From f35e2d548bd5e743414deeb61a7f4116fda0eba8 Mon Sep 17 00:00:00 2001 From: "Adam H. Sparks" Date: Mon, 4 Nov 2024 09:16:12 +0800 Subject: [PATCH 1/2] Fix package for Max to install from main branch --- .Rbuildignore | 1 + NAMESPACE | 1 - codemeta.json | 131 ++++++++++++++++++++++++++++++++++++++++++ man/download_gtiff.Rd | 69 ---------------------- man/read_cog.Rd | 1 - man/read_cog_dt.Rd | 1 - 6 files changed, 132 insertions(+), 72 deletions(-) create mode 100644 codemeta.json delete mode 100644 man/download_gtiff.Rd diff --git a/.Rbuildignore b/.Rbuildignore index 0870aec..894b93d 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -7,3 +7,4 @@ ^_pkgdown\.yml$ ^docs$ ^pkgdown$ +^codemeta\.json$ diff --git a/NAMESPACE b/NAMESPACE index 044bbc0..fb0a0d0 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -1,6 +1,5 @@ # Generated by roxygen2: do not edit by hand -export(download_gtiff) export(get_key) export(get_smips) export(plot) diff --git a/codemeta.json b/codemeta.json new file mode 100644 index 0000000..77cae6f --- /dev/null +++ b/codemeta.json @@ -0,0 +1,131 @@ +{ + "@context": "https://doi.org/10.5063/schema/codemeta-2.0", + "@type": "SoftwareSourceCode", + "identifier": "nert", + "description": "Provides access to Australia's TERN (Terrestrial Ecosystem Research Network) data through the API, .", + "name": "nert: An API Client for TERN Data", + "license": "https://spdx.org/licenses/MIT", + "version": "0.0.0.9000", + "programmingLanguage": { + "@type": "ComputerLanguage", + "name": "R", + "url": "https://r-project.org" + }, + "runtimePlatform": "R version 4.4.1 (2024-06-14)", + "author": [ + { + "@type": "Person", + "givenName": "Russell", + "familyName": "Edson", + "email": "russell.edson@adelaide.edu.au" + } + ], + "maintainer": [ + { + "@type": "Person", + "givenName": "Adam H.", + "familyName": "Sparks", + "email": "adamhsparks@gmail.com", + "@id": "https://orcid.org/0000-0002-0061-8359" + } + ], + "softwareSuggestions": [ + { + "@type": "SoftwareApplication", + "identifier": "testthat", + "name": "testthat", + "version": ">= 3.0.0", + "provider": { + "@id": "https://cran.r-project.org", + "@type": "Organization", + "name": "Comprehensive R Archive Network (CRAN)", + "url": "https://cran.r-project.org" + }, + "sameAs": "https://CRAN.R-project.org/package=testthat" + } + ], + "softwareRequirements": { + "1": { + "@type": "SoftwareApplication", + "identifier": "cli", + "name": "cli", + "provider": { + "@id": "https://cran.r-project.org", + "@type": "Organization", + "name": "Comprehensive R Archive Network (CRAN)", + "url": "https://cran.r-project.org" + }, + "sameAs": "https://CRAN.R-project.org/package=cli" + }, + "2": { + "@type": "SoftwareApplication", + "identifier": "curl", + "name": "curl", + "provider": { + "@id": "https://cran.r-project.org", + "@type": "Organization", + "name": "Comprehensive R Archive Network (CRAN)", + "url": "https://cran.r-project.org" + }, + "sameAs": "https://CRAN.R-project.org/package=curl" + }, + "3": { + "@type": "SoftwareApplication", + "identifier": "data.table", + "name": "data.table", + "provider": { + "@id": "https://cran.r-project.org", + "@type": "Organization", + "name": "Comprehensive R Archive Network (CRAN)", + "url": "https://cran.r-project.org" + }, + "sameAs": "https://CRAN.R-project.org/package=data.table" + }, + "4": { + "@type": "SoftwareApplication", + "identifier": "lubridate", + "name": "lubridate", + "provider": { + "@id": "https://cran.r-project.org", + "@type": "Organization", + "name": "Comprehensive R Archive Network (CRAN)", + "url": "https://cran.r-project.org" + }, + "sameAs": "https://CRAN.R-project.org/package=lubridate" + }, + "5": { + "@type": "SoftwareApplication", + "identifier": "rlang", + "name": "rlang", + "provider": { + "@id": "https://cran.r-project.org", + "@type": "Organization", + "name": "Comprehensive R Archive Network (CRAN)", + "url": "https://cran.r-project.org" + }, + "sameAs": "https://CRAN.R-project.org/package=rlang" + }, + "6": { + "@type": "SoftwareApplication", + "identifier": "terra", + "name": "terra", + "provider": { + "@id": "https://cran.r-project.org", + "@type": "Organization", + "name": "Comprehensive R Archive Network (CRAN)", + "url": "https://cran.r-project.org" + }, + "sameAs": "https://CRAN.R-project.org/package=terra" + }, + "7": { + "@type": "SoftwareApplication", + "identifier": "utils", + "name": "utils" + }, + "SystemRequirements": null + }, + "fileSize": "174.382KB", + "codeRepository": "https://github.com/AAGI-AUS/nert", + "readme": "https://github.com/AAGI-AUS/nert/blob/main/README.md", + "contIntegration": ["https://github.com/AAGI-AUS/nert/actions/workflows/R-CMD-check.yaml", "https://app.codecov.io/gh/AAGI-AUS/nert"] +} diff --git a/man/download_gtiff.Rd b/man/download_gtiff.Rd deleted file mode 100644 index 38bc7a8..0000000 --- a/man/download_gtiff.Rd +++ /dev/null @@ -1,69 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/download_gtiff.R -\name{download_gtiff} -\alias{download_gtiff} -\title{Download a Cloud Optimised Geotiff (\acronym{COG}) file to your local -device.