Merge branch 'develop'

.Rbuildignore

@@ -1,4 +1,8 @@
-^PFUPipelinesTools\.Rproj$
+^PFUPipelineTools\.Rproj$
 ^\.Rproj\.user$
 ^data-raw$
 ^LICENSE\.md$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+^README\.Rmd$

.gitignore

@@ -2,3 +2,4 @@
 .Rhistory
 .RData
 .Ruserdata
+docs

DESCRIPTION

@@ -1,18 +1,25 @@
-Package: PFUPipelinesTools
+Package: PFUPipelineTools
 Title: Tools for PFU Pipelines
-Version: 0.0.1
+Version: 0.1.1
+Date: 2023-06-06
 Authors@R: 
     person("Matthew", "Heun", , "[email protected]", role = c("aut", "cre"),
-           comment = c(ORCID = "YOUR-ORCID-ID"))
+           comment = c(ORCID = "0000-0002-7438-214X"))
 Description: There are several repositories that provide PFU pipelines for the PFU databases.
-             Several functions can be used for all pipelines.
-             This package hosts all common functions and constants.
+             Several functions can be used in common across all pipelines.
+             This package hosts common functions and constants.
 License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
 Imports:
-    assertthat
+    dplyr,
+    IEATools, 
+    lubridate,
+    magrittr,
+    parsedate,
+    pins,
+    rlang
 Depends: 
     R (>= 2.10)
 LazyData: true

LICENSE

@@ -1,2 +1,2 @@
 YEAR: 2023
-COPYRIGHT HOLDER: PFUPipelinesTools authors
+COPYRIGHT HOLDER: PFUPipelineTools authors

LICENSE.md

@@ -1,6 +1,6 @@
 # MIT License
 
-Copyright (c) 2023 PFUPipelinesTools authors
+Copyright (c) 2023 PFUPipelineTools 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

NAMESPACE

@@ -1,6 +1,12 @@
 # Generated by roxygen2: do not edit by hand
 
+export("%>%")
+export(":=")
+export(.data)
 export(filter_countries_years)
 export(release_target)
 export(stash_cache)
-export(trim_pipeline)
+export(tar_ungroup)
+importFrom(magrittr,"%>%")
+importFrom(rlang,":=")
+importFrom(rlang,.data)

NEWS.md

@@ -0,0 +1,7 @@
+# PFUPipelineTools 0.1.1 (2023-06-06)
+
+* Initial release
+* Added a `NEWS.md` file to track changes to the package.
+* Added first tests.
+    * Only 2 tests, both passing.
+    * Test coverage is low (17 %) but will improve.

R/data_functions.R

@@ -15,8 +15,8 @@
 #' @export
 #'
 #' @examples
-#' IEATools::sample_iea_data_path() %>%
-#'   IEATools::load_tidy_iea_df() %>%
+#' IEATools::sample_iea_data_path() |>
+#'   IEATools::load_tidy_iea_df() |>
 #'   filter_countries_years(countries = c("ZAF"), years = 1960:1999)
 filter_countries_years <- function(.df,
                                    countries,
@@ -32,14 +32,40 @@ filter_countries_years <- function(.df,
   }
   if (countries1) {
     if (countries == "all") {
-      return(.df %>% dplyr::filter(.data[[year]] %in% years))
+      return(.df |> dplyr::filter(.data[[year]] %in% years))
     }
   }
   if (years1) {
     if (years == "all") {
-      return(.df %>% dplyr::filter(.data[[country]] %in% countries))
+      return(.df |> dplyr::filter(.data[[country]] %in% countries))
     }
   }
-  .df %>%
+  .df |>
     dplyr::filter(.data[[country]] %in% countries, .data[[year]] %in% years)
 }
+
+
+#' Ungroups and removes tar_group column from a data frame
+#'
+#' The [tarchetypes::tar_group_by()] function
+#' adds a column named "tar_group".
+#' This function ungroups and removes the special column.
+#'
+#' @param .df The data frame to be ungrouped.
+#' @param tar_group_colname The name of the grouping column. Default is "tar_group".
+#' @param ungroup A boolean that tells whether to ungroup `.df`. Default is `TRUE`.
+#'
+#' @return A modified version of `.df`.
+#'
+#' @export
+tar_ungroup <- function(.df, tar_group_colname = "tar_group", ungroup = TRUE) {
+  out <- .df |>
+    dplyr::mutate(
+      "{tar_group_colname}" := NULL
+    )
+  if (ungroup) {
+    out <- out |>
+      dplyr::ungroup()
+  }
+  return(out)
+}

