From 3f6a950867eb5b0793380c2f86840081091d80c9 Mon Sep 17 00:00:00 2001 From: Eshaan Date: Sat, 6 Dec 2025 18:43:51 +1100 Subject: [PATCH 1/2] Improve PEcAn.SIPNET documentation and connect to PEcAn book Enhanced README with model description and integration details, updated book pages with proper metadata and current installation instructions, and connected all SIPNET documentation resources. Addresses #3703 --- CHANGELOG.md | 1 + .../03_topical_pages/05_models/sipnet.Rmd | 58 +++++------------- .../06_install_models/install_SIPNET.Rmd | 28 ++++----- models/sipnet/NEWS.md | 6 ++ models/sipnet/README.md | 61 +++++++++++++++---- 5 files changed, 83 insertions(+), 71 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 10c76509186..7a457be53a1 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). - `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..88ce06df420 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 | Bill Sacks, Liza Nicoll, others | | 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 comprehensive model documentation, see the [SIPNET documentation](https://pecanproject.github.io/sipnet). For the PEcAn.SIPNET package 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/install-models.html#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..673729962c5 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 +1,19 @@ -#### SIPNET {inst-sipnet} +#### SIPNET {#inst-sipnet} + +The recommended method to install SIPNET is from the official 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. \ No newline at end of file diff --git a/models/sipnet/NEWS.md b/models/sipnet/NEWS.md index 08a196e4e81..f779c7230ed 100644 --- a/models/sipnet/NEWS.md +++ b/models/sipnet/NEWS.md @@ -4,6 +4,12 @@ * `write.events.SIPNET()` to generate SIPNET `events.in` files from a `events.json` file. +## Documentation + +* 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..96d74344813 100644 --- a/models/sipnet/README.md +++ b/models/sipnet/README.md @@ -2,18 +2,43 @@ -[![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? + +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:** +- 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 +- Processes SIPNET outputs back to PEcAn standards +- 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 -``` r +You can install the development version of `PEcAn.SIPNET` from r-universe: + +```r # Enable repository from pecanproject options(repos = c( pecanproject = 'https://pecanproject.r-universe.dev', @@ -22,18 +47,28 @@ 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 From c593c22c906bc9d4401ab2f1b1896556f54c9ce1 Mon Sep 17 00:00:00 2001 From: David LeBauer Date: Sat, 6 Dec 2025 19:02:19 -0700 Subject: [PATCH 2/2] Revisions to docs during PR review --- CHANGELOG.md | 2 +- book_source/03_topical_pages/05_models/sipnet.Rmd | 6 +++--- .../03_install_OS/06_install_models/install_SIPNET.Rmd | 7 +++++-- models/sipnet/NEWS.md | 7 ++++--- models/sipnet/README.md | 6 ++++-- 5 files changed, 17 insertions(+), 11 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 7a457be53a1..43c4c91aad4 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -45,7 +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). +- 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 88ce06df420..e9cc54e4e3a 100644 --- a/book_source/03_topical_pages/05_models/sipnet.Rmd +++ b/book_source/03_topical_pages/05_models/sipnet.Rmd @@ -5,7 +5,7 @@ | Home Page | https://pecanproject.github.io/sipnet | | Source Code | https://github.com/PecanProject/sipnet | | License | BSD 3-Clause | -| Authors | Bill Sacks, Liza Nicoll, others | +| 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** @@ -14,7 +14,7 @@ SIPNET (Simplified Photosynthesis and Evapotranspiration Model) is a lightweight 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 comprehensive model documentation, see the [SIPNET documentation](https://pecanproject.github.io/sipnet). For the PEcAn.SIPNET package documentation, see the [package website](https://pecanproject.github.io/package-documentation/develop/PEcAn.SIPNET/). +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** @@ -36,7 +36,7 @@ SIPNET is configured using 3 files which are placed in the run folder, as well a For current SIPNET installation instructions, please see: -- [Installing SIPNET in the PEcAn documentation](https://pecanproject.github.io/pecan-documentation/develop/install-models.html#inst-sipnet) +- [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 673729962c5..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 @@ -1,6 +1,9 @@ #### SIPNET {#inst-sipnet} -The recommended method to install SIPNET is from the official repository: +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 # Clone the SIPNET repository @@ -16,4 +19,4 @@ sudo cp sipnet /usr/local/bin/sipnet For detailed installation instructions, build options, and dependencies, please see the [SIPNET Installation Guide](https://pecanproject.github.io/sipnet/install.html). -**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. \ 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 f779c7230ed..6eff15dbeb8 100644 --- a/models/sipnet/NEWS.md +++ b/models/sipnet/NEWS.md @@ -6,9 +6,10 @@ ## Documentation -* 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 +* 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 diff --git a/models/sipnet/README.md b/models/sipnet/README.md index 96d74344813..d83b72ffdb8 100644 --- a/models/sipnet/README.md +++ b/models/sipnet/README.md @@ -9,7 +9,9 @@ ## What is SIPNET? -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. +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 @@ -25,7 +27,7 @@ For comprehensive SIPNET documentation, see the [SIPNET project website](https:/ 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 -- Processes SIPNET outputs back to PEcAn standards +- Converts SIPNET outputs to netCDF in PEcAn standard format - Enables data assimilation, sensitivity analysis, and ensemble runs **Getting Started:**