Merge branch 'develop' into extend-workflows-api

.github/workflows/book.yml

@@ -52,19 +52,19 @@ jobs:
         path: book_source/_book/
     # download documentation repo
     - name: Checkout documentation repo
-      if: github.event_name != 'pull_request'
+      if: github.event_name == 'push'
       uses: actions/checkout@v3
       with:
         repository: ${{ github.repository_owner }}/pecan-documentation
         path: pecan-documentation
         token: ${{ secrets.GH_PAT }}
     # upload new documentation
     - name: publish to github
-      if: github.event_name != 'pull_request'
+      if: github.event_name == 'push'
       run: |
         git config --global user.email "[email protected]"
         git config --global user.name "GitHub Documentation Robot"
-        export VERSION=${GITHUB_REF##*/}
+        export VERSION=$(echo $GITHUB_REF | sed 's,.*/,,' )
         cd pecan-documentation
         mkdir -p $VERSION
         rsync -a --delete ../book_source/_book/ ${VERSION}/

.github/workflows/ci-weekly.yml

@@ -53,7 +53,8 @@ jobs:
     - name: check for out-of-date dependencies files
       uses: infotroph/tree-is-clean@v1
     - name: install newly-added dependencies
-      run: Rscript docker/depends/pecan.depends.R
+      working-directory: docker/depends
+      run: Rscript pecan.depends.R
 
     # initialize database
     - name: db setup
@@ -105,7 +106,7 @@ jobs:
     - name: install utils
       run: apt-get update && apt-get install -y postgresql-client qpdf
     - name: install new dependencies
-      run: Rscript scripts/generate_dependencies.R && Rscript docker/depends/pecan.depends.R
+      run: Rscript scripts/generate_dependencies.R && cd docker/depends && Rscript pecan.depends.R
 
     # run PEcAn checks
     - name: check
@@ -152,7 +153,7 @@ jobs:
     - name: install utils
       run: apt-get update && apt-get install -y postgresql-client qpdf
     - name: install new dependencies
-      run: Rscript scripts/generate_dependencies.R && Rscript docker/depends/pecan.depends.R
+      run: Rscript scripts/generate_dependencies.R && cd docker/depends && Rscript pecan.depends.R
 
     # initialize database
     - name: db setup

.github/workflows/ci.yml

@@ -38,7 +38,7 @@ jobs:
       fail-fast: false
       matrix:
         R:
-          - "4.0"
+          - "4.2"
           - "4.1"
 
     services:
@@ -65,7 +65,8 @@ jobs:
     - name: check for out-of-date dependencies files
       uses: infotroph/tree-is-clean@v1
     - name: install newly-added dependencies
-      run: Rscript docker/depends/pecan.depends.R
+      working-directory: docker/depends
+      run: Rscript pecan.depends.R
 
     # initialize database
     - name: db setup
@@ -89,8 +90,9 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
+        package: [check_base, check_modules, check_models]
         R:
-          - "4.0"
+          - "4.2"
           - "4.1"
 
     env:
@@ -127,14 +129,16 @@ jobs:
     - name: install utils
       run: apt-get update && apt-get install -y postgresql-client qpdf
     - name: install new dependencies
-      run: Rscript scripts/generate_dependencies.R && Rscript docker/depends/pecan.depends.R
+      run: Rscript scripts/generate_dependencies.R && cd docker/depends/ && Rscript pecan.depends.R
 
     # run PEcAn checks
+    # The package names of base, modules, and models are passed as matrix variables to avoid repeatability of code
     - name: check
-      run: make -j1 check
+      run: make -j1 ${{ matrix.package }}
       env:
         REBUILD_DOCS: "FALSE"
         RUN_TESTS: "FALSE"
+
     - name: check for out-of-date files
       uses: infotroph/tree-is-clean@v1
 
@@ -152,7 +156,7 @@ jobs:
       fail-fast: false
       matrix:
         R:
-          - "4.0"
+          - "4.2"
           - "4.1"
 
     services:
@@ -175,7 +179,7 @@ jobs:
     - name: install utils
       run: apt-get update && apt-get install -y postgresql-client qpdf
     - name: install new dependencies
-      run: Rscript scripts/generate_dependencies.R && Rscript docker/depends/pecan.depends.R
+      run: Rscript scripts/generate_dependencies.R && cd docker/depends/ && Rscript pecan.depends.R
 
     # initialize database
     - name: db setup

.github/workflows/depends.yml

@@ -29,6 +29,8 @@ jobs:
         R:
           - "4.0"
           - "4.1"
+          - "4.2"
+          - "4.3"
           - "devel"
 
     steps:

