CI: take the OpenMS core from the nightly SDK by default

.github/actions/openms-core/action.yml

@@ -17,12 +17,13 @@ description: >-
             no TOPP tools and no example data).
 
   THE DEFAULT MODE (used when 'mode' is empty) is set in the first step below,
-  DEFAULT_MODE: 'source', because the nightlies and releases of OpenMS up to now are
-  built WITH_GUI=ON: their tool registry lists ExecutePipeline and ImageCreator,
-  which cmake/find_openms.cmake rejects (both registries in one installation make
-  every TOPP tool fail). Once OpenMS no longer has the WITH_GUI option and a nightly
-  without the GUI is published, change it to 'sdk'. That is the only place to
-  change: the workflows pass a mode only where they need a specific one.
+  DEFAULT_MODE: 'sdk', the published nightly (or release) of OpenMS. Nightlies from
+  before the GUI moved here (before 2026-11-09) are built WITH_GUI=ON: their tool
+  registry lists ExecutePipeline and ImageCreator, which cmake/find_openms.cmake
+  rejects (both registries in one installation make every TOPP tool fail); build the
+  core with mode 'source' to test against such a commit, or against an OpenMS change
+  that is not in a nightly yet. That is the only place to change: the workflows pass
+  a mode only where they need a specific one.
 
 inputs:
   mode:
@@ -51,6 +52,12 @@ inputs:
       release X.Y.Z
     required: false
     default: "latest"
+  wait:
+    description: >-
+      sdk: minutes to wait for the folder given by 'version' while it is not complete yet
+      (it is still being uploaded); not used for 'latest'
+    required: false
+    default: "0"
   sdk:
     description: >-
       sdk: 'false' installs only the OpenMS installer (prefix_path is then empty), for
@@ -101,9 +108,8 @@ runs:
       shell: bash
       env:
         MODE: ${{ inputs.mode }}
-        # The default mode: 'source' while the OpenMS nightlies still contain the GUI,
-        # then 'sdk' (see the description of this action).
-        DEFAULT_MODE: source
+        # The default mode (see the description of this action).
+        DEFAULT_MODE: sdk
       run: |
         mode=${MODE:-$DEFAULT_MODE}
         case "$mode" in
@@ -391,6 +397,7 @@ runs:
         CHANNEL: ${{ inputs.channel }}
         VERSION: ${{ inputs.version }}
         NEED_SDK: ${{ inputs.sdk }}
+        OPENMS_SDK_WAIT_MINUTES: ${{ inputs.wait }}
       run: |
         bash "$GITHUB_ACTION_PATH/resolve-sdk.sh" "$CHANNEL" "$VERSION" "$RUNNER_OS" "$RUNNER_ARCH" "$NEED_SDK" |
           tee -a "$GITHUB_OUTPUT"
@@ -424,6 +431,7 @@ runs:
         CORE_DIR: ${{ steps.setup.outputs.core_dir }}
         DOWNLOAD_DIR: ${{ steps.setup.outputs.download_dir }}
         SDK_NAME: ${{ steps.sdk-resolve.outputs.sdk_name }}
+        FULLSTRING: ${{ steps.sdk-resolve.outputs.version_fullstring }}
       run: |
         set -euo pipefail
         rm -rf "$CORE_DIR"
@@ -440,6 +448,20 @@ runs:
           ls "$CORE_DIR"
           exit 1
         fi
+        # The SDK and the installer must come from one build of OpenMS: the GUI layer is
+        # compiled against the SDK and run against the installer. A folder of the archive
+        # can hold both from different builds while a later run of the same day is
+        # uploading. The SDK's CMake package names its full version string.
+        sdk_fullstring=$(sed -n 's/^set(OpenMS_VERSION_FULLSTRING "\(.*\)")[[:space:]]*$/\1/p' \
+          "$sdk_dir/lib/cmake/OpenMS/OpenMSConfig.cmake" "$sdk_dir/CMake/OpenMSConfig.cmake" 2>/dev/null | head -n 1 || true)
+        if [[ -z "$sdk_fullstring" ]]; then
+          echo >&2 "ERROR: the SDK's OpenMSConfig.cmake names no OpenMS_VERSION_FULLSTRING (an OpenMS from before 3.7, which this GUI layer cannot use)"
+          exit 1
+        fi
+        if [[ "$sdk_fullstring" != "$FULLSTRING" ]]; then
+          echo >&2 "ERROR: the SDK is OpenMS $sdk_fullstring, the installer OpenMS $FULLSTRING: they come from different builds (an upload in progress?)"
+          exit 1
+        fi
         echo "sdk_dir=$sdk_dir" >>"$GITHUB_OUTPUT"
 
