diff --git a/CHANGELOG.md b/CHANGELOG.md index 10c76509186..43c4c91aad4 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -45,6 +45,7 @@ For more information about this file see also [Keep a Changelog](http://keepacha - Package `PEcAn.uncertainty` has changed licensing. With approval from all its contributors, we now provide it under a BSD 3-clause license rather than the previously used NCSA Open Source license. - Ensemble and sensitivity analyses now assign an ensemble ID if one is not specified in the XML, even when running with no DB (#3654). +- Improved PEcAn.SIPNET documentation: enhanced README with comprehensive model description, updated book pages with proper metadata and current installation instructions, and connected all SIPNET documentation resources (#3703, #3705). - `download.ERA5_cds` now uses the R package ecmwfr (replacing python dependency of cdsapi via reticulate), enabling direct NetCDF downloads; and made flexible for both reanalysis and ensemble data product. - `extract_soil_gssurgo` now supports spatial sampling using a grid of user-defined size and spacing. And supports ensemble simulation of soil organic carbon (SOC) stocks, using area-weighted aggregation - The ERA5 NC extraction function can now handle multi-site instead of one diff --git a/book_source/03_topical_pages/05_models/sipnet.Rmd b/book_source/03_topical_pages/05_models/sipnet.Rmd index bbcef49aeaf..e9cc54e4e3a 100644 --- a/book_source/03_topical_pages/05_models/sipnet.Rmd +++ b/book_source/03_topical_pages/05_models/sipnet.Rmd @@ -1,16 +1,20 @@ -## SiPNET {#models-sipnet} +## SIPNET {#models-sipnet} | Model Information || | -- | -- | -| Home Page | | -| Source Code | | -| License | | -| Authors | | +| Home Page | https://pecanproject.github.io/sipnet | +| Source Code | https://github.com/PecanProject/sipnet | +| License | BSD 3-Clause | +| Authors | Michael Longfritz, William Sacks, David Moore, John M. Zobitz, Bobby H. Braswell, David S. Schimel, Rob Kooper, Michael C. Dietze, Istem Fer, Chris Black, David S. LeBauer| | PEcAn Integration | Michael Dietze, Rob Kooper | **Introduction** -Introduction about model +SIPNET (Simplified Photosynthesis and Evapotranspiration Model) is a lightweight ecosystem model designed to simulate complex environmental dynamics. It tracks carbon, water, nitrogen, and trace greenhouse-gas (N₂O, CH₄) interactions, supporting applications from forest carbon inventories to managed croplands. + +Key features include simulation of photosynthesis, respiration, allocation, soil water, soil temperature, and nitrogen cycling on sub-daily time steps. The model tracks vegetation, litter, soil, and mineral-N pools, and includes event-based management for agricultural processes. + +For model documentation including model structure, user guide, and developer guide, see the [SIPNET documentation](https://pecanproject.github.io/sipnet). For PEcAn.SIPNET documentation, see the [package website](https://pecanproject.github.io/package-documentation/develop/PEcAn.SIPNET/). **PEcAn configuration file additions** @@ -30,39 +34,9 @@ SIPNET is configured using 3 files which are placed in the run folder, as well a **Installation notes** -This section contains notes on how to compile the model. The notes for the VM might work on other machines or configurations as well. - -SIPNET version unk: - -``` -if [ ! -e ${HOME}/sipnet_unk ]; then - cd - curl -o sipnet_unk.tar.gz http://isda.ncsa.illinois.edu/~kooper/PEcAn/models/sipnet_unk.tar.gz - tar zxf sipnet_unk.tar.gz - rm sipnet_unk.tar.gz -fi -cd ${HOME}/sipnet_unk/ -make clean -make -sudo cp sipnet /usr/local/bin/sipnet.runk -make clean -``` - -SIPNET version 136: - -``` -if [ ! -e ${HOME}/sipnet_r136 ]; then - cd - curl -o sipnet_r136.tar.gz http://isda.ncsa.illinois.edu/~kooper/EBI/sipnet_r136.tar.gz - tar zxf sipnet_r136.tar.gz - rm sipnet_r136.tar.gz - sed -i 's#$(LD) $(LIBLINKS) \(.