Merge pull request #253 from cmu-delphi/post-1.0-release

1.1.0 pre-CRAN cleanup

Author: dsweber2

.Rbuildignore

@@ -23,3 +23,4 @@
 ^README\.Rmd$
 ^CRAN-SUBMISSION$
 ^LICENSE\.md$
+^revdep$

.github/pull_request_template.md

@@ -4,8 +4,8 @@ Please:
 
 - [ ] Make sure this PR is against "dev", not "main" (unless this is a release
       PR).
-- [ ] Request a review from one of the current epiprocess main reviewers:
-      brookslogan, nmdefries.
+- [ ] Request a review from one of the current epidatr main reviewers:
+      brookslogan, dshemetov, nmdefries, dsweber2.
 - [ ] Makes sure to bump the version number in `DESCRIPTION`. Always increment
       the patch version number (the third number), unless you are making a
       release PR from dev to main, in which case increment the minor version

DESCRIPTION

@@ -1,8 +1,7 @@
 Package: epidatr
 Type: Package
 Title: Client for Delphi's 'Epidata' API
-Version: 1.0.2
-Date: 2023-12-07
+Version: 1.1.0
 Authors@R:
   c(
     person("Logan", "Brooks", email = "[email protected]", role = c("aut")),

DEVELOPMENT.md

@@ -45,5 +45,20 @@ python -m http.server -d docs
 Please follow the guidelines in the [PR template document](.github/pull_request_template.md).
 
 ## Release process
+First, there's a handy function that makes a github issue; for example, at the time of writing we were doing:
+```R
+usethis::use_release_issue(version = "1.0.2")
+```
+If you want to extend it, add to the `release_bullets` function in [utils.R](https://github.com/cmu-delphi/epidatr/blob/dev/R/utils.R).
+ First, make sure that all the checks pass
+
+```R
+devtools::check(".", manual = TRUE, env_vars =c(NOT_CRAN = "false"))
+```
 
-TBD
+Aim for 10/10, no notes. Generally, follow the issue. `revdep_check` is likely to fail but doesn't seem to be terribly important. So for now ignore it.
+
+When this has gone smoothly enough, release to CRAN via
+```R
+devtools::release(check = TRUE)
+```

NAMESPACE

@@ -81,6 +81,7 @@ importFrom(openssl,md5)
 importFrom(purrr,map_chr)
 importFrom(purrr,map_lgl)
 importFrom(readr,read_csv)
+importFrom(stats,na.omit)
 importFrom(tibble,as_tibble)
 importFrom(tibble,tibble)
 importFrom(utils,help.search)

NEWS.md

@@ -1,29 +1,32 @@
 # 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 supports use of the `as_of` parameter (#209).
 - `pub_covid_hosp_state_timeseries` now correctly parses the `issue` field,
   instead of returning a missing value (#202).
-- `release_date` and `latest_update` fields are now parsed as `Date`, rather
-  than as text. This change impacts several endpoints..
 - In `pub_fluview_meta`, `latest_issue` field is now parsed as epiweek, rather
   than being parsed as `Date` and returning a missing value.
-- Support `Date` objects passed to version arguments `as_of` and `issues` in
-  endpoints (#192, #194).
 - `set_cache` cache size no longer runs into integer overflow (#189).
-- `clear_cache` now handles positional arguments just like `set_cache` (#197).
 - Improve line-wrapping of warning messages (#191).
-- `set_api_key` now available to help persist API key environment variables (#181, #217).
-- `get_auth_key` renamed to `get_api_key` (#181).
-- `get_api_key` no longer reads from R options and only uses environment variables (#217).
 - Fix documentation related to CRAN submission.
 - Fix some errors from passing "" as a key.
-- `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.
-- All endpoints now support the use of "\*" as a wildcard to fetch all dates or epiweeks (#234).
 - Fixed bug with NAs when parsing ints (#243).
-- Updated the default `timeout_seconds` to 15 minutes to allow large queries by default.
 