.github/workflows/integration-test.yml

@@ -0,0 +1,31 @@
+name : Integration Tests
+on :
+  # allow manual triggering
+  workflow_dispatch:
+
+  schedule:
+    # run Thursday 4:30 AM UTC
+  - cron: '30 4 * * 4'    
+jobs:
+  test:
+    runs-on: ubuntu-20.04
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    container: 
+      image: pecan/base:develop
+
+    steps:
+    - name: Checkout source code
+      uses: actions/checkout@v3
+
+    - name: Run tests
+      run: |
+        for FILE in modules/data.atmosphere/inst/integrationTests/*; do
+          if echo "$FILE" | grep -q "ERA5"; then
+            echo "Skipping file : $FILE"
+          else
+            Rscript "$FILE"
+          fi
+        done

.github/workflows/styler-actions.yml

@@ -62,7 +62,8 @@ jobs:
       - name: install any new dependencies
         env:
           GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-        run: Rscript docker/depends/pecan.depends.R
+        working-directory: docker/depends
+        run: Rscript pecan.depends.R
       - id: file_changes
         uses: trilom/[email protected]
       - name : make
@@ -82,7 +83,7 @@ jobs:
         run: |
           git config --global user.email "[email protected]"
           git config --global user.name "PEcAn stylebot"
-          git add \*.Rd \*NAMESPACE Makefile.depends docker/depends/pecan.depends.R
+          git add \*.Rd \*NAMESPACE Makefile.depends docker/depends/pecan_package_dependencies.R docker/depends/pecan_deps_from_github.txt
           if [ "$(git diff --name-only --cached)" != "" ]; then  git commit -m 'automated documentation update' ; fi
       - uses: r-lib/actions/pr-push@master
         with:

CHANGELOG.md

@@ -41,6 +41,10 @@ see if you need to change any of these:
 - Added Observation preparation functions into the SDA workflow, which supports AGB, LAI, Soil Carbon, and Soil moisture.
 - We are slowly change the license from NCSA opensource to BSD-3 to help with publishing PEcAn to CRAN.
 - Added an optional `pfts` argument to `PEcAn.uncertainty::run.sensitivity.analysis()` so that sensitivity analysis and variance decomposition can be run on a subset of PFTs defined in `settings` if desired (#3155).
+- Added new features of the SDA function including: 1) allow user-defined free-run mode; 
+2) allow user-defined parallel mode for the qsub submission; 3) allow user-defined email option to report the progress.
+- The analysis function now supports the parallelization of multi-chain MCMC sampling with the fully randomized inits function.
+- Added the new feature of the block-based SDA workflow, which supports the parallel computation.
 
 ### Fixed
 
@@ -80,6 +84,9 @@ convert data for a single PFT fixed (#1329, #2974, #2981)
 - DDBH (change in DBH over time) is no longer extracted and summarized from monthly -E- files by `PEcAn.ED2::model2netcdf.ED2()`.  We are not sure it makes sense to summarize this variable across cohorts of different sizes.
 - The `yr` and `yfiles` arguments of `PEcAn.ED2::read_E_files()` are no longer used and the simulation date is extracted from the names of the .h5 files output by ED2.
 - Update Dockerfile for sipnet/maespa/template to use pecan/models:tag to build.
+- Fixed a bug in `PEcAn.utils::ud_convert()` where it failed with objects of class "difftime" introduced by refactoring to use the `units` package instead of `udunits` (#3012)
+- The propagation of aqq and bqq for the SINGLE Q type has been corrected.
+- The issue where the indirect constraints will be increase with the increase of the covariance sizes.
 
 ### Changed
 
@@ -101,6 +108,7 @@ convert data for a single PFT fixed (#1329, #2974, #2981)
 - Internal changes to keep up to date with tidyselect v1.2.0
 - The `PEcAn.utils::download.file()` function has now been renamed to `PEcAn.utils::download_file()`
 - The `regrid()` and `grid2netcdf()` function from `PEcAn.utils` have been moved to `PEcAn.data.remote` package.
+- Web is now build using PHP 8 since PHP 7 is EOL.
 
