Merge branch 'develop' into 3.3.0_to_merge

Author: poshul

.devcontainer/devcontainer.json

@@ -1,6 +1,6 @@
 {
     "name": "OpenMS Dev Container",
-    "image": "ghcr.io/openms/contrib_manylinux_2_28:latest",
+    "image": "ghcr.io/openms/contrib_manylinux_2_34:latest",
     "customizations": {
         "vscode": {
             "extensions": [
@@ -31,4 +31,4 @@
         }
     },
     "postCreateCommand": "yum install openssh-clients -y"
-}
+}

.github/workflows/bioconda_deploy.yaml

@@ -0,0 +1,79 @@
+name: Deploy to Bioconda
+
+on:
+  workflow_dispatch:
+    inputs:
+      branch:
+        description: "Branch to deploy from"
+        required: true
+        default: "nightly"
+  push:
+    branches:
+      - nightly
+
+jobs:
+  bioconda-deploy:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -le {0}  # Important! Use login shell for proper conda initialization
+        
+    steps:
+      - name: Set up Conda
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          activate-environment: bioconda_env
+          auto-update-conda: true
+          #environment-file: environment.yml # Replace with your Conda environment file if necessary
+          python-version: 3.9
+          channels: conda-forge,bioconda,defaults
+          channel-priority: true
+
+      - name: Prepare output directory
+        run: |       
+          mkdir -p $GITHUB_WORKSPACE/output/noarch
+          touch $GITHUB_WORKSPACE/output/noarch/repodata.json
+          conda install bioconda-utils -y
+          conda index $GITHUB_WORKSPACE/output
+          ls -l
+          ls -l $GITHUB_WORKSPACE/output
+
+      - name: Configure Git
+        run: |
+          git config --global user.name "GitHub Actions"
+          git config --global user.email "[email protected]"
+          
+      - name: Clone Bioconda recipes repository and add our changes (e.g., version with 'dev') on top of it
+        run: |
+          git clone https://github.com/OpenMS/bioconda-recipes.git bioconda-recipes
+          cd bioconda-recipes
+          git checkout -b nightly origin/nightly
+          git remote add bioconda https://github.com/bioconda/bioconda-recipes.git
+          git fetch bioconda master
+          git rebase bioconda/master         
+
+      - name: Lint and build OpenMS Bioconda packages
+        run: |
+          cd bioconda-recipes
+          bioconda-utils lint --packages pyopenms openms-meta
+          bioconda-utils build --docker --pkg_dir $GITHUB_WORKSPACE/output --packages openms-meta || true
+          conda index $GITHUB_WORKSPACE/output
+          
+      - name: Build pyopenms package
+        run: |
+          cd bioconda-recipes
+          bioconda-utils build --docker --mulled-test --pkg_dir $GITHUB_WORKSPACE/output --packages pyopenms || true
+          conda index $GITHUB_WORKSPACE/output
+
+      - name: Upload Conda packages
+        run: |
+          cd bioconda-recipes
+          ls -l $GITHUB_WORKSPACE/output
+          anaconda -v -t ${{ secrets.ANACONDA_TOKEN }} upload -u openms --no-progress --force $GITHUB_WORKSPACE/output/linux-64/*.tar.bz2
+
+      - name: Check upload status
+        run: |
+          if [[ $? -ne 0 ]]; then
+            echo "Upload failed!"
+            exit 1
+          fi

