Adding testing infrastructure to rmot (#3)

*Added Authors and MIT license

* Simple unit tests for current functions

* Added code coverage and lifecycle badge

* Added GHA for R CMD check and test coverage

.Rbuildignore

@@ -3,3 +3,6 @@
 ^README\.Rmd$
 ^doc$
 ^Meta$
+^LICENSE\.md$
+^\.github$
+^codecov\.yml$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

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

@@ -0,0 +1,49 @@
+# 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]
+  pull_request:
+    branches: [main, master]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        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_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - 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@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true

.github/workflows/test-coverage.yaml

@@ -0,0 +1,55 @@
+# 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]
+  pull_request:
+    branches: [main, master]
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+          )
+        shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v3
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package
+
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v3
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

DESCRIPTION

@@ -2,11 +2,14 @@ Package: rmot
 Title: What the Package Does (One Line, Title Case)
 Version: 0.0.0.9000
 Authors@R: 
-    person("First", "Last", , "[email protected]", role = c("aut", "cre"),
-           comment = c(ORCID = "YOUR-ORCID-ID"))
+    c(
+  person(given = "Daniel", family = "Falster", role = c("aut", "ctb"), email = "[email protected]", comment = c(ORCID = "0000-0002-9814-092X")),
+  person(given = "Tess", family = "O'Brien", role = c("aut", "cre", "cph"), email = "[email protected]", comment = c(ORCID = "XXXX-XXXX-XXXX-XXXX")),
+  person(given = "Fonti", family = "Kar", role = c("ctb"), email = "[email protected]", comment = c(ORCID = "0000-0002-2760-3974")),
+  person(given = "David", family=  "Warton", role = c("aut", "ctb"), email = "[email protected]", comment = c(ORCID = "0000-0002-1642-628X"))
+    )
 Description: What the package does (one paragraph).
-License: `use_mit_license()`, `use_gpl3_license()` or friends to pick a
-    license
+License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
@@ -32,5 +35,7 @@ LinkingTo:
 SystemRequirements: GNU make
 Suggests: 
     knitr,
-    rmarkdown
+    rmarkdown,
+    testthat (>= 3.0.0)
 VignetteBuilder: knitr
+Config/testthat/edition: 3

LICENSE

@@ -1,21 +1,2 @@
-MIT License
-
-Copyright (c) 2023 Trait Ecology and Evolution
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+YEAR: 2023
+COPYRIGHT HOLDER: rmot authors

LICENSE.md

@@ -0,0 +1,21 @@
+# MIT License
+
+Copyright (c) 2023 rmot authors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

R/rmot_assign_data.R

@@ -7,7 +7,7 @@
 #' @export
 #'
 #' @examples
-#' rmot_assign_data(X = Loblolly$age, Y = Loblolly$height)
+#' rmot_model("linear") |> rmot_assign_data(X = Loblolly$age, Y = Loblolly$height)
 rmot_assign_data <- function(model_template, ...){
   # Grab user expressions
   user_code <- rlang::enexprs(..., .check_assign = TRUE)

R/rmot_run.R

@@ -9,9 +9,9 @@
 #' @examples
 #' rmot_model("linear") |>
 #'   rmot_assign_data(X = Loblolly$age,
-#'                  Y = Loblolly$height,
-#'                  N = nrow(Loblolly)) |>
-#'  rmot_run()
+#'                    Y = Loblolly$height,
+#'                    N = nrow(Loblolly)) |>
+#'   rmot_run()
 rmot_run <- function(model_template, ...) {
 
   # Detect model

README.Rmd

@@ -17,20 +17,23 @@ knitr::opts_chunk$set(
 # rmot
 
 <!-- badges: start -->
+[![R-CMD-check](https://github.com/traitecoevo/rmot/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/traitecoevo/rmot/actions/workflows/R-CMD-check.yaml)
+[![Codecov test coverage](https://codecov.io/gh/traitecoevo/rmot/branch/master/graph/badge.svg)](https://app.codecov.io/gh/traitecoevo/rmot?branch=master)
+[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
 <!-- badges: end -->
 
 The goal of 'rmot' is to ...
 
