Merge branch 'develop' into integ-testing

.github/workflows/book.yml

@@ -3,7 +3,7 @@ name: renderbook
 on:
   push:
     branches:
-      - master
+      - main
       - develop
     tags:
       - '*'
@@ -65,9 +65,12 @@ jobs:
         git config --global user.email "[email protected]"
         git config --global user.name "GitHub Documentation Robot"
         export VERSION=$(echo $GITHUB_REF | sed 's,.*/,,' )
+        if [ "$VERSION" = "main" ]; then
+          export VERSION=latest
+        fi
         cd pecan-documentation
         mkdir -p $VERSION
         rsync -a --delete ../book_source/_book/ ${VERSION}/
         git add --all *
         git commit -m "Build book from pecan revision ${GITHUB_SHA}" || true
-        git push -q origin master
+        git push -q origin main

.github/workflows/ci.yml

@@ -3,11 +3,10 @@ name: CI
 on:
   push:
     branches:
-      - master
+      - main
       - develop
-
     tags:
-      - '*'
+      - "v*.*.*"
   pull_request:
   merge_group:
   issue_comment:

.github/workflows/docker.yml

@@ -4,11 +4,11 @@ on:
   push:
     branches:
       - main
-      - master
       - develop
     tags:
       - "v*.*.*"
   pull_request:
+  merge_group:
   workflow_dispatch:
     inputs:
       r_version:

CHANGELOG.md

@@ -20,6 +20,7 @@ For more information about this file see also [Keep a Changelog](http://keepacha
     * Base packages `PEcAn.all`, `PEcAn.DB`, `PEcAn.QAQC`, `PEcAn.remote`, `PEcAn.settings`, `PEcAn.visualization`, and `PEcAn.workflow`
     * Model packages `PEcAn.BASGRA`, `PEcAn.CLM45`, `PEcAn.DALEC`, `PEcAn.dvmdostem`, `PEcAn.FATES`, `PEcAn.GDAY`, `PEcAn.JULES`, `PEcAn.LDNDC`, `PEcAn.LINKAGES`, `PEcAn.LPJGUESS`, `PEcAn.MAAT`, `PEcAn.MAESPA`, `PEcAn.PRELES`, `PEcAn.SIBCASA`, `PEcAn.SIPNET`, `PEcAn.STICS`, and the new model package template.
     * Modules `PEcAn.allometry`, `PEcAn.assim.batch`, `PEcAn.data.mining`, `PEcAn.emulator`, `PEcAn.MA`, `PEcAn.photosynthesis`, `PEcAn.priors`, and `PEcAn.RTM`.
+- Renamed master branch to main
 
 ### Removed
 

CONTRIBUTING.md

@@ -45,21 +45,21 @@ Switch pecan to your fork
 git remote set-url origin https://github.com/<your username>/pecan.git
 ```
 
-Setup pecan to be able to fetch from the master/develop
+Setup pecan to be able to fetch from the main/develop
 
