Windows: get OpenMS from a reusable workflow instead of a contrib build

.claude/skills/build-insight-dashboard/SKILL.md

@@ -140,7 +140,7 @@ One round:
    the first suspect is the cache and the first move is to clear it — before
    re-reading the config, before doubting the change, before restarting
    anything. Runs lose whole stretches to this by debugging the edit instead,
-   and it is the same symptom as the un-restarted server (`rounds.md`): what you
+   and it is the same symptom as the un-restarted server (`scaffold-workflow-app/rounds.md`): what you
    see is the previous configuration, faithfully served.
 2. **Resolve every candidate to its edit before offering it.** In thinking, name
    the file and the change that implements it. A candidate whose edit you cannot
@@ -292,7 +292,7 @@ print(page.frame_locator("iframe").first.locator("body")
 
 Only then shorten headers if the total overflows. Three builds on two notebooks had the 45px figure and the observed panel fits and still converged by trial across four and five gate cycles, because nothing here turned a panel width into a column width. A fourth had the formula and converged anyway, because the formula is only the numerator.
 
-**And do not buy the fit by dropping a column.** The same build removed one to make the sum work and disclosed it in its closing turn, which is the one place `handover.md` says a decision must never first appear. A column that does not fit is a question, not a silent edit.
+**And do not buy the fit by dropping a column.** The same build removed one to make the sum work and disclosed it in its closing turn, which is the one place `scaffold-workflow-app/handover.md` says a decision must never first appear. A column that does not fit is a question, not a silent edit.
 
 **The gate does not see the wrap.** A build reported *"875 wrapped onto a phantom row, 800 clipped 'Score', 815 fit"* and added that only the screenshot showed it — the gate returned 11/11 on the wrapped page. So a green gate is not evidence the table fits; the screenshot is. Read it before believing the count, and never treat a passing gate as the check for this. This rule used to name a fixed figure for a 1280px window until two builds on two notebooks sized their columns against it and wrapped anyway: one measured ~830px at a 1280px window, the other 864px with the wrap at a 865px sum. Both then re-derived the budget from a screenshot and repeated gate runs, which is the cost of a number that was one layout's measurement rather than something to compute. `verify-webapp-usability` measures the real property and fails on it; shorten a long header rather than widening its column |
 | **Normalise per side before a mirror plot** | The halves share one symmetric axis; raw counts (~7e4) against theoretical intensities (~1) flatten one onto the baseline |

.claude/skills/interview-parameters/probe.py

@@ -294,7 +294,7 @@ def main() -> int:
                 if (
                     re_eff > MATERIAL_THRESHOLD
                     and re_eff >= MASKING_RATIO * max(eff, EFFECT_THRESHOLD)
-                    and (best_unmask is None or re_eff > best_unmask[1])
+                    and (best_unmask is None or re_eff > best_unmask[1])  # pylint: disable=unsubscriptable-object
                 ):
                     best_unmask = (other["key"], re_eff)
             if best_unmask:

.claude/skills/notebook-to-webapp/SKILL.md

@@ -77,7 +77,7 @@ Four lines. The same build narrated step by step runs to eight: a line for the
 extracted file, one for the golden test, one for the workflow class and its
 pages, one for registering them, one for the template cleanup, one for the test
 lists. Each is a step inside a stage, and the last of them reads a phrase
-straight out of `cleanup.md` — a step that only exists because this framework
+straight out of `scaffold-workflow-app/cleanup.md` — a step that only exists because this framework
 has a rule about it is not a step the user is waiting on.
 