.github/workflows/codium-pr-agent.yml

@@ -1,4 +1,4 @@
-name: deploy-container-images
+name: Deploy container images
 on:
   workflow_dispatch:
   push:
@@ -40,18 +40,6 @@ jobs:
             ## Remove release/ from release branch name (or keep the non-release name)
             echo "tag=${BRANCH#release/}" >> $GITHUB_OUTPUT
         id: tag_name
-      - name: Define contrib image tag
-        id: contrib_tag
-        shell: bash
-        run: |
-            # the contrib image tag is the same as the main image tag for release branches
-            # for non-release branches, we use the latest contrib image
-            if [[ "${{ steps.extract_branch.outputs.branch }}" == "release/"* ]]
-            then
-              echo "contrib_tag=${{ steps.tag_name.outputs.tag }}" >> $GITHUB_OUTPUT
-            else
-              echo "contrib_tag=latest" >> $GITHUB_OUTPUT
-            fi
       - name: Downcase REPO
         run: echo "repo=${GITHUB_REPOSITORY,,}" >> $GITHUB_OUTPUT
         id: downcase_repo
@@ -67,22 +55,6 @@ jobs:
         uses: actions/checkout@v4
         with:
           fetch-depth: 1
-      - name: Checkout contrib submodule repository
-        run: git submodule update --init contrib
-        # we only need the contrib submodule if we're on a release branch
-        # otherwise, we use the latest contrib image built in the OpenMS/contrib
-        if: startsWith(steps.extract_branch.outputs.branch, 'release/')
-      - name: Build contrib container using the correct submodule hash
-        uses: docker/build-push-action@v6
-        with:
-          push: true
-          context: contrib
-          file: contrib/dockerfiles/Dockerfile
-          tags: |
-            ghcr.io/openms/contrib:${{ steps.tag_name.outputs.tag }}
-          cache-from: type=gha
-          cache-to: type=gha,mode=max
-        if: startsWith(steps.extract_branch.outputs.branch, 'release/')
       - name: Test docker build in runtime base
         uses: docker/build-push-action@v5
         with:
@@ -93,9 +65,8 @@ jobs:
             NUM_BUILD_CORES=4
             BUILDKIT_CONTEXT_KEEP_GIT_DIR=1
             OPENMS_VERSION_TAG=${{ steps.tag_name.outputs.tag }}
-            CONTRIB_IMAGE_TAG=${{ steps.contrib_tag.outputs.contrib_tag }}
-          cache-from: type=gha
-          cache-to: type=gha,mode=max
+          # cache-from: type=gha
+          # cache-to: type=gha,mode=max
       - name: Build and push library image
         uses: docker/build-push-action@v5
         with:
@@ -106,11 +77,10 @@ jobs:
             NUM_BUILD_CORES=4
             BUILDKIT_CONTEXT_KEEP_GIT_DIR=1
             OPENMS_VERSION_TAG=${{ steps.tag_name.outputs.tag }}
-            CONTRIB_IMAGE_TAG=${{ steps.contrib_tag.outputs.contrib_tag }}
           tags: |
             ghcr.io/${{ steps.downcase_repo.outputs.repo }}-library:${{ steps.tag_name.outputs.tag }}
-          cache-from: type=gha
-          cache-to: type=gha,mode=max
+          # cache-from: type=gha
+          # cache-to: type=gha,mode=max
       - name: Build and push tools image
         uses: docker/build-push-action@v6
         with:
@@ -121,12 +91,11 @@ jobs:
             NUM_BUILD_CORES=4
             BUILDKIT_CONTEXT_KEEP_GIT_DIR=1
             OPENMS_VERSION_TAG=${{ steps.tag_name.outputs.tag }}
-            CONTRIB_IMAGE_TAG=${{ steps.contrib_tag.outputs.contrib_tag }}
           tags: |
             ghcr.io/${{ steps.downcase_repo.outputs.repo }}-executables:${{ steps.tag_name.outputs.tag }}
             ghcr.io/${{ steps.downcase_repo.outputs.repo }}-tools:${{ steps.tag_name.outputs.tag }}
-          cache-from: type=gha
-          cache-to: type=gha,mode=max
+          # cache-from: type=gha
+          # cache-to: type=gha,mode=max
       - name: Build and push tools + thirdparty image
         uses: docker/build-push-action@v5
         with:
@@ -137,11 +106,10 @@ jobs:
             NUM_BUILD_CORES=4
             BUILDKIT_CONTEXT_KEEP_GIT_DIR=1
             OPENMS_VERSION_TAG=${{ steps.tag_name.outputs.tag }}
-            CONTRIB_IMAGE_TAG=${{ steps.contrib_tag.outputs.contrib_tag }}
           tags: |
             ghcr.io/${{ steps.downcase_repo.outputs.repo }}-tools-thirdparty:${{ steps.tag_name.outputs.tag }}
-          cache-from: type=gha
-          cache-to: type=gha,mode=max
+          # cache-from: type=gha
+          # cache-to: type=gha,mode=max
   deploy-singularity:
     runs-on: ubuntu-latest
     needs: deploy-docker
@@ -152,6 +120,11 @@ jobs:
           registry: ghcr.io
           username: ${{ github.actor }}
           password: ${{ secrets.GITHUB_TOKEN }}
+      # install glib2.0 development package needed by singularity
+      - name: Install Dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y libglib2.0-dev          
       - name: Singularity install with defaults
         uses: singularityhub/install-singularity@main
         with:

