Merge pull request #282 from cmu-delphi/dev

1.2.0 release

.github/workflows/pkgdown.yaml

@@ -16,6 +16,7 @@ name: pkgdown
 
 jobs:
   pkgdown:
+    # only build docs on the main repository and not forks
     if: github.repository_owner == 'cmu-delphi'
     runs-on: ubuntu-latest
     # Only restrict concurrency for non-PR jobs
@@ -39,19 +40,21 @@ jobs:
           needs: website
 
       - name: Build site
+        # - target_ref gets the ref from a different variable, depending on the event
+        # - override allows us to set the pkgdown mode and version_label
+        #   - mode: release is the standard build mode, devel places the site in /dev
+        #   - version_label: 'light' and 'success' are CSS labels for Bootswatch: Cosmo
+        #                    https://bootswatch.com/cosmo/
+        # - we use pkgdown:::build_github_pages to build the site because of an issue in pkgdown
+        #   https://github.com/r-lib/pkgdown/issues/2257
         run: |
-          override <- if (startsWith("${{ github.event_name }}", "pull_request")) {
-              if ("${{ github.base_ref }}" == "main") {
-                list(development = list(mode = "release", version_label = "light"))
-              } else {
-                list(development = list(mode = "devel", version_label = "success"))
-              }
+          target_ref <- "${{ github.event_name == 'pull_request' && github.base_ref || github.ref }}"
+          override <- if (target_ref == "main" || target_ref == "refs/heads/main") {
+            list(development = list(mode = "release", version_label = "light"))
+          } else if (target_ref == "dev" || target_ref == "refs/heads/dev") {
+            list(development = list(mode = "devel", version_label = "success"))
           } else {
-              if ("${{ github.ref_name }}" == "main") {
-                list(development = list(mode = "release", version_label = "light"))
-              } else {
-                list(development = list(mode = "devel", version_label = "success"))
-              }
+            stop("Unexpected target_ref: ", target_ref)
           }
           pkg <- pkgdown::as_pkgdown(".", override = override)
           cli::cli_rule("Cleaning files from old site...")

DESCRIPTION

@@ -1,13 +1,14 @@
 Package: epidatr
 Type: Package
 Title: Client for Delphi's 'Epidata' API
-Version: 1.1.1
+Version: 1.2.0
 Authors@R:
   c(
     person("Logan", "Brooks", email = "[email protected]", role = c("aut")),
     person("Dmitry", "Shemetov", email = "[email protected]", role = c("aut")),
     person("Samuel", "Gratzl", email = "[email protected]", role = c("aut")),
     person("David", "Weber", email = "[email protected]", role = c("ctb", "cre")),
+    person("Nat", "DeFries", role = c("ctb")),
     person("Alex", "Reinhart", role = c("ctb")),
     person("Daniel", "McDonald", role = c("ctb")),
     person("Kean Ming", "Tan", role = c("ctb")),

DEVELOPMENT.md

@@ -48,8 +48,12 @@ Please follow the guidelines in the [PR template document](.github/pull_request_
 
 Open a release issue and then copy and follow this checklist in the issue (modified from the checklist generated by `usethis::use_release_issue(version = "1.0.2")`):
 
-- [ ] `git pull`
-- [ ] Check [current CRAN check results](https://cran.rstudio.org/web/checks/check_results_epidatr.html)
+
+Open a release issue and then copy and follow this checklist in the issue (modified from the checklist generated by `usethis::use_release_issue(version = "1.0.2")`):
+
+- [ ] `git pull` on `dev` branch.
+- [ ] Make sure all changes are committed and pushed.
+- [ ] Check [current CRAN check results](https://cran.rstudio.org/web/checks/check_results_epidatr.html).
 - [ ] `devtools::check(".", manual = TRUE, env_vars = c(NOT_CRAN = "false"))`.
   - Aim for 10/10, no notes.
 - [ ] If check works well enough, merge to main. Otherwise open a PR to fix up.
@@ -61,20 +65,20 @@ Open a release issue and then copy and follow this checklist in the issue (modif
   - This may choke on the MIT license url, and that's ok.
 - [ ] `devtools::build_readme()`
 - [ ] `devtools::check_win_devel()`
-- [ ] Check email for problems
+- [ ] Have maintainer ("cre" in description) check email for problems.
 - [ ] `revdepcheck::revdep_check(num_workers = 4)`.
   - This may choke, it is very sensitive to the binary versions of packages on a given system. Either bypass or ask someone else to run it if you're concerned.
 - [ ] Update `cran-comments.md`
-- [ ] PR with any changes
+- [ ] PR with any changes (and go through the list again) into `dev` and run through the list again.
 