 ```bash
 git remote add upstream https://github.com/PecanProject/pecan.git
 ```
 
 ## PEcAn Branches
 
-PEcAn uses two protected branches, the master branch and the develop branch. The master branch will match the official releases, but all work will be done on the develop branch. Make sure that you create branches from the develop branch. This should be the default branch in your git repository.
+PEcAn uses two protected branches, the main branch and the develop branch. The main branch will match the official releases, but all work will be done on the develop branch. Make sure that you create branches from the develop branch. This should be the default branch in your git repository.
 
 ## Adding Features
 
 When you add a new feature always create an issue first, this allows others to comment and give you tips. It will also help us keep track of what people are adding and with new releases helps us to write new release notes and give you credit for your work.
 
-Secondly always work in a  branch, never work on the master or develop branch. Keep your master and develop branch in sync with the master and develop of the official PEcAn repository. This makes the pull requests (you do want your work to be in the main branch right?) easier for us.
+Secondly always work in a  branch, never work on the main or develop branch. Keep your main and develop branch in sync with the main and develop of the official PEcAn repository. This makes the pull requests (you do want your work to be in the main branch right?) easier for us.
 
 Finally try to keep your branches focused on fixing/adding only one feature and try not fall in the trap of doing a lot of things in a  single branch. This will not only make it harder for us to process your pull request but makes it take longer before you can submit your pull request. Small pull requests are more likely to be looked at faster and pulled into the develop branch faster.
 
@@ -112,7 +112,7 @@ git push -u origin GH-issuenumber-title-of-issue
 
 ## Additional Resources
 
-- [Adding models to PEcAn](https://pecanproject.github.io/pecan-documentation/master/adding-an-ecosystem-model.html)
-- [PEcAn configuration files](https://pecanproject.github.io/pecan-documentation/master/pecan-xml-configuration.html)
-- [Development help](https://pecanproject.github.io/pecan-documentation/master/developer-guide.html)
-- [PEcAn Code of Conduct](https://pecanproject.github.io/pecan-documentation/master/contributor-covenant-code-of-conduct.html)
+- [Adding models to PEcAn](https://pecanproject.github.io/pecan-documentation/latest/adding-an-ecosystem-model.html)
+- [PEcAn configuration files](https://pecanproject.github.io/pecan-documentation/latest/pecan-xml-configuration.html)
+- [Development help](https://pecanproject.github.io/pecan-documentation/latest/developer-guide.html)
+- [PEcAn Code of Conduct](CODE_OF_CONDUCT.md)

DEV-INTRO.md

@@ -1,6 +1,6 @@
 # PEcAn Development
 
-This is a minimal guide to getting started with PEcAn development under Docker. You can find more information about docker in the [pecan documentation](https://pecanproject.github.io/pecan-documentation/master/docker-index.html).
+This is a minimal guide to getting started with PEcAn development under Docker. You can find more information about docker in the [pecan documentation](https://pecanproject.github.io/pecan-documentation/latest/docker-index.html).
 
 ## Requirements and Recommendations
 
@@ -29,7 +29,7 @@ cd pecan
 
 ## Developing in Docker
 
-The use of Docker in PEcAn is described in detail in the [PEcAn documentation](https://pecanproject.github.io/pecan-documentation/master/docker-index.html). This is intended as a quick start.
+The use of Docker in PEcAn is described in detail in the [PEcAn documentation](https://pecanproject.github.io/pecan-documentation/latest/docker-index.html). This is intended as a quick start.
 
 ### Installing Docker
 
@@ -61,7 +61,7 @@ You can now use the command `docker compose` to work with the containers setup f
 
 ### First time setup
 
-The steps in this section only need to be done the first time you start working with the stack in docker. After this is done you can skip these steps. You can find more detail about the docker commands in the [pecan documentation](https://pecanproject.github.io/pecan-documentation/master/docker-index.html).
+The steps in this section only need to be done the first time you start working with the stack in docker. After this is done you can skip these steps. You can find more detail about the docker commands in the [pecan documentation](https://pecanproject.github.io/pecan-documentation/latest/docker-index.html).
 
 - setup .env file
 - create folders to hold the data

README.md

@@ -21,7 +21,7 @@ PEcAn is not itself an ecosystem model, and it can be used to with a variety of
 
 ## Documentation
 
-Consult documentation of the PEcAn Project; either the [latest stable development](https://pecanproject.github.io/pecan-documentation/develop/) branch, the latest [release](https://pecanproject.github.io/pecan-documentation/master/). Documentation from [earlier releases is here](https://pecanproject.github.io/documentation.html).
+Consult documentation of the PEcAn Project; either the [latest stable development](https://pecanproject.github.io/pecan-documentation/develop/) branch, the latest [release](https://pecanproject.github.io/pecan-documentation/latest/). Documentation from [earlier releases is here](https://pecanproject.github.io/documentation.html).
 
 ## Getting Started
 

book_source/02_demos_tutorials_workflows/01_install_pecan.Rmd

@@ -81,7 +81,7 @@ This will not go into much detail about about how to use Docker -- for more deta
 
     This should print the current version of docker-compose. We have tested the instruction below with versions of docker compose 1.22 and above.
    
-3. **Download the PEcAn docker compose file**. It is located in the root directory of the [PEcAn source code](https://github.com/pecanproject/pecan). For reference, here are direct links to the [latest stable version](https://raw.githubusercontent.com/PecanProject/pecan/master/docker-compose.yml) and the [bleeding edge development version](https://raw.githubusercontent.com/PecanProject/pecan/develop/docker-compose.yml). (To download the files, you should be able to right click the link and select "Save link as".) Make sure the file is saved as `docker-compose.yml` in a directory called `pecan`.
