Merge branch 'master' into JOSS

PIK-LPJmL · Nov 9, 2023 · b23d34c · b23d34c
2 parents 308286f + cfad25c
commit b23d34c
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diff --git a/.buildlibrary b/.buildlibrary
@@ -1,4 +1,4 @@
-ValidationKey: '2307608'
+ValidationKey: '2336684'
 AutocreateReadme: yes
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'

diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml
@@ -1,5 +1,3 @@
-# Run CI for R using https://eddelbuettel.github.io/r-ci/
-
 name: check
 
 on:
@@ -8,92 +6,44 @@ on:
   pull_request:
     branches: [main, master]
 
-env:
-  USE_BSPM: "true"
-  _R_CHECK_FORCE_SUGGESTS_: "false"
-  NO_BINARY_INSTALL_R_PACKAGES: 'c("madrat", "magclass", "citation", "gms", "goxygen", "GDPuc", "roxygen2")'
-
 jobs:
   check:
     runs-on: ubuntu-latest
 
     steps:
       - uses: actions/checkout@v3
 
-      - name: Bootstrap
-        run: |
-          sudo chown runner -R .
-          sudo locale-gen en_US.UTF-8
-          sudo add-apt-repository -y ppa:ubuntugis/ppa
-          curl -OLs https://eddelbuettel.github.io/r-ci/run.sh
-          chmod 0755 run.sh
-          ./run.sh bootstrap
-          rm -f bspm_*.tar.gz
-
-      - name: Enable r-universe repo, modify bspm integration
-        run: |
-          # install packages from https://pik-piam.r-universe.dev and CRAN
-          echo '
-          options(repos = c(universe = "https://pik-piam.r-universe.dev",
-                            CRAN = "https://cloud.r-project.org"))
-          ' >> .Rprofile
-          cat .Rprofile
-          # modify bspm integration to never install binary builds of PIK CRAN packages
-          sudo sed -i '/bspm::enable()/d' /etc/R/Rprofile.site
-          # need double % because of printf, %s is replaced with "$NO_BINARY_INSTALL_R_PACKAGES" (see "env:" above)
-          printf '
-          local({
-            expr <- quote({
-              if (!is.null(repos)) {
-                noBinaryInstallRPackages <- %s
-                pkgs <- c(bspm::install_sys(pkgs[!pkgs %%in%% noBinaryInstallRPackages]),
-                          pkgs[pkgs %%in%% noBinaryInstallRPackages])
-              }
-              type <- "source"
-            })
-            trace(utils::install.packages, expr, print = FALSE)
-          })
-          ' "$NO_BINARY_INSTALL_R_PACKAGES" | sudo tee --append /etc/R/Rprofile.site >/dev/null
-          cat /etc/R/Rprofile.site
-
-      - name: Set up Pandoc
-        uses: r-lib/actions/setup-pandoc@v2
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - name: Set up Python 3.9
-        uses: actions/setup-python@v4
+      - uses: r-lib/actions/setup-r@v2
         with:
-          python-version: 3.9
+          use-public-rspm: true
+          extra-repositories: "https://rse.pik-potsdam.de/r/packages"
 
-      - name: Cache R libraries
-        if: ${{ !env.ACT }} # skip when running locally via nektos/act
-        uses: pat-s/always-upload-cache@v3
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: /usr/local/lib/R/
-          key: 3-${{ runner.os }}-usr-local-lib-R-${{ hashFiles('DESCRIPTION') }}
-          restore-keys: |
-            3-${{ runner.os }}-usr-local-lib-R-
-
-      - name: Restore R library permissions
-        run: |
-          sudo chmod 2777 /usr/local/lib/R /usr/local/lib/R/site-library
-
-      - name: Install dependencies
-        run: |
-          ./run.sh install_aptget libhdf5-dev libharfbuzz-dev libfribidi-dev
-          ./run.sh install_all
-          ./run.sh install_r_binary covr rstudioapi
-          ./run.sh install_r lucode2
+          extra-packages: |
+            any::lucode2
+            any::covr
+            any::madrat
+            any::magclass
+            any::citation
+            any::gms
+            any::goxygen
+            any::GDPuc
+          # piam packages also available on CRAN (madrat, magclass, citation,
+          # gms, goxygen, GDPuc) will usually have an outdated binary version
+          # available; by using extra-packages we get the newest version
+
+      - uses: actions/setup-python@v4
+        with:
+          python-version: 3.9
 
       - name: Install python dependencies if applicable
         run: |
           [ -f requirements.txt ] && python -m pip install --upgrade pip wheel || true
           [ -f requirements.txt ] && pip install -r requirements.txt || true
 
-      - name: Remove bspm integration # to get rid of error when running install.packages
-        run: |
-          sudo sed -i '/  trace(utils::install.packages, expr, print = FALSE)/d' /etc/R/Rprofile.site
-          cat /etc/R/Rprofile.site
-
       - name: Verify validation key
         shell: Rscript {0}
         run: lucode2:::validkey(stopIfInvalid = TRUE)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -15,7 +15,7 @@ repos:
     -   id: mixed-line-ending
 
