Pre commit (#22)

* Adding the pre-commit hook

* Removing adding README.md back to pre-commit

.github/workflows/coverage.yaml

@@ -15,7 +15,7 @@ jobs:
       - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
-      
+
       - uses: r-lib/actions/[email protected]
 
       - uses: r-lib/actions/setup-r-dependencies@v2
@@ -36,4 +36,3 @@ jobs:
         shell: Rscript {0}
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
-

.github/workflows/pre-commit.yaml

@@ -0,0 +1,23 @@
+name: Pre-commit
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v3
+
+      - name: Run pre-commit hooks
+        uses: pre-commit/[email protected]

.github/workflows/r.yml

@@ -12,7 +12,7 @@ on:
 
 name: R-CMD-check-final
 
-env: 
+env:
   GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
 jobs:
@@ -82,7 +82,7 @@ jobs:
           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
@@ -98,7 +98,7 @@ jobs:
         run: |
           install2.r -n 2 shinyjs shinydashboard DT shinycssloaders plotly
           installGithub.r UofUEpiBio/epiworldR@${{ github.sha }}
-      
+
       - name: Check the package
         run: |
           R CMD build .
@@ -118,11 +118,7 @@ jobs:
         run: |
           install2.r -n 2 shinyjs shinydashboard DT shinycssloaders plotly
           installGithub.r UofUEpiBio/epiworldR@${{ github.sha }}
-      
+
       - name: Check the package
         run: |
           R CMD check --no-manual epiworldRShiny_*tar.gz
-
-        
-          
-

.pre-commit-config.yaml

@@ -0,0 +1,31 @@
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v3.2.0
+    hooks:
+    -   id: trailing-whitespace
+        exclude: ^(inst/|man/|src/cpp11.cpp|playgroud/|R/cpp11.R)
+    -   id: end-of-file-fixer
+        exclude: ^(inst/|man/|src/cpp11.cpp|playgroud/|R/cpp11.R)
+    -   id: check-yaml
+        exclude: ^(inst/|man/|src/cpp11.cpp|playgroud/|R/cpp11.R)
+    -   id: check-added-large-files
+        exclude: ^(inst/|man/|src/cpp11.cpp|playgroud/|R/cpp11.R)
+    -   id: detect-private-key
+        exclude: ^(inst/|man/|src/cpp11.cpp|playgroud/|R/cpp11.R)
+
+-   repo: https://github.com/lorenzwalthert/precommit
+    rev: v0.4.2
+    hooks:
+      - id: style-files
+        args:
+          [
+            '--ignore-start="^# styler: off$"',
+            '--ignore-stop="^# styler: on$"',
+            '--strict=FALSE'
+          ]
+        exclude: ^(inst/|man/|src/cpp11.cpp|playgroud/|R/cpp11.R)
+      - id: readme-rmd-rendered
+      # - id: lintr
+      #   args: [--warn_only]
+      #   verbose: true
+      #   exclude: ^(inst/|man/|src/cpp11.cpp|playgroud/|R/cpp11.R)

.vscode/c_cpp_properties.json

@@ -17,4 +17,4 @@
         }
     ],
     "version": 4
-}
+}

.vscode/settings.json

@@ -62,4 +62,4 @@
         "editor.insertSpaces": true,
         "editor.detectIndentation": false
     }
-}
+}

CODE_OF_CONDUCT.md

@@ -59,7 +59,7 @@ representative at an online or offline event.
 ## Enforcement
 
 Instances of abusive, harassing, or otherwise unacceptable behavior may be
-reported to the community leaders responsible for enforcement at [email protected]. 
+reported to the community leaders responsible for enforcement at [email protected].
 All complaints will be reviewed and investigated promptly and fairly.
 
 All community leaders are obligated to respect the privacy and security of the

DESCRIPTION

@@ -5,7 +5,7 @@ Version: 0.3-2
 Authors@R: c(
   person(given="George", family="Vega Yon", role=c("aut","cre"),
   email="[email protected]", comment = c(ORCID = "0000-0002-3171-0844")),
-  person(given="Derek", family="Meyer", role=c("aut"), 
+  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")),
@@ -17,20 +17,20 @@ Authors@R: c(
 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.
 URL: https://github.com/UofUEpiBio/epiworldR,
     https://uofuepibio.github.io/epiworldR/,
-    https://uofuepibio.github.io/epiworldR-workshop/ 
+    https://uofuepibio.github.io/epiworldR-workshop/
 BugReports: https://github.com/UofUEpiBio/epiworldR/issues
 License: MIT + file LICENSE
 RoxygenNote: 7.3.2
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 LinkingTo: cpp11
-Suggests: 
+Suggests:
     knitr,
     rmarkdown,
     tinytest,
     netplot,
     igraph,
     data.table
-Imports: 
+Imports:
     utils
 VignetteBuilder: knitr

Makefile

@@ -2,11 +2,11 @@
 VERSION := $(shell grep Version DESCRIPTION | sed -e 's/Version: //')
 