 # epidatr 1.0.0
 

R/cache.R

@@ -90,6 +90,8 @@ cache_environ$epidatr_cache <- NULL
 #'   variable is `EPIDATR_CACHE_LOGFILE`.
 #' @param confirm whether to confirm directory creation. default is `TRUE`;
 #'   should only be set in non-interactive scripts
+#' @param startup indicates whether the function is being called on
+#'   startup. Affects suppressability of the messages. Default is `FALSE`.
 #' @return [`NULL`] no return value, all effects are stored in the package
 #'         environment
 #' @seealso [`clear_cache`] to delete the old cache while making a new one,
@@ -102,7 +104,8 @@ set_cache <- function(cache_dir = NULL,
                       days = NULL,
                       max_size = NULL,
                       logfile = NULL,
-                      confirm = TRUE) {
+                      confirm = TRUE,
+                      startup = FALSE) {
   if (is.null(cache_dir)) {
     cache_dir <- Sys.getenv("EPIDATR_CACHE_DIR", unset = rappdirs::user_cache_dir("R", version = "epidatr"))
   } else if (is.null(cache_dir)) {
@@ -171,9 +174,10 @@ set_cache <- function(cache_dir = NULL,
   cli::cli_inform(c(
     "!" = "epidatr cache is being used (set env var EPIDATR_USE_CACHE=FALSE if not intended).",
     "i" = "The cache directory is {cache_dir}.",
-    "i" = "The cache will be cleared after {days} days and will be pruned if it exceeds {max_size} MB.",
+    "i" = "The cache will be cleared after {days} day{ifelse(days>1,'s','')}
+           and will be pruned if it exceeds {max_size} MB.",
     "i" = "The log of cache transactions is stored at {file.path(cache_dir, logfile)}."
-  ))
+  ), class = if (startup) "packageStartupMessage" else NULL)
 }
 
 #' Manually reset the cache, deleting all currently saved data and starting afresh

R/epidatr-package.R

@@ -11,6 +11,6 @@
   cache_environ$use_cache <- Sys.getenv("EPIDATR_USE_CACHE", unset = FALSE)
   cache_environ$use_cache <- (cache_environ$use_cache == "TRUE")
   if (cache_environ$use_cache) {
-    set_cache()
+    set_cache(startup = TRUE)
   }
 }

R/model.R

@@ -165,6 +165,7 @@ print.EpidataFieldInfo <- function(x, ...) {
   cli::cli_dl(x[attr(x, "names")])
 }
 
+#' @importFrom stats na.omit
 parse_value <- function(info, value, disable_date_parsing = FALSE) {
   stopifnot(inherits(info, "EpidataFieldInfo"))
 

R/utils.R

@@ -61,3 +61,9 @@ get_wildcard_equivalent_dates <- function(time_value, time_type = c("day", "week
   }
   return(time_value)
 }
+
+#' inserts each string as a bullet at the end of the "Prepare for release" section
+#' @keywords internal
+release_bullets <- function() {
+  c("merge to main")
+}

README.Rmd

@@ -112,6 +112,6 @@ See also the [Terms of Use](https://delphi.cmu.edu/covidcast/terms-of-use/), not
 
 
 [mit-image]: https://img.shields.io/badge/License-MIT-yellow.svg
-[mit-url]: https://opensource.org/license/mit/
+[mit-url]: https://opensource.org/license/mit
 [github-actions-image]: https://github.com/cmu-delphi/epidatr/workflows/ci/badge.svg
 [github-actions-url]: https://github.com/cmu-delphi/epidatr/actions

README.md

@@ -6,7 +6,7 @@
 <!-- badges: start -->
 
 [![License:
-MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/license/mit/)
+MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/license/mit)
 [![Github
 Actions](https://github.com/cmu-delphi/epidatr/workflows/ci/badge.svg)](https://github.com/cmu-delphi/epidatr/actions)
 [![codecov](https://codecov.io/gh/dsweber2/epidatr/branch/dev/graph/badge.svg?token=jVHL9eHZNZ)](https://app.codecov.io/gh/dsweber2/epidatr)
@@ -39,6 +39,13 @@ also provide packages for downstream data processing
 
 ``` r
 library(epidatr)
+#> ! epidatr cache is being used (set env var EPIDATR_USE_CACHE=FALSE if not
+#>   intended).
+#> ℹ The cache directory is /fasterHome/workingDataDir/epidatr.
+#> ℹ The cache will be cleared after 1 day and will be pruned if it exceeds 1024
+#>   MB.
+#> ℹ The log of cache transactions is stored at
+#>   /fasterHome/workingDataDir/epidatr/logfile.txt.
 # Obtain the smoothed covid-like illness (CLI) signal from Delphi's US COVID-19
 # Trends and Impact Survey (CTIS), in partnership with Facebook, as it was on
 # April 10, 2021 for the US at the national level