 -   repo: https://github.com/lorenzwalthert/precommit
-    rev: v0.3.2.9013
+    rev: v0.3.2.9019
     hooks:
     -   id: parsable-R
     -   id: deps-in-desc

diff --git a/CITATION.cff b/CITATION.cff
@@ -2,8 +2,8 @@ cff-version: 1.2.0
 message: If you use this software, please cite it using the metadata from this file.
 type: software
 title: 'lpjmlkit: Toolkit for Basic LPJmL Handling'
-version: 1.1.8
-date-released: '2023-07-18'
+version: 1.1.9
+date-released: '2023-10-06'
 abstract: A collection of basic functions to facilitate the work with the Dynamic
   Global Vegetation Model (DGVM) Lund-Potsdam-Jena managed Land (LPJmL) hosted at
   the Potsdam Institute for Climate Impact Research (PIK). It provides functions for

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -0,0 +1,86 @@
+# Contributing to lpjmlkit
+
+Thank you for your interest in contributing to *lpjmlkit*, an open-source R
+package for operating LPJmL and processing related data.
+We currently prefer contributions in the form of bug reports, feature requests,
+and suggestions of code improvements as issues in the
+[lpjmlkit GitHub repository](https://github.com/PIK-LPJmL/lpjmlkit/issues).
+If you want to contribute code, please follow the instructions below.
+Please note that due to our current worflow information on the authorship of
+code contributions may get lost.
+
+
+## Getting Started
+
+Before you start contributing to *lpjmlkit*, here are a few steps to get you
+set up:
+
+1. Fork the [lpjmlkit GitHub repository](https://github.com/PIK-LPJmL/lpjmlkit)
+to your own GitHub account.
+2. Clone your forked repository to your local machine.
+   ```shell
+   git clone https://github.com/YourUsername/lpjmlkit.git
+   cd lpjmlkit
+   ```
+3. Install the package and its dependencies following the instructions in the
+documentation.
+
+Now you're ready to start making contributions!
+
+## Contributing
+
+To contribute to *lpjmlkit*, please follow these steps:
+
+1. Check for existing issues in the
+[**issue tracker**](https://github.com/PIK-LPJmL/lpjmlkit/issues) to see if your
+contribution idea has already been discussed or reported.
+2. If the issue doesn't already exist, create a **new issue** to discuss the
+problem or feature you want to address. Be sure to provide as much detail as
+possible to help others understand the context and purpose.
+3. **Fork the repository** if you haven't already and create a **new branch**
+for your contribution.
+4. Make your changes in that new branch, following best practices and 
+adhering to the **coding style** of the project.
+5. Write **unit tests** if applicable and ensure that all tests pass.
+6. Submit a **pull request (PR)** referencing the issue you created earlier.
+Describe your changes, and our team will review it as soon as possible.
+7. All discussion threads of the PR need to be resolved before the PR can be merged.
+
+Your contributions will be greatly appreciated and will help make *lpjmlkit*
+even better.
+
+
+## Code Quality
+We use the the [**Advanced R Style Guide**](https://style.tidyverse.org/) for R
+code.
+
+Furthermore we use the following tools to ensure code quality:
+* [**roxygen2**](https://roxygen2.r-lib.org/) for documentation.
+* [**testthat**](https://testthat.r-lib.org/) for unit tests.
+* [**lintr**](https://lintr.r-lib.org/) for static code analysis.
+
+Please make sure that your code passes all tests and static code analysis before
+submitting a pull request.
+
+## Code of Conduct
+
+Please note that by contributing to *lpjmlkit*, you are expected to adhere to
+our Code of Conduct. We strive to maintain a welcoming and inclusive community,
+and we expect respectful and considerate behavior from all contributors:
+* **Be Respectful**: Treat all community members with respect and kindness.
+* **Inclusivity**: Ensure that your language and actions are inclusive and
+respectful of diversity.
+* **Collaboration**: Encourage a collaborative and supportive atmosphere.
+
+We do not tolerate:
+* **Harassment**: Any form of harassment, trolling, or offensive behavior.
+* **Discrimination**: Discrimination, derogatory comments, or exclusionary
+practices.
+* **Bullying**: Bullying or aggressive behavior towards others.
+
+Reporting Incidents  
+If you witness or experience any violations, please report them to
+[[email protected]](mailto:[email protected]).
+All reports will be handled confidentially and promptly.
+
+Thank you for being part of the *lpjmlkit* community!
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: lpjmlkit
 Type: Package
 Title: Toolkit for Basic LPJmL Handling
-Version: 1.1.8
+Version: 1.1.9
 Authors@R: c(
     person("Jannes", "Breier", , "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-9055-6904")),
     person("Sebastian","Ostberg", , "[email protected]", role = "aut", comment = c(ORCID = "0000-0002-2368-7015")),
@@ -54,4 +54,4 @@ Suggests:
     sf
 Config/testthat/edition: 3
 VignetteBuilder: knitr
-Date: 2023-07-18
+Date: 2023-10-06
diff --git a/R/LPJmLMetaData.R b/R/LPJmLMetaData.R
@@ -75,7 +75,7 @@ LPJmLMetaData <- R6::R6Class( # nolint
       cat(
         paste0(spaces,
                col_var(
-                paste0("$", print_fields)
+                 paste0("$", print_fields)
                ),
                " ",
                to_char1,
@@ -106,13 +106,14 @@ LPJmLMetaData <- R6::R6Class( # nolint
       )
       cat("\n")
 
