OpenMS · Copilot · Dec 3, 2025 · Dec 3, 2025 · Dec 3, 2025 · Dec 3, 2025
diff --git a/.github/workflows/build-windows-executable-app-with-pyinstaller.yaml b/.github/workflows/build-windows-executable-app-with-pyinstaller.yaml
@@ -3,12 +3,16 @@ on:
   workflow_dispatch:
 env:
   OPENMS_VERSION: 3.2.0 
+  # Control whether to build pyOpenMS from source (true) or use pip (false). Default: false
+  BUILD_PYOPENMS: false
   # Define needed TOPP tools here
   TOPP_TOOLS: "FeatureFinderMetabo MetaboliteAdductDecharger SiriusExport"
 
 jobs:
   build-openms:
     runs-on: windows-latest
+    env:
+      PYTHON_VERSION: 3.11.0
 
     steps:
     - name: Checkout
@@ -53,6 +57,19 @@ jobs:
         # 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: Set up Python for pyOpenMS build
+      if: env.BUILD_PYOPENMS == 'true'
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ env.PYTHON_VERSION }}
+
+    - name: Install Python dependencies for pyOpenMS build
+      if: env.BUILD_PYOPENMS == 'true'
+      shell: bash
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install setuptools wheel nose 'cython<3.1' 'autowrap<0.23' numpy
+
     - name: Extract branch/PR infos
       shell: bash
       run: |
@@ -133,6 +150,7 @@ jobs:
           BUILD_TYPE: "Release"
           OPENMP: "Off"
           USE_STATIC_BOOST: "On"
+          PYOPENMS: "${{ env.BUILD_PYOPENMS == 'true' && 'ON' || 'OFF' }}"
           #  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"
@@ -142,6 +160,28 @@ jobs:
           CCACHE_COMPRESSLEVEL: 12
           CCACHE_MAXSIZE: 400M
 
+    - name: Build pyOpenMS
+      if: env.BUILD_PYOPENMS == 'true'
+      shell: bash
+      run: |
+          cd $GITHUB_WORKSPACE/OpenMS/bld/
+          ninja pyopenms
+
+    - name: Package pyOpenMS wheel
+      if: env.BUILD_PYOPENMS == 'true'
+      shell: bash
+      run: |
+          cd $GITHUB_WORKSPACE/OpenMS/bld/pyOpenMS
+          python -m pip install wheel
+          python setup.py bdist_wheel
+
+    - name: Upload pyOpenMS wheel as artifact
+      if: env.BUILD_PYOPENMS == 'true'
+      uses: actions/upload-artifact@v4
+      with:
+        name: pyopenms-wheel
+        path: ${{ github.workspace }}/OpenMS/bld/pyOpenMS/dist/*.whl
+
     - name: Package
       shell: bash
       run: |
@@ -197,14 +237,27 @@ jobs:
       with:
         python-version: ${{ env.PYTHON_VERSION }}
 
+    - name: Download pyOpenMS wheel (if built from source)
+      if: env.BUILD_PYOPENMS == 'true'
+      uses: actions/download-artifact@v4
+      with:
+        name: pyopenms-wheel
+        path: pyopenms-wheel
+
     - name: Setup virtual environment
       shell: cmd
       run: |
         python -m venv myenv
 
         call myenv\Scripts\activate.bat   
 
-        pip install -r requirements.txt
+        if "${{ env.BUILD_PYOPENMS }}" == "true" (
+          pip install pyopenms-wheel/*.whl
+          findstr /v /r /c:"^pyopenms" requirements.txt > requirements_filtered.txt
+          pip install -r requirements_filtered.txt
+        ) else (
+          pip install -r requirements.txt
+        )
 
         pip install pyinstaller
 

diff --git a/.github/workflows/build-windows-executable-app.yaml b/.github/workflows/build-windows-executable-app.yaml
@@ -15,6 +15,8 @@ permissions:
 env:
   OPENMS_VERSION: 3.2.0 
   PYTHON_VERSION: 3.11.0
+  # Control whether to build pyOpenMS from source (true) or use pip (false). Default: false
+  BUILD_PYOPENMS: false
   # Name of the installer
   APP_NAME: OpenMS-StreamlitTemplateApp
   # Define unique GUID for UpgradeCode
@@ -70,6 +72,19 @@ jobs:
         # 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: Set up Python for pyOpenMS build
+      if: env.BUILD_PYOPENMS == 'true'
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ env.PYTHON_VERSION }}
+
+    - name: Install Python dependencies for pyOpenMS build
+      if: env.BUILD_PYOPENMS == 'true'
+      shell: bash
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install setuptools wheel nose 'cython<3.1' 'autowrap<0.23' numpy
+
     - name: Extract branch/PR infos
       shell: bash
       run: |
@@ -150,6 +165,7 @@ jobs:
           BUILD_TYPE: "Release"
           OPENMP: "Off"
           USE_STATIC_BOOST: "On"
+          PYOPENMS: "${{ env.BUILD_PYOPENMS == 'true' && 'ON' || 'OFF' }}"
           #  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"
@@ -159,6 +175,28 @@ jobs:
           CCACHE_COMPRESSLEVEL: 12
           CCACHE_MAXSIZE: 400M
 
