From eb81d4bb41f89d2544c23cf6b5e005e196d0a499 Mon Sep 17 00:00:00 2001 From: Adriaan Dokter Date: Tue, 5 Sep 2023 10:57:48 -0400 Subject: [PATCH 1/9] bump version --- DESCRIPTION | 2 +- NEWS.md | 4 +++- README.md | 2 +- 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index ed104227..cf8c8a55 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: bioRad Title: Biological Analysis and Visualization of Weather Radar Data -Version: 0.7.1.9000 +Version: 0.7.2 Description: Extract, visualize and summarize aerial movements of birds and insects from weather radar data. See Dokter, A. M. et al. (2018) "bioRad: biological analysis and visualization of weather radar data" diff --git a/NEWS.md b/NEWS.md index 0b5e39ea..66c1fcdd 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# bioRad 0.7.1.9000 +# bioRad 0.7.2 * changed default aloft bucket to aloftdata (#622) @@ -6,6 +6,8 @@ * fix a bug in the calculation of flight altitude quantiles (#627), which caused underestimation of flight altitude quantiles by up to one altitude bin. +* updates for compatibility with testthat package 3rd edition ($630) + # bioRad 0.7.1 Rebuilds documentation with examples formatted as per CRAN requirements. diff --git a/README.md b/README.md index 3b48cb74..3ac8c152 100644 --- a/README.md +++ b/README.md @@ -97,7 +97,7 @@ Then load the package with: ``` r library(bioRad) -#> Welcome to bioRad version 0.7.1.9000 +#> Welcome to bioRad version 0.7.2 #> using vol2birdR version 1.0.1 (MistNet installed) ``` From 2078f55db9a20cc01b0af6d3c2528d72523c5a1f Mon Sep 17 00:00:00 2001 From: Adriaan Dokter Date: Tue, 5 Sep 2023 17:01:20 -0400 Subject: [PATCH 2/9] update codemeta --- codemeta.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/codemeta.json b/codemeta.json index ef75215b..1bb7d8f7 100644 --- a/codemeta.json +++ b/codemeta.json @@ -8,7 +8,7 @@ "codeRepository": "https://github.com/adokter/bioRad/", "issueTracker": "https://github.com/adokter/bioRad/issues", "license": "https://spdx.org/licenses/MIT", - "version": "0.7.1.9000", + "version": "0.7.2", "programmingLanguage": { "@type": "ComputerLanguage", "name": "R", @@ -500,7 +500,7 @@ }, "SystemRequirements": null }, - "fileSize": "9100.234KB", + "fileSize": "4886.285KB", "citation": [ { "@type": "ScholarlyArticle", From 51d0669db5d8464c08efff68985d1941ab908fac Mon Sep 17 00:00:00 2001 From: Adriaan Dokter Date: Tue, 5 Sep 2023 17:03:37 -0400 Subject: [PATCH 3/9] update cran release hash --- CRAN-SUBMISSION | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION index 272c6adf..ba149aad 100644 --- a/CRAN-SUBMISSION +++ b/CRAN-SUBMISSION @@ -1,3 +1,3 @@ -Version: 0.7.1 -Date: 2023-07-17 16:11:14 UTC -SHA: bab8c99165d91822e5bacd5c62ddf4c6cc94c3d7 +Version: 0.7.2 +Date: 2023-09-05 21:02:55 UTC +SHA: 2078f55db9a20cc01b0af6d3c2528d72523c5a1f From 8b97beff2a90cd54322e33edf5b957f1931f146f Mon Sep 17 00:00:00 2001 From: Adriaan Dokter Date: Wed, 6 Sep 2023 09:41:01 -0400 Subject: [PATCH 4/9] reduce download size by download_pvolfiles() example --- R/download_pvolfiles.R | 6 +++--- man/download_pvolfiles.Rd | 6 +++--- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/R/download_pvolfiles.R b/R/download_pvolfiles.R index 36ebf5f4..4f319ecb 100644 --- a/R/download_pvolfiles.R +++ b/R/download_pvolfiles.R @@ -24,9 +24,9 @@ #' temp_dir <- paste0(tempdir(),"/bioRad_tmp_files") #' dir.create(temp_dir) #' download_pvolfiles( -#' date_min = as.POSIXct("2016-10-02 20:00", tz = "UTC"), -#' date_max = as.POSIXct("2016-10-02 20:05", tz = "UTC"), -#' radar = "KBBX", +#' date_min = as.POSIXct("2002-10-01 00:00", tz = "UTC"), +#' date_max = as.POSIXct("2002-10-01 00:05", tz = "UTC"), +#' radar = "KBRO", #' directory = temp_dir, #' overwrite = TRUE #' ) diff --git a/man/download_pvolfiles.Rd b/man/download_pvolfiles.Rd index 278e5644..f11ea834 100644 --- a/man/download_pvolfiles.Rd +++ b/man/download_pvolfiles.Rd @@ -44,9 +44,9 @@ Download a selection of polar volume (\code{pvol}) files from the temp_dir <- paste0(tempdir(),"/bioRad_tmp_files") dir.create(temp_dir) download_pvolfiles( - date_min = as.POSIXct("2016-10-02 20:00", tz = "UTC"), - date_max = as.POSIXct("2016-10-02 20:05", tz = "UTC"), - radar = "KBBX", + date_min = as.POSIXct("2002-10-01 00:00", tz = "UTC"), + date_max = as.POSIXct("2002-10-01 00:05", tz = "UTC"), + radar = "KBRO", directory = temp_dir, overwrite = TRUE ) From d0ea28369dc8259af2d44956df5e7fb475a1e8eb Mon Sep 17 00:00:00 2001 From: Adriaan Dokter Date: Wed, 6 Sep 2023 09:43:26 -0400 Subject: [PATCH 5/9] update cran hash --- CRAN-SUBMISSION | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION index ba149aad..6191eb25 100644 --- a/CRAN-SUBMISSION +++ b/CRAN-SUBMISSION @@ -1,3 +1,3 @@ Version: 0.7.2 -Date: 2023-09-05 21:02:55 UTC -SHA: 2078f55db9a20cc01b0af6d3c2528d72523c5a1f +Date: 2023-09-06 13:43:18 UTC +SHA: 8b97beff2a90cd54322e33edf5b957f1931f146f From 7f86ff5f6fcc919cc447ff051a80f1f42e19692a Mon Sep 17 00:00:00 2001 From: Adriaan Dokter Date: Wed, 6 Sep 2023 15:51:07 -0400 Subject: [PATCH 6/9] disable ubuntu-latest (devel) and enable windows --- .github/workflows/R-CMD-check.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 35affa05..22ca63f7 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -19,8 +19,8 @@ jobs: matrix: config: - {os: macos-latest, r: 'release'} - # - {os: windows-latest, r: 'release'} # disabled until vol2birdR CRAN release - - {os: ubuntu-latest, r: 'devel'} + - {os: windows-latest, r: 'release'} + # - {os: ubuntu-latest, r: 'devel'} # disabled, runtime > 45 min. - {os: ubuntu-latest, r: 'release'} - {os: ubuntu-latest, r: 'oldrel-1'} From 1824a4b546dc3bf9ab79a83600bacc7b085125d8 Mon Sep 17 00:00:00 2001 From: Adriaan Dokter Date: Thu, 7 Sep 2023 15:59:17 -0400 Subject: [PATCH 7/9] change download method to libcurl for Windows compatibility --- NEWS.md | 2 ++ R/apply_mistnet.R | 2 +- 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/NEWS.md b/NEWS.md index 66c1fcdd..09b21d2b 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,7 @@ # bioRad 0.7.2 +## Bugfixes + * changed default aloft bucket to aloftdata (#622) * skip tests for `calculate_vp()` when vol2birdR package is not installed (#624) diff --git a/R/apply_mistnet.R b/R/apply_mistnet.R index 6dede5eb..46337ca2 100644 --- a/R/apply_mistnet.R +++ b/R/apply_mistnet.R @@ -94,7 +94,7 @@ #' # Download a NEXRAD file and save as KBGM_example #' download.file( #' "https://noaa-nexrad-level2.s3.amazonaws.com/2019/10/01/KBGM/KBGM20191001_000542_V06", -#' tempfile +#' method="libcurl", mode="wb", tempfile #' ) #' #' # Calculate MistNet segmentation From 929c98e9cc32e00162f62f5b8c79d60f1efce87e Mon Sep 17 00:00:00 2001 From: Adriaan Dokter Date: Thu, 7 Sep 2023 16:03:08 -0400 Subject: [PATCH 8/9] rebuild documentation, switch to libcurl download --- R/nexrad_odim.R | 2 +- man/apply_mistnet.Rd | 2 +- man/nexrad_to_odim.Rd | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/R/nexrad_odim.R b/R/nexrad_odim.R index f2598ee6..5174b12e 100644 --- a/R/nexrad_odim.R +++ b/R/nexrad_odim.R @@ -23,7 +23,7 @@ #' path = file.path(tempdir(), "KBGM_example") #' #' download.file(paste("https://noaa-nexrad-level2.s3.amazonaws.com/", -#' "2019/10/01/KBGM/KBGM20191001_000542_V06", +#' "2019/10/01/KBGM/KBGM20191001_000542_V06", method="libcurl", mode="wb", #' sep = "" #' ), path) #' diff --git a/man/apply_mistnet.Rd b/man/apply_mistnet.Rd index b40880df..0d89e220 100644 --- a/man/apply_mistnet.Rd +++ b/man/apply_mistnet.Rd @@ -112,7 +112,7 @@ tempfile=tempfile("KBGM_example") # Download a NEXRAD file and save as KBGM_example download.file( "https://noaa-nexrad-level2.s3.amazonaws.com/2019/10/01/KBGM/KBGM20191001_000542_V06", - tempfile + method="libcurl", mode="wb", tempfile ) # Calculate MistNet segmentation diff --git a/man/nexrad_to_odim.Rd b/man/nexrad_to_odim.Rd index 29da0113..ba19b890 100644 --- a/man/nexrad_to_odim.Rd +++ b/man/nexrad_to_odim.Rd @@ -34,7 +34,7 @@ Convert a NEXRAD polar volume file to an ODIM polar volume file path = file.path(tempdir(), "KBGM_example") download.file(paste("https://noaa-nexrad-level2.s3.amazonaws.com/", - "2019/10/01/KBGM/KBGM20191001_000542_V06", + "2019/10/01/KBGM/KBGM20191001_000542_V06", method="libcurl", mode="wb", sep = "" ), path) From 1e065e52dd567f68f4f743a81aa2448d4359c902 Mon Sep 17 00:00:00 2001 From: Adriaan Dokter Date: Thu, 7 Sep 2023 19:40:55 -0400 Subject: [PATCH 9/9] fix typo in example --- R/nexrad_odim.R | 6 ++---- man/nexrad_to_odim.Rd | 6 ++---- 2 files changed, 4 insertions(+), 8 deletions(-) diff --git a/R/nexrad_odim.R b/R/nexrad_odim.R index 5174b12e..c69c3952 100644 --- a/R/nexrad_odim.R +++ b/R/nexrad_odim.R @@ -22,10 +22,8 @@ #' # download a NEXRAD file, save as KBGM_example #' path = file.path(tempdir(), "KBGM_example") #' -#' download.file(paste("https://noaa-nexrad-level2.s3.amazonaws.com/", -#' "2019/10/01/KBGM/KBGM20191001_000542_V06", method="libcurl", mode="wb", -#' sep = "" -#' ), path) +#' download.file(paste0("https://noaa-nexrad-level2.s3.amazonaws.com/", +#' "2019/10/01/KBGM/KBGM20191001_000542_V06"), path, method="libcurl", mode="wb") #' #' # convert to ODIM format #' diff --git a/man/nexrad_to_odim.Rd b/man/nexrad_to_odim.Rd index ba19b890..a05fe263 100644 --- a/man/nexrad_to_odim.Rd +++ b/man/nexrad_to_odim.Rd @@ -33,10 +33,8 @@ Convert a NEXRAD polar volume file to an ODIM polar volume file # download a NEXRAD file, save as KBGM_example path = file.path(tempdir(), "KBGM_example") -download.file(paste("https://noaa-nexrad-level2.s3.amazonaws.com/", - "2019/10/01/KBGM/KBGM20191001_000542_V06", method="libcurl", mode="wb", - sep = "" -), path) +download.file(paste0("https://noaa-nexrad-level2.s3.amazonaws.com/", + "2019/10/01/KBGM/KBGM20191001_000542_V06"), path, method="libcurl", mode="wb") # convert to ODIM format