ci: replace Jenkins with Gitea Actions, modernize DESCRIPTION

- Add real R CMD check workflow via Gitea Actions (rocker/r-ver:4.4)
- Remove Jenkinsfile and demo workflow
- Modernize DESCRIPTION: Authors@R, R >= 4.1.0, URL/BugReports fields,
  move tidycensus from Imports to Suggests, testthat edition 3
- Fix agresti_coull_interval: correct implementation, export it
- Convert get_fips/get_stabbr to use requireNamespace for tidycensus
- Remove civilytics:: self-reference in rnh()

.Rbuildignore

@@ -3,6 +3,5 @@
 ^\.github$
 ^README\.Rmd$
 ^Makefile$
-^Jenkinsfile$
 ^Dockerfile$
 ^LICENSE\.md$

.gitea/workflows/check.yaml

@@ -0,0 +1,46 @@
+name: R-CMD-check
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+jobs:
+  check:
+    name: R CMD check
+    runs-on: ubuntu-latest
+    container: rocker/r-ver:4.4
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install system dependencies
+        run: |
+          apt-get update -qq
+          apt-get install -y --no-install-recommends \
+            libcurl4-openssl-dev \
+            libssl-dev \
+            libxml2-dev \
+            libcairo2-dev \
+            libjpeg-dev \
+            libpng-dev \
+            libfontconfig1-dev \
+            libharfbuzz-dev \
+            libfribidi-dev \
+            libfreetype6-dev \
+            libtiff5-dev
+
+      - name: Install R dependencies
+        run: |
+          install.packages(c("remotes", "rcmdcheck"))
+          remotes::install_deps(dependencies = TRUE)
+        shell: Rscript {0}
+
+      - name: Run R CMD check
+        run: rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "warning")
+        shell: Rscript {0}
+
+      - name: Run tests
+        run: testthat::test_local(".", reporter = "progress")
+        shell: Rscript {0}

.gitea/workflows/demo.yaml

@@ -1,19 +0,0 @@
-name: Gitea Actions Demo
-run-name: ${{ gitea.actor }} is testing out Gitea Actions 🚀
-on: [push]
-
-jobs:
-  Explore-Gitea-Actions:
-    runs-on: ubuntu-latest
-    steps:
-      - run: echo "🎉 The job was automatically triggered by a ${{ gitea.event_name }} event."
-      - run: echo "🐧 This job is now running on a ${{ runner.os }} server hosted by Gitea!"
-      - run: echo "🔎 The name of your branch is ${{ gitea.ref }} and your repository is ${{ gitea.repository }}."
-      - name: Check out repository code
-        uses: actions/checkout@v4
-      - run: echo "💡 The ${{ gitea.repository }} repository has been cloned to the runner."
-      - run: echo "🖥️ The workflow is now ready to test your code on the runner."
-      - name: List files in the repository
-        run: |
-          ls ${{ gitea.workspace }}
-      - run: echo "🍏 This job's status is ${{ job.status }}."

DESCRIPTION

@@ -2,25 +2,29 @@ Package: civilytics
 Type: Package
 Title: Utilities Functions for Civilytics
 Version: 0.2.0
-Author: Jared E. Knowles <jared@civilytics.com>
-Maintainer: Jared E. Knowles <jared@civilytics.com>
-Description: House R functions for Civilytics Consulting LLC
-    This package implements a variety of useful functions for creating and 
-    branding analyses produced by Civilytics Consulting LLC. 
+Authors@R:
+    person("Jared", "E. Knowles", email = "jared@civilytics.com",
+           role = c("aut", "cre"))
+Description: House R functions for Civilytics Consulting LLC. This package
+    implements a variety of useful functions for creating and branding analyses
+    produced by Civilytics Consulting LLC.
 License: LGPL (>= 3)
+URL: https://gitea.civilytics.org/Civilytics/civilyticsR
+BugReports: https://gitea.civilytics.org/Civilytics/civilyticsR/issues
 Depends:
-    R (>= 2.15.1)
+    R (>= 4.1.0)
 Imports:
     ggplot2,
     jpeg,
     png,
     stringr,
     gridExtra,
-    tidycensus,
     grid,
     stringdist
 Encoding: UTF-8
 LazyData: true
 Suggests:
-    testthat
+    testthat (>= 3.0.0),
+    tidycensus
 RoxygenNote: 7.3.2
+Config/testthat/edition: 3

