 32bit.
+    # Skipped when the openms-core action has set up the environment already
+    # (VCINSTALLDIR): vcvars run twice can make PATH too long for cmd.
+    - name: Emulate a Visual Studio shell (Windows)
+      if: ${{ runner.os == 'Windows' && env.VCINSTALLDIR == '' }}
+      uses: egor-tensin/vs-shell@v2
+      with: { arch: x64 }
+
+    ############################################################################
+    - name: Compute the Compiler Version
+      id: compiler
+      env:
+        compiler: ${{ inputs.compiler }}
+      shell: bash
+      run: |
+        case ${compiler:-gcc} in
+        clang*)
+          ver=$(clang -dumpversion)
+          name=$(type -p clang++)
+          cc_name=$(type -p clang)
+          ;;
+
+        cl*)
+          ver=$(cl.exe 2>&1 |
+            grep -E 'Version [0-9.]+' |
+            sed -E 's/^.* Version ([0-9.]+) .*$/\1/')
+          name=$compiler
+          cc_name=$compiler
+          ;;
+
+        gcc | g++)
+          ver=$(gcc -dumpversion)
+          name=$(type -p g++)
+          cc_name=$(type -p gcc)
+          ;;
+
+        xcode)
+          ver=$(clang -dumpversion)
+          name=$(xcrun -f clang++)
+          cc_name=$(xcrun -f clang)
+          ;;
+
+        *)
+          ver="0.0"
+          name=$compiler
+          cc_name=$compiler
+          ;;
+        esac
+
+        major=$(cut -d. -f1 <<<"$ver")
+
+        {
+          echo "ver=$ver"
+          echo "major=$major"
+          echo "name=$name"
+        } >>"$GITHUB_OUTPUT"
+
+        {
+          # All remaining steps should use this compiler.
+          echo "CXX=$name"
+          echo "CC=$cc_name"
+        } >>"$GITHUB_ENV"
+
+    ############################################################################
+    # The tests and the documentation run the GUI applications, which then need
+    # no display (src/tests sets it per test as well).
+    - name: Set CI-specific Environment Variables
+      shell: bash
+      run: echo "QT_QPA_PLATFORM=offscreen" >>"$GITHUB_ENV"
+
+    ############################################################################
+    # This is only really needed so we can set cache keys.
+    - name: Extract the PR Number or Branch Name
+      id: pr
+      shell: bash
+      run: echo "name=${{ github.event.pull_request && github.event.number || github.ref_name }}" >>"$GITHUB_OUTPUT"
+
+    ############################################################################
+    # Restore and save are separate steps so that every run saves a fresh cache
+    # (under a key unique to the run) while the restore-keys ladder finds the
+    # newest one: of the branch or pull request, else of develop (the default
+    # branch, whose caches every pull request can read), else any in scope.
+    - name: Try to Fetch Existing Build Cache
+      id: ccache-restore
+      uses: actions/cache/restore@v5
+      with:
+        path: .ccache
+        key: ${{ runner.os }}-${{ runner.arch }}-${{ inputs.compiler }}-${{ steps.compiler.outputs.major }}-ccache-${{ steps.pr.outputs.name }}-${{ github.run_id }}-${{ github.run_attempt }}
+        restore-keys: |
+          ${{ runner.os }}-${{ runner.arch }}-${{ inputs.compiler }}-${{ steps.compiler.outputs.major }}-ccache-${{ steps.pr.outputs.name }}-
+          ${{ runner.os }}-${{ runner.arch }}-${{ inputs.compiler }}-${{ steps.compiler.outputs.major }}-ccache-develop-
+          ${{ runner.os }}-${{ runner.arch }}-${{ inputs.compiler }}-${{ steps.compiler.outputs.major }}-ccache-
+
+    ############################################################################
+    - name: Configure Build Caching
+      id: ccache-configure
+      shell: bash
+      env:
+        # MSVC objects are considerably larger than the gcc/clang ones
+        maxsize: ${{ runner.os == 'Windows' && '1G' || '500M' }}
+      run: |
+        mkdir -p "$GITHUB_WORKSPACE/.ccache"
+
+        {
+          echo "CCACHE_COMPRESS=true"
+          echo "CCACHE_COMPRESSLEVEL=6"
+          echo "CCACHE_DIR=$GITHUB_WORKSPACE/.ccache"
+          echo "CCACHE_MAXSIZE=$maxsize"
+          echo "CMAKE_C_COMPILER_LAUNCHER=ccache"
+          echo "CMAKE_CXX_COMPILER_LAUNCHER=ccache"
+        } >>"$GITHUB_ENV"
+
+    ############################################################################
+    # Reset the hit/miss counters (not the cached objects) so the statistics
+    # printed after the build describe this run only.