+    - name: Build pyOpenMS
+      if: env.BUILD_PYOPENMS == 'true'
+      shell: bash
+      run: |
+          cd $GITHUB_WORKSPACE/OpenMS/bld/
+          ninja pyopenms
+
+    - name: Package pyOpenMS wheel
+      if: env.BUILD_PYOPENMS == 'true'
+      shell: bash
+      run: |
+          cd $GITHUB_WORKSPACE/OpenMS/bld/pyOpenMS
+          python -m pip install wheel
+          python setup.py bdist_wheel
+
+    - name: Upload pyOpenMS wheel as artifact
+      if: env.BUILD_PYOPENMS == 'true'
+      uses: actions/upload-artifact@v4
+      with:
+        name: pyopenms-wheel
+        path: ${{ github.workspace }}/OpenMS/bld/pyOpenMS/dist/*.whl
+
     - name: Test Windows
       shell: bash
       run: ctest --output-on-failure -V -S $GITHUB_WORKSPACE/OpenMS/tools/ci/citest.cmake
@@ -251,8 +289,26 @@ jobs:
       run: |
         sed -i 's/#import site/import site/' python-${{ env.PYTHON_VERSION }}/python311._pth
 
-    - name: Install Required Packages
-      run: .\python-${{ env.PYTHON_VERSION }}\python -m pip install --force-reinstall -r requirements.txt --no-warn-script-location
+    - name: Download pyOpenMS wheel (if built from source)
+      if: env.BUILD_PYOPENMS == 'true'
+      uses: actions/download-artifact@v4
+      with:
+        name: pyopenms-wheel
+        path: pyopenms-wheel
+
+    - name: Install pyOpenMS from wheel (if built from source)
+      if: env.BUILD_PYOPENMS == 'true'
+      run: |
+        .\python-${{ env.PYTHON_VERSION }}\python -m pip install pyopenms-wheel/*.whl --no-warn-script-location
+
+    - name: Install Required Packages (excluding pyOpenMS if built from source)
+      run: |
+        if ("${{ env.BUILD_PYOPENMS }}" -eq "true") {
+          Get-Content requirements.txt | Where-Object { $_ -notmatch '^pyopenms([=<>!~\s]|$)' } | Set-Content requirements_filtered.txt
+          .\python-${{ env.PYTHON_VERSION }}\python -m pip install --force-reinstall -r requirements_filtered.txt --no-warn-script-location
+        } else {
+          .\python-${{ env.PYTHON_VERSION }}\python -m pip install --force-reinstall -r requirements.txt --no-warn-script-location
+        }
 
     - name: Set to offline deployment
       run: |

diff --git a/Dockerfile b/Dockerfile
@@ -2,6 +2,7 @@
 # It also adds a basic streamlit server that serves a pyOpenMS-based app.
 # hints:
 # build image and give it a name (here: streamlitapp) with: docker build --no-cache -t streamlitapp:latest --build-arg GITHUB_TOKEN=<your-github-token> . 2>&1 | tee build.log
+# To install pyOpenMS from conda instead of building from source: docker build --no-cache -t streamlitapp:latest --build-arg BUILD_PYOPENMS=OFF --build-arg GITHUB_TOKEN=<your-github-token> . 2>&1 | tee build.log
 # check if image was build: docker image ls
 # run container: docker run -p 8501:8501 streamlitappsimple:latest
 # debug container after build (comment out ENTRYPOINT) and run container with interactive /bin/bash shell
@@ -11,6 +12,8 @@ FROM ubuntu:22.04 AS setup-build-system
 ARG OPENMS_REPO=https://github.com/OpenMS/OpenMS.git
 ARG OPENMS_BRANCH=release/3.4.1
 ARG PORT=8501
+# Control whether to build pyOpenMS from source (ON) or install from conda (OFF). Default: ON
+ARG BUILD_PYOPENMS=ON
 # GitHub token to download latest OpenMS executable for Windows from Github action artifact.
 ARG GITHUB_TOKEN
 ENV GH_TOKEN=${GITHUB_TOKEN}
@@ -56,65 +59,82 @@ RUN echo "mamba activate streamlit-env" >> ~/.bashrc
 SHELL ["/bin/bash", "--rcfile", "~/.bashrc"]
 SHELL ["mamba", "run", "-n", "streamlit-env", "/bin/bash", "-c"]
 
