Merge pull request #301 from aappling-usgs/develop

updates in support of htcondor mle & bayes runs

DESCRIPTION

@@ -2,8 +2,8 @@ Package: mda.streams
 Type: Package
 Title: Data Preparation, Access, and Analysis Functions for the Powell Center
     Continental Stream Metabolism Project
-Version: 0.9.15
-Date: 2017-01-19
+Version: 0.9.19
+Date: 2017-02-11
 Author: Alison P Appling, Luke A Winslow, Jordan S Read, Lindsay Carr
 Maintainer: Alison Appling <aappling@usgs.gov>
 Description: Back end tools for powstreams.
@@ -20,7 +20,7 @@ Imports:
     geoknife (>= 1.5.2),
     sbtools (>= 1.0.2),
     streamMetabolizer (>= 0.9.18),
-    unitted (>= 0.2.7),
+    unitted (>= 0.2.8),
     dplyr (>= 0.5.0),
     tibble (>= 1.2.0),
     foreign,
@@ -39,4 +39,4 @@ Suggests:
     yaml
 LazyLoad: yes
 LazyData: yes
-RoxygenNote: 5.0.1
+RoxygenNote: 6.0.1

NAMESPACE

@@ -147,7 +147,6 @@ importFrom(tools,write_PACKAGES)
 importFrom(unitted,deunitted)
 importFrom(unitted,get_units)
 importFrom(unitted,is.unitted)
-importFrom(unitted,rbind.unitted)
 importFrom(unitted,read_unitted)
 importFrom(unitted,u)
 importFrom(unitted,v)

R/archive_ts.R

@@ -17,7 +17,7 @@
 #' @param filename character. the filename[s] to archive
 #' @param verbose logical. give status messages?
 #' @import sbtools
-archive_ts <- function(var_src, site_name, version=c('tsv','rds'), ts_id, filename, verbose=TRUE) {
+archive_ts <- function(var_src, site_name, version=c('rds','tsv'), ts_id, filename, verbose=TRUE) {
 
   # check session
   sb_require_login("stop")

R/config_to_metab.R

@@ -129,6 +129,8 @@ config_to_metab <- function(config, rows, verbose=TRUE, prep_only=FALSE) {
     error=function(e) {
       out <- "error in model run"
       attr(out, "errors") <- as.character(e$message)
+      attr(out, "error_object") <- e
+      attr(out, "inputs") <- list(specs=metab_args$specs, data=metab_data, data_daily=metab_data_daily, info=metab_args$info)
       out
     })
 

R/download_ts.R

@@ -7,7 +7,7 @@
 #'   \code{get_var_src_codes(data_type=='ts')$var_src})
 #' @param folder string for a folder location
 #' @param version character string indicating whether you want to download the 
-#'   ts as a .tsv or .rds
+#'   ts as an .rds or .tsv
 #' @param on_remote_missing character indicating what to do if the remote file 
 #'   is missing
 #' @param on_local_exists character indicating what to do if the folder already 

R/login_sb.R

@@ -1,7 +1,7 @@
 #' Log into ScienceBase with your myUSGS credentials
 #' 
 #' BE CAREFUL NOT TO POST OR SHARE YOUR PASSWORD! Even better, set up your 
-#' ~/.R/stream_metab.yaml with fields for sb_user and sb_password so you never
+#' ~/.R/stream_metab.yaml with fields for sb_user and sb_password so you never 
 #' again have to bring your password into the R global environment. If that file
 #' exists and you call \code{login_sb()} with no arguments, the file contents 
 #' will be used to log you in.
@@ -11,17 +11,24 @@
 #' \code{sbtools::\link[sbtools]{authenticate_sb}} but easier to type.
 #' 
 #' @param username Your ScienceBase/myUSGS username, usually an email address
+#' @param filename The file path to a yaml file where fields for sb_user and
+#'   sb_password can be found. This file will be ignored if \code{username} is
+#'   given.
 #' @import sbtools
 #' @export
-login_sb <- function(username) {
+login_sb <- function(username, filename='~/.R/stream_metab.yaml') {
   # if username is provided, assume the user wants to log in manually
   if(!missing(username)) {
     return(authenticate_sb(username))
   }
 
-  # next possibility is that yaml pkg is available and a profile exists
-  filename <- file.path(Sys.getenv("HOME"), ".R", "stream_metab.yaml")
-  if(requireNamespace('yaml', quietly=TRUE) && file.exists(filename)) {
+  # next possibility is that yaml pkg is available and a profile exists. putting
+  # the yaml in ~/.R is preferred. putting the yaml in the current working
+  # directory is also an option (useful for cluster runs) but not widely
+  # advertised because it increases the risk of accidentally committing a
+  # password file to a versioning system
+  if(file.exists(filename)) {
+    if(!requireNamespace('yaml', quietly=TRUE)) stop("need the yaml package to log in by file")
     profile <- yaml::yaml.load_file(filename)
     if(exists('sb_user', profile) && exists('sb_password', profile)) {    
       return(authenticate_sb(profile$sb_user, profile$sb_password))

