openms-api-surface-exposure
Summary
Expose and verify OpenMS C++ API surface through nanobind-based Python bindings, enabling downstream Python code to access mass spectrometry data structures and algorithms. This skill bridges compiled C++ library functionality into importable Python modules for rapid prototyping and algorithm development.
When to use
When you need to make OpenMS C++ classes, functions, or data structures callable from Python code, or when verifying that a newly bound C++ component can be imported and instantiated without errors in a Python environment. Triggers: adding new C++ bindings to src/pyOpenMS/bindings/, building the pyOpenMS extension module from source, or testing binding completeness after CMake compilation.
When NOT to use
- Input is already a pre-built binary wheel (.whl) or conda package; use package installation instead.
- No C++ source changes are needed and only existing Python APIs are being called.
- The goal is to use OpenMS algorithms without rebuilding the extension module (use existing pyOpenMS installation from bioconda or conda-forge).
Inputs
- C++ source files in src/pyOpenMS/bindings/ with nanobind binding declarations
- CMakeLists.txt with nanobind compilation rules
- OpenMS C++ library headers and compiled object files
Outputs
- Compiled pyOpenMS Python extension module (.so on Linux, .pyd on Windows, .dylib on macOS)
- Importable Python module with bound C++ classes and functions
- Module load verification and runtime function call test results
How to apply
Navigate to src/pyOpenMS/bindings/ and review or create nanobind binding specifications according to the wrapping instructions in CLAUDE.md. Configure the CMake build system to compile the nanobind binding files into a Python extension module (.so/.pyd). Execute the CMake build process to generate the compiled pyOpenMS module. Import the generated pyOpenMS module in a Python environment (e.g., import pyOpenMS) and verify that the module loads without ImportError or missing symbol errors. Execute a simple function call or attribute access on a bound C++ class (e.g., instantiate a spectrum object, call a peak-finding method) to confirm that the binding is complete and functional. Check for runtime type errors, segmentation faults, or attribute access failures that would indicate incomplete or incorrect binding specifications.
Related tools
- nanobind (Binding code generator and C++/Python interop framework used to specify and compile OpenMS C++ classes into importable Python extension modules)
- CMake (Build system configuration tool that orchestrates nanobind compilation, linking, and extension module generation)
- OpenMS C++ library (Upstream C++ API being exposed through nanobind bindings) — https://github.com/OpenMS/OpenMS
Evaluation signals
- pyOpenMS module imports without ImportError, ModuleNotFoundError, or unresolved symbol errors.
- A bound C++ class can be instantiated from Python (e.g.,
spectrum = pyOpenMS.MSSpectrum()).
- Methods and attributes on bound objects are callable and return expected types without segmentation faults.
- No AttributeError or TypeError when accessing bound functions with correct argument types.
- CMake build log shows zero compilation warnings or errors in nanobind binding code.
Limitations
- The provided document fragment does not contain the full technical specification of binding file structure or module import verification process, limiting detailed guidance on binding specification syntax.
- Nanobind binding completeness depends on manual specification of each C++ class/function to expose; not all OpenMS C++ API is automatically bound.
- Platform-specific compilation issues may occur on Windows, macOS, and Linux due to different C++ toolchains and nanobind ABI requirements.
- Binding layer may introduce performance overhead compared to native C++ for computationally intensive workflows.
Evidence
- [other] Navigate to the src/pyOpenMS/bindings/ directory and review nanobind binding specifications according to CLAUDE.md wrapping instructions.: "Navigate to the src/pyOpenMS/bindings/ directory and review nanobind binding specifications according to CLAUDE.md wrapping instructions."
- [other] Configure the build system (CMake) to compile nanobind binding files into a Python extension module.: "Configure the build system (CMake) to compile nanobind binding files into a Python extension module."
- [other] Import the generated pyOpenMS module in a Python environment and verify that the module loads without errors.: "Import the generated pyOpenMS module in a Python environment and verify that the module loads without errors."
- [readme] With pyOpenMS, OpenMS offers Python bindings to a large part of the OpenMS API to enable rapid algorithm development.: "With pyOpenMS, OpenMS offers Python bindings to a large part of the OpenMS API to enable rapid algorithm development."
- [other] Execute a simple function call or attribute access on the imported module to confirm binding completeness.: "Execute a simple function call or attribute access on the imported module to confirm binding completeness."