 **The bad version is described here and not written out, deliberately.** It used

.github/scripts/ci-assertions.sh

@@ -916,6 +916,7 @@ assert_doc_links_resolve() {
     # `docs/a16-storage-runbook.md`, while a sibling reference inside docs/
     # may reasonably write just `build_app.md`.
     _ci_dangling=""
+    _ci_dangling_at=""
     _ci_checked=0
     for _ci_ref in $_ci_refs; do
         _ci_checked=$((_ci_checked + 1))
@@ -925,14 +926,36 @@ assert_doc_links_resolve() {
         if git ls-files --error-unmatch "docs/$_ci_ref" >/dev/null 2>&1; then
             continue
         fi
+        # Skills cite their own supporting files by bare name (`cleanup.md`)
+        # or relative to the skills root (`scaffold-workflow-app/handover.md`).
+        if git ls-files --error-unmatch ".claude/skills/$_ci_ref" >/dev/null 2>&1; then
+            continue
+        fi
+        # Last, relative to the directory of the Markdown file citing it. Every
+        # citing file has to resolve it on its own: one file with a sibling of
+        # that name says nothing about another file citing the same name.
+        _ci_unresolved=""
+        for _ci_citer in $(git ls-files '*.md' -z 2>/dev/null \
+                | xargs -0 grep -l -- "\`$_ci_ref\`" 2>/dev/null); do
+            if ! git ls-files --error-unmatch "$(dirname "$_ci_citer")/$_ci_ref" >/dev/null 2>&1; then
+                _ci_unresolved="$_ci_unresolved $_ci_citer"
+            fi
+        done
+        if [ -z "$_ci_unresolved" ]; then
+            continue
+        fi
         _ci_dangling="$_ci_dangling $_ci_ref"
+        for _ci_citer in $_ci_unresolved; do
+            _ci_dangling_at="$_ci_dangling_at $_ci_citer:$_ci_ref"
+        done
     done
 
     if [ -n "$_ci_dangling" ]; then
         _ci_fail "tracked Markdown cites .md paths that do not exist:$_ci_dangling"
-        printf '%s\n' "$_ci_dangling" | tr ' ' '\n' | grep -v '^$' | while read -r _ci_d; do
-            git ls-files '*.md' -z 2>/dev/null \
-                | xargs -0 grep -n -- "\`$_ci_d\`" 2>/dev/null | sed 's|^|  |' >&2 || true
+        # Only the citing files that cannot resolve the reference.
+        for _ci_d in $_ci_dangling_at; do
+            grep -n -- "\`${_ci_d#*:}\`" "${_ci_d%%:*}" 2>/dev/null \
+                | sed "s|^|  ${_ci_d%%:*}:|" >&2 || true
         done
         _ci_rc=1
     fi

.github/workflows/build-windows-executable-app.yaml

@@ -13,10 +13,6 @@ permissions:
   contents: write
 
 env:
-  OPENMS_VERSION: 3.5.0
-  # Override to pin contrib to a specific release when OPENMS_VERSION is a non-release branch (e.g. "develop").
-  # Leave empty to use OPENMS_VERSION.
-  OPENMS_CONTRIB_VERSION: ""
   PYTHON_VERSION: 3.11.0
   # Name of the installer
   APP_NAME: OpenMS-StreamlitTemplateApp
@@ -26,160 +22,28 @@ env:
   TOPP_TOOLS: "FeatureFinderMetabo FeatureLinkerUnlabeledKD SiriusExport"
 
 jobs:
-  build-openms:
-    runs-on: windows-2022
-
+  # `with:` of a reusable-workflow call cannot read `env`, so this job hands
+  # TOPP_TOOLS over as an output and it stays defined in one place.
+  config:
+    runs-on: ubuntu-latest
+    outputs:
+      topp-tools: ${{ steps.out.outputs.topp-tools }}
     steps:
-    - name: Checkout
-      uses: actions/checkout@v4
-      with:
-        repository: OpenMS/OpenMS
-        ref: release/${{ env.OPENMS_VERSION }}
-        path: 'OpenMS'
-
-    - name: Install Qt (Windows)
-      uses: jurplel/install-qt-action@v4
-      with:
-        version: '6.8.3'    ## Note this version is build with win64_msvc2022_64 and should always match what we use
-        arch: 'win64_msvc2022_64'
-        cache: 'false'
-        archives: 'qtsvg qtimageformats qtbase'
-
-    # https://github.com/marketplace/actions/visual-studio-shell
-    - name: Set up Visual Studio shell
-      uses: egor-tensin/vs-shell@v2
-      with:
-        arch: x64
+    - id: out
+      run: echo "topp-tools=$TOPP_TOOLS" >> "$GITHUB_OUTPUT"
 
