Merge pull request #83 from NOAA-EDAB/dev

Dev

..Rcheck/00check.log

@@ -0,0 +1,13 @@
+* using log directory ‘/home/rklasky/R/packages/Rpath/..Rcheck’
+* using R version 4.3.1 (2023-06-16)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* R was compiled by
+    gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
+    GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
+* running under: Linux Mint 20
+* using session charset: UTF-8
+* checking for file ‘./DESCRIPTION’ ... ERROR
+Required fields missing or empty:
+  ‘Author’ ‘Maintainer’
+* DONE
+Status: 1 ERROR

.Rbuildignore

@@ -5,3 +5,6 @@
 ^_pkgdown\.yml$
 ^docs$
 ^pkgdown$
+^data-raw$
+^doc$
+^Meta$

.Renviron

@@ -0,0 +1 @@
+_R_CHECK_DONTTEST_EXAMPLES_=FALSE

.github/workflows/R-CMD-check.yaml

@@ -1,8 +1,8 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master]
+    branches: [main, master, UnitTests]
   pull_request:
     branches: [main, master]
 
@@ -18,7 +18,7 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-latest,   r: 'release'}
+          - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
@@ -29,30 +29,21 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
       - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: rcmdcheck
-
-      - uses: r-lib/actions/check-r-package@v1
-
-      - name: Show testthat output
-        if: always()
-        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
-        shell: bash
+          extra-packages: any::rcmdcheck
+          needs: check
 
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
+      - uses: r-lib/actions/check-r-package@v2
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+          upload-snapshots: true

.github/workflows/pkgdown.yaml

@@ -22,7 +22,7 @@ jobs:
     permissions:
       contents: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 

.github/workflows/secretScan.yml

@@ -11,3 +11,4 @@ jobs:
         fetch-depth: '2'
     - name: gitleaks-action
       uses: gitleaks/[email protected]
+

.github/workflows/tests.yml

@@ -0,0 +1,94 @@
+
+on:
+  push:
+    paths:
+    - '.github/workflows/tests.yml'
+    - 'R/*'
+    - 'tests/testthat/*'
+    - 'README.md'
+    - 'DESCRIPTION'
+  pull_request:
+    paths:
+    - '.github/workflows/tests.yml'
+    - 'R/*'
+    - 'tests/testthat/*'
+
+name: Unit-Tests
+
+jobs:
+  # build:
+  #   runs-on: ubuntu-latest
+  #   steps:
+  #     - uses: actions/checkout@v2
+  #     - uses: r-lib/actions/setup-r@v2
+  #     - uses: r-lib/actions/setup-pandoc@v2
+  #     - name: Install dependencies
+  #       run: Rscript -e "install.packages(c('testthat', 'tidyverse', 'here'))"
+  #     - name: Run tests
+  #       run: Rscript -e "source('tests/testthat.R')"
+
+  Unit-Tests:
+    runs-on: ${{matrix.config.os}}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        #os: [macos-latest, ubuntu-latest, windows-latest]
+        #os: [ubuntu-latest]
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,  r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,  r: 'release'}
+          - {os: ubuntu-latest,  r: 'oldrel-1'}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+#      R_REMOTES_NO_ERRORS_FROM_WARNINGS: false
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+#        with:
+#          fetch-depth: 0
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+#          r-version: '4.3.1'
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+
+      - name: Install command line packages
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt update
+          sudo apt-get install libcurl4-openssl-dev libgit2-dev
+
+      - name: Install dependencies
+        #run: Rscript -e "install.packages(c('remotes','testthat', 'tidyverse', 'here'))"
+        run: |
+          install.packages(c('usethis','remotes','testthat','tidyverse','here','rmarkdown','qpdf','distillery','ggpubr','rlist'))
+          remotes::install_github("NOAA-EDAB/Rpath")
+        shell: Rscript {0}
+
+      - name: Run tests
+        #run: Rscript -e "source('tests/testthat.R')"
+        run: |
+          source(here::here("data-raw/REcosystem.R"))
+          source(here::here("tests/testthat.R"))
+        shell: Rscript {0}
+
+      # - name: commit data files
+      #   run: |
+      #     git config user.name  github-actions
+      #     git config user.email [email protected]
+      #     file.copy('here::here("tests/testthat/Rplots.pdf")",to=here::here("inst/extdata/Rplots.pdf"))
+      #     git add inst/extdata/Rplots.pdf
+      #     git commit -m "automated commit from testthat yml"
+      #     git push

