Merge pull request #217 from cmu-delphi/r-tests

Try some basic unit tests

Author: capnrefsmmat

R-packages/covidcast/DESCRIPTION

@@ -39,18 +39,22 @@ LazyData: true
 Roxygen: list(markdown = TRUE)
 Imports:
   dplyr,
+  ggplot2,
+  grDevices,
   httr,
-  purrr,
   jsonlite,
-  usmap,
   maptools,
-  ggplot2,
-  grDevices,
+  purrr,
   rlang,
-  tidyr
+  tidyr,
+  usmap
 RoxygenNote: 7.1.1
 Suggests: 
+    gridExtra,
     knitr,
+    mockery,
     rmarkdown,
-    gridExtra
+    testthat,
+    tibble,
+    vdiffr
 VignetteBuilder: knitr

R-packages/covidcast/DEVELOP.md

@@ -0,0 +1,80 @@
+# covidcast development guide
+
+A short checklist for submitting pull requests:
+
+1. Run the unit tests with `devtools::test()` and ensure they pass.
+2. If you have added any new features (new functions, new options, etc.), add a
+   brief description to `NEWS.md` to the next listed version number. Also ensure
+   that new functions or datasets are listed in the reference in `_pkgdown.yml`
+   so they appear in a good place in the documentation website.
+3. If you changed any documentation, rebuild the documentation with
+   `devtools::document()` and then `pkgdown::build_site()`. (This can be slow,
+   because our vignettes take a long time to build.)
+4. Submit the pull request and see if the CI can also successfully run the
+   tests.
+
+## Unit tests
+
+Unit tests are provided in `tests/testthat/` and use the [testthat
+package](https://testthat.r-lib.org/). Tests are automatically run as part of `R
+CMD check`, but during package development, the easiest way to run all tests is
+via `devtools::test()` from within the package working directory.
+
+Our continuous integration (CI) on GitHub will automatically run the unit tests
+when you open a pull request, as part of running `R CMD check`. Failed tests and
+check errors will both result in the build failing and errors being visible in
+the pull request.
+
+### Testing plots
+
+We test our plots and maps with the [vdiffr](https://github.com/r-lib/vdiffr)
+package, which renders plots and then visually compares them to a saved
+reference image.
+
+See `tests/testthat/test-plot.R` for examples. Each test case uses
+`vdiffr::expect_doppelganger` with two arguments: a name (which will be the
+filename of the saved plot, so ensure this is descriptive and unique) and a
+plot, such as a ggplot object.
+
+When you add new test case or change how a plotting feature works, you will need
+to "validate" the tests, meaning vdiffr will render the plots and ask you if
+they look correct. To do this, run `vdiffr::manage_cases()` from within the
+package working directory. A Shiny app will open up and present you with each
+plot. For new plots, it will simply show you the plot, and a "Validate" button
+will let you indicate that the plot looks good. For changed plots, it will show
+you the difference between the saved image and the new plot. You must ensure
+that the changes look correct, then press Validate.
+
+Once you've validated all changes, press Quit and you will be able to commit the
+changed images and run the tests successfully.
+
+### Using data files in tests
+
+Unit tests should not depend on being able to load data from the COVIDcast API,
+since that data is subject to change. It is preferable to either use toy
+examples or to store static datasets to be loaded and used.
+
+Small static datasets can be kept in `tests/testthat/data/` in RDS form (using
+`saveRDS` and `loadRDS`). The `testthat::test_path` function locates files
+relative to the `tests/testthat/` directory regardless of your current working
+directory, so for example you can use
+
+```r
+foo <- readRDS(test_path("data/foo.rds"))
+```
+
+to load `tests/testthat/data/foo.rds`.
+
+## Documentation
+
+We use
+[roxygen2](https://cran.r-project.org/web/packages/roxygen2/vignettes/roxygen2.html)
+and [pkgdown](https://pkgdown.r-lib.org/index.html) to build good-looking
+documentation automatically. We should strive to have clear documentation for
+all exported functions and data, as well as vignettes giving examples of all
+major package features.
+
+After changing a vignette or documentation, you'll need to rebuild the
+documentation. Use `devtools::document()` to do this. Then
+`pkgdown::build_site(".")` (from within the package directory) will rebuild the
+HTML documentation site.

R-packages/covidcast/R/covidcast.R

@@ -396,13 +396,15 @@ covidcast_meta <- function() {
   meta <- .request(list(source='covidcast_meta', cached="true"))
 
   if (meta$message != "success") {
-    stop("Failed to obtain metadata: ", meta$message, ".")
+    abort(paste0("Failed to obtain metadata: ", meta$message, "."),
+          err_msg = meta$message,
+          class = "covidcast_meta_fetch_failed")
   }
 
   meta <- meta$epidata %>%
     dplyr::mutate(min_time = as.Date(as.character(.data$min_time), format = "%Y%m%d"),
                   max_time = as.Date(as.character(.data$max_time), format = "%Y%m%d"),
-                  max_issue = as.Date(as.character(.data$max_issue), format = "%Y%m%d")) 
+                  max_issue = as.Date(as.character(.data$max_issue), format = "%Y%m%d"))
 
   class(meta) <- c("covidcast_meta", "data.frame")
   return(meta)

R-packages/covidcast/tests/figs/deps.txt

@@ -0,0 +1,3 @@
+- vdiffr-svg-engine: 1.0
+- vdiffr: 0.3.3
+- freetypeharfbuzz: 0.2.5