} -\usage{ -download_gtiff( - data = "smips", - collection = "totalbucket", - day, - api_key = get_key(), - file = getwd(), - quiet = FALSE, - cache = TRUE -) -} -\arguments{ -\item{collection}{A character vector of the data collection to be queried, -on of: -\itemize{ -\item SMindex -\item bucket1 -\item bucket2 -\item deepD -\item runoff -\item totalbucket -Defaults to \dQuote{totalbucket}. -}} - -\item{day}{A single day's date to query, \emph{e.g.}, \code{day = "2017-12-31"}, both -\code{Character} and \code{Date} classes are accepted.} - -\item{api_key}{A \code{character} string containing your \acronym{API} key, -a random string provided to you by \acronym{TERN}, for the request. -Defaults to automatically detecting your key from your local .Renviron, -.Rprofile or similar. Alternatively, you may directly provide your key as -a string here or use functionality like that from \CRANpkg{keyring}. If -nothing is provided, you will be prompted on how to set up your \R session -so that it is auto-detected and a browswer window will open at the -\acronym{TERN} website for you to request a key.} - -\item{file}{The filename including the full file path. Defaults to the -current working directory through \code{getwd()}.} - -\item{quiet}{Show file download progress bar if TRUE} -} -\value{ -A \code{nert.files} object, , a \code{list} of Geotiff files that are locally -available. -} -\description{ -Download an entire \acronym{COG} file to your local machine -} -\examples{ -download_gtiff() -} -\references{ -\url{https://portal.tern.org.au/metadata/TERN/d1995ee8-53f0-4a7d-91c2-ad5e4a23e5e0https://geonetwork.tern.org.au/geonetwork/srv/eng/catalog.search#/metadata/d1995ee8-53f0-4a7d-91c2-ad5e4a23e5e0} -} -\seealso{ -Other COGs: -\code{\link{read_cog}()}, -\code{\link{read_cog_dt}()} -} -\author{ -Adam Sparks, adam.sparks@curtin.edu.au -} -\concept{COGs} diff --git a/man/read_cog.Rd b/man/read_cog.Rd index 259f7d1..1aaca61 100644 --- a/man/read_cog.Rd +++ b/man/read_cog.Rd @@ -59,7 +59,6 @@ plot(r) } \seealso{ Other COGs: -\code{\link{download_gtiff}()}, \code{\link{read_cog_dt}()} } \concept{COGs} diff --git a/man/read_cog_dt.Rd b/man/read_cog_dt.Rd index db34226..dd71190 100644 --- a/man/read_cog_dt.Rd +++ b/man/read_cog_dt.Rd @@ -63,7 +63,6 @@ r } \seealso{ Other COGs: -\code{\link{download_gtiff}()}, \code{\link{read_cog}()} } \concept{COGs} From 0cb74f7a208d49afa82ca185182cbb563956a951 Mon Sep 17 00:00:00 2001 From: "Adam H. Sparks" Date: Mon, 4 Nov 2024 09:17:21 +0800 Subject: [PATCH 2/2] Remove curl from imports --- DESCRIPTION | 1 - codemeta.json | 22 +++++----------------- 2 files changed, 5 insertions(+), 18 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index edfeeb2..5319bf4 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -17,7 +17,6 @@ Roxygen: list(markdown = TRUE) RoxygenNote: 7.3.2 Imports: cli, - curl, data.table, lubridate, rlang, diff --git a/codemeta.json b/codemeta.json index 77cae6f..ea91284 100644 --- a/codemeta.json +++ b/codemeta.json @@ -58,18 +58,6 @@ "sameAs": "https://CRAN.R-project.org/package=cli" }, "2": { - "@type": "SoftwareApplication", - "identifier": "curl", - "name": "curl", - "provider": { - "@id": "https://cran.r-project.org", - "@type": "Organization", - "name": "Comprehensive R Archive Network (CRAN)", - "url": "https://cran.r-project.org" - }, - "sameAs": "https://CRAN.R-project.org/package=curl" - }, - "3": { "@type": "SoftwareApplication", "identifier": "data.table", "name": "data.table", @@ -81,7 +69,7 @@ }, "sameAs": "https://CRAN.R-project.org/package=data.table" }, - "4": { + "3": { "@type": "SoftwareApplication", "identifier": "lubridate", "name": "lubridate", @@ -93,7 +81,7 @@ }, "sameAs": "https://CRAN.R-project.org/package=lubridate" }, - "5": { + "4": { "@type": "SoftwareApplication", "identifier": "rlang", "name": "rlang", @@ -105,7 +93,7 @@ }, "sameAs": "https://CRAN.R-project.org/package=rlang" }, - "6": { + "5": { "@type": "SoftwareApplication", "identifier": "terra", "name": "terra", @@ -117,14 +105,14 @@ }, "sameAs": "https://CRAN.R-project.org/package=terra" }, - "7": { + "6": { "@type": "SoftwareApplication", "identifier": "utils", "name": "utils" }, "SystemRequirements": null }, - "fileSize": "174.382KB", + "fileSize": "174.372KB", "codeRepository": "https://github.com/AAGI-AUS/nert", "readme": "https://github.com/AAGI-AUS/nert/blob/main/README.md", "contIntegration": ["https://github.com/AAGI-AUS/nert/actions/workflows/R-CMD-check.yaml", "https://app.codecov.io/gh/AAGI-AUS/nert"]