Shifted convert.input.R from utils to DB

CHANGELOG.md

@@ -27,6 +27,8 @@ see if you need to change any of these:
   package the version that was provided with this release and the version that
   is currently installed. Use it in scripts to record your system state for
   reproducibility, or for debugging.
+- Added a new function `unit_is_parseable` in PEcAn.utils to replace `udunits2::ud.is.parseable`.
+  (#3002; @nanu1605)
 - Initial LDNDC model coupling
 
 We are slowly change the license from NCSA opensource to BSD-3 to help with publishing PEcAn to CRAN.
@@ -62,6 +64,9 @@ convert data for a single PFT fixed (#1329, #2974, #2981)
 - api is now open by default (was auth required in the past)
 - Installation instructions updated in documentation
 - PEcAn.assim.sequential is renamed to PEcAnAssimSequential
+- `convert.input` is moved from PEcAn.utils to PEcAn.DB and renamed as `convert_input`.
+  This was needed to resolve a cyclic dependency between PEcAn.DB and PEcAn.utils.
+  (#3026; @nanu1605)
 
 ### Removed
 

base/db/DESCRIPTION

@@ -1,7 +1,7 @@
 Package: PEcAn.DB
 Type: Package
 Title: PEcAn Functions Used for Ecological Forecasts and Reanalysis
-Version: 1.7.2
+Version: 1.7.2.9000
 Date: 2021-10-04
 Authors@R: c(person("David", "LeBauer", role = c("aut", "cre"),
                      email = "[email protected]"),
@@ -49,16 +49,19 @@ Imports:
     knitr,
     lubridate,
     magrittr,
+    methods,
     ncdf4,
     PEcAn.logger,
     PEcAn.remote,
     PEcAn.utils,
     purrr,
     R.utils,
+    RCurl,
     rlang,
     tibble,
     tidyr,
-    units
+    units,
+    XML
 Suggests:
     bit64,
     data.table,

base/db/NAMESPACE

@@ -5,6 +5,7 @@ export(append.covariate)
 export(assign.treatments)
 export(bety2pecan)
 export(betyConnect)
+export(convert_input)
 export(db.close)
 export(db.exists)
 export(db.getShowQueries)

base/db/NEWS.md

@@ -5,6 +5,9 @@
 * New functions `stamp_started` and `stamp_finished`, used to record the start
   and end time of model runs in the database. Both used to live in
   `PEcAn.remote` and were moved to resolve a circular dependency.
+* New function `convert_input`, used to convert between formats while reusing
+  existing files where possible. It previously lived in package `PEcAn.utils`,
+  but was moved here to simplify dependencies. (#3026; @nanu1605)
 
 # PEcAn.DB 1.7.2
 

base/db/R/insert_table.R

@@ -44,8 +44,8 @@ match_dbcols <- function(values, table, con, coerce_col_class = TRUE, drop = TRU
   # Load one row to get column types
   sql_row <- dplyr::tbl(con, table) %>% utils::head(1) %>% dplyr::collect()
   sql_types <- purrr::map(sql_row, class) %>%
-    purrr::map_chr(1) %>%
-    .[use_cols]
+    purrr::map_chr(1) 
+  sql_types <- sql_types[use_cols]
   values_types <- purrr::map(values_sub, class) %>% purrr::map_chr(1)
   type_mismatch <- sql_types != values_types
   if (sum(type_mismatch) > 0) {
@@ -69,7 +69,7 @@ match_dbcols <- function(values, table, con, coerce_col_class = TRUE, drop = TRU
         "Coercing local column types to match SQL."
       )
       # Coerce values data frame to these types
-      values_fixed <- purrr::map2_dfc(values_sub, sql_types, as)
+      values_fixed <- purrr::map2_dfc(values_sub, sql_types, methods::as)
     }
   } else {
     values_fixed <- values_sub

base/utils/DESCRIPTION

@@ -50,7 +50,6 @@ Suggests:
     data.table,
     ggplot2,
     MASS,
-    PEcAn.DB,
     randtoolbox,
     raster,
     rjags,

base/utils/NEWS.md

@@ -0,0 +1,7 @@
+# PEcAn.DB 1.7.2.9000
+
+## Added
+
+* Shifted `convert.input` function from `PEcAn.utils` to `PEcAn.DB` with a new name `convert_input`to remove circular dependency.
+  (#3026; @nanu1605)
+* Added a stub function `convert.input`. (#3026; @nanu1605)

base/utils/R/Defunct.R

@@ -0,0 +1,17 @@
+#' @title Defunct functions in PEcAn.utils
+#' @description The functions listed below are defunct and have been removed from the package.
+#'  Calling them will produce a message indicating what function, if any, has replaced it.
+#'
+#' @name PEcAn.utils-defunct
+#' @keywords internal
+NULL
+
+
+#' @rdname PEcAn.utils-defunct
+#' @section `convert.input`: Use `PEcAn.DB::convert_input` instead.
+#' @usage NULL
+#' @aliases convert.input convert.input-defunct
+#' @export
+convert.input <- function(...){
+  .Defunct("PEcAn.DB::convert_input", package = NULL)
+} # convert.input()

base/utils/R/help.R

@@ -33,5 +33,5 @@
 ##'
 ##' @docType package
 ##' @name PEcAn
-##' @aliases PECAn, pecan, package-pecan
+##' @aliases PECAn pecan package-pecan
 NULL

base/utils/R/utils.R

@@ -205,6 +205,7 @@ zero.bounded.density <- function(x, bw = "SJ", n = 1001) {
 ##' @export summarize.result
 ##' @usage summarize.result(result)
 ##' @importFrom rlang .data
+##' @importFrom magrittr %>%
 ##' @author David LeBauer, Alexey Shiklomanov
 summarize.result <- function(result) {
   ans1 <- result %>%