Adding check to main and cran versions of epiworldRShiny (#21)

* Adding check to main and cran versions of epiworldRShiny * Adding environment * Correcting env * Handling prev versiono of epiworldRShiny * Adding missing comma * Addressing issues * Avoiding building manuals * Adding step to save the built package * Update r.yml * Update r.yml * Updating who is the maintainer * Adding given and family explicitly * Fix bug in description * Updating news and makefile [skip ci]
UofUEpiBio · Oct 7, 2024 · 6ea9a61 · 6ea9a61
1 parent 8bd6b18
commit 6ea9a61
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diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile
@@ -12,7 +12,8 @@ RUN \
   wget https://github.com/jgm/pandoc/releases/download/3.2.1/pandoc-3.2.1-1-amd64.deb && \
   dpkg -i pandoc-3.2.1-1-amd64.deb
 
-RUN install2.r cpp11 rmarkdown roxygen2 tinytest data.table netplot
+RUN install2.r cpp11 rmarkdown roxygen2 tinytest data.table netplot \
+  devtools
 
 RUN apt-get install -y --no-install-recommends && \
   install2.r languageserver

diff --git a/.github/workflows/r.yml b/.github/workflows/r.yml
@@ -12,7 +12,11 @@ on:
 
 name: R-CMD-check-final
 
+env: 
+  GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
 jobs:
+
   R-CMD-check:
     runs-on: ${{ matrix.config.os }}
 
@@ -26,7 +30,7 @@ jobs:
           - {os: windows-latest, r: 'release'}
           - {os: macOS-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: windows-latest, r: 'devel', http-user-agent: 'release'}
-          # Use older ubuntu to maximise backward compatibility
+          # se older ubuntu to maximise backward compatibility
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
           - {os: ubuntu-latest,   r: 'oldrel'}
@@ -68,14 +72,56 @@ jobs:
           check-dir: '"check"'
           error-on: '"warning"'
 
-      # Upload the built package as an artifact
+      - name: Build the package
+        if: ${{ matrix.config.os == 'ubuntu-latest' && (matrix.config.r == 'release' || matrix.config.r == 'devel') }}
+        run: R CMD build .
+
       - uses: actions/upload-artifact@v4
-        if: ${{ matrix.config.os == 'ubuntu-latest' && matrix.config.r == 'release' }}
+        if: ${{ matrix.config.os == 'ubuntu-latest' && (matrix.config.r == 'release' || matrix.config.r == 'devel') }}
+        with:
+          name: epiworldR-built-package-${{ matrix.config.os }}-${{ matrix.config.r }}
+          path: epiworldR_*.tar.gz
+          retention-days: 7
+
+  epiworldShiny:
+    runs-on: ubuntu-latest
+    container: rocker/tidyverse:4.4.0
+
+    steps:
+      - uses: actions/checkout@v4
         with:
-          name: ${{ matrix.config.os }}-pkg
-          path: ${{ github.workspace }}/*.tar.gz
+          repository: 'UofUEpiBio/epiworldRShiny'
+          ref: 'main'
+          fetch-depth: 1
+
+      - name: Install dependencies
+        run: |
+          install2.r -n 2 shinyjs shinydashboard DT shinycssloaders plotly
+          installGithub.r UofUEpiBio/epiworldR@${{ github.sha }}
       
+      - name: Check the package
+        run: |
+          R CMD build .
+          R CMD check  --no-manual epiworldRShiny_*tar.gz
+
+  epiworldRShiny-cran:
+    runs-on: ubuntu-latest
+    container: rocker/tidyverse:4.4.0
+
+    steps:
+      - name: Get epiworldRShiny
+        run: |
+          wget \
+            https://cran.r-project.org/src/contrib/epiworldRShiny_0.1-0.tar.gz
+
+      - name: Install dependencies
+        run: |
+          install2.r -n 2 shinyjs shinydashboard DT shinycssloaders plotly
+          installGithub.r UofUEpiBio/epiworldR@${{ github.sha }}
       
+      - name: Check the package
+        run: |
+          R CMD check --no-manual epiworldRShiny_*tar.gz
 
         
           

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -3,15 +3,15 @@ Type: Package
 Title: Fast Agent-Based Epi Models
 Version: 0.3-2
 Authors@R: c(
-  person("Derek", "Meyer", role=c("aut","cre"), 
-  email="[email protected]", comment = c(ORCID = "0009-0005-1350-6988")),
-  person("George", "Vega Yon", role=c("aut"),
+  person(given="George", family="Vega Yon", role=c("aut","cre"),
   email="[email protected]", comment = c(ORCID = "0000-0002-3171-0844")),
-  person("Susan", "Holmes", role = "rev", comment =
+  person(given="Derek", family="Meyer", role=c("aut"), 
+  email="[email protected]", comment = c(ORCID = "0009-0005-1350-6988")),
+  person(given="Susan", family="Holmes", role = "rev", comment =
          c(what = "JOSS reviewer", ORCID="0000-0002-2208-8168")),
-  person("Abinash", "Satapathy", role = "rev", comment =
+  person(given="Abinash", family="Satapathy", role = "rev", comment =
          c(what = "JOSS reviewer", ORCID="0000-0002-2955-2744")),
-  person("Carinogurjao", role = "rev"),
+  person(given="Carinogurjao", role = "rev"),
   person("Centers for Disease Control and Prevention", role="fnd", comment = "Award number 1U01CK000585; 75D30121F00003"
   ))
 Description: A flexible framework for Agent-Based Models (ABM), the 'epiworldR' package provides methods for prototyping disease outbreaks and transmission models using a 'C++' backend, making it very fast. It supports multiple epidemiological models, including the Susceptible-Infected-Susceptible (SIS), Susceptible-Infected-Removed (SIR), Susceptible-Exposed-Infected-Removed (SEIR), and others, involving arbitrary mitigation policies and multiple-disease models. Users can specify infectiousness/susceptibility rates as a function of agents' features, providing great complexity for the model dynamics. Furthermore, 'epiworldR' is ideal for simulation studies featuring large populations.