 Submit to CRAN:
 
-- [ ] `devtools::submit_cran()`
-- [ ] Approve email
+- [ ] `devtools::submit_cran()`.
+- [ ] Maintainer approves email.
 
 Wait for CRAN...
 
-- [ ] Accepted :tada:
-- [ ] `dev`
-- [ ] `usethis::use_github_release(publish = FALSE)` (publish off, otherwise it won't push).
-- [ ] check the release notes and publish the branch on github
+- [ ] If accepted :tada:, move to next steps. If rejected, fix and resubmit.
+- [ ] Open and merge a PR containing any updates made to `main` back to `dev`.
+- [ ] `usethis::use_github_release(publish = FALSE)` (publish off, otherwise it won't push) will create a draft release based on the commit hash in CRAN-SUBMISSION and push a tag to the GitHub repo.
+- [ ] Go to the repo, verify the release notes, and publish when ready.

NEWS.md

@@ -1,31 +1,52 @@
+# epidatr 1.2.0
+
+## Changes
+
+- Improve handling of the `EPIDATR_USE_CACHE` environment variable, allowing it
+  to be any value convertable by `as.logical()` and handle the case when it
+  can't be converted.
+- Support more date formats in function to convert dates to epiweeks. Use `parse_api_date` since it already supports both common formats. #276
+- `EPIDATR_USE_CACHE` only supported exactly "TRUE" before. Now it supports all logical values and includes a warning when any value that can't be converted to logical is provided. #273
+- `missing` doesn't count default values as non-missing. If a user doesn't pass `geo_values` or `time_values` (both of which default to `"*"` in `pub_covidcast`), or `dates` (in `pub_covid_hosp_state_timeseries`), the missing check fails. To avoid this, just don't check missingness of those two arguments.
+
 # epidatr 1.1.1
 
 ## Changes
 
 ## Features
 
 ## Patches
-- Fixed failure when passing `as_of` values in `Date` format to
-  `pub_covidcast` while caching is enabled (#259)
+
+- Fix failure when passing `as_of` values in `Date` format to
+  `pub_covidcast` while caching is enabled (#259).
+- For `pub_covidcast` data source `nchs-mortality`, parse dates as `epiweek`
+  and expect `epiweek` inputs from user (#260).
+- Fix failure in `pub_covidcast` when user doesn't pass `geo_values` or
+  `time_values`, even though those arguments have defaults (#268).
 
 # epidatr 1.1.0
 
 ## Changes
+
 - `pub_covid_hosp_state_timeseries` now supports use of the `as_of` parameter (#209).
 - `release_date` and `latest_update` fields are now parsed as `Date`, rather
   than as text. This change impacts several endpoints.
 - `get_auth_key` renamed to `get_api_key` (#181).
 - `get_api_key` no longer reads from R options and only uses environment variables (#217).
 - `pvt_twitter` and `pub_wiki` now use `time_type` and `time_values` args instead of mutually exclusive `dates` and `epiweeks` (#236). This matches the interface of the `pub_covidcast` endpoint.
 - Updated the default `timeout_seconds` to 15 minutes to allow large queries by default.
+
 ## Features
+
 - Function reference now displays commonly-used functions first (#205).
 - Support `Date` objects passed to version arguments `as_of` and `issues` in
   endpoints (#192, #194).
 - `clear_cache` now handles positional arguments just like `set_cache` (#197).
 - `set_api_key` now available to help persist API key environment variables (#181, #217).
 - All endpoints now support the use of "\*" as a wildcard to fetch all dates or epiweeks (#234).
+
 ## Patches
+
 - Endpoints now fail when passed misspelled arguments (#187, #201).
 - `pub_fluview_meta` fixed to `fetch` the response automatically.
 - `pub_covid_hosp_state_timeseries` now correctly parses the `issue` field,