.gitignore

@@ -1,18 +1,28 @@
 .Rproj.user
 .Rhistory
 .RData
-*.png
+.Renviron
 *.jpg
 *.tif
-data
+*.tar
+*.so
 outputs
 code
 *.xlsx
 *.docx
+*.pdf
 Ecopath_dev
 Rpath.Rcheck*
 src/*.o
 src/*.dll
-NAMESPACE
-
+tests/testthat/data/output/*
+tests/testthat/data/bkup/*
+tests/testthat/data/input/REcosystem_Current_*.dat
+tests/testthat/data/input/REcosystem_Current_*.csv
+tests/testthat/old/*
+tests/testthat/bkup/*
+tests/testthat/old dat files/*
 docs
+doc
+Meta
+Rpath.Rproj

DESCRIPTION

@@ -1,32 +1,49 @@
-Package: Rpath
-Type: Package
-Title: R implementation of Ecopath with Ecosim
-Version: 0.0.1.3
-Date: 2021-04-25
-Authors@R: c(
-    person("Kerim", "Aydin",   email = "[email protected]",   role = "aut"),
-    person("Sean", "Lucey",    email = "[email protected]",    
-           role = c("aut", "cre")),
-    person("Sarah", "Gaichas", email = "[email protected]", role = "aut"))
-Description: This package implements the core mass balance equations made popular
-    by Ecopath with Ecosim. There are two parts to the package, the static snapshot
-    of energy flow through the system using rpath and dynamic simulations run using 
-    the rsim family of functions.
-License: file LICENSE
-Encoding: UTF-8
-Imports:
-    data.table,
-    graphics,
-    grDevices,
-    MASS,
-    Rcpp (>= 0.11.3),
-    stats,
-    utils
-LinkingTo: Rcpp
-Suggests:
-    knitr,
-    rmarkdown
-VignetteBuilder: knitr
-RoxygenNote: 7.1.1
-URL: https://github.com/NOAA-EDAB/Rpath
-BugReports: https://github.com/NOAA-EDAB/Rpath/issues
+Package: Rpath
+Type: Package
+Title: R implementation of Ecopath with Ecosim
+Version: 0.9.0
+Date: 2024-05-31
+Authors@R: c(
+    person("Kerim", "Aydin",   email = "[email protected]",   role = "aut"),
+    person("Sean", "Lucey",    email = "[email protected]",    
+           role = c("aut", "cre")),
+    person("Sarah", "Gaichas", email = "[email protected]", role = "aut"))
+Description: This package implements the core mass balance equations made popular
+    by Ecopath with Ecosim. There are two parts to the package, the static snapshot
+    of energy flow through the system using rpath and dynamic simulations run using 
+    the rsim family of functions.
+License: file LICENSE
+Encoding: UTF-8
+Imports:
+    data.table,
+    methods,
+    graphics,
+    grDevices,
+    MASS,
+    Rcpp (>= 0.11.3),
+    stats,
+    utils
+LinkingTo: Rcpp
+Suggests:
+    here,
+    knitr,
+    rmarkdown,
+    distillery,
+    ggplot2,
+    ggpubr,
+    rlist,
+    stringr,
+    qpdf,
+    usethis,
+    dplyr,
+    generics,
+    testthat (>= 3.0.0)
+VignetteBuilder: knitr
+RoxygenNote: 7.2.3
+URL: https://github.com/NOAA-EDAB/Rpath
+BugReports: https://github.com/NOAA-EDAB/Rpath/issues
+Depends: 
+    R (>= 2.10)
+Config/testthat/edition: 3
+LazyData: true
+

NAMESPACE

@@ -53,4 +53,5 @@ import(stats)
 import(utils)
 importFrom(Rcpp,sourceCpp)
 importFrom(grDevices,rainbow)
+importFrom(methods,is)
 useDynLib(Rpath)