+3. **Download the PEcAn docker compose file**. It is located in the root directory of the [PEcAn source code](https://github.com/pecanproject/pecan). For reference, here are direct links to the [latest stable version](https://raw.githubusercontent.com/PecanProject/pecan/main/docker-compose.yml) and the [bleeding edge development version](https://raw.githubusercontent.com/PecanProject/pecan/develop/docker-compose.yml). (To download the files, you should be able to right click the link and select "Save link as".) Make sure the file is saved as `docker-compose.yml` in a directory called `pecan`.
 
 4. **Initialize the PEcAn database and data images**. The following `docker compose` commands are used to download all the data PEcAn needs to start working. For more on how they work, see our [Docker topical pages](#pecan-docker-quickstart-init).
 

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

@@ -13,16 +13,16 @@ The following Tutorials assume you have installed PEcAn. If you have not, please
 |Type|Title|Web Link| Source Rmd|
 |:--:|:---:|:------:|:---------:|
 |Demo| Basic Run| [html](#demo-1) | [Rmd](https://github.com/PecanProject/pecan/blob/develop/documentation/tutorials/01_Demo_Basic_Run/Demo01.Rmd)|
-|Demo| Uncertainty Analysis| [html](#demo-2)	| [Rmd](https://github.com/PecanProject/pecan/tree/master/documentation/tutorials/02_Demo_Uncertainty_Analysis)|
+|Demo| Uncertainty Analysis| [html](#demo-2)	| [Rmd](https://github.com/PecanProject/pecan/tree/main/documentation/tutorials/02_Demo_Uncertainty_Analysis)|
 |Demo| Output Analysis|html |[Rmd](https://github.com/PecanProject/pecan/tree/develop/documentation/tutorials/AnalyzeOutput)|
 |Demo| MCMC |html|[Rmd](https://github.com/PecanProject/pecan/tree/develop/documentation/tutorials/MCMC)|
 |Demo|Parameter Assimilation |html |[Rmd](https://github.com/PecanProject/pecan/tree/develop/documentation/tutorials/ParameterAssimilation)|
 |Demo|State Assimilation|html|[Rmd](https://github.com/PecanProject/pecan/tree/develop/documentation/tutorials/StateAssimilation)|
 |Demo| Sensitivity|html|[Rmd](https://github.com/PecanProject/pecan/tree/develop/documentation/tutorials/sensitivity)|
-|Vignette|Allometries|html|[Rmd](https://github.com/PecanProject/pecan/blob/master/modules/allometry/vignettes/AllomVignette.Rmd)|
-|Vignette|MCMC|html|[Rmd](https://github.com/PecanProject/pecan/blob/master/modules/assim.batch/vignettes/AssimBatchVignette.Rmd)|
-|Vignette|Meteorological Data|html|[Rmd](https://github.com/PecanProject/pecan/tree/master/modules/data.atmosphere/vignettes)|
-|Vignette|Meta-Analysis|html|[Rmd](https://github.com/PecanProject/pecan/blob/master/modules/meta.analysis/vignettes/single.MA_demo.Rmd)|
-|Vignette|Photosynthetic Response Curves|html|[Rmd](https://github.com/PecanProject/pecan/blob/master/modules/photosynthesis/vignettes/ResponseCurves.Rmd)|
-|Vignette|Priors|html|[Rmd](https://github.com/PecanProject/pecan/blob/master/modules/priors/vignettes/priors_demo.Rmd)|
-|Vignette|Leaf Spectra:PROSPECT inversion|html|[Rmd](https://github.com/PecanProject/pecan/blob/master/modules/rtm/vignettes/pecanrtm.vignette.Rmd)|
+|Vignette|Allometries|html|[Rmd](https://github.com/PecanProject/pecan/blob/main/modules/allometry/vignettes/AllomVignette.Rmd)|
+|Vignette|MCMC|html|[Rmd](https://github.com/PecanProject/pecan/blob/main/modules/assim.batch/vignettes/AssimBatchVignette.Rmd)|
+|Vignette|Meteorological Data|html|[Rmd](https://github.com/PecanProject/pecan/tree/main/modules/data.atmosphere/vignettes)|
+|Vignette|Meta-Analysis|html|[Rmd](https://github.com/PecanProject/pecan/blob/main/modules/meta.analysis/vignettes/single.MA_demo.Rmd)|
+|Vignette|Photosynthetic Response Curves|html|[Rmd](https://github.com/PecanProject/pecan/blob/main/modules/photosynthesis/vignettes/ResponseCurves.Rmd)|
+|Vignette|Priors|html|[Rmd](https://github.com/PecanProject/pecan/blob/main/modules/priors/vignettes/priors_demo.Rmd)|
+|Vignette|Leaf Spectra:PROSPECT inversion|html|[Rmd](https://github.com/PecanProject/pecan/blob/main/modules/rtm/vignettes/pecanrtm.vignette.Rmd)|

book_source/02_demos_tutorials_workflows/03_web_workflow.Rmd

@@ -200,7 +200,7 @@ At the moment, what is functional is a prototype workflow that works for invento
 This tool works with an internal copy of the FIA that is uploaded to a postGRES database along side BETY, however for space reasons this database does not ship with the PEcAn VM. To turn this feature on:
 
 1. Download and Install the FIA database. Instructions in [Installing data for PEcAn]
-2. For web-base runs, specify the database settings in the [config.php](https://github.com/PecanProject/pecan/blob/master/web/config.example.php)
+2. For web-base runs, specify the database settings in the [config.php](https://github.com/PecanProject/pecan/blob/main/web/config.example.php)
 3. For R-based runs, specify the database settings in the [THE PEcAn XML]
 
 More detailed information on how PEcAn processes inputs can be found on our [Input Conversion]page.

book_source/02_demos_tutorials_workflows/05_developer_workflows/02_git/01_using-git.Rmd

@@ -48,7 +48,7 @@ We follow branch organization laid out on [this page](http://nvie.com/posts/a-su
 In short, there are three main branches you must be aware of:
 
 * **develop** - Main Branch containing the latest code. This is the main branch you will make changes to. 
-* **master** - Branch containing the latest stable code. DO NOT MAKE CHANGES TO THIS BRANCH. 
+* **main** - Branch containing the latest stable code. DO NOT MAKE CHANGES TO THIS BRANCH. 
 * **release/vX.X.X** - Named branches containing code specific to a release. Only make changes to this branch if you are fixing a bug on a release branch.
 
 #### Milestones, Issues, Tasks
@@ -121,7 +121,7 @@ git remote add upstream [email protected]:PecanProject/pecan.git
 
 ##### Hint: Keeping your fork in sync
 
-If you have used the instructions above, you can use the helper script called [`scripts/syncgit.sh`](https://github.com/PecanProject/pecan/blob/master/scripts/syncgit.sh) to keep the master and develop branches of your own fork in sync with the PEcAnProject/pecan repository.
+If you have used the instructions above, you can use the helper script called [`scripts/syncgit.sh`](https://github.com/PecanProject/pecan/blob/main/scripts/syncgit.sh) to keep the main and develop branches of your own fork in sync with the PEcAnProject/pecan repository.
 
 After following the above, your .git/config file will include the following:
 
@@ -144,7 +144,7 @@ Then, you can run:
 ./scripts/syncgit.sh
 ```
 
