Merge branch 'release-0.1.14'

EnergyEconomyDecoupling · Aug 18, 2023 · d4a4c00 · d4a4c00
2 parents 08ec74d + 4a58866
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: PFUSetup
 Title: Functions to Set Up the Directory Structure of the PFU Database
-Version: 0.1.13
-Date: 2023-04-24
+Version: 0.1.15
+Date: 2023-08-18
 Authors@R: 
     person(given = "Matthew",
            family = "Heun",

diff --git a/NEWS.md b/NEWS.md
@@ -3,7 +3,22 @@ title: "Release notes for `PFUSetup`"
 output: html_document
 ---
 
-# PFUSetup 0.1.13 (2023-04-24)
+
+Cite all releases with doi [10.5281/zenodo.5228359](https://doi.org/10.5281/zenodo.5228359), 
+which always resolves to the latest release.
+
+
+# PFUSetup 0.1.14 (2023-08-18)
+
+* Now uses DOI for long-term citation.
+* Relative paths if `home_path` and `cloud_storage_path` are both
+  set to an empty string (`""`).
+* New tests for relative paths.
+    - Now at 58 tests, all passing.
+    - Test coverage remains at 100%.
+
+
+# PFUSetup 0.1.13 (2023-04-24) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7859068.svg)](https://doi.org/10.5281/zenodo.7859068)
 
 * Now defaulting to 2022 release of IEA World Extended Energy Balance (WEEB) data.
 * No new tests.