NEWS.md

@@ -1,3 +1,12 @@
+# Rpath 0.9.0
+
+## Major Changes
+- Added Ecosense routines and vignettes
+- Added example ecosystems
+- Added Unit Tests
+- Fixed bug in stanza month calculations that affected some species
+- Changed versioning to reflect near-release status.
+=======
 # Rpath 0.0.1.3
 
 ## Major Changes

R/RcppExports.R

@@ -1,23 +1,23 @@
-# Generated by using Rcpp::compileAttributes() -> do not edit by hand
-# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
-
-rk4_run <- function(params, instate, forcing, fishing, stanzas, StartYear, EndYear) {
-    .Call('_Rpath_rk4_run', PACKAGE = 'Rpath', params, instate, forcing, fishing, stanzas, StartYear, EndYear)
-}
-
-Adams_run <- function(params, instate, forcing, fishing, stanzas, StartYear, EndYear, InitDeriv) {
-    .Call('_Rpath_Adams_run', PACKAGE = 'Rpath', params, instate, forcing, fishing, stanzas, StartYear, EndYear, InitDeriv)
-}
-
-deriv_vector <- function(params, state, forcing, fishing, stanzas, inyear, m, tt) {
-    .Call('_Rpath_deriv_vector', PACKAGE = 'Rpath', params, state, forcing, fishing, stanzas, inyear, m, tt)
-}
-
-SplitSetPred <- function(stanzas, state) {
-    .Call('_Rpath_SplitSetPred', PACKAGE = 'Rpath', stanzas, state)
-}
-
-SplitUpdate <- function(stanzas, state, forcing, deriv, yr, mon) {
-    .Call('_Rpath_SplitUpdate', PACKAGE = 'Rpath', stanzas, state, forcing, deriv, yr, mon)
-}
-
+# Generated by using Rcpp::compileAttributes() -> do not edit by hand
+# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
+
+rk4_run <- function(params, instate, forcing, fishing, stanzas, StartYear, EndYear) {
+    .Call('_Rpath_rk4_run', PACKAGE = 'Rpath', params, instate, forcing, fishing, stanzas, StartYear, EndYear)
+}
+
+Adams_run <- function(params, instate, forcing, fishing, stanzas, StartYear, EndYear, InitDeriv) {
+    .Call('_Rpath_Adams_run', PACKAGE = 'Rpath', params, instate, forcing, fishing, stanzas, StartYear, EndYear, InitDeriv)
+}
+
+deriv_vector <- function(params, state, forcing, fishing, stanzas, inyear, m, tt) {
+    .Call('_Rpath_deriv_vector', PACKAGE = 'Rpath', params, state, forcing, fishing, stanzas, inyear, m, tt)
+}
+
+SplitSetPred <- function(stanzas, state) {
+    .Call('_Rpath_SplitSetPred', PACKAGE = 'Rpath', stanzas, state)
+}
+
+SplitUpdate <- function(stanzas, state, forcing, deriv, yr, mon) {
+    .Call('_Rpath_SplitUpdate', PACKAGE = 'Rpath', stanzas, state, forcing, deriv, yr, mon)
+}
+

R/Rpath_support.R

@@ -1,12 +1,18 @@
+library(methods)
+
 ########################################################################################
 # Set of functions for returning functional group names (character vector)
 # using the type input column
 #
 # Internal supporting function for group names to check type 
-grouptype <- function(Rpath){
-  if(class(Rpath)=="Rpath"){gt<-list(type=Rpath$type, grp=Rpath$Group)}
-  else{
-    if(class(Rpath)=="Rpath.params"){
+#'
+#' @importFrom methods is
+#'
+grouptype <- function(Rpath) {
+  if (is(Rpath,"Rpath")) {
+    gt<-list(type=Rpath$type, grp=Rpath$Group)
+  } else {
+    if (is(Rpath,"Rpath.params")) {
       gt<-list(type=Rpath$model$Type, grp=Rpath$model$Group)}
     else{
       stop("Input must be an Rpath (balanced) or Rpath.params (unbalanced) object.")