Change AUTHORS File, added Nils Bender

.devcontainer/Dockerfile

@@ -0,0 +1,6 @@
+# TARGETARCH is set automatically by Docker BuildKit (default since Docker 23.0).
+# Falls back to amd64 when BuildKit is not available.
+# ARM64/Apple Silicon users: if auto-detection fails, add to devcontainer.json:
+#   "build": { "args": { "TARGETARCH": "arm64" } }
+ARG TARGETARCH=amd64
+FROM ghcr.io/openms/contrib_manylinux_2_34:latest-${TARGETARCH}

.gitattributes

@@ -12,4 +12,6 @@
 # XML files with potential byte-counting indices that will lose function
 # if the windows CR byte is added
 *.mzML binary
-*.mzXML binary
+*.mzXML binary
+
+.github/workflows/*.lock.yml linguist-generated=true merge=ours

.github/ISSUE_TEMPLATE/01-question.yml

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+name: Request for Help
+description: Ask a question or request support
+labels:
+  - question
+body:
+  - type: markdown
+    attributes:
+      value: |
+        <br>
+  - type: markdown
+    attributes:
+      value: "## Please Read Before Continuing"
+  - type: markdown
+    attributes:
+      value: |
+        Before opening an issue *please* consider using the following options instead:
+
+        * [Search existing issues](/OpenMS/OpenMS/issues) for similar requests.
+        * Start a [new discussion](/OpenMS/OpenMS/discussions/categories/q-a) in the Q&A section.
+
+        Thank you!
+
+        <br>
+  - type: markdown
+    attributes:
+      value: "## Details About Your Environment"
+  - type: input
+    id: os
+    attributes:
+      label: Operating System and Hardware
+      description: What operating system are you using?  Which version?  On what hardware?
+      placeholder: "Example: Windows 11 on x86"
+    validations:
+      required: true
+  - type: input
+    id: version
+    attributes:
+      label: OpenMS Version
+      description: Which version and distribution of OpenMS are you using?
+      placeholder: "Example: pyOpenMS 3.4"
+    validations:
+      required: true
+  - type: markdown
+    attributes:
+      value: |
+        <br>
+  - type: markdown
+    attributes:
+      value: "## Describe Your Request"
+  - type: textarea
+    id: description
+    attributes:
+      label: Your Question
+      description: |
+        Please provide a detailed question along with any information
+        you think we would need to help you.
+    validations:
+      required: true

.github/ISSUE_TEMPLATE/02-bug-report.yml

@@ -0,0 +1,69 @@
+name: Bug Report
+description: Create a report to help us improve OpenMS
+labels:
+  - bug
+body:
+  - type: markdown
+    attributes:
+      value: |
+        <br>
+  - type: markdown
+    attributes:
+      value: "## Details About Your Environment"
+  - type: input
+    id: os
+    attributes:
+      label: Operating System and Hardware
+      description: What operating system are you using?  Which version?  On what hardware?
+      placeholder: "Example: Windows 11 on x86"
+    validations:
+      required: true
+  - type: input
+    id: version
+    attributes:
+      label: OpenMS Version
+      description: Which version and distribution of OpenMS are you using?
+      placeholder: "Example: pyOpenMS 3.4"
+    validations:
+      required: true
+  - type: dropdown
+    id: installer
+    attributes:
+      label: Installation Method
+      description: How did you install OpenMS?
+      options:
+        - "Official Installer"
+        - "Docker"
+        - "Python: Conda"
+        - "Python: Bioconda"
+        - "Python: pip"
+        - "Linux Package"
+        - "Other"
+    validations:
+      required: true
+  - type: markdown
+    attributes:
+      value: |
+        <br>
+  - type: markdown
+    attributes:
+      value: "## Describe the Bug"
+  - type: markdown
+    attributes:
+      value: |
+        When describing the problem you are experiencing please provide as much information as possible, including:
+
+        * What triggered the bug?
+        * The full text of any error message.
+        * Output from the tool you were using.
+        * Screenshots of misbehaving GUI tools.
+        * Example source code for problems with pyOpenMS.
+
+        Thank you!
+  - type: textarea
+    id: description
+    attributes:
+      label: Bug Description
+      description: Please describe the problem you are experiencing.
+    validations:
+      required: true

