preparing 2.1.5 CRAN submission

.github/workflows/rhub.yaml

@@ -0,0 +1,95 @@
+# R-hub's generic GitHub Actions workflow file. It's canonical location is at
+# https://github.com/r-hub/actions/blob/v1/workflows/rhub.yaml
+# You can update this file to a newer version using the rhub2 package:
+#
+# rhub::rhub_setup()
+#
+# It is unlikely that you need to modify this file manually.
+
+name: R-hub
+run-name: "${{ github.event.inputs.id }}: ${{ github.event.inputs.name || format('Manually run by {0}', github.triggering_actor) }}"
+
+on:
+  workflow_dispatch:
+    inputs:
+      config:
+        description: 'A comma separated list of R-hub platforms to use.'
+        type: string
+        default: 'linux,windows,macos'
+      name:
+        description: 'Run name. You can leave this empty now.'
+        type: string
+      id:
+        description: 'Unique ID. You can leave this empty now.'
+        type: string
+
+jobs:
+
+  setup:
+    runs-on: ubuntu-latest
+    outputs:
+      containers: ${{ steps.rhub-setup.outputs.containers }}
+      platforms: ${{ steps.rhub-setup.outputs.platforms }}
+
+    steps:
+    # NO NEED TO CHECKOUT HERE
+    - uses: r-hub/actions/setup@v1
+      with:
+        config: ${{ github.event.inputs.config }}
+      id: rhub-setup
+
+  linux-containers:
+    needs: setup
+    if: ${{ needs.setup.outputs.containers != '[]' }}
+    runs-on: ubuntu-latest
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.containers) }}
+    container:
+      image: ${{ matrix.config.container }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+
+  other-platforms:
+    needs: setup
+    if: ${{ needs.setup.outputs.platforms != '[]' }}
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.platforms) }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/setup-r@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: photosynthesis
-Version: 2.1.4.9000
+Version: 2.1.5
 Date: 2024-11-23
 Title: Tools for Plant Ecophysiology & Modeling
 Authors@R: c(

NEWS.md

@@ -1,4 +1,4 @@
-# photosynthesis (development version)
+# photosynthesis 2.1.5
 
 * Added `photoinhibition()` to light response models. This allows users to estimate photoinhibitation at high light.
 

R/models.R

@@ -49,7 +49,7 @@ get_all_models = function(method) {
 #' @param k_sat Light saturated rate of process k
 #' @param phi_J Quantum efficiency of process k
 #' @param theta_J Curvature of the light response
-#' @param b_inb Inhibition parameter
+#' @param b_inh Inhibition parameter
 #' @md
 #' 
 #' @export

R/photosynthesis-package.R

@@ -5,7 +5,6 @@
 #' See the README on
 #' [GitHub](https://github.com/cdmuir/photosynthesis)
 #'
-#' @docType _PACKAGE
 #' @name photosynthesis-package
 #' @importFrom ggplot2 ggplot
 #' @importFrom magrittr %>% %<>%
@@ -15,6 +14,8 @@
 #' @importFrom rlang .data
 #' @importFrom stats coef lm optim plogis resid rnorm
 #' @importFrom units as_units drop_units set_units
+#' @keywords internal
+"_PACKAGE"
 NULL
 
 ## quiets concerns of R CMD check re: the .'s that appear in pipelines

cran-comments.md

@@ -1,20 +1,19 @@
 ## Summary of new changes
 
-* Removed imports of unexported **tealeaves** functions using `:::` operator
-* `read_licor()` removes lines where parameter settings are changed between logging
+* Added `photoinhibition()` to light response models. This allows users to estimate photoinhibitation at high light.
 
 ## Test environments
-* local R installation, R 4.3.1
-* ubuntu 22.04.3 (on Github actions), R 4.3.1
-* win-builder (release)
-* win-builder (devel)
-* win-builder (oldrelease)
-* R-hub builder: Windows Server 2022, R-devel, 64 bit
-* R-hub builder: Fedora Linux, R-devel, clang, gfortran
+* local R installation, R 4.4.2
+* ubuntu 22.04.3 (on Github actions), R 4.3.1 # NEED TO DO
+* win-builder (release) # NEED TO DO
+* win-builder (devel) # NEED TO DO
+* win-builder (oldrelease) # NEED TO DO
+* R-hub builder: Windows Server 2022, R-devel, 64 bit # NEED TO DO
+* R-hub builder: Fedora Linux, R-devel, clang, gfortran # NEED TO DO
 
 ## R CMD check results
 
 ❯ checking installed package size ... NOTE
-    installed size is  7.3Mb
+    installed size is  7.4Mb
     sub-directories of 1Mb or more:
-      doc   6.1Mb
+      doc   6.2Mb