 ## Installation
 
-You can install the development version of 'rmot' from [GitHub](https://github.com/) with:
+'rmot' is under active development. You can install the current developmental version of 'rmot' from [GitHub](https://github.com/) with:
 
 ``` r
 # install.packages("remotes")
 remotes::install_github("traitecoevo/rmot")
 ```
 
-## Demo
+## Quick demo
 
 ```{r example}
 rmot_model("linear") |>
@@ -42,4 +45,4 @@ rmot_model("linear") |>
 
 ## Found a bug? 
 
-Please lodge a GitHub Issue with details of the bug
+Please submit a [GitHub issue](https://github.com/traitecoevo/rmot/issues) with details of the bug. A [reprex](https://reprex.tidyverse.org/) would be particularly helpful with the bug-proofing process!  

README.md

@@ -4,21 +4,27 @@
 # rmot
 
 <!-- badges: start -->
+
+[![R-CMD-check](https://github.com/traitecoevo/rmot/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/traitecoevo/rmot/actions/workflows/R-CMD-check.yaml)
+[![Codecov test
+coverage](https://codecov.io/gh/traitecoevo/rmot/branch/master/graph/badge.svg)](https://app.codecov.io/gh/traitecoevo/rmot?branch=master)
+[![Lifecycle:
+experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
 <!-- badges: end -->
 
 The goal of ‘rmot’ is to …
 
 ## Installation
 
-You can install the development version of ‘rmot’ from
-[GitHub](https://github.com/) with:
+‘rmot’ is under active development. You can install the current
+developmental version of ‘rmot’ from [GitHub](https://github.com/) with:
 
 ``` r
 # install.packages("remotes")
 remotes::install_github("traitecoevo/rmot")
 ```
 
-## Demo
+## Quick demo
 
 ``` r
 rmot_model("linear") |>
@@ -30,4 +36,7 @@ rmot_model("linear") |>
 
 ## Found a bug?
 
-Please lodge a GitHub Issue with details of the bug
+Please submit a [GitHub
+issue](https://github.com/traitecoevo/rmot/issues) with details of the
+bug. A [reprex](https://reprex.tidyverse.org/) would be particularly
+helpful with the bug-proofing process!

codecov.yml

@@ -0,0 +1,14 @@
+comment: false
+
+coverage:
+  status:
+    project:
+      default:
+        target: auto
+        threshold: 1%
+        informational: true
+    patch:
+      default:
+        target: auto
+        threshold: 1%
+        informational: true

tests/testthat.R

@@ -0,0 +1,12 @@
+# This file is part of the standard setup for testthat.
+# It is recommended that you do not modify it.
+#
+# Where should you do additional test configuration?
+# Learn more about the roles of various files in:
+# * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
+# * https://testthat.r-lib.org/articles/special-files.html
+
+library(testthat)
+library(rmot)
+
+test_check("rmot")

tests/testthat/test-rmot_assign_data.R

@@ -0,0 +1,17 @@
+test_that("Execution and output", {
+
+  lm_loblloy <- rmot_model("linear") |>
+    rmot_assign_data(X = Loblolly$age)
+
+  expect_named(lm_loblloy)
+
+  expect_visible(lm_loblloy)
+
+  expect_type(lm_loblloy, "list")
+
+  lm_empty <- rmot_model("linear")
+
+  expect_null(lm_empty$X)
+
+  expect_true(length(lm_loblloy$X) > 0)
+})

tests/testthat/test-rmot_models.R

@@ -0,0 +1,19 @@
+test_that("Execution and output", {
+  expect_named(rmot_model("linear"))
+  expect_type(rmot_model("linear"), "list")
+  expect_visible(rmot_model("linear"))
+
+  expect_named(rmot_model("constant_single"))
+  expect_type(rmot_model("constant_single"), "list")
+  expect_visible(rmot_model("constant_single"))
+
+  lm_test <- rmot_model("linear") |>
+    rmot_assign_data(X = Loblolly$age,
+                     Y = Loblolly$height,
+                     N = nrow(Loblolly)) |>
+    rmot_run(chains = 2, iter = 300, verbose = FALSE, show_messages = FALSE)
+
+  expect_visible(lm_test)
+
+  expect_s4_class(lm_test, "stanfit")
+})