*\)#$(LD) \1 $(LIBLINKS)#' ${HOME}/sipnet_r136/Makefile -fi -cd ${HOME}/sipnet_r136/ -make clean -make -sudo cp sipnet /usr/local/bin/sipnet.r136 -make clean -``` - -**VM** +For current SIPNET installation instructions, please see: + +- [Installing SIPNET in the PEcAn documentation](https://pecanproject.github.io/pecan-documentation/develop/osinstall.html#sipnet-inst-sipnet) +- [SIPNET Installation Guide](https://pecanproject.github.io/sipnet/install.html) + +The recommended approach is to install SIPNET from the official [SIPNET repository](https://github.com/PecanProject/sipnet) diff --git a/book_source/03_topical_pages/93_installation/03_install_OS/06_install_models/install_SIPNET.Rmd b/book_source/03_topical_pages/93_installation/03_install_OS/06_install_models/install_SIPNET.Rmd index 6a105823ecc..9dd02a803fb 100644 --- a/book_source/03_topical_pages/93_installation/03_install_OS/06_install_models/install_SIPNET.Rmd +++ b/book_source/03_topical_pages/93_installation/03_install_OS/06_install_models/install_SIPNET.Rmd @@ -1,23 +1,22 @@ -#### SIPNET {inst-sipnet} +#### SIPNET {#inst-sipnet} + +You can download a compiled binary from the [SIPNET releases page](https://github.com/PecanProject/sipnet/releases). + +You can also install SIPNET is from the repository: + ```bash -cd -curl -o sipnet_unk.tar.gz http://isda.ncsa.illinois.edu/~kooper/EBI/sipnet_unk.tar.gz -tar zxf sipnet_unk.tar.gz -rm sipnet_unk.tar.gz +# Clone the SIPNET repository +git clone https://github.com/PecanProject/sipnet.git +cd sipnet -cd sipnet_unk +# Build SIPNET make -sudo cp sipnet /usr/local/bin/sipnet.runk + +# Install the executable (optional - adjust path as needed) +sudo cp sipnet /usr/local/bin/sipnet ``` -##### SIPNET testrun +For detailed installation instructions, build options, and dependencies, please see the [SIPNET Installation Guide](https://pecanproject.github.io/sipnet/install.html). -```bash -cd -curl -o testrun.sipnet.tar.gz http://isda.ncsa.illinois.edu/~kooper/EBI/testrun.sipnet.tar.gz -tar zxf testrun.sipnet.tar.gz -rm testrun.sipnet.tar.gz -cd testrun.sipnet -sipnet.runk -``` \ No newline at end of file +**Note:** Previous installation methods using tarballs (`sipnet_unk.tar.gz`, `sipnet_r136.tar.gz`) are deprecated. Please use the repository method above for the most up-to-date version. All previous tagged releases are available as source code and compiled binaries from the SIPNET releases page. \ No newline at end of file diff --git a/models/sipnet/NEWS.md b/models/sipnet/NEWS.md index 08a196e4e81..6eff15dbeb8 100644 --- a/models/sipnet/NEWS.md +++ b/models/sipnet/NEWS.md @@ -4,6 +4,13 @@ * `write.events.SIPNET()` to generate SIPNET `events.in` files from a `events.json` file. +## Documentation + +* Updated Package Documentation #3705 + * Improved README with comprehensive description of SIPNET model and its integration with PEcAn + * Updated PEcAn book SIPNET page with model metadata and proper documentation links + * Replaced outdated installation instructions with current methods pointing to official SIPNET repository + # PEcAn.SIPNET 1.9.1 ## Changed diff --git a/models/sipnet/README.md b/models/sipnet/README.md index 8fee3a08770..d83b72ffdb8 100644 --- a/models/sipnet/README.md +++ b/models/sipnet/README.md @@ -2,18 +2,45 @@ -[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental) +[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental) [![PEcAn.SIPNET status badge](https://pecanproject.r-universe.dev/badges/PEcAn.SIPNET)](https://pecanproject.r-universe.dev/PEcAn.SIPNET) -PEcAn Functions Used for Ecological Forecasts and Reanalysis +## What is SIPNET? + +The SIPNET v1 (**S**implified PnET (**P**hotosynthesis** and **E**vapo**t**ranspiration)) model is a lightweight ecosystem model designed to simulate ecosystem carbon and water dynamics. + +SIPNET v2 added a nitrogen cycle, trace greenhouse-gas (N₂O, CH₄) fluxes, and support for cropland and ecosystem management. As of PEcAn v1.10, support for SIPNET v2 is partially implemented and under active development. + +**Key Features:** +- Simulates photosynthesis, respiration, allocation, soil water, soil temperature, and nitrogen cycling +- Operates on sub-daily time steps +- Tracks vegetation, litter, soil, and mineral-N pools +- Event-based management for agricultural processes (planting, harvest, tillage, irrigation) +- Clean, modular, BSD-licensed codebase suitable for research and production + +For comprehensive SIPNET documentation, see the [SIPNET project website](https://pecanproject.github.io/sipnet). + +## Using SIPNET via PEcAn + +PEcAn.SIPNET is the PEcAn interface package that enables SIPNET integration with the PEcAn workflow system. This package: +- Converts PEcAn-standard inputs to SIPNET format +- Manages SIPNET model configuration and execution +- Converts SIPNET outputs to netCDF in PEcAn standard format +- Enables data assimilation, sensitivity analysis, and ensemble runs + +**Getting Started:** +- [Demo 1: Basic PEcAn Run](https://pecanproject.github.io/pecan-documentation/develop/basic-users-guide.html) +- [SIPNET in the PEcAn Book](https://pecanproject.github.io/pecan-documentation/develop/models-sipnet.html) ## Installation -You can install the development version of `PEcAn.SIPNET` from r-universe like so: +### Install PEcAn.SIPNET Package + +You can install the development version of `PEcAn.SIPNET` from r-universe: -``` r +```r # Enable repository from pecanproject options(repos = c( pecanproject = 'https://pecanproject.r-universe.dev', @@ -22,18 +49,28 @@ options(repos = c( install.packages('PEcAn.SIPNET') ``` -Or you can install directly from GitHub with the remotes package like so: +Or install directly from GitHub: -``` r +```r library(remotes) -install_github('pecanproject/pecan', subdir = "models/sipnet") +install_github('pecanproject/pecan', subdir = "models/sipnet") ``` -## Example +### Install SIPNET Model -This is a basic example which shows you how to solve a common problem: +To use PEcAn.SIPNET, you also need the SIPNET model executable installed on your system. For installation instructions, see: +- [Installing SIPNET](https://pecanproject.github.io/pecan-documentation/develop/install-models.html#inst-sipnet) +- [SIPNET Installation Guide](https://pecanproject.github.io/sipnet/install.html) -``` r -library(PEcAn.SIPNET) -## basic example code -``` +## Documentation + +- **PEcAn.SIPNET Package Docs:** https://pecanproject.github.io/package-documentation/develop/PEcAn.SIPNET/ +- **SIPNET Model Docs:** https://pecanproject.github.io/sipnet +- **PEcAn Book - SIPNET Chapter:** https://pecanproject.github.io/pecan-documentation/develop/models-sipnet.html +- **Source Code:** https://github.com/PecanProject/pecan/tree/develop/models/sipnet + +## Learn More + +- **PEcAn Project:** https://pecanproject.github.io +- **Tutorials:** https://pecanproject.github.io/tutorials.html +- **SIPNET Repository:** https://github.com/PecanProject/sipnet