Jenkinsfile

@@ -1,60 +0,0 @@
-pipeline {
-  agent {
-    dockerfile true
-  }
-    stages {
-      stage('Docker setup') {
-        steps {
-         sh '''
-          R --version
-          java --version
-          '''
-        }
-
-      }
-      stage('Build and test') {
-        stages {
-          stage("Build package") {
-           steps {
-                sh '''
-                R CMD build .
-                '''
-            }
-          }
-        stage('Check') {
-          steps {
-            sh '''
-            R CMD check --no-manual civilytics_0.2.0.tar.gz
-            '''
-
-            sh '''
-            R CMD INSTALL civilytics_0.2.0.tar.gz
-            '''
-          }
-        }
-        stage('testthat'){
-         steps {
-         sh '''
-         R -e 'testthat::test_local(".")'
-         '''
-         }
-      }
-       stage('test coverage') {
-        steps {
-         sh '''
-         R -e 'covr::package_coverage(".")'
-         '''
-         }
-        }
-      stage('Clean') {
-        steps {
-
-          sh '''
-          rm -rf civilytics_0.2.0.tar.gz civilytics.Rcheck
-          '''
-      }
-    }
-  }
-}
-}
-}

NAMESPACE

@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+export(agresti_coull_interval)
 export(add_logo)
 export(add_logo_ga)
 export(clopper_pearson)
@@ -39,7 +40,6 @@ export(waldInterval)
 export(z_gap_test)
 export(z_univariate)
 import(ggplot2)
-import(tidycensus)
 importFrom(ggplot2,theme)
 importFrom(graphics,plot)
 importFrom(graphics,rasterImage)

R/prop_conf.R

@@ -72,14 +72,21 @@ waldInterval <- function(x, n, conf.level = 0.95){
 
 #' Calculate the Agresti-Coull interval
 #'
-#' @param num a number of successes
-#' @param den a number of trials
-#' @param conf.level default 0.95, set the confidence interval to return
+#' @param num number of successes
+#' @param den number of trials
+#' @param conf.level default 0.95, confidence level for the interval
 #'
-#' @return an interval
-agresti_coull_interval <- function(num, den, conf.level) {
-  num <- num + 2
-  den <- den + 4
-  return(num/den)
-
+#' @return three values forming the lower bound, observed proportion, and upper bound
+#' @export
+#'
+#' @examples
+#' agresti_coull_interval(20, 40)
+#' agresti_coull_interval(2, 100, conf.level = 0.99)
+agresti_coull_interval <- function(num, den, conf.level = 0.95) {
+  z <- qnorm(1 - (1 - conf.level) / 2)
+  n_tilde <- den + z^2
+  p_tilde <- (num + z^2 / 2) / n_tilde
+  margin <- z * sqrt(p_tilde * (1 - p_tilde) / n_tilde)
+  obs <- num / den
+  return(c("low" = p_tilde - margin, "observed" = obs, "high" = p_tilde + margin))
 }

R/utils.R

@@ -234,14 +234,21 @@ outersect <- function(x, y, ...) {
 #' @param stabbr a two letter abbreviation for a US state
 #'
 #' @return FIPS codes that match the abbreviation
-#' @import tidycensus
 #' @export
 #'
 #' @examples
+#' \dontrun{
 #' get_fips("MT")
 #' get_fips("PR")
-#' get_fips("CC")
+#' }
 get_fips <- function(stabbr) {
+  if (!requireNamespace("tidycensus", quietly = TRUE)) {
+    stop(
+      "Package 'tidycensus' is required for get_fips(). ",
+      "Install it with: install.packages('tidycensus')",
+      call. = FALSE
+    )
+  }
   fips <- tidycensus::fips_codes[, 1:2]
   fips <- fips[!duplicated(fips),]
   out <- fips[fips$state == stabbr, 2]
@@ -253,12 +260,20 @@ get_fips <- function(stabbr) {
 #' @param fips a character value that captures the FIPS code with leading 0
 #'
 #' @return a character value, length 2, with the state abbreviation
-#' @import tidycensus
 #' @export
 #'
 #' @examples
+#' \dontrun{
 #' get_stabbr("06")
+#' }
 get_stabbr <- function(fips) {
+  if (!requireNamespace("tidycensus", quietly = TRUE)) {
+    stop(
+      "Package 'tidycensus' is required for get_stabbr(). ",
+      "Install it with: install.packages('tidycensus')",
+      call. = FALSE
+    )
+  }
   fips_codes <- tidycensus::fips_codes[, 1:2]
   fips_codes <- fips_codes[!duplicated(fips_codes),]
   if (length(fips) != 1) {
@@ -442,6 +457,6 @@ round_to_nearest_half <- function(x) {
 #' @examples
 #' rnh(c(0.2, 0.3, 0.4, 0.8, 0.09, 0.9))
 rnh <- function(x) {
-  tmp <- Vectorize(civilytics::round_to_nearest_half)
+  tmp <- Vectorize(round_to_nearest_half)
   tmp(x)
 }