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 e46d1d4830f..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, @@ -31,23 +32,23 @@ test_download_AmerifluxLBL <- function(start_date, end_date, sitename, lat.in, l lon.in = lon.in, sitename = sitename ) - }) - - # checking if the file is downloaded - test_that("Downloaded files are present at the desired location", { - expect_true(file.exists(paste0(tmpdir, "/AMF_US-Akn_BASE_HH_6-5.csv"))) - }) - test_that("Downloaded data files have the right format", { - firstline <- system(paste0("head -4 ", paste0(tmpdir, "/AMF_US-Akn_BASE_HH_6-5.csv")), intern = TRUE) - lastline <- system(paste0("tail -1 ", paste0(tmpdir, "/AMF_US-Akn_BASE_HH_6-5.csv")), intern = TRUE) - - # checking if first line of CSV has the sitename - expect_true(grepl(sitename, firstline[1])) - - # fourth and last row checked to contain non-alphabetical data since these are used to verify start and end dates - expect_false(grepl("[A-Za-z]", firstline[4])) - expect_false(grepl("[A-Za-z]", lastline[1])) + # checking if the file is downloaded + test_that("Downloaded files are present at the desired location", { + expect_true(file.exists(paste0(tmpdir, "/AMF_US-Akn_BASE_HH_6-5.csv"))) + }) + + test_that("Downloaded data files have the right format", { + firstline <- system(paste0("head -4 ", paste0(tmpdir, "/AMF_US-Akn_BASE_HH_6-5.csv")), intern = TRUE) + lastline <- system(paste0("tail -1 ", paste0(tmpdir, "/AMF_US-Akn_BASE_HH_6-5.csv")), intern = TRUE) + + # checking if first line of CSV has the sitename + expect_true(grepl(sitename, firstline[1])) + + # fourth and last row checked to contain non-alphabetical data since these are used to verify start and end dates + expect_false(grepl("[A-Za-z]", firstline[4])) + expect_false(grepl("[A-Za-z]", lastline[1])) + }) }) } 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 90f37c8e0c0..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, @@ -37,51 +38,51 @@ test_download_ERA5 <- function(start_date, end_date, lat.in, lon.in, product_typ product_types = product_types, reticulate_python = reticulate_python ) - }) - - test_that("All the required files are downloaded and stored at desired location", { - expect_true(file.exists(paste0(tmpdir, "/era5.2m_dewpoint_temperature.nc"))) - expect_true(file.exists(paste0(tmpdir, "/era5.2m_temperature.nc"))) - expect_true(file.exists(paste0(tmpdir, "/era5.10m_u_component_of_wind.nc"))) - expect_true(file.exists(paste0(tmpdir, "/era5.10m_v_component_of_wind.nc"))) - expect_true(file.exists(paste0(tmpdir, "/era5.surface_pressure.nc"))) - expect_true(file.exists(paste0(tmpdir, "/era5.surface_solar_radiation_downwards.nc"))) - expect_true(file.exists(paste0(tmpdir, "/era5.surface_thermal_radiation_downwards.nc"))) - expect_true(file.exists(paste0(tmpdir, "/era5.total_precipitation.nc"))) - }) + + test_that("All the required files are downloaded and stored at desired location", { + expect_true(file.exists(paste0(tmpdir, "/era5.2m_dewpoint_temperature.nc"))) + expect_true(file.exists(paste0(tmpdir, "/era5.2m_temperature.nc"))) + expect_true(file.exists(paste0(tmpdir, "/era5.10m_u_component_of_wind.nc"))) + expect_true(file.exists(paste0(tmpdir, "/era5.10m_v_component_of_wind.nc"))) + expect_true(file.exists(paste0(tmpdir, "/era5.surface_pressure.nc"))) + expect_true(file.exists(paste0(tmpdir, "/era5.surface_solar_radiation_downwards.nc"))) + expect_true(file.exists(paste0(tmpdir, "/era5.surface_thermal_radiation_downwards.nc"))) + expect_true(file.exists(paste0(tmpdir, "/era5.total_precipitation.nc"))) + }) - test_that("All ERA5 data files have the correct variable units", { - nc <- nc_open(paste0(tmpdir, "/era5.2m_dewpoint_temperature.nc")) - expect_equal(nc$var$d2m$units, "K") - nc_close(nc) + test_that("All ERA5 data files have the correct variable units", { + nc <- nc_open(paste0(tmpdir, "/era5.2m_dewpoint_temperature.nc")) + expect_equal(nc$var$d2m$units, "K") + nc_close(nc) - nc <- nc_open(paste0(tmpdir, "/era5.2m_temperature.nc")) - expect_equal(nc$var$t2m$units, "K") - nc_close(nc) + nc <- nc_open(paste0(tmpdir, "/era5.2m_temperature.nc")) + expect_equal(nc$var$t2m$units, "K") + nc_close(nc) - nc <- nc_open(paste0(tmpdir, "/era5.10m_u_component_of_wind.nc")) - expect_equal(nc$var$u10$units, "m s**-1") - nc_close(nc) + nc <- nc_open(paste0(tmpdir, "/era5.10m_u_component_of_wind.nc")) + expect_equal(nc$var$u10$units, "m s**-1") + nc_close(nc) - nc <- nc_open(paste0(tmpdir, "/era5.10m_v_component_of_wind.nc")) - expect_equal(nc$var$v10$units, "m s**-1") - nc_close(nc) + nc <- nc_open(paste0(tmpdir, "/era5.10m_v_component_of_wind.nc")) + expect_equal(nc$var$v10$units, "m s**-1") + nc_close(nc) - nc <- nc_open(paste0(tmpdir, "/era5.surface_pressure.nc")) - expect_equal(nc$var$sp$units, "Pa") - nc_close(nc) + nc <- nc_open(paste0(tmpdir, "/era5.surface_pressure.nc")) + expect_equal(nc$var$sp$units, "Pa") + nc_close(nc) - nc <- nc_open(paste0(tmpdir, "/era5.surface_solar_radiation_downwards.nc")) - expect_equal(nc$var$ssrd$units, "J m**-2") - nc_close(nc) + nc <- nc_open(paste0(tmpdir, "/era5.surface_solar_radiation_downwards.nc")) + expect_equal(nc$var$ssrd$units, "J m**-2") + nc_close(nc) - nc <- nc_open(paste0(tmpdir, "/era5.surface_thermal_radiation_downwards.nc")) - expect_equal(nc$var$strd$units, "J m**-2") - nc_close(nc) + nc <- nc_open(paste0(tmpdir, "/era5.surface_thermal_radiation_downwards.nc")) + expect_equal(nc$var$strd$units, "J m**-2") + nc_close(nc) - nc <- nc_open(paste0(tmpdir, "/era5.total_precipitation.nc")) - expect_equal(nc$var$tp$units, "m") - nc_close(nc) + nc <- nc_open(paste0(tmpdir, "/era5.total_precipitation.nc")) + expect_equal(nc$var$tp$units, "m") + nc_close(nc) + }) }) }