diff --git a/R/path_functions.R b/R/path_functions.R
@@ -5,16 +5,25 @@
 #'
 #' The default argument for `home_path` gets the value for `fs::path_home()`.
 #'
+#' Although this function is called [get_abs_paths()],
+#' it can return relative paths if both `home_path` and `cloud_storage_path`
+#' are set to "" (an empty string) and
+#' `project_path` is set to the root folder of the project.
+#' In that event, the leading file separator (`fsep`) is removed
+#' from the path (if it exists).
+#'
 #' @param home_path The absolute path to the user's home directory.
-#' @param dropbox_path The path to the user's Dropbox directory, relative to `home_path`.
+#' @param cloud_storage_path The path to the user's cloud storage directory, relative to `home_path`.
 #' @param project_path The path to the project directory, relative to `home_path`.
+#' @param iea_year The year of IEA data release, as a string.
 #' @param iea_folder_path The path to the IEA data directory, relative to `home_path`.
 #' @param iea_data_path The path to the IEA data file, relative to `home_path`.
 #' @param version The version of the input data.
-#' @param input_data_path The path to the input data directory.
-#' @param output_data_path The path to the output data directory.
+#' @param input_data_path The path to the input data directory, relative to `home_path`.
+#' @param output_data_path The path to the output data directory, relative to `home_path`.
 #' @param fao_data_path The path to the FAO live animals data file, relative to `home_path`.
-#' @param ilo_data_path The path to the ILO employment data file, relative to `home_path`.
+#' @param ilo_employment_data_path The path to the ILO employment data file, relative to `home_path`.
+#' @param ilo_working_hours_data_path The path to the ILO working hours data file, relative to `home_path`.
 #' @param hmw_analysis_data_path The path to the human muscle work analysis file, relative to `home_path`.
 #' @param amw_analysis_data_path The path to the animal muscle work file, relative to `home_path`.
 #' @param mw_concordance_path The path to the muscle work country concordance file, relative to `home_path`.
@@ -27,24 +36,27 @@
 #' @param ceda_data_folder The path to the folder containing CEDA (Centre for Environmental Data Analysis) data, relative to `home_path`.
 #' @param reports_source_folders A string vector of paths to folders containing report sources.
 #' @param reports_dest_folder The path to the folder into which reports will be written, relative to `home_path`.
-#' @param pipeline_caches_folder The path to a folder containing zipped versions of the pipeline cache.
+#' @param pipeline_caches_folder The path to a folder containing zipped versions of the pipeline cache, relative to `home_path`.
 #'                               Data are stored as .zip files
 #'                               Default is "PipelineCaches" relative to `project_path`.
-#' @param pipeline_releases_folder The path to a folder containing released versions of the PSUT target data frame.
+#' @param pipeline_releases_folder The path to a folder containing released versions of the PSUT target data frame, relative to `home_path`.
 #'                                 Data are stored using the `pins` package.
 #'                                 Default is "PipelineReleases" relative to `project_path`.
+#' @param fsep The file separator used when constructing paths.
+#'             Default is `.Platform$file.sep`.
 #'
 #' @return A named list containing paths to important directories and files, including:
 #' \itemize{
 #'  \item{home_path}{The absolute path to the user's home.}
-#'  \item{dropbox_path}{The absolute path of the user's Dropbox folder.}
+#'  \item{cloud_storage_path}{The absolute path of the user's cloud storage folder.}
 #'  \item{project_path}{The absolute path to the project folder.}
 #'  \item{iea_folder_path}{The absolute path to a folder containing IEA data.}
 #'  \item{iea_data_path}{The absolute path to the IEA data file for the OECD countries.}
 #'  \item{input_data_path}{The absolute path to the input data directory.}
 #'  \item{output_data_path}{The absolute path to the output data directory.}
 #'  \item{fao_data_path}{The absolute path to the FAO live animals data file.}
-#'  \item{ilo_data_path}{The absolute path to the ILO employment data file.}
+#'  \item{ilo_employment_data_path}{The absolute path to the ILO employment data file.}
+#'  \item{ilo_working_hours_data_path}{The absolute path to the ILO working hours data file.}
 #'  \item{hmw_analysis_data_path}{The absolute path to the human muscle work analysis file.}
 #'  \item{amw_analysis_data_path}{The absolute path to the animal muscle work file.}
 #'  \item{mw_concordance_path}{The absolute path to the muscle work country concordance file.}
@@ -67,20 +79,25 @@
 #'
 #' @examples
 #' get_abs_paths()
+#' # Set relative paths with empty strings
+#' get_abs_paths(home_path = "", cloud_storage_path = "",
+#'               project_path = "my_project_path")
 get_abs_paths <- function(home_path = fs::path_home() %>% as.character(),
-                          dropbox_path = "Dropbox",
-                          project_path =  file.path(dropbox_path,
+                          cloud_storage_path = "Dropbox",
+                          project_path =  file.path(cloud_storage_path,
                                                     "Fellowship 1960-2015 PFU database"),
+                          iea_year = "2022",
                           iea_folder_path = file.path(project_path,
                                                       "IEA extended energy balance data",
-                                                      "IEA 2022 energy balance data"),
+                                                      paste("IEA", iea_year, "energy balance data")),
                           iea_data_path = file.path(iea_folder_path,
-                                                    "IEA Extended Energy Balances 2022 (TJ).csv"),
+                                                    paste("IEA Extended Energy Balances", iea_year, "(TJ).csv")),
                           version = "v1.1",
                           input_data_path = file.path(project_path, "InputData", version),
                           output_data_path = file.path(project_path, "OutputData"),
                           fao_data_path = file.path(input_data_path, "fao_qcl_data.rds"),
-                          ilo_data_path = file.path(input_data_path, "ilo_hmw_data.rds"),
+                          ilo_employment_data_path = file.path(input_data_path, "ilo_employment_data.rds"),
+                          ilo_working_hours_data_path = file.path(input_data_path, "ilo_working_hours_data.rds"),
                           hmw_analysis_data_path = file.path(input_data_path, "hmw_analysis_data.xlsx"),
                           amw_analysis_data_path = file.path(input_data_path, "amw_analysis_data.xlsx"),
                           mw_concordance_path = file.path(input_data_path, "FAO_ISO_MW_Mapping.xlsx"),
@@ -89,34 +106,49 @@ get_abs_paths <- function(home_path = fs::path_home() %>% as.character(),
                           phi_constants_path = file.path(input_data_path, "phi_constants.xlsx"),
                           exemplar_table_path = file.path(input_data_path, "Exemplar_Table.xlsx"),
                           fu_analysis_folder = file.path(input_data_path, "FU analysis data"),
-                          ceda_data_folder = file.path(input_data_path, "CEDA Data"),
                           machine_data_folder = file.path(input_data_path, "Machines - Data"),
+                          ceda_data_folder = file.path(input_data_path, "CEDA Data"),
                           reports_source_folders = "reports",
                           reports_dest_folder = file.path(output_data_path, "Reports"),
                           pipeline_caches_folder = file.path(output_data_path, "PipelineCaches"),
-                          pipeline_releases_folder = file.path(output_data_path, "PipelineReleases")) {
+                          pipeline_releases_folder = file.path(output_data_path, "PipelineReleases"),
+                          fsep = .Platform$file.sep) {
 