1---2name: openms-api-surface-exposure-23description: Use when when you need to make OpenMS C++ classes, functions, or data structures callable from Python code, or when verifying that a newly bound C++ component can be imported and instantiated without errors in a Python environment.4license: CC-BY-4.05---67# openms-api-surface-exposure89## Summary1011Expose and verify OpenMS C++ API surface through nanobind-based Python bindings, enabling downstream Python code to access mass spectrometry data structures and algorithms. This skill bridges compiled C++ library functionality into importable Python modules for rapid prototyping and algorithm development.1213## When to use1415When you need to make OpenMS C++ classes, functions, or data structures callable from Python code, or when verifying that a newly bound C++ component can be imported and instantiated without errors in a Python environment. Triggers: adding new C++ bindings to src/pyOpenMS/bindings/, building the pyOpenMS extension module from source, or testing binding completeness after CMake compilation.1617## When NOT to use1819- Input is already a pre-built binary wheel (.whl) or conda package; use package installation instead.20- No C++ source changes are needed and only existing Python APIs are being called.21- The goal is to use OpenMS algorithms without rebuilding the extension module (use existing pyOpenMS installation from bioconda or conda-forge).2223## Inputs2425- C++ source files in src/pyOpenMS/bindings/ with nanobind binding declarations26- CMakeLists.txt with nanobind compilation rules27- OpenMS C++ library headers and compiled object files2829## Outputs3031- Compiled pyOpenMS Python extension module (.so on Linux, .pyd on Windows, .dylib on macOS)32- Importable Python module with bound C++ classes and functions33- Module load verification and runtime function call test results3435## How to apply3637Navigate to src/pyOpenMS/bindings/ and review or create nanobind binding specifications according to the wrapping instructions in CLAUDE.md. Configure the CMake build system to compile the nanobind binding files into a Python extension module (.so/.pyd). Execute the CMake build process to generate the compiled pyOpenMS module. Import the generated pyOpenMS module in a Python environment (e.g., `import pyOpenMS`) and verify that the module loads without ImportError or missing symbol errors. Execute a simple function call or attribute access on a bound C++ class (e.g., instantiate a spectrum object, call a peak-finding method) to confirm that the binding is complete and functional. Check for runtime type errors, segmentation faults, or attribute access failures that would indicate incomplete or incorrect binding specifications.3839## Related tools4041- **nanobind** (Binding code generator and C++/Python interop framework used to specify and compile OpenMS C++ classes into importable Python extension modules)42- **CMake** (Build system configuration tool that orchestrates nanobind compilation, linking, and extension module generation)43- **OpenMS C++ library** (Upstream C++ API being exposed through nanobind bindings) — https://github.com/OpenMS/OpenMS4445## Evaluation signals4647- pyOpenMS module imports without ImportError, ModuleNotFoundError, or unresolved symbol errors.48- A bound C++ class can be instantiated from Python (e.g., `spectrum = pyOpenMS.MSSpectrum()`).49- Methods and attributes on bound objects are callable and return expected types without segmentation faults.50- No AttributeError or TypeError when accessing bound functions with correct argument types.51- CMake build log shows zero compilation warnings or errors in nanobind binding code.5253## Limitations5455- The provided document fragment does not contain the full technical specification of binding file structure or module import verification process, limiting detailed guidance on binding specification syntax.56- Nanobind binding completeness depends on manual specification of each C++ class/function to expose; not all OpenMS C++ API is automatically bound.57- Platform-specific compilation issues may occur on Windows, macOS, and Linux due to different C++ toolchains and nanobind ABI requirements.58- Binding layer may introduce performance overhead compared to native C++ for computationally intensive workflows.5960## Evidence6162- [other] Navigate to the src/pyOpenMS/bindings/ directory and review nanobind binding specifications according to CLAUDE.md wrapping instructions.: "Navigate to the src/pyOpenMS/bindings/ directory and review nanobind binding specifications according to CLAUDE.md wrapping instructions."63- [other] Configure the build system (CMake) to compile nanobind binding files into a Python extension module.: "Configure the build system (CMake) to compile nanobind binding files into a Python extension module."64- [other] Import the generated pyOpenMS module in a Python environment and verify that the module loads without errors.: "Import the generated pyOpenMS module in a Python environment and verify that the module loads without errors."65- [readme] With pyOpenMS, OpenMS offers Python bindings to a large part of the OpenMS API to enable rapid algorithm development.: "With pyOpenMS, OpenMS offers Python bindings to a large part of the OpenMS API to enable rapid algorithm development."66- [other] Execute a simple function call or attribute access on the imported module to confirm binding completeness.: "Execute a simple function call or attribute access on the imported module to confirm binding completeness."
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