+    - name: Reset ccache Statistics
+      id: ccache-reset
+      shell: bash
+      run: |
+        ccache --version
+        ccache --zero-stats
+
+    ############################################################################
+    # The preset input, or else the CI preset of the runner.
+    - name: Resolve CMake presets
+      id: preset
+      shell: bash
+      env:
+        preset: ${{ inputs.preset }}
+      run: |
+        if [[ -n "$preset" ]]; then
+          echo "name=$preset" >> "$GITHUB_OUTPUT"
+          exit 0
+        fi
+        case "$RUNNER_OS-$RUNNER_ARCH" in
+          Linux-X64) preset=linux-x64-ci ;;
+          Linux-ARM64) preset=linux-arm64-ci ;;
+          macOS-ARM64) preset=macos-arm64-ci ;;
+          Windows-X64) preset=windows-x64-ci ;;
+          *)
+            echo >&2 "ERROR: no CI preset mapped for $RUNNER_OS-$RUNNER_ARCH"
+            exit 1
+            ;;
+        esac
+        echo "name=$preset" >> "$GITHUB_OUTPUT"
+
+    ############################################################################
+    - name: Build
+      id: build
+      shell: bash
+      env:
+        PRESET: ${{ steps.preset.outputs.name }}
+        PREFIX_PATH: ${{ inputs.prefix_path }}
+        TOPP_BIN_DIR: ${{ inputs.topp_bin_dir }}
+        EXAMPLES_DIR: ${{ inputs.examples_dir }}
+        CORE_VERSION_FULLSTRING: ${{ inputs.core_version_fullstring }}
+        CMAKE_ARGS: ${{ inputs.cmake_args }}
+        # Also sets LSMinimumSystemVersion of the GUI apps and the installer's minimum macOS.
+        MACOSX_DEPLOYMENT_TARGET: "${{ inputs.macosx_deployment_target }}"
+      run: |
+        set -euxo pipefail
+
+        options=(
+          "-DCMAKE_PREFIX_PATH=$PREFIX_PATH"
+          "-DCMAKE_INSTALL_PREFIX=$GITHUB_WORKSPACE/install"
+        )
+        if [[ -n "$TOPP_BIN_DIR" ]]; then
+          options+=("-DOPENMS_TOPP_BIN_DIR=$TOPP_BIN_DIR")
+        fi
+        if [[ -n "$EXAMPLES_DIR" ]]; then
+          options+=("-DOPENMS_EXAMPLES_DIR=$EXAMPLES_DIR")
+        fi
+        if [[ -n "$CORE_VERSION_FULLSTRING" ]]; then
+          options+=("-DOPENMS_CORE_VERSION_FULLSTRING=$CORE_VERSION_FULLSTRING")
+        fi
+        while IFS= read -r arg; do
+          if [[ -n "$arg" ]]; then
+            options+=("$arg")
+          fi
+        done <<<"$CMAKE_ARGS"
+
+        cmake --preset "$PRESET" "${options[@]}"
+        cmake --build --preset "$PRESET"
+
+    - name: Verify public headers
+      if: ${{ runner.os == 'Linux' && runner.arch == 'X64' && inputs.preset == '' }}
+      shell: bash
+      run: cmake --build --preset "${{ steps.preset.outputs.name }}" --target all_verify_interface_header_sets
+
+    ############################################################################
+    # Hit rate and cache size for this run. A diagnostic that must never decide
+    # the fate of the job (an older ccache without --verbose would otherwise skip
+    # the tests).
+    - name: Report ccache Statistics
+      if: ${{ !cancelled() && steps.ccache-configure.outcome == 'success' && steps.ccache-reset.outcome == 'success' }}
+      continue-on-error: true
+      shell: bash
+      run: ccache --show-stats --verbose
+
+    ############################################################################
+    - name: Test
+      if: ${{ inputs.run_tests == 'true' }}
+      shell: bash
+      run: ctest --preset "${{ steps.preset.outputs.name }}"
+
+    ############################################################################
+    # Saved only when the build succeeded (a failed build would pin a partial
+    # cache as the newest of the branch); test failures still save.
+    - name: Save Build Cache
+      if: ${{ !cancelled() && steps.build.outcome == 'success' }}
+      uses: actions/cache/save@v5
+      with:
+        path: .ccache
+        # Reuse the restore step's primary key so the two can never drift apart.
+        key: ${{ steps.ccache-restore.outputs.cache-primary-key }}