.github/workflows/containerdeploy.yml

@@ -216,11 +216,10 @@ jobs:
 
     - name: Install Qt (Windows)
       if: startsWith(matrix.os, 'windows')
-      uses: jurplel/install-qt-action@v3
+      uses: jurplel/install-qt-action@v4
       with:
-        version: '5.15.2' # 5.12.7 is broken https://bugreports.qt.io/browse/QTBUG-81715, > 5.15.2 is not available on official archives (https://github.com/miurahr/aqtinstall/issues/636)
+        version: '6.7.2'
         cache: 'false'
-        aqtversion: '==3.1.*'
         archives: 'qtsvg qtimageformats qtbase'
 
     - name: Setup build tools (and system contrib on Linux and Mac)
@@ -234,7 +233,7 @@ jobs:
           sudo add-apt-repository universe
           sudo apt update   
           sudo apt-get -qq install -y build-essential cmake autoconf patch libtool git automake ninja-build xvfb ccache
-          sudo apt-get -qq install -y qtbase5-dev libqt5svg5-dev libqt5opengl5-dev
+          sudo apt-get -qq install -y qt6-base-dev libqt6svg6-dev libqt6opengl6-dev libqt6openglwidgets6 libgl-dev
           sudo apt-get -qq install -y libeigen3-dev libboost-random-dev libboost-regex-dev libboost-iostreams-dev \
            libboost-date-time-dev libboost-math-dev libxerces-c-dev zlib1g-dev libsvm-dev libbz2-dev coinor-libcoinmp-dev libhdf5-dev
           echo "cmake_prefix=" >> $GITHUB_OUTPUT
@@ -245,8 +244,8 @@ jobs:
         fi
         
         if [[ "${{ matrix.os }}" == windows-* ]]; then
-          # Qt5_DIR set by Install Qt5 step
-          echo "cmake_prefix=$Qt5_DIR/lib/cmake;$Qt5_DIR" >> $GITHUB_OUTPUT
+          # QT_ROOT_DIR set by Install Qt step
+          echo "cmake_prefix=$QT_ROOT_DIR/lib/cmake;$QT_ROOT_DIR" >> $GITHUB_OUTPUT
           choco install ccache ninja -y --no-progress
           choco install cmake -y --no-progress
           ## GH CLI "SHOULD BE" installed. Sometimes I had to manually install nonetheless. Super weird.
@@ -270,10 +269,11 @@ jobs:
           brew update
           ## Needed for Qt. Install before to overwrite the default softlinks on the GH runners
           brew install [email protected] --force --overwrite
-          brew install --quiet ccache autoconf automake libtool ninja && brew link --overwrite ccache
-          brew install libsvm xerces-c boost eigen sqlite coinutils cbc cgl clp qt@5
-          echo "cmake_prefix=$(brew --prefix qt@5)/lib/cmake;$(brew --prefix qt@5)" >> $GITHUB_OUTPUT
-          echo "Qt5_DIR=$(brew --prefix qt@5)/lib/cmake/Qt5" >> $GITHUB_ENV
+          brew install --quiet ccache autoconf automake libtool ninja libomp && brew link --overwrite ccache
+          # attempt to fix https://github.com/Homebrew/homebrew-core/issues/113176
+          brew link --force libomp
+          brew install libsvm xerces-c boost eigen sqlite coinutils cbc cgl clp qt
+          echo "cmake_prefix=$(brew --prefix qt)/lib/cmake;$(brew --prefix qt);$(brew --prefix libomp)" >> $GITHUB_OUTPUT
           brew install --quiet doxygen ghostscript graphviz
         fi
 
@@ -384,6 +384,7 @@ jobs:
           ENABLE_GCC_WERROR: "OFF" # TODO think about that
           SEARCH_ENGINES_DIRECTORY: ${{ github.workspace }}/_thirdparty
           WITH_GUI: "ON"
+          SIGNING_IDENTITY: "-"
           ADDRESS_SANITIZER: "Off"
           BUILD_TYPE: "Release"
           OPENMP: "ON"