-# Install up-to-date cmake via mamba and packages for pyOpenMS build.
+# Install up-to-date cmake via mamba and packages for pyOpenMS build (if building from source).
 RUN mamba install cmake
-RUN pip install --upgrade pip && python -m pip install -U setuptools nose 'cython<3.1' 'autowrap<0.23' pandas numpy pytest
+ARG BUILD_PYOPENMS
+RUN if [ "$BUILD_PYOPENMS" = "ON" ]; then \
+        pip install --upgrade pip && python -m pip install -U setuptools nose 'cython<3.1' 'autowrap<0.23' pandas numpy pytest; \
+    fi
 
 # Clone OpenMS branch and the associcated contrib+thirdparties+pyOpenMS-doc submodules.
-RUN git clone --recursive --depth=1 -b ${OPENMS_BRANCH} --single-branch ${OPENMS_REPO} && cd /OpenMS
+RUN if [ "$BUILD_PYOPENMS" = "ON" ]; then \
+        git clone --recursive --depth=1 -b ${OPENMS_BRANCH} --single-branch ${OPENMS_REPO} && cd /OpenMS; \
+    fi
 
 # Pull Linux compatible third-party dependencies and store them in directory thirdparty.
 WORKDIR /OpenMS
-RUN mkdir /thirdparty && \
-    git submodule update --init THIRDPARTY && \
-    cp -r THIRDPARTY/All/* /thirdparty && \
-    cp -r THIRDPARTY/Linux/x86_64/* /thirdparty && \
-    chmod -R +x /thirdparty
+ARG BUILD_PYOPENMS
+RUN if [ "$BUILD_PYOPENMS" = "ON" ]; then \
+        mkdir /thirdparty && \
+        git submodule update --init THIRDPARTY && \
+        cp -r THIRDPARTY/All/* /thirdparty && \
+        cp -r THIRDPARTY/Linux/x86_64/* /thirdparty && \
+        chmod -R +x /thirdparty; \
+    fi
 ENV PATH="/thirdparty/LuciPHOr2:/thirdparty/MSGFPlus:/thirdparty/Sirius:/thirdparty/ThermoRawFileParser:/thirdparty/Comet:/thirdparty/Fido:/thirdparty/MaRaCluster:/thirdparty/MyriMatch:/thirdparty/OMSSA:/thirdparty/Percolator:/thirdparty/SpectraST:/thirdparty/XTandem:/thirdparty/crux:${PATH}"
 
 # Build OpenMS and pyOpenMS.
 FROM setup-build-system AS compile-openms
 WORKDIR /
 
-# Set up build directory.
-RUN mkdir /openms-build
-WORKDIR /openms-build
-
-# Configure.
-RUN /bin/bash -c "cmake -DCMAKE_BUILD_TYPE='Release' -DCMAKE_PREFIX_PATH='/OpenMS/contrib-build/;/usr/;/usr/local' -DHAS_XSERVER=OFF -DBOOST_USE_STATIC=OFF -DPYOPENMS=ON ../OpenMS -DPY_MEMLEAK_DISABLE=On"
-
-# Build TOPP tools and clean up.
-RUN make -j4 TOPP
-RUN rm -rf src doc CMakeFiles
-
-# Build pyOpenMS wheels and install via pip.
-RUN make -j4 pyopenms
-WORKDIR /openms-build/pyOpenMS
-RUN pip install dist/*.whl
+ARG BUILD_PYOPENMS
+# Set up build directory and build pyOpenMS from source if enabled.
+RUN if [ "$BUILD_PYOPENMS" = "ON" ]; then \
+        mkdir /openms-build && \
+        cd /openms-build && \
+        /bin/bash -c "cmake -DCMAKE_BUILD_TYPE='Release' -DCMAKE_PREFIX_PATH='/OpenMS/contrib-build/;/usr/;/usr/local' -DHAS_XSERVER=OFF -DBOOST_USE_STATIC=OFF -DPYOPENMS=ON ../OpenMS -DPY_MEMLEAK_DISABLE=On" && \
+        make -j4 TOPP && \
+        rm -rf src doc CMakeFiles && \
+        make -j4 pyopenms && \
+        cd /openms-build/pyOpenMS && \
+        pip install dist/*.whl; \
+    fi
 
