neptoon
neptoon is a Python package for processing Cosmic-Ray Neutron Sensor (CRNS) data and estimating field-scale soil moisture. It supports stationary and roving workflows, quality assessment, sensor calibration and field-sampling planning.
Key Features
- Modular Correction Pipeline: Apply multiple correction methods for pressure, incoming intensity, humidity, and biomass
- Quality Assessment: Built-in data quality checks integrated with SaQC
- Sensor Calibration: Method-aware N0/I_D calibration using soil sampling data
- External Data Integration: Automatic integration with NMDB.eu for incoming neutron corrections
- Roving CRNS: Process mobile surveys with track-aware QA/corrections, shared geospatial adapters, gridding, footprints, interpolation, maps, and terrain products
- Multiple Interfaces: Use via Python API, configuration files, or GUI
- Published Science: Implementations based on peer-reviewed methodologies
- Reproducibility: Built-in reporting, reproducible workflows, and comprehensive documentation
Installation
pip install neptoon
Isolated Environment with uv (recommended):
uv venv --python 3.11
uv pip install neptoon
These commands install Neptoon into a local .venv without creating a new
project or modifying an existing pyproject.toml.
Isolated Environment with conda:
conda create -n neptoon python=3.11 ipykernel
conda activate neptoon
pip install neptoon
For more detailed instructions, see the installation documentation.
Quick Start
from neptoon.config import ConfigurationManager
from neptoon.workflow import ProcessWithConfig
# Load configurations
config = ConfigurationManager()
config.load_configuration(file_path="path/to/sensor_config.yaml")
config.load_configuration(file_path="path/to/processing_config.yaml")
# Process data
yaml_processor = ProcessWithConfig(configuration_object=config)
yaml_processor.run_full_process()
Ready-to-use configurations, sample data, scripts, and notebooks are indexed in examples/README.md.
Documentation
The documentation is published at www.neptoon.org. The same source pages can also be opened directly in the GitLab repository:
- Documentation home — All documentation entry points.
- Beginner's guide — First steps with Neptoon.
- CRNS history — Background and development of CRNS.
- Scientific literature — Primary references for the implemented methods.
- Site planning and sampling — Sampling schemes and the interactive Site planer.
- Workflow guide — Detailed processing workflow.
- Examples — Practical examples and tutorials.
These relative .md links work in the GitLab Markdown view; MkDocs resolves the
corresponding source-page links in docs/index.md into published website URLs.
Project Status
Neptoon 1.0 is the first stable release. Since 1.0, breaking configuration changes should be limited to major versions. Development continues; see the roadmap for planned work.
Support and Contribution
- Contact: Email us at contact@neptoon.org
- Issues: Report bugs or request features through GitLab issues
- Contributing: See the contribution guidelines for details on how to contribute
Authors and Acknowledgments
Lead Developers:
- Daniel Power — ORCID · Email
- Martin Schrön — ORCID · Homepage · Email
- Louis Trinkle — ORCID · Email
- Markus Köhli — ORCID · Homepage · Email
Acknowledgments:
- Fredo Erxleben — ORCID
- Steffen Zacharias — ORCID
- Rafael Rosolem — ORCID · Homepage
- Miguel Rico-Ramirez — ORCID
- Till Francke — ORCID
- Daniel Rasche — ORCID
License
Neptoon's original code is licensed under MIT. The bundled PARMA/EXPACS model and data are not covered by the MIT grant and have separate JAEA terms restricting commercial use. Supplemental detector-response files also need a provenance and redistribution review. See THIRD-PARTY-LICENSES.md before redistributing the package, especially for commercial use.
Citation
Cite the archived version you used. The exact-version citation below points to
the latest archived Zenodo release; the source-tree package VERSION may be
ahead while the next release is being prepared. The badge above uses the concept
DOI, which covers all versions.
Power, D., Köhli, M., Schrön, M., Trinkle, L., Erxleben, F., Rosolem, R., & Zacharias, S. (2026). Neptoon (Version 1.12.7) [Software]. Zenodo. https://doi.org/10.5281/zenodo.23621795
BibTex
@software{Neptoon,
author = {Power, Daniel and Köhli, Markus and Schrön, Markus and Trinkle, Louis and Erxleben, Fredo and Rosolem, Rafael and Zacharias, Steffen},
title = {Neptoon},
year = 2026,
publisher = {Zenodo},
version = {v1.12.7},
doi = {10.5281/zenodo.23621795},
url = {https://doi.org/10.5281/zenodo.23621795},
}
More Detailed Documentation
Scientific literature
The scientific methods implemented or discussed by Neptoon are linked to their primary and supporting references in the scientific literature documentation.
Conventions
These documents define the coding standards and architectural patterns used throughout the project. They serve as the single source of truth for both human contributors and AI assistants.
- Logging - Logger setup and log level conventions.
- Testing - Test organization, fixtures, markers, and CI pipeline.
- ColumnInfo - Column naming system and enum usage.
- Configuration - Pydantic config models and YAML loading.
- Hub Pattern - CRNSDataHub, DataFrames, and quality flags.
- Corrections - Factory/Builder pattern for the correction pipeline.
- Git Workflow - Branching, CI pipeline, and release process.
AI-Assisted Development
The repository includes durable guidance for coding agents and contributors:
AGENTS.md— universal entry point and toolchain rulesagent/code-overview.md— detailed find/edit/test mapagent/architecture.md— stable architecture summaryagent/conventions/— recurring implementation conventionsagent/decisions/— architecture and policy recordsagent/playbooks/convention-audit.md— project-specific guidance auditagent/playbooks/add-meteo-provider.md— provider integration checklistagent/playbooks/add-report-figure.md— report figure/config/PDF integrationagent/playbooks/debug-ci-regression.md— reproduce and diagnose CI regressions
Temporary plans, session memory, current priorities, contributor profiles, and agent
personas are local concerns and are intentionally not tracked. See
agent/README.md for the repository/local boundary.
3 maintainers
Metadata
3 maintainers
Release files for neptoon 1.12.7
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Total release size: 27.9 MB
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