     - name: Install the OpenMS Installer (Linux)

.github/actions/openms-core/resolve-sdk.sh

@@ -22,7 +22,8 @@
 #
 # Prints shell assignments (version, sdk_name, sdk_url, installer_name,
 # installer_url, version_fullstring), e.g. for >> "$GITHUB_OUTPUT".
-# OPENMS_ARCHIVE_URL overrides the base URL.
+# OPENMS_ARCHIVE_URL overrides the base URL. OPENMS_SDK_WAIT_MINUTES (default 0) waits for a
+# given version (not latest) whose folder is not complete yet.
 set -euo pipefail
 
 if [[ $# -lt 4 || $# -gt 5 ]]; then
@@ -93,13 +94,13 @@ find_in_folder() {
 if [[ "$version" == latest ]]; then
   # newest first; a folder of a release or nightly that is still being uploaded,
   # or whose build failed on this platform, is passed over
-  mapfile -t folders < <(listing "$base/$channel" | sed 's#/$##' | grep -E "$folder_regex" | sort -rV | head -n 10)
-  for folder in "${folders[@]}"; do
+  # (a read loop, not mapfile: macOS has bash 3.2; fd 3 keeps the loop's stdin free)
+  while IFS= read -r folder <&3; do
     if find_in_folder "$folder"; then
       exit 0
     fi
     echo >&2 "note: $base/$channel/$folder has no complete set for $os-$arch, trying the one before"
-  done
+  done 3< <(listing "$base/$channel" | sed 's#/$##' | grep -E "$folder_regex" | sort -rV | head -n 10)
   echo >&2 "ERROR: none of the newest folders of $base/$channel has the SDK ($sdk_suffix) and the installer ($installer_suffix)"
   exit 1
 fi
@@ -111,7 +112,16 @@ if ! grep -qE "$folder_regex" <<<"$version"; then
   echo >&2 "ERROR: '$version' is not a version of the $channel channel"
   exit 2
 fi
-if ! find_in_folder "$version"; then
-  echo >&2 "ERROR: $base/$channel/$version has no SDK OpenMS-SDK-$version-$sdk_suffix and installer OpenMS-<version>-$installer_suffix"
-  exit 1
-fi
+# A given folder may still be uploading (the nightly of the GUI layer can start before
+# OpenMS's nightly is published): wait up to OPENMS_SDK_WAIT_MINUTES for it.
+wait_minutes=${OPENMS_SDK_WAIT_MINUTES:-0}
+waited=0
+until find_in_folder "$version"; do
+  if (( waited >= wait_minutes )); then
+    echo >&2 "ERROR: $base/$channel/$version has no SDK OpenMS-SDK-$version-$sdk_suffix and installer OpenMS-<version>-$installer_suffix"
+    exit 1
+  fi
+  echo >&2 "note: $base/$channel/$version is not complete for $os-$arch yet, waiting ($waited of $wait_minutes minutes)"
+  sleep 300
+  waited=$((waited + 5))
+done

.github/workflows/release.yml

@@ -136,11 +136,14 @@ jobs:
         id: core
         uses: ./.github/actions/openms-core
         with:
-          mode: ${{ inputs.core_mode }}
+          # an explicit core_ref is built from source (the SDK has no ref to choose)
+          mode: ${{ inputs.core_mode || (inputs.core_ref != '' && 'source') || '' }}
           ref: ${{ needs.version.outputs.core_ref }}
           exact: "true"
           channel: ${{ needs.version.outputs.core_channel }}
           version: ${{ needs.version.outputs.version }}
+          # the nightly of OpenMS may still be uploading when the GUI nightly starts
+          wait: ${{ needs.version.outputs.core_channel == 'nightly' && '120' || '0' }}
           ssh_key: ${{ secrets.ARCHIVE_RRSYNC_SSH }}
           ssh_host: ${{ secrets.ARCHIVE_RRSYNC_HOST }}
           ssh_port: ${{ secrets.ARCHIVE_RRSYNC_PORT }}

.github/workflows/test.yml

@@ -98,7 +98,8 @@ jobs:
         id: core
         uses: ./.github/actions/openms-core
         with:
-          mode: ${{ inputs.core_mode }}
+          # an explicit core_ref is built from source (the SDK has no ref to choose)
+          mode: ${{ inputs.core_mode || (inputs.core_ref != '' && 'source') || '' }}
           ref: ${{ inputs.core_ref || env.OPENMS_CORE_DEFAULT_REF }}
           exact: ${{ inputs.core_exact && 'true' || 'false' }}
           channel: ${{ inputs.core_channel || 'nightly' }}