.github/ISSUE_TEMPLATE/03-feature-request.yml

@@ -0,0 +1,12 @@
+name: Feature Request
+description: Suggest an idea for this project
+labels:
+  - enhancement
+body:
+  - type: textarea
+    id: enhancement
+    attributes:
+      label: Enhancement Description
+      description: Please describe the feature you would like added to OpenMS.
+    validations:
+      required: true

.github/ISSUE_TEMPLATE/04-maintainer.yml

@@ -0,0 +1,13 @@
+name: OpenMS Maintainer Report
+description: A way for OpenMS core team members to submit reports.
+body:
+  - type: markdown
+    attributes:
+      value: |
+        **NOTE:** This form is for OpenMS maintainers and core team members.  If you want to file a bug report or request help please use [another form](/OpenMS/OpenMS/issues/new) instead.
+  - type: textarea
+    id: report
+    attributes:
+      label: Report
+    validations:
+      required: true

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1 @@
+blank_issues_enabled: false

.github/copilot-instructions.md

@@ -0,0 +1,156 @@
+# GitHub Copilot Instructions for OpenMS
+
+## Important Build Instructions
+
+**DO NOT attempt to build OpenMS unless asked to do so** - The build process is extremely resource-intensive and costly. Building OpenMS requires significant computational resources and time.
+
+## Project Overview
+
+OpenMS is an open-source software C++ library for LC-MS data management and analyses. It offers an infrastructure for rapid development of mass spectrometry related software. OpenMS is free software available under the three-clause BSD license and runs under Windows, macOS, and Linux.
+
+### Key Features
+
+- **Core C++ library** with modern C++20 standards
+- **Python bindings** (pyOpenMS) for rapid algorithm development
+- **150+ command-line tools** (TOPP Tools) for MS data processing
+- **Visualization tools** (TOPPView) for 1D, 2D, and 3D data
+- **Support for major file formats** (mzML, mzXML, mzIdentML, pepXML, mzTab)
+- **Comprehensive quantitation support** (label-free, SILAC, iTRAQ, TMT, SRM, SWATH)
+- **Integration with workflow systems** (KNIME, Galaxy, nextflow)
+
+### Architecture Components
+
+1. **OpenMS Library**
+   - Core data structures (MSSpectrum, MSExperiment, Feature, FeatureMap)
+   - Signal processing and analysis algorithms
+   - File format handling and conversion
+
+2. **TOPP Tools**
+   - Command-line tools built on the OpenMS library
+   - Standardized parameter handling via CTD scheme
+   - Tools for identification, quantification, and data processing
+
+3. **User Interfaces**
+   - TOPPView for data visualization
+   - TOPPAS for workflow creation
+   - pyOpenMS for Python scripting
+
+4. **pyOpenMS**
+   - Hand-maintained nanobind C++ bindings (no code generation)
+   - 13 domain-based modules compiled in parallel
+   - Pure Python addon system for DataFrame export and convenience methods
+   - Custom type casters for OpenMS::String, DataValue, ParamValue, DPosition
+   - Integration with scientific Python ecosystem (numpy, pandas, pyarrow)
+   - Located in `src/pyOpenMS/`; see `src/pyOpenMS/CLAUDE.md` for detailed binding guide
+
+## Development Guidelines
+
+1. **Code Style**
+   - Follow the existing C++ coding conventions in the codebase
+   - Use the established naming patterns for classes, methods, and variables
+   - Maintain consistency with the surrounding code
+
+2. **Testing**
+   - Write unit tests for new functionality
+   - Ensure existing tests pass before suggesting changes
+   - Test files are located in `src/tests/`
+
+3. **Documentation**
+   - Add Doxygen comments for new public methods and classes
+   - Update relevant documentation when modifying existing functionality
+
+4. **Common Patterns**
+   - Use OpenMS data structures (e.g., `MSExperiment`, `FeatureMap`, `PeptideIdentification`)
+   - Follow the established error handling patterns
