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Merge branch 'develop' into model-run-workflow
2 parents 2cba6f0 + 80e1b7a commit 9571570

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lines changed

‎.github/workflows/pkgdown.yml‎

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name: renderpkgdown
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on:
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push:
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branches:
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- main
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- develop
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tags:
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- '*'
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pull_request:
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merge_group:
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workflow_dispatch:
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jobs:
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pkgdown:
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runs-on: ubuntu-latest
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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container:
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image: pecan/depends:develop
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steps:
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# Checkout source code
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- uses: actions/checkout@v4
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# Install pkgdown
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- name: Install dependencies
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run: Rscript -e 'install.packages("pkgdown")'
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# Generate documentation using Makefile
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- name: Generate Package Documentation
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run: make pkgdocs
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# Check if package documentation repo exists
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- name: Check if package documentation repo exists
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id: pkgdoc_exists
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run: |
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if git ls-remote https://github.com/${{ github.repository_owner }}/package-documentation.git > /dev/null 2>&1; then
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echo "exists=true" >> $GITHUB_OUTPUT
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else
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echo "exists=false" >> $GITHUB_OUTPUT
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fi
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# Checkout package documentation repo
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- name: Checkout package documentation repo
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if: ${{ github.event_name == 'push' && steps.pkgdoc_exists.outputs.exists == 'true' }}
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uses: actions/checkout@v4
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with:
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repository: ${{ github.repository_owner }}/package-documentation
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path: package-documentation
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token: ${{ secrets.GH_PAT }}
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# Deploy Pkgdown documentation
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- name: Publish to github
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if: github.event_name == 'push'
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run: |
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git config --global user.email "[email protected]"
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git config --global user.name "GitHub Documentation Robot"
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export VERSION=$(echo $GITHUB_REF | sed 's,.*/,,' )
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if [ "$VERSION" = "main" ]; then
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export VERSION=latest
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fi
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cd package-documentation
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mkdir -p $VERSION
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rsync -a --delete pkgdocs/ ${VERSION}/
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git add --all *
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git commit -m "Build pkgdown docs from pecan revision ${GITHUB_SHA}" || true
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git push -q origin main

‎CHANGELOG.md‎

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@@ -13,6 +13,10 @@ For more information about this file see also [Keep a Changelog](http://keepacha
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- Add make option to document a single package with `make documentation pathto/package`
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- `settings$host$qsub` and `settings$host$modellauncher$qsub.extra` will now expand `@NJOBS@` to the number of models in the run, allowing e.g. `--array=1-@NJOBS@`. Note that qsub still by default submits every model as a separate job, so for now this is mostly useful for custom modellauncher scripts
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- Added automated pkgdown documentation for all PEcAn packages (@divine7022, #3482):
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- Compiled pages are live at https://pecanproject.github.io/package-documentation and inside Docker at `pecan.localhost/pkgdocs/`, and these are automatically updated each time a PR to the source packages is merged.
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- You can compile all pkgdown pages locally at any time with `make pkgdocs`.
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### Fixed
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- updated github action to build docker images
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- PEcAn.SIPNET now accepts relative paths in its input XML (#3418). Previously all files referenced in the autogenerated `job.sh` needed to be specified as absolute paths.

‎Makefile‎

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SHELL = /bin/bash
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NCPUS ?= 1
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BASE := logger utils db settings visualization qaqc remote workflow
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### Rules
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.PHONY: all install check test document clean shiny \
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check_base check_models check_modules document help
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.PHONY: all install check test document clean shiny pkgdocs \
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check_base check_models check_modules help
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all: install document
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# Note: Installs base first as Modules has a circular dependency on base
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# Note: Installs base first as Modules has a circular dependency on base
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check_base: $(BASE_C)
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check_models: $(MODELS_C)
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check_modules: $(BASE_I) $(MODULES_C)
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document: $(ALL_PKGS_D) .doc/base/all
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pkgdocs:
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Rscript scripts/build_pkgdown.R $(ALL_PKGS) base/all || exit 1
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install: $(ALL_PKGS_I) .install/base/all
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check: $(ALL_PKGS_C) .check/base/all
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test: $(ALL_PKGS_T) .test/base/all
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@echo " test Run unit tests on all packages"
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@echo " shiny Install dependencies for Shiny apps"
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@echo " book Render the PEcAn bookdown documentation"
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@echo " pkgdocs Build package documentation websites using pkgdown"
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@echo " clean Remove build artifacts"
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@echo " help Show this help message"
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‎base/settings/R/inst/tests/test.xml‎