R/endpoints.R

@@ -576,9 +576,10 @@ pub_covid_hosp_state_timeseries <- function(
   # Check parameters
   rlang::check_dots_empty()
 
-  if (missing(states) || missing(dates)) {
-    stop(
-      "`states` and `dates` are both required"
+  if (missing(states)) {
+    cli::cli_abort(
+      "`states` is required",
+      class = "epidatr__pub_covid_hosp_state_timeseries__missing_required_args"
     )
   }
 
@@ -960,9 +961,9 @@ pub_covidcast_meta <- function(fetch_args = fetch_args_list()) {
 #'   <https://cmu-delphi.github.io/delphi-epidata/api/covidcast_geography.html>).
 #' @param time_type string. The temporal resolution of the data (either "day" or
 #' "week", depending on signal).
-#' @param geo_values character. The geographies to return. "*" fetches
-#'   all. (See:
-#'   <https://cmu-delphi.github.io/delphi-epidata/api/covidcast_geography.html>.)
+#' @param geo_values character. The geographies to return. Defaults to all
+#'  ("*") geographies within requested geographic resolution (see:
+#'  <https://cmu-delphi.github.io/delphi-epidata/api/covidcast_geography.html>.).
 #' @param time_values [`timeset`]. Dates to fetch. Defaults to all ("*") dates.
 #' @param ... not used for values, forces later arguments to bind by name
 #' @param as_of Date. Optionally, the as of date for the issues to fetch. If not
@@ -999,17 +1000,19 @@ pub_covidcast <- function(
     missing(source) ||
       missing(signals) ||
       missing(time_type) ||
-      missing(geo_type) ||
-      missing(time_values) ||
-      missing(geo_values)
+      missing(geo_type)
   ) {
-    stop(
-      "`source`, `signals`, `time_type`, `geo_type`, `time_values`, and `geo_values` are all required"
+    cli::cli_abort(
+      "`source`, `signals`, `time_type`, and `geo_type` are all required",
+      class = "epidatr__pub_covidcast__missing_required_args"
     )
   }
 
   if (sum(!is.null(issues), !is.null(lag), !is.null(as_of)) > 1) {
-    stop("`issues`, `lag`, and `as_of` are mutually exclusive")
+    cli::cli_abort(
+      "`issues`, `lag`, and `as_of` are mutually exclusive",
+      class = "epidatr__pub_covidcast__too_many_issue_params"
+    )
   }
 
   assert_character_param("data_source", source, len = 1)
@@ -1025,6 +1028,13 @@ pub_covidcast <- function(
   as_of <- parse_timeset_input(as_of)
   issues <- parse_timeset_input(issues)
 
+  if (source == "nchs-mortality" && time_type != "week") {
+    cli::cli_abort(
+      "{source} data is only available at the week level",
+      class = "epidatr__nchs_week_only"
+    )
+  }
+
   create_epidata_call(
     "covidcast/",
     list(
@@ -1051,8 +1061,14 @@ pub_covidcast <- function(
           c("day", "week")
       ),
       create_epidata_field_info("geo_value", "text"),
-      create_epidata_field_info("time_value", "date"),
-      create_epidata_field_info("issue", "date"),
+      create_epidata_field_info("time_value", switch(time_type,
+        day = "date",
+        week = "epiweek"
+      )),
+      create_epidata_field_info("issue", switch(time_type,
+        day = "date",
+        week = "epiweek"
+      )),
       create_epidata_field_info("lag", "int"),
       create_epidata_field_info("value", "float"),
       create_epidata_field_info("stderr", "float"),

R/epidatr-package.R

@@ -8,8 +8,14 @@
 "_PACKAGE"
 