+   - Utilize OpenMS logging mechanisms
+
+5. **Performance Considerations**
+   - Be mindful of memory usage when processing large datasets
+   - Consider algorithmic complexity for data processing operations
+   - Use appropriate OpenMS containers and algorithms
+
+## Key Directories
+
+- `src/openms/` - Core library source code
+- `src/openms/include/OpenMS/` - Header files
+- `src/topp/` - TOPP tools (command-line applications)
+- `src/tests/` - Unit and integration tests
+- `src/pyOpenMS/` - Python bindings (nanobind)
+- `doc/` - Documentation
+
+## Project Structure
+
+```
+OpenMS/
+├── cmake/                       # CMake build system files
+├── doc/                         # Documentation
+├── share/OpenMS/                # Shared data (enzymes, mods, CV, etc.)
+├── src/
+│   ├── openms/                  # Core library
+│   │   ├── include/OpenMS/      # Header files
+│   │   └── source/              # Implementation files
+│   ├── openms_gui/              # GUI components
+│   ├── pyOpenMS/                # Python bindings
+│   │   ├── bindings/            # Hand-maintained nanobind C++ binding files
+│   │   │   ├── bind_kernel.cpp  # KERNEL/ classes
+│   │   │   ├── bind_spectrum.cpp      # MSSpectrum
+│   │   │   ├── bind_chromatogram.cpp  # MSChromatogram
+│   │   │   ├── bind_experiment.cpp    # MSExperiment
+│   │   │   ├── bind_metadata.cpp      # METADATA/ classes
+│   │   │   ├── bind_chemistry.cpp     # CHEMISTRY/ classes
+│   │   │   ├── bind_analysis.cpp      # ANALYSIS/ classes
+│   │   │   ├── bind_format.cpp        # FORMAT/ classes
+│   │   │   ├── bind_processing.cpp    # PROCESSING/ classes
+│   │   │   ├── bind_featurefinder.cpp # FEATUREFINDER/ classes
+│   │   │   ├── bind_datastructures.cpp # DATASTRUCTURES/, MATH/ classes
+│   │   │   ├── bind_ml.cpp            # ML/ classes
+│   │   │   ├── bind_misc.cpp          # Everything else
+│   │   │   ├── binding_utils.h        # Helper templates for inheritance
+│   │   │   └── type_casters/          # Custom nanobind type casters
+│   │   ├── pyopenms/            # Python package
+│   │   │   ├── __init__.py      # Module imports and addon injection
+│   │   │   ├── addons/          # Pure Python addon methods
+│   │   │   └── _dataframes.py   # DataFrame mixin (pandas optional)
+│   │   └── tests/               # pyOpenMS tests
+│   ├── tests/                   # C++ test suites
+│   │   ├── class_tests/         # Unit tests
+│   │   └── topp/                # TOPP tool tests
+│   └── topp/                    # TOPP tools
+└── tools/                       # Development and CI utilities
+```
+
+## Testing Infrastructure
+
+- **Class tests**: Unit tests in `src/tests/class_tests/openms/source/`
+- **TOPP tests**: Integration tests in `src/tests/topp/`
+- **Python tests**: pyOpenMS tests in `src/pyOpenMS/tests/`
+- Test naming convention: `ClassName_test.cpp` for C++ class `ClassName`
+
+## Build Commands
+
+```bash
+# Full build
+cmake --build OpenMS-build -j$(nproc)
+
+# pyOpenMS only
+cmake --build OpenMS-build --target pyopenms -j$(nproc)
+
+# Run C++ tests
+ctest --test-dir OpenMS-build
+
+# Run pyOpenMS tests (from /tmp to avoid import shadowing)
+cd /tmp && PYTHONPATH=.../OpenMS-build/pyOpenMS python3 -m pytest .../src/pyOpenMS/tests/ -v
+```
+
+## Assistance Focus
+
+When providing code suggestions:
+- Analyze existing code patterns before suggesting changes
+- Respect the established architecture
+- Consider cross-platform compatibility (Windows, Linux, macOS)
+- Be aware of OpenMS dependencies and external libraries
+- Use existing OpenMS data structures and algorithms
+- Follow the established error handling patterns
+- Maintain consistency with surrounding code style
+- When CI tests fail, investigate the root cause first before patching reference files
+- For pyOpenMS bindings, follow patterns in `src/pyOpenMS/CLAUDE.md`