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<?xml version="1.0"?>
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<pecan>
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<info>
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<notes></notes>
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<userid>-1</userid>
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<username></username>
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<date>2025/03/24 10:37:56 +0000</date>
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</info>
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<outdir>/data/workflows/PEcAn_99000000005</outdir>
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<database>
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<bety>
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<user>bety</user>
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<password>bety</password>
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<host>postgres</host>
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<port>5432</port>
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<dbname>bety</dbname>
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<driver>PostgreSQL</driver>
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<write>true</write>
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</bety>
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<dbfiles>/data/dbfiles</dbfiles>
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</database>
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<pfts>
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<pft>
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<name>temperate.coniferous</name>
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</pft>
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</pfts>
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<meta.analysis>
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<iter>3000</iter>
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<random.effects>
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<on>FALSE</on>
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<use_ghs>TRUE</use_ghs>
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</random.effects>
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</meta.analysis>
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<ensemble>
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<size>1</size>
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<variable>NPP</variable>
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<samplingspace>
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<parameters>
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<method>uniform</method>
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</parameters>
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<met>
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<method>sampling</method>
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</met>
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</samplingspace>
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</ensemble>
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<model>
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<id>99000000003</id>
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</model>
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<workflow>
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<id>99000000005</id>
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</workflow>
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<run>
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<site>
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<id>772</id>
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<met.start>2004/01/01</met.start>
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<met.end>2004/12/31</met.end>
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</site>
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<inputs>
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<met>
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<source>AmerifluxLBL</source>
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<output>SIPNET</output>
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<username>Aritra_2023</username>
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</met>
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</inputs>
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<start.date>2004/01/01</start.date>
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<end.date>2004/12/31</end.date>
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</run>
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<host>
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<name>localhost</name>
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<rabbitmq>
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<uri>amqp://guest:guest@rabbitmq/%2F</uri>
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<queue>SIPNET_git</queue>
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</rabbitmq>
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</host>
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</pecan>

‎base/settings/R/read.settings.R‎

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#'
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#' settings <- read.settings()
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#' settings <- read.settings(file="willowcreek.xml")
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#' test.settings.file <- system.file("tests/test.xml", package = "PEcAn.all")
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#' test.settings.file <- system.file("tests/test.xml", package = "PEcAn.settings")
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#' settings <- read.settings(test.settings.file)
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#' }
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read.settings <- function(inputfile = "pecan.xml") {

‎base/settings/man/read.settings.Rd‎

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‎book_source/02_demos_tutorials_workflows/02_user_demos/01_introductions_user.Rmd‎