 .onLoad <- function(libname, pkgname) {
-  cache_environ$use_cache <- Sys.getenv("EPIDATR_USE_CACHE", unset = FALSE)
-  cache_environ$use_cache <- (cache_environ$use_cache == "TRUE")
+  cache_environ$use_cache <- as.logical(Sys.getenv("EPIDATR_USE_CACHE", unset = FALSE))
+  if (is.na(cache_environ$use_cache)) {
+    cli::cli_warn(
+      "Failed to read EPIDATR_USE_CACHE environment variable.
+        Should be a logical. Defaulting to FALSE."
+    )
+    cache_environ$use_cache <- FALSE
+  }
   if (cache_environ$use_cache) {
     set_cache(startup = TRUE)
   }

R/model.R

@@ -239,7 +239,7 @@ parse_data_frame <- function(epidata_call, df, disable_date_parsing = FALSE) {
 #' @importFrom MMWRweek MMWRweek
 #' @keywords internal
 date_to_epiweek <- function(value) {
-  date_components <- MMWRweek::MMWRweek(as.Date(as.character(value), "%Y%m%d"))
+  date_components <- MMWRweek::MMWRweek(parse_api_date(value))
   as.numeric(paste0(
     date_components$MMWRyear,
     # Pad with zeroes up to 2 digits (x -> 0x)

_pkgdown.yml

@@ -1,5 +1,6 @@
-# Colors should stay consistent across epipredict & epidatr, using Carnegie
-# Red https://www.cmu.edu/brand/brand-guidelines/visual-identity/colors.html
+# Colors should stay consistent across epipredict, epiprocess, and epidatr,
+# using Carnegie Red
+# https://www.cmu.edu/brand/brand-guidelines/visual-identity/colors.html
 
 # This is to give a default value to the `mode` parameter in the
 # `pkgdown::build_site` function. This is useful when building the site locally,
@@ -15,11 +16,14 @@ template:
   bslib:
     font_scale: 1.0
     primary: "#C41230"
+    success: "#B4D43C"
     link-color: "#C41230"
 
 navbar:
   bg: primary
-  type: dark
+  type: light
+
+url: https://cmu-delphi.github.io/epidatr/
 
 home:
   links:

tests/testthat/test-cache.R

@@ -18,7 +18,7 @@ test_set_cache <- function(cache_dir = new_temp_dir,
 }
 
 test_that("cache set as expected", {
-  test_set_cache()
+  expect_message(test_set_cache())
   if (grepl("/", as.character(new_temp_dir))) {
     # this is what check produces
     expect_equal(cache_info()$dir, normalizePath(new_temp_dir))
@@ -38,7 +38,7 @@ test_that("cache set as expected", {
 
 # use an existing example to save, then load and compare the values
 test_that("cache saves & loads", {
-  test_set_cache()
+  expect_message(test_set_cache())
   epidata_call <- pub_covidcast(
     source = "jhu-csse",
     signals = "confirmed_7dav_incidence_prop",
@@ -128,7 +128,7 @@ test_that("check_is_cachable", {
       expect_false(check_is_cachable(epidata_call, fetch_args))
     }
   }
-  test_set_cache()
+  expect_message(test_set_cache())
   check_fun(expected_result = FALSE) # doesn't specify issues or as_of
   check_fun(as_of = "2020-01-01", expected_result = TRUE) # valid as_of
   check_fun(issues = "2020-01-01", expected_result = TRUE) # valid issues
@@ -178,14 +178,14 @@ test_that("check_is_cachable", {
   # cases where the cache isn't active
   disable_cache()
   check_fun(as_of = "2020-01-01", expected_result = FALSE)
-  test_set_cache()
+  expect_message(test_set_cache())
   cache_environ$epidatr_cache <- NULL
   check_fun(as_of = "2020-01-01", expected_result = FALSE)
-  test_set_cache()
+  expect_message(test_set_cache())
   check_fun(as_of = "2020-01-01", expected_result = TRUE)
 })
 
-test_set_cache()
+expect_message(test_set_cache())
 cache_environ$epidatr_cache$prune()
 clear_cache(disable = TRUE)
 rm(new_temp_dir)