Merge pull request #3510 from divine7022/package-documentation

fix: "/pkgdoc/package_documentation/pkgdocs": not found

Author: dlebauer

.github/workflows/pkgdown.yml

@@ -16,6 +16,7 @@ jobs:
     runs-on: ubuntu-latest  
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      PECAN_GIT_BRANCH: ${{ github.event_name == 'pull_request' && github.base_ref || github.ref_name }}
 
     container: 
       image: pecan/depends:develop
@@ -24,7 +25,7 @@ jobs:
     # Checkout source code
     - uses: actions/checkout@v4
 
-    # Install pkgdown
+    # Install dependencies
     - name: Install dependencies
       run: Rscript -e 'install.packages("pkgdown")'
 

base/all/DESCRIPTION

@@ -43,6 +43,8 @@ Description: The Predictive Ecosystem Carbon Analyzer
     PEcAn is to streamline the interaction between data and
     models, and to improve the efficacy of scientific
     investigation.
+URL: https://pecanproject.github.io
+BugReports: https://github.com/PecanProject/pecan/issues
 Depends:
     PEcAn.DB,
     PEcAn.settings,

base/db/DESCRIPTION

@@ -39,6 +39,8 @@ Description: The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
     model parameterization, execution, and analysis. The goal of PECAn is to
     streamline the interaction between data and models, and to improve the
     efficacy of scientific investigation.
+URL: https://pecanproject.github.io
+BugReports: https://github.com/PecanProject/pecan/issues
 Imports:
     DBI,
     dbplyr (>= 2.4.0),

base/db/man/PEcAn.DB-package.Rd

@@ -19,8 +19,8 @@ Description: Convenience functions for logging outputs from 'PEcAn',
    and lenience when running large batches of simulations that should not be
    terminated by errors in individual models. It is loosely based on
    the 'log4j' package.
-BugReports: https://github.com/PecanProject/pecan/issues
 URL: https://pecanproject.github.io/
+BugReports: https://github.com/PecanProject/pecan/issues
 Imports: 
     utils,
     stringi

base/logger/DESCRIPTION

@@ -10,6 +10,8 @@ Authors@R: c(person("David", "LeBauer", role = c("aut", "cre"),
 Author: David LeBauer, Tess McCabe
 Maintainer: David LeBauer <dlebauer@illinois.edu>
 Description: PEcAn integration and model skill testing
+URL: https://pecanproject.github.io
+BugReports: https://github.com/PecanProject/pecan/issues
 Imports:
     dplyr,
     graphics,

base/qaqc/DESCRIPTION

@@ -15,6 +15,8 @@ Authors@R: c(person("David", "LeBauer", role = c("aut"),
              person("University of Illinois, NCSA", role = c("cph")))
 Description: This package contains utilities for communicating with and executing code on local and remote hosts.
     In particular, it has PEcAn-specific utilities for starting ecosystem model runs.
+URL: https://pecanproject.github.io
+BugReports: https://github.com/PecanProject/pecan/issues
 Imports:
     dplyr,
     foreach,

base/remote/DESCRIPTION

@@ -12,6 +12,8 @@ LazyLoad: yes
 LazyData: FALSE
 Require: hdf5
 Description: Contains functions to read PEcAn settings files.
+URL: https://pecanproject.github.io
+BugReports: https://github.com/PecanProject/pecan/issues
 Depends:
     methods
 Imports:

base/settings/DESCRIPTION

@@ -30,6 +30,8 @@ Description: The Predictive Ecosystem Carbon Analyzer
     PEcAn is to streamline the interaction between data and
     models, and to improve the efficacy of scientific
     investigation.
+URL: https://pecanproject.github.io
+BugReports: https://github.com/PecanProject/pecan/issues
 Imports:
     abind (>= 1.4.5),
     curl,