R/storing.R

@@ -26,21 +26,21 @@
 #' # Establish the pinboard
 #' pinboard <- pins::board_folder("~/Dropbox/Fellowship 1960-2015 PFU database/OutputData/PipelineReleases/")
 #' # Get information about the `PSUT` target in the pinboard
-#' pinboard %>%
+#' pinboard |>
 #'   pins::pin_meta(name = "psut")
 #' # Find versions of the `PSUT` target
-#' pinboard %>%
+#' pinboard |>
 #'   pins::pin_versions(name = "psut")
 #' # Get the latest copy of the `PSUT` target.
-#' my_psut <- pinboard %>%
+#' my_psut <- pinboard |>
 #'   pins::pin_read(name = "psut")
 #' # Retrieve a previous version of the `PSUT` target.
-#' my_old_psut <- pinboard %>%
+#' my_old_psut <- pinboard |>
 #'   pins::pin_read(name = "psut", version = "20220218T023112Z-1d9e1")}
 release_target <- function(pipeline_releases_folder, targ, pin_name, type = "rds", release = FALSE) {
   if (release) {
     # Establish the pinboard
-    out <- pins::board_folder(pipeline_releases_folder, versioned = TRUE) %>%
+    out <- pins::board_folder(pipeline_releases_folder, versioned = TRUE) |>
       # Returns the fully-qualified name of the file written to the pinboard.
       pins::pin_write(targ, name = pin_name, type = type, versioned = TRUE)
   } else {
@@ -76,12 +76,12 @@ stash_cache <- function(pipeline_caches_folder, cache_folder, file_prefix, depen
     return("Release not requested.")
   }
   # Zip the drake cache
-  zipped_cache_filename <- paste0(file_prefix, parsedate::format_iso_8601(Sys.time()), ".zip") %>%
+  zipped_cache_filename <- paste0(file_prefix, parsedate::format_iso_8601(Sys.time()), ".zip") |>
     # Change file name format to be equivalent to the pins file format.
     # Eliminate "-" characters
-    gsub(pattern = "-", replacement = "") %>%
+    gsub(pattern = "-", replacement = "") |>
     # Eliminate ":" characters, because they cause problems on some OSes.
-    gsub(pattern = ":", replacement = "") %>%
+    gsub(pattern = ":", replacement = "") |>
     # Change "+0000" to "Z", where "Z" means Zulu time (GMT offset of 00:00)
     gsub(pattern = "\\+0000", replacement = "Z")
   invisible(utils::zip(zipfile = zipped_cache_filename, files = cache_folder, extras = "-q"))

R/utils-.data.R

@@ -0,0 +1,11 @@
+#' Data pronoun
+#'
+#' See [rlang::.data] for details.
+#'
+#' @name .data
+#' @rdname data
+#' @keywords internal
+#' @export
+#' @importFrom rlang .data
+#' @usage .data
+NULL

R/utils-pipe.R

@@ -0,0 +1,11 @@
+#' Pipe operator
+#'
+#' See \code{magrittr::\link[magrittr]{\%>\%}} for details.
+#'
+#' @name %>%
+#' @rdname pipe
+#' @keywords internal
+#' @export
+#' @importFrom magrittr %>%
+#' @usage lhs \%>\% rhs
+NULL

R/utils-qqassign.R

@@ -0,0 +1,11 @@
+#' Assignment
+#'
+#' See \code{rlang::\link[rlang]{:=}} for details.
+#'
+#' @name :=
+#' @rdname quasi-quote-assign
+#' @keywords internal
+#' @export
+#' @importFrom rlang :=
+#' @usage x := y
+NULL