-  list(home_path = home_path,
-       dropbox_path = file.path(home_path, dropbox_path),
-       project_path = file.path(home_path, project_path),
-       iea_folder_path = file.path(home_path, iea_folder_path),
-       input_data_path = file.path(home_path, input_data_path),
-       output_data_path = file.path(home_path, output_data_path),
-       iea_data_path = file.path(home_path, iea_data_path),
-       fao_data_path = file.path(home_path, fao_data_path),
-       ilo_data_path = file.path(home_path, ilo_data_path),
-       hmw_analysis_data_path = file.path(home_path, hmw_analysis_data_path),
-       amw_analysis_data_path = file.path(home_path, amw_analysis_data_path),
-       mw_concordance_path = file.path(home_path, mw_concordance_path),
-       country_concordance_path = file.path(home_path, country_concordance_path),
-       aggregation_mapping_path = file.path(home_path, aggregation_mapping_path),
-       exemplar_table_path = file.path(home_path, exemplar_table_path),
-       phi_constants_path = file.path(home_path, phi_constants_path),
-       fu_analysis_folder = file.path(home_path, fu_analysis_folder),
-       machine_data_folder = file.path(home_path, machine_data_folder),
-       ceda_data_folder = file.path(home_path, ceda_data_folder),
-       reports_source_folders = reports_source_folders,
-       reports_dest_folder = file.path(home_path, reports_dest_folder),
-       pipeline_caches_folder = file.path(home_path, pipeline_caches_folder),
-       pipeline_releases_folder = file.path(home_path, pipeline_releases_folder))
+  if (home_path == "" & cloud_storage_path == "") {
+    csp <- ""
+    remove_leading_file_seps <- TRUE
+  } else {
+    csp <- file.path(home_path, cloud_storage_path)
+    remove_leading_file_seps <- FALSE
+  }
+  out <- list(home_path = home_path,
+              cloud_storage_path = csp,
+              project_path = file.path(home_path, project_path, fsep = fsep),
+              iea_folder_path = file.path(home_path, iea_folder_path, fsep = fsep),
+              input_data_path = file.path(home_path, input_data_path, fsep = fsep),
+              output_data_path = file.path(home_path, output_data_path, fsep = fsep),
+              iea_data_path = file.path(home_path, iea_data_path, fsep = fsep),
+              fao_data_path = file.path(home_path, fao_data_path, fsep = fsep),
+              ilo_employment_data_path = file.path(home_path, ilo_employment_data_path, fsep = fsep),
+              ilo_working_hours_data_path = file.path(home_path, ilo_working_hours_data_path, fsep = fsep),
+              hmw_analysis_data_path = file.path(home_path, hmw_analysis_data_path, fsep = fsep),
+              amw_analysis_data_path = file.path(home_path, amw_analysis_data_path, fsep = fsep),
+              mw_concordance_path = file.path(home_path, mw_concordance_path, fsep = fsep),
+              country_concordance_path = file.path(home_path, country_concordance_path, fsep = fsep),
+              aggregation_mapping_path = file.path(home_path, aggregation_mapping_path, fsep = fsep),
+              exemplar_table_path = file.path(home_path, exemplar_table_path, fsep = fsep),
+              phi_constants_path = file.path(home_path, phi_constants_path, fsep = fsep),
+              fu_analysis_folder = file.path(home_path, fu_analysis_folder, fsep = fsep),
+              machine_data_folder = file.path(home_path, machine_data_folder, fsep = fsep),
+              ceda_data_folder = file.path(home_path, ceda_data_folder, fsep = fsep),
+              reports_source_folders = reports_source_folders,
+              reports_dest_folder = file.path(home_path, reports_dest_folder, fsep = fsep),
+              pipeline_caches_folder = file.path(home_path, pipeline_caches_folder, fsep = fsep),
+              pipeline_releases_folder = file.path(home_path, pipeline_releases_folder, fsep = fsep))
+  if (remove_leading_file_seps) {
+    out <- lapply(out, FUN = function(path) {
+      gsub(pattern = paste0("^", fsep), replacement = "", x = path)
+    })
+  }
+  return(out)
 }
diff --git a/docs/reference/get_abs_paths.html b/docs/reference/get_abs_paths.html
diff --git a/inst/CITATION b/inst/CITATION
@@ -4,14 +4,14 @@ citEntry(entry = "Manual",
   title        = "PFUSetup: Automated setup for the PFU database project.",
   author       = personList(as.person("Matthew Kuperus Heun")),
   year         = "2023",
-  note         = "R package version 0.1.13",
-  url          = "https://EnergyEconomyDecoupling.github.io/PFUSetup/",
+  note         = "R package version 0.1.14",
+  url          = "https://doi.org/10.5281/zenodo.5228359",
   doi          = "10.5281/zenodo.5228359",
 
   textVersion  =
   paste("Matthew Kuperus Heun (2023).",
         "PFUSetup: Automated setup for the PFU database project.",
-        "R package version 0.1.13.",
+        "R package version 0.1.14.",
         "https://EnergyEconomyDecoupling.github.io/PFUSetup/",
         "https://doi.org/10.5281/zenodo.5228359")
 )
diff --git a/inst/WORDLIST b/inst/WORDLIST
@@ -6,6 +6,7 @@ Centre
 CMD
 Codecov
 DOI
+doi
 dest
 dropbox
 EnergyEconomyDecoupling
@@ -34,3 +35,4 @@ PipelineReleases
 PSUT
 Sys
 WEEB
+zenodo
-Original file line number
+Diff line change
@@ Expand Up / @@ -6,6 +6,7 @@ Centre @@
     CMD
     Codecov
     DOI
+    doi
     dest
     dropbox
     EnergyEconomyDecoupling
@@ Expand Down Expand Up / @@ -34,3 +35,4 @@ PipelineReleases @@
     PSUT
     Sys
     WEEB
+    zenodo