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|Type|Title|Web Link| Source Rmd|
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|:--:|:---:|:------:|:---------:|
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|Demo| Basic Run| [html](#demo-1) | [Rmd](https://github.com/PecanProject/pecan/blob/develop/documentation/tutorials/01_Demo_Basic_Run/Demo01.Rmd)|
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|Demo| Uncertainty Analysis| [html](#demo-2) | [Rmd](https://github.com/PecanProject/pecan/tree/main/documentation/tutorials/02_Demo_Uncertainty_Analysis)|
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|Demo| Output Analysis|html |[Rmd](https://github.com/PecanProject/pecan/tree/develop/documentation/tutorials/AnalyzeOutput)|
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|Demo| MCMC |html|[Rmd](https://github.com/PecanProject/pecan/tree/develop/documentation/tutorials/MCMC)|
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|Demo|Parameter Assimilation |html |[Rmd](https://github.com/PecanProject/pecan/tree/develop/documentation/tutorials/ParameterAssimilation)|
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|Demo|State Assimilation|html|[Rmd](https://github.com/PecanProject/pecan/tree/develop/documentation/tutorials/StateAssimilation)|
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|Demo| Sensitivity|html|[Rmd](https://github.com/PecanProject/pecan/tree/develop/documentation/tutorials/sensitivity)|
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|Vignette|Allometries|html|[Rmd](https://github.com/PecanProject/pecan/blob/main/modules/allometry/vignettes/AllomVignette.Rmd)|
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|Vignette|MCMC|html|[Rmd](https://github.com/PecanProject/pecan/blob/main/modules/assim.batch/vignettes/AssimBatchVignette.Rmd)|
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|Vignette|Meteorological Data|html|[Rmd](https://github.com/PecanProject/pecan/tree/main/modules/data.atmosphere/vignettes)|
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|Vignette|Meta-Analysis|html|[Rmd](https://github.com/PecanProject/pecan/blob/main/modules/meta.analysis/vignettes/single.MA_demo.Rmd)|
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|Vignette|Photosynthetic Response Curves|html|[Rmd](https://github.com/PecanProject/pecan/blob/main/modules/photosynthesis/vignettes/ResponseCurves.Rmd)|
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|Vignette|Priors|html|[Rmd](https://github.com/PecanProject/pecan/blob/main/modules/priors/vignettes/priors_demo.Rmd)|
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|Vignette|Leaf Spectra:PROSPECT inversion|html|[Rmd](https://github.com/PecanProject/pecan/blob/main/modules/rtm/vignettes/pecanrtm.vignette.Rmd)|
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|Demo| Basic Run| [html](#demo-1) | <a href="https://github.com/PecanProject/pecan/blob/develop/documentation/tutorials/01_Demo_Basic_Run/Demo01.Rmd" target = "_blank">Rmd</a> |
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|Demo| Uncertainty Analysis| [html](#demo-2)| <a href="https://github.com/PecanProject/pecan/blob/develop/documentation/tutorials/02_Demo_Uncertainty_Analysis/Demo02.Rmd" target = "_blank">Rmd</a> |
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|Demo| Output Analysis|html | <a href="https://github.com/PecanProject/pecan/blob/develop/documentation/tutorials/AnalyzeOutput/modelVSdata.Rmd" target="_blank">Rmd</a> |
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|Demo| MCMC |html| <a href= "https://github.com/PecanProject/pecan/blob/develop/documentation/tutorials/MCMC/MCMC_Concepts.Rmd" target = "_blank">Rmd</a> |
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|Demo|Parameter Assimilation |html | <a href="https://github.com/PecanProject/pecan/blob/develop/documentation/tutorials/ParameterAssimilation/PDA.Rmd" target = "_blank">Rmd</a> |
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|Demo|State Assimilation|html| <a href="https://github.com/PecanProject/pecan/blob/develop/documentation/tutorials/StateAssimilation/TreeRingSDA.Rmd" target = "_blank">Rmd</a> |
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|Demo| Sensitivity|html| <a href="https://github.com/PecanProject/pecan/blob/develop/documentation/tutorials/sensitivity/PEcAn_sensitivity_tutorial_v1.0.Rmd" target = "_blank">Rmd</a> |
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|Vignette|Allometries|html| <a href="https://github.com/PecanProject/pecan/blob/develop/modules/allometry/vignettes/AllomVignette.Rmd" target = "_blank">Rmd</a> |
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|Vignette|MCMC|html| <a href="https://github.com/PecanProject/pecan/blob/develop/modules/assim.batch/vignettes/AssimBatchVignette.Rmd" target = "_blank">Rmd</a> |
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|Vignette|Meteorological Data|html| <a href="https://github.com/PecanProject/pecan/tree/develop/modules/data.atmosphere/vignettes" target = "_blank">Rmd</a> |
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|Vignette|Meta-Analysis|html| <a href="https://github.com/PecanProject/pecan/blob/develop/modules/meta.analysis/vignettes/single.MA_demo.Rmd" target = "_blank">Rmd</a> |
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|Vignette|Photosynthetic Response Curves|html| <a href="https://github.com/PecanProject/pecan/blob/develop/modules/photosynthesis/vignettes/ResponseCurves.Rmd" target = "_blank">Rmd</a> |
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|Vignette|Priors|html| <a href="https://github.com/PecanProject/pecan/blob/develop/modules/priors/vignettes/priors_demo.Rmd" target = "_blank">Rmd</a> |
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|Vignette|Leaf Spectra:PROSPECT inversion|html| <a href="https://github.com/PecanProject/pecan/blob/develop/modules/rtm/vignettes/pecanrtm.vignette.Rmd" target = "_blank">Rmd</a> |