-    - name: Setup build tools
-      shell: bash
-      run: |
-        choco install ccache ninja -y --no-progress
-        choco install cmake --version=3.31.12 -y --no-progress --force
-        ## GH CLI "SHOULD BE" installed. Sometimes I had to manually install nonetheless. Super weird.
-        # https://github.com/actions/runner-images/blob/main/images/win/scripts/Installers/Install-GitHub-CLI.ps1
-        echo "C:/Program Files (x86)/GitHub CLI" >> $GITHUB_PATH
-
-    - name: Extract branch/PR infos
-      shell: bash
-      run: |
-        cd OpenMS
-        RUN_NAME_LOCAL=$(echo ${GITHUB_REF#refs/heads/} | tr / -)
-        echo "RUN_NAME=${RUN_NAME_LOCAL}" >> $GITHUB_ENV
-        echo "BASE_REF=$(gh pr view --json baseRefName -q .baseRefName || echo ${RUN_NAME_LOCAL})" >> $GITHUB_ENV
-      id: extract_branch
-      env:
-        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-
-    - name: Cache contrib
-      id: cache-contrib-win
-      uses: actions/cache@v4
-      with:
-        path: ${{ github.workspace }}/OpenMS/contrib
-        key: ${{ runner.os }}-contrib-${{ env.OPENMS_CONTRIB_VERSION || env.OPENMS_VERSION }}
-
-    - name: Load contrib build
-      if: steps.cache-contrib-win.outputs.cache-hit != 'true'
-      env:
-        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      run: |
-        cd OpenMS/contrib
-        # Download the file using the URL fetched from GitHub
-        gh release download release/${{ env.OPENMS_CONTRIB_VERSION || env.OPENMS_VERSION }} -R OpenMS/contrib --pattern 'contrib_build-Windows.tar.gz'
-        # Extract the archive
-        7z x -so contrib_build-Windows.tar.gz | 7z x -si -ttar
-        rm contrib_build-Windows.tar.gz
-        ls
-
-    - name: Add contrib to PATH
-      shell: bash
-      run: |
-        # Add contrib library path for runtime DLL resolution
-        echo "${{ github.workspace }}/OpenMS/contrib/lib" >> $GITHUB_PATH
-
-    - name: Setup ccache cache
-      uses: actions/cache@v4
-      with:
-        path: .ccache
-        key: ${{ runner.os }}-ccache-${{ env.RUN_NAME }}-${{ github.run_number }}
-        # Restoring: From current branch, otherwise from base branch, otherwise from any branch.
-        restore-keys: |
-          ${{ runner.os }}-ccache-${{ env.RUN_NAME }}
-          ${{ runner.os }}-ccache-${{ env.BASE_REF }}
-          ${{ runner.os }}-ccache-
-
-    - name: Add THIRDPARTY
-      shell: bash
-      run: |
-          # initialize THIRDPARTY
-          cd OpenMS
-          git submodule update --init THIRDPARTY
-          cd ..
-          # add third-party binaries to PATH
-          # use flat THIRDPARTY structure
-          mkdir -p _thirdparty
-          cp -R OpenMS/THIRDPARTY/Windows/x86_64/* _thirdparty/
-          cp -R OpenMS/THIRDPARTY/All/* _thirdparty/
-          # add third-party binaries to PATH
-          for thirdpartytool in ${{ github.workspace }}/_thirdparty/*
-          do