diff --git a/Makefile b/Makefile
@@ -38,15 +38,15 @@ check: build
 	cd .. && R CMD check epiworldR_*.tar.gz
 
 clean: 
-	Rscript --vanilla -e 'devtools::clean_dll()'
+	rm -f src/*.dll src/*.so src/*.o
 	sed -i -E 's/@useDynLib\s+[a-zA-Z]+/@useDynLib epiworldR/g' R/epiworldR-package.R
 	sed -i -E 's/useDynLib\(+[a-zA-Z]+/useDynLib(epiworldR/g' NAMESPACE
 	sed -i -E 's/^Package:.+/Package: epiworldR/g' DESCRIPTION 
 	# sed -i -E 's/^\\(name|alias|title)\{[a-zA-Z]+/\\\1{epiworldR/g' man/epiworldR-package.Rd
 	sed -i -E 's/^library\(epiworldRdev\)/library(epiworldR)/g' README.*
 
 docs:
-	Rscript --vanilla -e 'devtools::document()'
+	Rscript --vanilla -e 'roxygen2::roxigenize()'
 
 .PHONY: build update check clean docs docker-debug
 

diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,4 @@
-# epiworldR 0.3-2 (dev)
+# epiworldR 0.3-2
 
 * Starting version 0.3-0, `epiworldR` is versioned using the same version as the C++ library, `epiworld`.
 
@@ -17,7 +17,7 @@
   among agents: `distribute_viruses`, `distribute_tools`, and `distribute_entities`.
 
 
-# epiworldR 0.1-0`
+# epiworldR 0.1-0
 
 * Force model to update agents' states when running a simulation.
   This was causing issues when calling `run_multiple()` after a single

diff --git a/R/tool.R b/R/tool.R
@@ -76,6 +76,20 @@ tool <- function(
     death_reduction
 ) {
 
+  uses_deprecated <- FALSE
+  if (missing(prevalence)) {
+
+    warning(
+      "Starting version 0.3-0, the 'prevalence' argument is required.",
+      " It will be set to be 0.5. Next versions will fail with an error."
+      )
+
+    prevalence <- 0.5
+    as_proportion <- TRUE
+    uses_deprecated <- TRUE
+
+  }
+
   structure(
     tool_cpp(
       name,
@@ -86,7 +100,12 @@ tool <- function(
       recovery_enhancer,
       death_reduction
     ),
-    class = "epiworld_tool"
+    class = "epiworld_tool",
+    uses_deprecated = uses_deprecated,
+    deprecated_args = list(
+      prevalence = prevalence,
+      as_proportion = as_proportion
+    )
   )
 
 }
@@ -168,8 +187,18 @@ add_tool <- function(model, tool, proportion) {
       )
 
     set_distribution_tool(
-      tool,
-      distribute_tool_randomly(proportion, TRUE)
+      tool = tool,
+      distfun = distribute_tool_randomly(proportion, TRUE)
+    )
+
+  } else if (isTRUE(attr(tool, "uses_deprecated"))) {
+
+    set_distribution_tool(
+      tool = tool,
+      distfun = distribute_tool_randomly(
+        prevalence = attr(tool, "deprecated_args")$prevalence,
+        as_proportion = attr(tool, "deprecated_args")$as_proportion
+      )
     )
 
   }

diff --git a/R/virus.R b/R/virus.R
@@ -63,15 +63,29 @@
 #' @export
 #' @aliases epiworld_virus
 virus <- function(
-    name,
-    prevalence,
-    as_proportion,
-    prob_infecting,
-    recovery_rate = 0.5,
-    prob_death    = 0.0,
-    post_immunity = -1.0,
-    incubation    = 7.0
-    ) {
+  name,
+  prevalence,
+  as_proportion,
+  prob_infecting,
+  recovery_rate = 0.5,
+  prob_death    = 0.0,
+  post_immunity = -1.0,
+  incubation    = 7.0
+  ) {
+
+  uses_deprecated <- FALSE
+  if (missing(prevalence)) {
+
+    warning(
+      "Starting version 0.3-0, the 'prevalence' argument is required.",
+      " It will be set to be 0.5. Next versions will fail with an error."
+      )
+
+    prevalence <- 0.5
+    as_proportion <- TRUE
+    uses_deprecated <- TRUE
+
+  }
 
   structure(
     virus_cpp(
@@ -84,7 +98,12 @@ virus <- function(
       post_immunity,
       incubation
       ),
-    class = "epiworld_virus"
+    class = "epiworld_virus",
+    uses_deprecated = uses_deprecated,
+    deprecated_args = list(
+      prevalence = prevalence,
+      as_proportion = as_proportion
+    )
   )
 
 }
@@ -172,6 +191,16 @@ add_virus <- function(model, virus, proportion) {
       distfun=distribute_virus_randomly(proportion, as_proportion = TRUE)
     )
 
+  } else if (isTRUE(attr(tool, "uses_deprecated"))) {
+
+    set_distribution_virus(
+      virus = tool,
+      distfun = distribute_virus_randomly(
+        prevalence = attr(tool, "deprecated_args")$prevalence,
+        as_proportion = attr(tool, "deprecated_args")$as_proportion
+      )
+    )
+
   }
 
   UseMethod("add_virus")