 ### Removed
 

CONTRIBUTING.md

@@ -1,13 +1,13 @@
 # How to contribute
 
-Third-party contributions are highly encouraged for PEcAn and will grow the code as well as the understanding of PEcAn and its applications.  The core development team can not add all models that exist to PEcAn or all possible scenarios and analysis that people want to conduct.  Our goal is to keep it as easy as possible for you contribute changes that get things working in your environment. 
+Third-party contributions are highly encouraged for PEcAn and will grow the code as well as the understanding of PEcAn and its applications.  The core development team can not add all models that exist to PEcAn or all possible scenarios and analysis that people want to conduct.  Our goal is to keep it as easy as possible for you contribute changes that get things working in your environment.
 There are a few guidelines that we need contributors to follow so that we can have a chance of keeping on top of things.
 
 ## PEcAn CORE vs Models vs Modules
 
 New functionality is typically directed toward modules to provide a slimmer PEcAn Core, reducing the requirements to get PEcAn running on different platforms, especially HPC machines, and to allow greater freedom for modules and models.
 
-Generally, new model should be added to the models folder and new modules should be added to the modules folder. 
+Generally, new model should be added to the models folder and new modules should be added to the modules folder.
 Exceptions include code that is reused in many models or modules and wrapper functions that call specific implementations in models; these can be placed in the core packages.
 
 If you are unsure of whether your contribution should be implemented as a model, module or part of PEcAn Core, you may visit [Chat Room](https://join.slack.com/t/pecanproject/shared_invite/enQtMzkyODUyMjQyNTgzLWEzOTM1ZjhmYWUxNzYwYzkxMWVlODAyZWQwYjliYzA0MDA0MjE4YmMyOTFhMjYyMjYzN2FjODE4N2Y4YWFhZmQ) or ask on the pecan-develop mailing list for advice.
@@ -16,9 +16,9 @@ If you are unsure of whether your contribution should be implemented as a model,
 
 - Make sure you have a GitHub account.
 - Search GitHub and Google to see if your issue has already been reported
-        - Create an issue in GitHub, assuming one does not already exist.
-	- Clearly describe the issue including steps to reproduce when it is a bug.
-	- Make sure you fill in the earliest version that you know has the issue.
+  - Create an issue in GitHub, assuming one does not already exist.
+  - Clearly describe the issue including steps to reproduce when it is a bug.
+  - Make sure you fill in the earliest version that you know has the issue.
 - Ask @dlebauer, @mdietze or @robkooper to add you to the PEcAn project if you plan on fixing the issue.
 
 ## Getting Started
@@ -33,17 +33,20 @@ At this point you will have a copy of PEcAn and you are almost ready to work on
 At this point you will have a copy of the pecan repo in your personal space. Next steps are to setup your local copy to work with the forked version.
 
 Introduce your self to GIT (if you have not done this yet), make sure you use an email associated with your GitHub account.
+
 ```bash
 git config --global user.name "John Doe"
 git config --global user.email [email protected]
 ```
 
 Switch pecan to your fork
+
 ```bash
 git remote set-url origin https://github.com/<your username>/pecan.git
 ```
 
 Setup pecan to be able to fetch from the master/develop
+
 ```bash
 git remote add upstream https://github.com/PecanProject/pecan.git
 ```
@@ -66,30 +69,30 @@ Here is a simplified workflow on how add a new feature:
 
 Update your develop (both locally and on GitHub)
 
-```
+```bash
 git fetch upstream
 git checkout develop
 git merge upstream/develop
 git push
 ```
 
-### Create a branch to do your work.
+### Create a branch to do your work
 
-A good practice is to call the branch in the form of GH-<issue-number> followed by the title of the issue. This makes it easier to find out the issue you are trying to solve and helps us to understand what is done in the branch. Calling a branch my-work is confusing. Names of branch can not have a space, and should be replaced with a hyphen.
+A good practice is to call the branch in the form of `GH-<issue-number>` followed by the title of the issue. This makes it easier to find out the issue you are trying to solve and helps us to understand what is done in the branch. Calling a branch my-work is confusing. Names of branch can not have a space, and should be replaced with a hyphen.
 
-```
+```bash
 git checkout -b GH-issuenumber-title-of-issue
 ```
 
 ### Work and commit
 
-Do you work, and commit as you see fit.Make your commit messages helpful. 
+Do you work, and commit as you see fit.Make your commit messages helpful.
 
-### Push your changes up to GitHub.
+### Push your changes up to GitHub
 
 If this is the first time pushing to GitHub you will need to extended command, other wise you can simply do a `git push`.
 
-```
+```bash
 git push -u origin GH-issuenumber-title-of-issue
 ```
 

DEBUGING.md

@@ -1,3 +1,5 @@
+# DEBUGGING.MD
+
 Adding the following to the workflow.R or to your .Rprofile will enable
 printing of a stacktrace in case something goes wrong. This will help
 with the development of PEcAn.