-            echo $thirdpartytool >> $GITHUB_PATH
-          done
-
-    - name: Build Windows
-      shell: bash
-      run: |
-          mkdir $GITHUB_WORKSPACE/OpenMS/bld/
-          bash OpenMS/tools/ci/capture-env.sh -v $GITHUB_WORKSPACE/OpenMS/bld/CMakeCache.txt
-          ctest --output-on-failure -V -S $GITHUB_WORKSPACE/OpenMS/tools/ci/cibuild.cmake
-      env:
-          OPENMS_CONTRIB_LIBS: "${{ github.workspace }}/OpenMS/contrib"
-          CI_PROVIDER: "GitHub-Actions"
-          CMAKE_GENERATOR: "Ninja"
-          SOURCE_DIRECTORY: "${{ github.workspace }}/OpenMS"
-          BUILD_NAME: "${{ env.RUN_NAME }}-Win64-class-topp-${{ github.run_number }}"
-          ENABLE_STYLE_TESTING: "OFF"
-          ENABLE_TOPP_TESTING: "ON"
-          ENABLE_CLASS_TESTING: "ON"
-          WITH_GUI: "OFF"
-          WITH_PARQUET: "OFF"
-          ADDRESS_SANITIZER: "Off"
-          BUILD_TYPE: "Release"
-          OPENMP: "Off"
-          USE_STATIC_BOOST: "On"
-          #  BUILD_FLAGS: "-p:CL_MPCount=2" # For VS Generator and MSBuild
-          BUILD_FLAGS: "-j2" # Ninja will otherwise use all cores (doesn't go well in GHA)
-          CMAKE_CCACHE_EXE: "ccache"
-          CCACHE_BASEDIR: ${{ github.workspace }}
-          CCACHE_DIR: ${{ github.workspace }}/.ccache
-          CCACHE_COMPRESS: true
-          CCACHE_COMPRESSLEVEL: 12
-          CCACHE_MAXSIZE: 400M
-
-    - name: Test Windows
-      shell: bash
-      run: ctest --output-on-failure -V -S $GITHUB_WORKSPACE/OpenMS/tools/ci/citest.cmake
-      env:
-          SOURCE_DIRECTORY: "${{ github.workspace }}/OpenMS"
-          CI_PROVIDER: "GitHub-Actions"
-          BUILD_NAME: "${{ env.RUN_NAME }}-Win64-class-topp-${{ github.run_number }}"
-
-    - name: Package
-      shell: bash
-      run: |
-          ctest --output-on-failure -V -S $GITHUB_WORKSPACE/OpenMS/tools/ci/cipackage.cmake
-      env:
-          SOURCE_DIRECTORY: "${{ github.workspace }}/OpenMS"
-          PACKAGE_TYPE: zip
-          SEARCH_ENGINES_DIRECTORY: "${{ github.workspace }}/_thirdparty"
-          CI_PROVIDER: "GitHub-Actions"
-          CPACK_PACKAGE_FILE_NAME: "openms-package"
-
-    - name: Upload package as artifact
-      uses: actions/upload-artifact@v4
-      with:
-        name: openms-package
-        path: ${{ github.workspace }}/OpenMS/bld/*.zip
+  # OpenMS TOPP tools, DLLs and share/ from the official Windows installer.
+  # See docs/openms-windows-workflow.md for the inputs, including `mode: source`
+  # for building a branch or fork. App repositories call the same workflow as
+  # OpenMS/streamlit-template/.github/workflows/openms-windows.yml@<ref>.
+  build-openms:
+    needs: config
+    uses: ./.github/workflows/openms-windows.yml
+    with:
+      openms-version: "3.5.0"
+      mode: installer
+      topp-tools: ${{ needs.config.outputs.topp-tools }}
+      artifact-name: openms-package
 
   build-executable:
     runs-on: windows-2022