README.Rmd

@@ -0,0 +1,49 @@
+---
+output: github_document
+---
+
+<!-- *********** -->
+<!-- Note: README.md is generated from README.Rmd.   -->
+<!-- Be sure to edit README.Rmd and generate the README.md file by Cmd/Ctl-shift-K -->
+<!-- *********** -->
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>",
+  fig.path = "man/figures/README-",
+  out.width = "100%"
+)
+```
+
+# PFUPipelineTools
+
+
+<!-- badges: start -->
+[![CRAN status](https://www.r-pkg.org/badges/version/Recca)](https://cran.r-project.org/package=Recca)
+[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
+[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
+[![R-CMD-check](https://github.com/EnergyEconomyDecoupling/PFUPipelineTools/workflows/R-CMD-check/badge.svg)](https://github.com/EnergyEconomyDecoupling/PFUPipelineTools/actions)
+[![Codecov test coverage](https://codecov.io/gh/EnergyEconomyDecoupling/PFUPipelineTools/branch/master/graph/badge.svg)](https://app.codecov.io/gh/EnergyEconomyDecoupling/PFUPipelineTools?branch=main)
+<!-- [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5226085.svg)](https://doi.org/10.5281/zenodo.5226085) -->
+<!-- badges: end -->
+
+
+PFUPipelineTools provides a single package for several functions
+that are used across various PFU pipelines.
+
+
+## Installation
+
+You can install the development version of PFUPipelineTools from [GitHub](https://github.com/) with:
+
+``` r
+# install.packages("devtools")
+devtools::install_github("EnergyEconomyDecoupling/PFUPipelineTools")
+```
+
+
+## More Information
+
+Find more information, including vignettes and function documentation, at 
+<https://MatthewHeun.github.io/PFUPipelineTools/>.

README.md

@@ -0,0 +1,40 @@
+
+<!-- *********** -->
+<!-- Note: README.md is generated from README.Rmd.   -->
+<!-- Be sure to edit README.Rmd and generate the README.md file by Cmd/Ctl-shift-K -->
+<!-- *********** -->
+
+# PFUPipelineTools
+
+<!-- badges: start -->
+
+[![CRAN
+status](https://www.r-pkg.org/badges/version/Recca)](https://cran.r-project.org/package=Recca)
+[![Lifecycle:
+experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
+[![Project Status: Active – The project has reached a stable, usable
+state and is being actively
+developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
+[![R-CMD-check](https://github.com/EnergyEconomyDecoupling/PFUPipelineTools/workflows/R-CMD-check/badge.svg)](https://github.com/EnergyEconomyDecoupling/PFUPipelineTools/actions)
+[![Codecov test
+coverage](https://codecov.io/gh/EnergyEconomyDecoupling/PFUPipelineTools/branch/master/graph/badge.svg)](https://app.codecov.io/gh/EnergyEconomyDecoupling/PFUPipelineTools?branch=main)
+<!-- [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5226085.svg)](https://doi.org/10.5281/zenodo.5226085) -->
+<!-- badges: end -->
+
+PFUPipelineTools provides a single package for several functions that
+are used across various PFU pipelines.
+
+## Installation
+
+You can install the development version of PFUPipelineTools from
+[GitHub](https://github.com/) with:
+
+``` r
+# install.packages("devtools")
+devtools::install_github("EnergyEconomyDecoupling/PFUPipelineTools")
+```
+
+## More Information
+
+Find more information, including vignettes and function documentation,
+at <https://MatthewHeun.github.io/PFUPipelineTools/>.

_pkgdown.yml

@@ -0,0 +1,3 @@
+template:
+  bootstrap: 5
+  bootswatch: sandstone

data-raw/create_constants.R

@@ -2,7 +2,6 @@
 # If there are any changes to these constants,
 # source this script before building the package.
 
-library(magrittr)
 library(IEATools)
 
 #

inst/CITATION

@@ -0,0 +1,15 @@
+citHeader("To cite PFUPipelineTools in publications use:")
+
+citEntry(entry = "Manual",
+  title        = "PFUPipelineTools: Tools for PFU Pipelines",
+  author       = personList(as.person("Matthew Kuperus Heun")),
+  year         = "2023",
+  note         = "R package version 0.1.1",
+  url          = "https://github.com/EnergyEconomyDecoupling/PFUAggDatabase",
+
+  textVersion  =
+  paste("Matthew Kuperus Heun (2023).",
+        "PFUAggWorkflow: Calculate Aggregations and Efficiencies For Energy Conversion Chains in PSUT Format",
+        "R package version 0.1.1.",
+        "https://github.com/EnergyEconomyDecoupling/PFUAggDatabase")
+)