Merge branch 'release/3.10.0'

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

@@ -29,7 +29,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -51,3 +51,4 @@ jobs:
           MYSQL_PASSWORD: ${{ secrets.MYSQL_PASSWORD }}
         with:
           upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/lint.yaml

@@ -14,7 +14,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:

.github/workflows/pkgdown.yaml

@@ -22,7 +22,7 @@ jobs:
     permissions:
       contents: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -41,7 +41,7 @@ jobs:
 
       - name: Deploy to GitHub pages 🚀
         if: github.event_name != 'pull_request'
-        uses: JamesIves/github-pages-deploy-action@v4.4.1
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
         with:
           clean: false
           branch: gh-pages

.github/workflows/test-coverage.yaml

@@ -15,7 +15,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
@@ -43,12 +43,12 @@ jobs:
         if: always()
         run: |
           ## --------------------------------------------------------------------
-          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
         shell: bash
 
       - name: Upload test results
         if: failure()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: coverage-test-failures
           path: ${{ runner.temp }}/package

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: tarflow.iquizoo
 Title: Setup "targets" Workflows for "iquizoo" Data Processing
-Version: 3.9.3
+Version: 3.10.0
 Authors@R: c(
     person("Liang", "Zhang", , "psychelzh@outlook.com", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-9041-1150")),
@@ -22,26 +22,23 @@ Imports:
     cli,
     data.iquizoo (>= 2023.10.22),
     DBI,
-    dplyr,
     memoise,
-    purrr,
     rlang (>= 1.0.0),
     stringr,
     tarchetypes,
-    targets,
-    tidyr
+    targets
 Suggests:
     bit64,
     covr,
     digest,
     lifecycle,
     odbc,
     preproc.iquizoo (>= 2.6.0),
+    purrr,
     RMariaDB (>= 1.3.1),
     roxygen2,
     testthat (>= 3.0.0),
     tibble,
-    tidytable,
     withr
 Remotes:
     psychelzh/data.iquizoo,

NAMESPACE

@@ -7,8 +7,9 @@ export(fetch_iquizoo_mem)
 export(setup_option_file)
 export(setup_source)
 export(setup_templates)
+export(tar_fetch_data)
 export(tar_prep_iquizoo)
+export(tar_prep_proj)
+export(tar_prep_raw)
 export(use_targets_pipeline)
-import(dplyr)
 import(rlang)
-import(tidyr)

NEWS.md

@@ -1,3 +1,17 @@
+# tarflow.iquizoo 3.10.0
+
+## Breaking Changes
+
+* Now `query` argument of `fetch_data()` is optional. If not specified, the default query stored in the package will be used.
+
+## Enhancements
+
+* Added `suffix_format` argument to `fetch_data()` to specify the format of suffix in the query file. This is useful when you want to use a different format of suffix in the query file.
+* Enhanced the documentation of `fetch_data()`.
+* Let package not depend on dplyr, tidyr and purrr packages (#84).
+* Exported more targets factory functions: `tar_prep_proj()`, `tar_fetch_data()`, `tar_prep_raw()`.
+* Do not add `progress_hash` objects when `check_progress` is set to `FALSE` in `tar_prep_iquizoo()`.
+
 # tarflow.iquizoo 3.9.3
 