R/mda_helpers.R

@@ -572,7 +572,7 @@ parse_metab_model_path <- function(file_path, out=c("dir_name","file_name","mode
   dir_name <- sapply(file_path, dirname, USE.NAMES=FALSE)
   file_name <- sapply(file_path, basename, USE.NAMES=FALSE)
 
-  version <- if(substring(file_name, 1, 3) == "mmm") "modern" else "original"
+  version <- ifelse(substring(file_name, 1, 3) == "mmm", "modern", "original")
   parsed <- data.frame(
     dir_name = dir_name,
     file_name = file_name, 

R/stage_meta_basic.R

@@ -6,7 +6,7 @@
 #' @param verbose logical. print status messages?
 #' @import dplyr
 #' @import tibble
-#' @importFrom unitted u v get_units
+#' @importFrom unitted u v is.unitted get_units write_unitted
 #' @export
 #' @examples 
 #' \dontrun{
@@ -78,7 +78,7 @@ stage_meta_basic <- function(sites=list_sites(), on_exists=c('replace','add_rows
       }
 
       # add truly new rows
-      new_meta <- rbind.unitted(old_meta, sites_meta)
+      new_meta <- rbind(old_meta, sites_meta)
     } else {
       new_meta <- sites_meta
     }

R/stage_meta_indy.R

@@ -8,7 +8,7 @@
 #'   function is called (except that this copying is currently only implemented 
 #'   for the 'basic' metadata table).
 #' @inheritParams stage_meta_styx
-#' @importFrom unitted u is.unitted get_units
+#' @importFrom unitted u v is.unitted get_units write_unitted
 #' @export
 stage_meta_indy <- function(
   rows=u(data.frame(
@@ -41,7 +41,7 @@ stage_meta_indy <- function(
     }
 
     # add truly new rows
-    new_meta <- rbind.unitted(old_meta, rows)
+    new_meta <- rbind(old_meta, rows)
   } else {
     new_meta <- rows
   }

R/stage_meta_styx.R

@@ -10,7 +10,7 @@
 #'   by the new rows.
 #' @param folder where to store the staged file
 #' @param verbose logical. give status messages?
-#' @importFrom unitted u write_unitted is.unitted rbind.unitted
+#' @importFrom unitted u write_unitted is.unitted
 #' @import dplyr
 #' @export
 stage_meta_styx <- function(rows, on_exists=c("stop","replace"), folder = tempdir(), verbose = FALSE) {
@@ -38,7 +38,7 @@ stage_meta_styx <- function(rows, on_exists=c("stop","replace"), folder = tempdi
     }
 
     # add truly new rows
-    new_meta <- rbind.unitted(old_meta, rows)
+    new_meta <- rbind(old_meta, rows)
   } else {
     new_meta <- rows
   }

R/stage_nwis_ts.R

@@ -8,7 +8,7 @@
 #' @param folder a folder to place the file outputs in (defaults to temp 
 #'   directory)
 #' @param version character string indicating whether you want to stage the 
-#'   \code{ts} as a .tsv or .rds
+#'   \code{ts} as an .rds or .tsv
 #' @param verbose provide verbose output (currently not implemented)
 #' @return a character vector of file handles
 #' @importFrom dataRetrieval readNWISuv

R/ts_has_file.R

@@ -4,7 +4,7 @@
 #' file meeting the criteria
 #' 
 #' @param ts_items a list of timeseries sbitems
-#' @param with_ts_version one or more of \code{c('tsv','rds')} to limit the 
+#' @param with_ts_version one or more of \code{c('rds','tsv')} to limit the 
 #'   dataset extension to anything in with_ts_version (if the dataset is a ts)
 #' @param with_ts_archived one or more of \code{c(TRUE,FALSE)} to limit the list
 #'   to sites that have a ts that's archived, not archived, or either

R/write_ts.R

@@ -8,7 +8,7 @@
 #' @param var the variable name of the output, e.g., 'doobs'
 #' @param src the source of the data, e.g., 'nwis' or 'nldas'
 #' @param folder the folder to write the file in
-#' @param version the output version for the file (tsv, rds)
+#' @param version the output version for the file (rds, tsv)
 #' @keywords internal
 #' @importFrom lubridate tz
 #' @importFrom unitted u