-Now the master and develop branches on your fork will be up to date. 
+Now the main and develop branches on your fork will be up to date. 
 
 #### Using Branching
 
@@ -199,7 +199,7 @@ git push origin <branchname>
 
 #### After pull request is merged
 
-1. Make sure you start in master 
+1. Make sure you start in main 
 
 ```sh
 git checkout develop`

book_source/03_topical_pages/02_pecan_standards.Rmd

@@ -10,11 +10,11 @@ Internal PEcAn standard time follows ISO_8601 format for dates and time (https:/
 
 To aid in the conversion between PEcAn internal ISO_8601 standard and CF convention used in all met drivers and PEcAn standard output you can utilize the functions: "cf2datetime","datetime2doy","cf2doy", and for SIPNET "sipnet2datetime"
 
-### Input Standards
+## Input Standards
 
-#### Meterology Standards 
+### Meteorology Standards 
 
-##### Dimensions:
+#### Dimensions:
 
 
 |CF standard-name | units |
@@ -26,7 +26,8 @@ To aid in the conversion between PEcAn internal ISO_8601 standard and CF convent
 General Note: dates in the database should be date-time (preferably with timezone), and datetime passed around in PEcAn should be of type POSIXct.
 
 
-##### The variable names should be `standard_name`
+#### Variable names should be `standard_name`
+
 ```{r, echo=FALSE,warning=FALSE,message=FALSE}
 names<-c("<b>air_temperature</b>", "air_temperature_max", "air_temperature_min", "<b>air_pressure</b>", 
          "mole_fraction_of_carbon_dioxide_in_air", "moisture_content_of_soil_layer", "soil_temperature ",
@@ -75,15 +76,15 @@ The key is to process each type of met data (site, reanalysis, forecast, climate
 
 ### Soils and Vegetation Inputs
 
-##### Soil Data 
+#### Soil Data 
 
 See the [Soil Data] section on more into on creating a standard soil data file.
 
-##### Vegetation Data
+#### Vegetation Data
 
 See the [Vegetation Data] section on more info on creating a standard vegetation data file
 
-### Output Standards {#OutputStandards}
+## Output Standards {#OutputStandards}
 
 * created by `model2netcdf` functions
 * based on format used by [MsTMIP](http://nacp.ornl.gov/MsTMIP_variables.shtml)