 ## Breaking Changes

R/database.R

@@ -70,32 +70,54 @@ fetch_iquizoo_mem <- function(cache = NULL) {
 
 #' Fetch data from iQuizoo database
 #'
-#' @param query A parameterized SQL query. Note the query should also contain
-#'   a `glue` expression to inject the table name, i.e., `"{ table_name }"`.
+#' This function is a wrapper of [fetch_iquizoo()], which is used as a helper
+#' function to fetch data from the iQuizoo database.
+#'
+#' The data essentially means one of the two types of data: raw data or scores.
+#' The raw data is the original data collected from the game, while the scores
+#' are the scores calculated by the iQuizoo system. While scores can also be
+#' calculated from the raw data, the pre-calculated scores are used to for some
+#' quick analysis.
+#'
+#' The data is separated by project date, so the table name is suffixed by the
+#' project date, which is automatically fetched from the database by this
+#' function. You could set the format of the date suffix by `suffix_format`,
+#' although currently you should not need to change it because it probably will
+#' not change in the future. Finally, this suffix should be substituted into the
+#' query, which should contain an expression to inject the table name, i.e.,
+#' `"{table_name}"`.
+#'
 #' @param project_id The project id to be bound to the query.
 #' @param game_id The game id to be bound to the query.
 #' @param ... Further arguments passed to [fetch_iquizoo()].
 #' @param what What to fetch. Can be either "raw_data" or "scores".
+#' @param query A parameterized SQL query. A default query file is stored in the
+#'   package, which is often enough for most cases. You can also specify your
+#'   own query file by this argument. See details for more information.
+#' @param suffix_format The format of the date suffix. See details for more
+#'   information.
 #' @return A [data.frame] contains the fetched data.
 #' @export
-fetch_data <- function(query, project_id, game_id, ...,
-                       what = c("raw_data", "scores")) {
+fetch_data <- function(project_id, game_id, ...,
+                       what = c("raw_data", "scores"),
+                       query = NULL,
+                       suffix_format = "%Y0101") {
   check_dots_used()
   what <- match.arg(what)
-  # the database stores data from each year into a separate table with the
-  # suffix of course date with the format "<year>0101"
+  # data separated by project date, so we need to get the project date first
   suffix <- package_file("sql", "project_date.sql") |>
     read_file() |>
     fetch_iquizoo(params = project_id) |>
     .subset2("project_date") |>
-    format("%Y0101")
+    format(suffix_format)
   table_name <- paste0(
     switch(what,
       raw_data = "content_orginal_data_",
       scores = "content_ability_score_"
     ),
     suffix
   )
+  query <- query %||% read_file(package_file("sql", paste0(what, ".sql")))
   fetch_iquizoo(
     stringr::str_glue(
       query,
@@ -105,96 +127,3 @@ fetch_data <- function(query, project_id, game_id, ...,
     params = list(project_id, game_id)
   )
 }
-
-#' Set data source
-#'
-#' @param driver The driver used. Set as an option of `"tarflow.driver"`.
-#'   Options are [odbc::odbc()] and [RMariaDB::MariaDB()], both of which need
-#'   pre-configurations. Default to first available one.
-#' @param dsn The data source name of an **ODBC** database connector. See
-#'   [odbc::dbConnect()] for more information. Used when `driver` is set as
-#'   [odbc::odbc()].
-#' @param groups Section identifier in the `default.file`. See
-#'   [RMariaDB::MariaDB()] for more information. Used when `driver` is set as
-#'   [RMariaDB::MariaDB()].
-#' @return An S3 class of `tarflow.source` with the options.
-#' @export
-setup_source <- function(driver = getOption("tarflow.driver"),
-                         dsn = getOption("tarflow.dsn"),
-                         groups = getOption("tarflow.groups")) {
-  structure(
-    list(
-      driver = driver,
-      dsn = dsn,
-      groups = groups
-    ),
-    class = "tarflow.source"
-  )
-}
-
-#' Check if the database based on the given data source is ready
-#'
-#' @param source The data source from which data is fetched. See
-#'    [setup_source()] for details.
-#' @return TRUE if the database is ready, FALSE otherwise.
-#' @export
-check_source <- function(source = setup_source()) {
-  if (!inherits(source, "tarflow.source")) {
-    cli::cli_abort(
-      "{.arg source} must be created by {.fun setup_source}.",
-      class = "tarflow_bad_source"
-    )
-  }
-  # nocov start
-  if (inherits(source$driver, "OdbcDriver")) {
-    return(DBI::dbCanConnect(source$driver, dsn = source$dsn))
-  }
-  # nocov end
-  if (inherits(source$driver, "MariaDBDriver")) {
-    return(DBI::dbCanConnect(source$driver, groups = source$groups))
-  }
-  return(FALSE)
-}
-
-# nocov start
-
-#' Setup MySQL database connection option file
-#'
-#' This function will create a MySQL option file at the given path. To ensure it
-#' works, set these environment variables before calling this function:
-#' - `MYSQL_HOST`: The host name of the MySQL server.
-#' - `MYSQL_USER`: The user name of the MySQL server.
-#' - `MYSQL_PASSWORD`: The password of the MySQL server.
-#'
-#' @param path The path to the option file. Default location is operating system
-#'   dependent. On Windows, it is `C:/my.cnf`. On other systems, it is
-#'   `~/.my.cnf`.
-#' @param overwrite Whether to overwrite the existing option file.
-#' @param quietly A logical indicates whether message should be suppressed.
-#' @return NULL (invisible).
-#' @export
-setup_option_file <- function(path = NULL, overwrite = FALSE, quietly = FALSE) {
-  my_cnf_tmpl <- read_file(package_file("database", "my.cnf.tmpl"))
-  path <- path %||% default_file()
-  if (file.exists(path) && !overwrite) {
-    if (!quietly) {
-      cli::cli_alert_warning(
-        "Option file already exists. Use {.arg overwrite = TRUE} to overwrite.",
-        class = "tarflow_option_file_exists"
-      )
-    }
-    return(invisible())
-  }
-  writeLines(stringr::str_glue(my_cnf_tmpl), path)
-}
-
-# helper functions
-default_file <- function() {
-  if (Sys.info()["sysname"] == "Windows") {
-    return("C:/my.cnf")
-  } else {
-    return("~/.my.cnf")
-  }
-}
-
-# nocov end