‎docker/depends/pecan_deps_from_github.txt‎

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ropensci/traits
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SticsRPacks/SticsOnR
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SticsRPacks/SticsRFiles
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VangiElia/GEDI4R

‎docker/depends/pecan_package_dependencies.csv‎

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"future","*","modules/data.atmosphere","Suggests",FALSE
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"future","*","modules/data.land","Imports",FALSE
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"future","*","modules/data.remote","Imports",FALSE
80-
"GEDI4R","*","modules/data.remote","Suggests",FALSE
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"geonames","> 0.998","modules/data.atmosphere","Imports",FALSE
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"getPass","*","base/remote","Suggests",FALSE
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"getPass","*","modules/data.atmosphere","Suggests",FALSE
@@ -165,7 +164,7 @@
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"lubridate",">= 1.6.0","modules/assim.sequential","Imports",FALSE
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"lubridate",">= 1.6.0","modules/benchmark","Imports",FALSE
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"lubridate",">= 1.6.0","modules/data.atmosphere","Imports",FALSE
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"lubridate",">= 1.6.0","modules/rtm","Imports",FALSE
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"lubridate",">= 1.6.0","modules/rtm","Suggests",FALSE
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"lubridate",">= 1.7.0","models/biocro","Imports",FALSE
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"Maeswrap","*","models/maespa","Suggests",FALSE
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"magic",">= 1.5.0","modules/assim.sequential","Suggests",FALSE
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"rlang","*","modules/assim.sequential","Imports",FALSE
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"rlang","*","modules/benchmark","Imports",FALSE
489488
"rlang","*","modules/data.land","Imports",FALSE
490-
"rlang","*","modules/data.remote","Imports",FALSE
491489
"rlang","*","modules/uncertainty","Imports",FALSE
492490
"rlang",">= 0.2.0","modules/data.atmosphere","Imports",FALSE
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"rlist","*","modules/assim.sequential","Suggests",FALSE
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565563
"stats","*","modules/assim.batch","Imports",FALSE
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"stats","*","modules/assim.sequential","Suggests",FALSE
567565
"stats","*","modules/photosynthesis","Imports",FALSE
566+
"stats","*","modules/rtm","Imports",FALSE
568567
"SticsRFiles","*","models/stics","Suggests",FALSE
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"stringi","*","base/logger","Imports",FALSE
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"stringi","*","base/utils","Imports",FALSE

‎docker/docs/Dockerfile‎

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-e 'remotes::install_version("rmarkdown", ">= 2.19", dependencies = TRUE, upgrade = FALSE, repos = repos)' \
1616
-e 'remotes::install_version("knitr", ">= 1.42", dependencies = TRUE, upgrade = FALSE, repos = repos)' \
1717
-e 'remotes::install_version("bookdown", ">= 0.31", dependencies = TRUE, upgrade = FALSE, repos = repos)' \
18+
-e 'install.packages("pkgdown", repos = repos)' \
1819
&& rm -rf /var/lib/apt/lists/*
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# ----------------------------------------------------------------------
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# Compile bookdown documentation
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# ----------------------------------------------------------------------
2024
WORKDIR /src/book_source/
2125
COPY book_source /src/book_source/
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COPY documentation /src/documentation/
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COPY docker-compose.yml /src/
2428
COPY docker/env.example /src/docker/
2529
RUN make build
2630

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# ----------------------------------------------------------------------
32+
# Build pkgdown documentation
33+
# ----------------------------------------------------------------------
34+
WORKDIR /pkgdoc/
35+
COPY Makefile Makefile.depends /pkgdoc/
36+
COPY scripts/build_pkgdown.R /pkgdoc/scripts/build_pkgdown.R
37+
COPY base /pkgdoc/base/
38+
COPY modules /pkgdoc/modules/
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COPY models /pkgdoc/models/
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RUN make clean && make pkgdocs
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# ----------------------------------------------------------------------
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# copy html pages to container
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# ----------------------------------------------------------------------
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COPY docker/docs/index.html /usr/local/apache2/htdocs/
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COPY --from=pecandocs /src/book_source/_book/ /usr/local/apache2/htdocs/docs/pecan/
54+
COPY --from=pecandocs /pkgdoc/package_documentation/pkgdocs/ /usr/local/apache2/htdocs/pkgdocs/
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# ----------------------------------------------------------------------
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# PEcAn version information

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