+      # Print information about subset if subsetted
       cat(
         paste0(
           spaces,
           col_var("$subset"),
           " ",
           # Color red if subset.
-          ifelse(self$subset, col_warn(self$subset), ""),
+          ifelse(self$subset, col_warn(self$subset), self$subset),
           "\n"
         )
       )
@@ -170,7 +171,7 @@ LPJmLMetaData <- R6::R6Class( # nolint
       # Update cell fields - distinguish between character -> LPJmL C index
       #   starting from 0 and numeric/integer -> R index starting from 1 -> -1.
       if (!is.null(subset$cell) ||
-          !is.null(subset$lon) || !is.null(subset$lat)) {
+            !is.null(subset$lon) || !is.null(subset$lat)) {
 
         # Subset of subset$cell, subset$lon or subset$lat always have to be
         #   accompanied by cell_dimnames.
@@ -276,39 +277,39 @@ LPJmLMetaData <- R6::R6Class( # nolint
             "bigendian" = ifelse(x$endian == "big", TRUE, FALSE),
             # "descr" = tolower(x$name), # nolint
             "lastyear" = x$header[["firstyear"]] +
-                         x$header[["timestep"]] *
-                         (x$header[["nyear"]] - 1),
+              x$header[["timestep"]] *
+                (x$header[["nyear"]] - 1),
             "name" = ifelse(is.null(x$name), "LPJDUMMY", x$name)
           )) %>%
           `[[<-`("order",
-                switch(as.character(.$order),
-                       `1` = "cellyear",
-                       `2` = "yearcell",
-                       `3` = "cellindex",
-                       `4` = "cellseq",
-                       stop(
-                         paste(
-                           "Invalid order value", sQuote(.$order), "in header"
-                         )
-                       )
-                  )
-                ) %>%
+            switch(as.character(.$order),
+              `1` = "cellyear",
+              `2` = "yearcell",
+              `3` = "cellindex",
+              `4` = "cellseq",
+              stop(
+                paste(
+                  "Invalid order value", sQuote(.$order), "in header"
+                )
+              )
+            )
+          ) %>%
           `[[<-`("datatype",
-                switch(as.character(.$datatype),
-                       `0` = "byte",
-                       `1` = "short",
-                       `2` = "int",
-                       `3` = "float",
-                       `4` = "double",
-                       stop(
-                         paste(
-                           "Invalid datatype value", sQuote(.$datatype),
-                           "in header"
-                         )
-                       )
-                    )
+            switch(as.character(.$datatype),
+              `0` = "byte",
+              `1` = "short",
+              `2` = "int",
+              `3` = "float",
+              `4` = "double",
+              stop(
+                paste(
+                  "Invalid datatype value", sQuote(.$datatype),
+                  "in header"
                 )
-          private$init_list(header_to_meta, additional_attributes)
+              )
+            )
+          )
+        private$init_list(header_to_meta, additional_attributes)
 
       } else {
         private$init_list(x, additional_attributes)
@@ -574,19 +575,19 @@ LPJmLMetaData <- R6::R6Class( # nolint
         "filename"
       ) %>%
 
-      # Only append scalar if != 1
-      append(
-        ifelse(
-          !is.null(private$.scalar),
-          ifelse(private$.scalar == 1, "scalar", NA),
-          NA
-        )
-      ) %>%
+        # Only append scalar if != 1
+        append(
+          ifelse(
+            !is.null(private$.scalar),
+            ifelse(private$.scalar == 1, "scalar", NA),
+            NA
+          )
+        ) %>%
 
-      # Workaround to deal with NAs (NULL not possible in ifelse)
-      stats::na.omit() %>%
-      as.vector() %>%
-      return()
+        # Workaround to deal with NAs (NULL not possible in ifelse)
+        stats::na.omit() %>%
+        as.vector() %>%
+        return()
     },
 
     .sim_name = NULL,
@@ -681,8 +682,7 @@ LPJmLMetaData <- R6::R6Class( # nolint
                     "name",
                     "map",
                     "version",
-                    "offset"
-                   ),
+                    "offset"),
 
     .dimension_map = list(space_format = c("cell", "lon_lat"),
                           time_format = c("time", "year_month_day"),