Merge branch 'develop' into fix_warnings_mining

PecanProject · Oct 5, 2023 · 8ecd9fe · 8ecd9fe
2 parents eb25f94 + 341bf6c
commit 8ecd9fe
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Showing 4 changed files with 15 additions and 12 deletions.
diff --git a/book_source/_bookdown.yml b/book_source/_bookdown.yml
@@ -1,2 +1,2 @@
 rmd_subdir: true
-edit: https://github.com/tonygardella/pecan/edit/release/vtonydoc/book_source/%s
+edit: https://github.com/PecanProject/pecan/edit/develop/book_source/%s
diff --git a/modules/data.atmosphere/inst/integrationTests/test.download.AmerifluxLBL.R b/modules/data.atmosphere/inst/integrationTests/test.download.AmerifluxLBL.R
@@ -1,4 +1,5 @@
 library(testthat)
+library(PEcAn.DB)
 
 test_download_AmerifluxLBL <- function(start_date, end_date, sitename, lat.in, lon.in) {
   # putting logger to debug mode
@@ -7,13 +8,13 @@ test_download_AmerifluxLBL <- function(start_date, end_date, sitename, lat.in, l
   PEcAn.logger::logger.setLevel("DEBUG")
 
   # mocking functions
-  mockery::stub(PEcAn.DB::convert_input, 'dbfile.input.check', data.frame())
-  mockery::stub(PEcAn.DB::convert_input, 'db.query', data.frame(id = 1))
+  mockery::stub(convert_input, 'dbfile.input.check', data.frame())
+  mockery::stub(convert_input, 'db.query', data.frame(id = 1))
 
   withr::with_dir(tempdir(), {
     tmpdir <- getwd()
     # calling download function
-    res <- PEcAn.DB::convert_input(
+    res <- convert_input(
       input.id = NA,
       outfolder = tmpdir,
       formatname = NULL,

diff --git a/modules/data.atmosphere/inst/integrationTests/test.download.CRUNCEP.R b/modules/data.atmosphere/inst/integrationTests/test.download.CRUNCEP.R
@@ -1,5 +1,6 @@
 library(testthat)
 library(ncdf4)
+library(PEcAn.DB)
 
 test_download_CRUNCEP <- function(start_date, end_date, lat.in, lon.in, method, maxErrors, sleep) {
   # putting logger to debug mode
@@ -8,12 +9,12 @@ test_download_CRUNCEP <- function(start_date, end_date, lat.in, lon.in, method,
   PEcAn.logger::logger.setLevel("DEBUG")
 
   # mocking functions
-  mockery::stub(PEcAn.DB::convert_input, 'dbfile.input.check', data.frame())
-  mockery::stub(PEcAn.DB::convert_input, 'db.query', data.frame(id = 1))
+  mockery::stub(convert_input, 'dbfile.input.check', data.frame())
+  mockery::stub(convert_input, 'db.query', data.frame(id = 1))
 
   withr::with_dir(tempdir(), {
     tmpdir <- getwd()
-    PEcAn.DB::convert_input(
+    convert_input(
       input.id = NA,
       outfolder = tmpdir,
       formatname = NULL,

diff --git a/modules/data.atmosphere/inst/integrationTests/test.download.ERA5.R b/modules/data.atmosphere/inst/integrationTests/test.download.ERA5.R
@@ -1,5 +1,6 @@
 library(testthat)
 library(ncdf4)
+library(PEcAn.DB)
 
 test_download_ERA5 <- function(start_date, end_date, lat.in, lon.in, product_types, reticulate_python) {
   # putting logger to debug mode
@@ -9,16 +10,16 @@ test_download_ERA5 <- function(start_date, end_date, lat.in, lon.in, product_typ
 
 
   # mocking functions
-  mockery::stub(PEcAn.DB::convert_input, 'dbfile.input.check', data.frame())
-  mockery::stub(PEcAn.DB::convert_input, 'db.query', data.frame(id = 1))
+  mockery::stub(convert_input, 'dbfile.input.check', data.frame())
+  mockery::stub(convert_input, 'db.query', data.frame(id = 1))
 
   # additional mocks needed since download.ERA5 does not return data as other download functions
-  mockery::stub(PEcAn.DB::convert_input, 'length', 2)
-  mockery::stub(PEcAn.DB::convert_input, 'purrr::map_dfr', data.frame(missing = c(FALSE), empty = c(FALSE)))
+  mockery::stub(convert_input, 'length', 2)
+  mockery::stub(convert_input, 'purrr::map_dfr', data.frame(missing = c(FALSE), empty = c(FALSE)))
 
   withr::with_dir(tempdir(), {
     tmpdir <- getwd()
-    PEcAn.DB::convert_input(
+    convert_input(
       input.id = NA,
       outfolder = tmpdir,
       formatname = NULL,