 
-build: 
+build:
 	cd .. && R CMD build epiworldR
 
 debug: clean
-	docker run --rm -ti -w/mnt -v $(PWD):/mnt uofuepibio/epiworldr:debug make docker-debug 
+	docker run --rm -ti -w/mnt -v $(PWD):/mnt uofuepibio/epiworldr:debug make docker-debug
 
 docker-debug:
 	EPI_CONFIG="-DEPI_DEBUG -Wall -pedantic -g" R CMD INSTALL \
@@ -15,33 +15,33 @@ docker-debug:
 install-dev: clean
 	sed -i -E 's/@useDynLib\s+[a-zA-Z]+/@useDynLib epiworldRdev/g' R/epiworldR-package.R
 	sed -i -E 's/useDynLib\(+[a-zA-Z]+/useDynLib(epiworldRdev/g' NAMESPACE
-	sed -i -E 's/^Package:.+/Package: epiworldRdev/g' DESCRIPTION 
+	sed -i -E 's/^Package:.+/Package: epiworldRdev/g' DESCRIPTION
 	sed -i -E 's/^library\(epiworldR\)/library(epiworldRdev)/g' README.*
 	Rscript --vanilla -e 'roxygen2::roxygenize()'
 	EPI_DEV=yes R CMD INSTALL .& $(MAKE) clean
 
-install: 
+install:
 	cd .. && \
 		R CMD INSTALL epiworldR_$(VERSION).tar.gz
-		
+
 
 README.md: README.Rmd
 	Rscript --vanilla -e 'rmarkdown::render("README.Rmd")'
 
 # update:
 # 	wget https://raw.githubusercontent.com/UofUEpiBio/epiworld/master/epiworld.hpp && \
-# 		mv epiworld.hpp inst/include/epiworld.hpp 
+# 		mv epiworld.hpp inst/include/epiworld.hpp
 local-update:
 	rsync -avz ../epiworld/include/epiworld inst/include/.
 
 check: build
 	cd .. && R CMD check epiworldR_*.tar.gz
 
-clean: 
+clean:
 	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/^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.*
 
@@ -52,4 +52,3 @@ docs:
 
 checkv: build
 	R CMD check --as-cran --use-valgrind epiworldR*.tar.gz
-

NEWS.md

@@ -7,7 +7,7 @@
 * Ports the `Entity` class. Entities are used to group agents within a model.
 
 * Refactors `add_tool`, `add_virus`, and `add_entity` simplifying syntax. Now,
-  these functions only receive the model and object. Prevalence is 
+  these functions only receive the model and object. Prevalence is
   specified in the object itself. `add_tool_n` and `add_virus_n` are now
   deprecated.
 

R/ModelDiffNet.R

@@ -1,10 +1,10 @@
 #' Network Diffusion Model
-#' 
-#' The network diffusion model is a simple model that assumes that 
-#' the probability of adoption of a behavior is proportional to the 
+#'
+#' The network diffusion model is a simple model that assumes that
+#' the probability of adoption of a behavior is proportional to the
 #' number of adopters in the network.
-#' 
-#' @export 
+#'
+#' @export
 #' @param name Name of the model.
 #' @param prevalence Prevalence of the disease.
 #' @param prob_adopt Probability of adoption.
@@ -22,52 +22,52 @@
 #' \deqn{
 #' P(adopt) = \mbox{Logit}^{-1}(prob\_adopt + params * data + exposure)
 #' }
-#' Where exposure is the number of adopters in the agent's network. 
-#' 
+#' Where exposure is the number of adopters in the agent's network.
+#'
 #' Another important difference is that the transmission network is not
 #' necesary useful since adoption in this model is not from a particular
 #' neighbor.
-#' 
+#'
 #' @examples
 #' set.seed(2223)
 #' n <- 10000
-#' 
+#'
 #' # Generating synthetic data on a matrix with 2 columns.
 #' X <- cbind(
-#'  age = sample(1:100, n, replace = TRUE),
-#'  female = sample.int(2, n, replace = TRUE) - 1
+#'   age = sample(1:100, n, replace = TRUE),
+#'   female = sample.int(2, n, replace = TRUE) - 1
 #' )
-#' 
+#'
 #' adopt_chatgpt <- ModelDiffNet(
 #'   "ChatGPT",
 #'   prevalence = .01,
 #'   prob_adopt = .1,
 #'   data       = X,
 #'   params     = c(1, 4)
 #' )
-#' 
+#'
 #' # Simulating a population from smallworld
 #' agents_smallworld(adopt_chatgpt, n, 8, FALSE, .01)
-#' 
+#'
 #' # Running the model for 50 steps
 #' run(adopt_chatgpt, 50)
-#' 
+#'
 #' # Plotting the model
 #' plot(adopt_chatgpt)
 #' @aliases epiworld_diffnet
 ModelDiffNet <- function(
-  name,
-  prevalence,
-  prob_adopt,
-  normalize_exposure = TRUE,
-  data               = matrix(nrow = 0, ncol = 0),
-  data_cols          = 1L:ncol(data),
-  params             = vector("double")
-  ) {
+    name,
+    prevalence,
+    prob_adopt,
+    normalize_exposure = TRUE,
+    data               = matrix(nrow = 0, ncol = 0),
+    data_cols          = 1L:ncol(data),
+    params             = vector("double")
+    ) {
 
   if (length(data) == 0L)
     data_cols <- vector("integer")
-  else 
+  else
     data_cols <- as.integer(data_cols) - 1L
 
   structure(
@@ -80,7 +80,7 @@ ModelDiffNet <- function(
       ncol(data),
       data_cols,
       params
-      ),
+    ),
     class = c("epiworld_diffnet", "epiworld_model")
   )
 
@@ -94,4 +94,3 @@ ModelDiffNet <- function(
 plot.epiworld_diffnet <- function(x, main = get_name(x), ...) {
   plot_epi(x, main = main, ...)
 }
-