diff --git a/book_source/_bookdown.yml b/book_source/_bookdown.yml index 45407cef0bc..fb22b3b1e6e 100644 --- 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 index 659f016e5dd..372f5bfb11d 100644 --- 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 index 8512b49f34d..cfad888104b 100644 --- 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 index fbcff615fd6..bf84c31dd85 100644 --- 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,