Make pyOpenMS build optional in Dockerfile and Windows workflows

[Copilot]

The Dockerfile built pyOpenMS from source while Windows workflows installed from pip, creating an inconsistency.

Changes

Dockerfile

• Added BUILD_PYOPENMS build arg (default: ON)
  • ON: Builds OpenMS and pyOpenMS from source (existing behavior)
  • OFF: Installs pyOpenMS from conda
• Wrapped all OpenMS/pyOpenMS build steps in conditional blocks

ARG BUILD_PYOPENMS=ON
RUN if [ "$BUILD_PYOPENMS" = "ON" ]; then \
        mkdir /openms-build && cd /openms-build && \
        cmake -DPYOPENMS=ON ../OpenMS && \
        make -j4 pyopenms && \
        pip install dist/*.whl; \
    fi

Windows Workflows

• Added BUILD_PYOPENMS env var (default: false) to both build-windows-executable-app.yaml and build-windows-executable-app-with-pyinstaller.yaml
  • false: Installs from pip (existing behavior)
  • true: Builds from source
• Added conditional build steps in build-openms job:
  • Python setup and build dependencies (cython, autowrap, numpy)
  • CMake configuration with PYOPENMS flag
  • Ninja build and wheel packaging
  • Artifact upload
• Added conditional install in build-executable job:
  • Downloads wheel artifact when built from source
  • Filters pyOpenMS from requirements.txt to avoid conflicts

Documentation

• Updated README with build configuration options
• Added usage examples for both Docker and workflow configurations

Defaults preserve existing behavior: Dockerfile builds from source, Windows workflows use pip.

Original prompt

---

This section details on the original issue you should resolve

<issue_title>Make pyOpenMS build Optional</issue_title>
<issue_description>I noticed our process is a bit inconsistent at the moment. The Dockerfile builds pyOpenMS from source but the windows installer workflow does not. To make it consistent I suggest the following:

• Add an environment variable to Dockerfile to not build pyOpenMS but get it from conda
• Add the option to build pyOpenMS for the windows installers</issue_description>

Comments on the Issue (you are @copilot in this section)

• Fixes Make pyOpenMS build Optional #245

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