-# Install other dependencies (excluding pyopenms)
+# Install dependencies.
 COPY requirements.txt ./requirements.txt 
-RUN grep -Ev '^pyopenms([=<>!~].*)?$' requirements.txt > requirements_cleaned.txt && mv requirements_cleaned.txt requirements.txt
+RUN if [ "$BUILD_PYOPENMS" = "ON" ]; then \
+        # If building from source, exclude pyopenms from requirements.txt \
+        grep -Ev '^pyopenms([=<>!~].*)?$' requirements.txt > requirements_cleaned.txt && mv requirements_cleaned.txt requirements.txt; \
+    fi
 RUN pip install -r requirements.txt
 
 WORKDIR /
 RUN mkdir openms
 
-# Copy TOPP tools bin directory, add to PATH.
-RUN cp -r openms-build/bin /openms/bin
+ARG BUILD_PYOPENMS
+# Copy TOPP tools bin directory, add to PATH (only if built from source).
+RUN if [ "$BUILD_PYOPENMS" = "ON" ]; then \
+        cp -r openms-build/bin /openms/bin; \
+    fi
 ENV PATH="/openms/bin/:${PATH}"
 
-# Copy TOPP tools bin directory, add to PATH.
-RUN cp -r openms-build/lib /openms/lib
+# Copy TOPP tools lib directory, add to LD_LIBRARY_PATH (only if built from source).
+RUN if [ "$BUILD_PYOPENMS" = "ON" ]; then \
+        cp -r openms-build/lib /openms/lib; \
+    fi
 ENV LD_LIBRARY_PATH="/openms/lib/:${LD_LIBRARY_PATH}"
 
-# Copy share folder, add to PATH, remove source directory.
-RUN cp -r OpenMS/share/OpenMS /openms/share
-RUN rm -rf OpenMS
+# Copy share folder, add to PATH, remove source directory (only if built from source).
+RUN if [ "$BUILD_PYOPENMS" = "ON" ]; then \
+        cp -r OpenMS/share/OpenMS /openms/share && \
+        rm -rf OpenMS; \
+    fi
 ENV OPENMS_DATA_PATH="/openms/share/"
 
-# Remove build directory.
-RUN rm -rf openms-build
+# Remove build directory (only if built from source).
+RUN if [ "$BUILD_PYOPENMS" = "ON" ]; then \
+        rm -rf openms-build; \
+    fi
 
 # Prepare and run streamlit app.
 FROM compile-openms AS run-app

diff --git a/README.md b/README.md
@@ -50,6 +50,7 @@ To run the app locally:
 This repository contains two Dockerfiles.
 
 1. `Dockerfile`: This Dockerfile builds all dependencies for the app including Python packages and the OpenMS TOPP tools. Recommended for more complex workflows where you want to use the OpenMS TOPP tools for instance with the **TOPP Workflow Framework**.
+   - By default, it builds pyOpenMS from source. To install pyOpenMS from conda instead, use `--build-arg BUILD_PYOPENMS=OFF`.
 2. `Dockerfile_simple`: This Dockerfile builds only the Python packages. Recommended for simple apps using pyOpenMS only.
 
 1. **Install Docker**
@@ -116,6 +117,23 @@ This repository contains two Dockerfiles.
       docker run -p 8505:8501 openms_streamlit_template
       ```
 
+## ⚙️ Build Configuration
+
+### pyOpenMS Build Options
+
+You can control whether pyOpenMS is built from source or installed from conda/pip:
+
+#### Docker
+- **Build from source (default)**: `docker build -t streamlitapp:latest .`
+- **Install from conda**: `docker build --build-arg BUILD_PYOPENMS=OFF -t streamlitapp:latest .`
+
+#### Windows Workflows
+The GitHub Actions workflows (`build-windows-executable-app.yaml` and `build-windows-executable-app-with-pyinstaller.yaml`) can be configured via the `BUILD_PYOPENMS` environment variable:
+- **Install from pip (default)**: `BUILD_PYOPENMS: false`
+- **Build from source**: `BUILD_PYOPENMS: true`
+
+Change this value in the workflow file under the `env:` section to enable building pyOpenMS from source.
+
 ## Documentation
 
 Documentation for **users** and **developers** is included as pages in [this template app](https://abi-services.cs.uni-tuebingen.de/streamlit-template/), indicated by the 📖 icon.