From 2396776cb35110fac096bb5fd367468c01667e2a Mon Sep 17 00:00:00 2001 From: Thierry Onkelinx Date: Wed, 12 Aug 2020 16:41:15 +0200 Subject: [PATCH 01/13] Upgrade to roxygen2 7.1.1 --- DESCRIPTION | 2 +- man/commit.Rd | 9 ++++++--- man/git2rdata-package.Rd | 8 ++++---- man/is_git2rdata.Rd | 6 ++++-- man/is_git2rmeta.Rd | 6 ++++-- man/list_data.Rd | 11 +++++++---- man/meta.Rd | 14 +++++++------- man/prune_meta.Rd | 14 ++++++++------ man/pull.Rd | 9 ++++++--- man/push.Rd | 9 ++++++--- man/read_vc.Rd | 9 ++++++--- man/recent_commit.Rd | 9 ++++++--- man/relabel.Rd | 9 ++++++--- man/repository.Rd | 9 ++++++--- man/rm_data.Rd | 22 +++++++++++++++------- man/status.Rd | 9 ++++++--- man/upgrade_data.Rd | 17 +++++++++++++---- man/write_vc.Rd | 35 ++++++++++++++++++++++++++++------- 18 files changed, 139 insertions(+), 68 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 6167c9a..33be424 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -39,7 +39,7 @@ License: GPL-3 Encoding: UTF-8 LazyData: true Roxygen: list(markdown = TRUE) -RoxygenNote: 6.1.1 +RoxygenNote: 7.1.1 URL: https://github.com/ropensci/git2rdata, https://doi.org/10.5281/zenodo.1485309 BugReports: https://github.com/ropensci/git2rdata/issues Collate: diff --git a/man/commit.Rd b/man/commit.Rd index 55f2914..92e152c 100644 --- a/man/commit.Rd +++ b/man/commit.Rd @@ -7,8 +7,11 @@ See \code{\link[git2r]{commit}} in \code{git2r}. } \seealso{ -Other version_control: \code{\link{pull}}, - \code{\link{push}}, \code{\link{recent_commit}}, - \code{\link{repository}}, \code{\link{status}} +Other version_control: +\code{\link{pull}()}, +\code{\link{push}()}, +\code{\link{recent_commit}()}, +\code{\link{repository}()}, +\code{\link{status}()} } \concept{version_control} diff --git a/man/git2rdata-package.Rd b/man/git2rdata-package.Rd index 91ae826..f1dc2b7 100644 --- a/man/git2rdata-package.Rd +++ b/man/git2rdata-package.Rd @@ -18,13 +18,13 @@ Useful links: } \author{ -\strong{Maintainer}: Thierry Onkelinx \email{thierry.onkelinx@inbo.be} (0000-0001-8804-4216) +\strong{Maintainer}: Thierry Onkelinx \email{thierry.onkelinx@inbo.be} (\href{https://orcid.org/0000-0001-8804-4216}{ORCID}) Other contributors: \itemize{ - \item Floris Vanderhaeghe \email{floris.vanderhaeghe@inbo.be} (0000-0002-6378-6229) [contributor] - \item Peter Desmet \email{peter.desmet@inbo.be} (0000-0002-8442-8025) [contributor] - \item Els Lommelen \email{els.lommelen@inbo.be} (0000-0002-3481-5684) [contributor] + \item Floris Vanderhaeghe \email{floris.vanderhaeghe@inbo.be} (\href{https://orcid.org/0000-0002-6378-6229}{ORCID}) [contributor] + \item Peter Desmet \email{peter.desmet@inbo.be} (\href{https://orcid.org/0000-0002-8442-8025}{ORCID}) [contributor] + \item Els Lommelen \email{els.lommelen@inbo.be} (\href{https://orcid.org/0000-0002-3481-5684}{ORCID}) [contributor] \item Research Institute for Nature and Forest \email{info@inbo.be} [copyright holder, funder] } diff --git a/man/is_git2rdata.Rd b/man/is_git2rdata.Rd index 31cd867..86bdf6b 100644 --- a/man/is_git2rdata.Rd +++ b/man/is_git2rdata.Rd @@ -55,7 +55,9 @@ is_git2rdata("iris", root) junk <- file.remove(list.files(root, full.names = TRUE), root) } \seealso{ -Other internal: \code{\link{is_git2rmeta}}, - \code{\link{meta}}, \code{\link{upgrade_data}} +Other internal: +\code{\link{is_git2rmeta}()}, +\code{\link{meta}()}, +\code{\link{upgrade_data}()} } \concept{internal} diff --git a/man/is_git2rmeta.Rd b/man/is_git2rmeta.Rd index b86ab4a..e5e085c 100644 --- a/man/is_git2rmeta.Rd +++ b/man/is_git2rmeta.Rd @@ -58,7 +58,9 @@ is_git2rdata("iris", root) junk <- file.remove(list.files(root, full.names = TRUE), root) } \seealso{ -Other internal: \code{\link{is_git2rdata}}, - \code{\link{meta}}, \code{\link{upgrade_data}} +Other internal: +\code{\link{is_git2rdata}()}, +\code{\link{meta}()}, +\code{\link{upgrade_data}()} } \concept{internal} diff --git a/man/list_data.Rd b/man/list_data.Rd index b5105c0..96953a3 100644 --- a/man/list_data.Rd +++ b/man/list_data.Rd @@ -34,7 +34,7 @@ dir.create(root) # screen output junk <- write_vc(iris[1:6, ], "iris", root, sorting = "Sepal.Length") # write a standard tab separate file (non git2rdata object) -write.table(iris, file = file.path(root, "standard.tsv"), sep = "\\t") +write.table(iris, file = file.path(root, "standard.tsv"), sep = "\t") # write a YAML file yml <- list( authors = list( @@ -99,8 +99,11 @@ junk <- file.remove( repo_path) } \seealso{ -Other storage: \code{\link{prune_meta}}, - \code{\link{read_vc}}, \code{\link{relabel}}, - \code{\link{rm_data}}, \code{\link{write_vc}} +Other storage: +\code{\link{prune_meta}()}, +\code{\link{read_vc}()}, +\code{\link{relabel}()}, +\code{\link{rm_data}()}, +\code{\link{write_vc}()} } \concept{storage} diff --git a/man/meta.Rd b/man/meta.Rd index 2b83b2c..d1f617b 100644 --- a/man/meta.Rd +++ b/man/meta.Rd @@ -15,8 +15,7 @@ meta(x, ...) \method{meta}{character}(x, na = "NA", ...) -\method{meta}{factor}(x, optimize = TRUE, na = "NA", index, - strict = TRUE, ...) +\method{meta}{factor}(x, optimize = TRUE, na = "NA", index, strict = TRUE, ...) \method{meta}{logical}(x, optimize = TRUE, ...) @@ -24,8 +23,7 @@ meta(x, ...) \method{meta}{Date}(x, optimize = TRUE, ...) -\method{meta}{data.frame}(x, optimize = TRUE, na = "NA", sorting, - strict = TRUE, ...) +\method{meta}{data.frame}(x, optimize = TRUE, na = "NA", sorting, strict = TRUE, ...) } \arguments{ \item{x}{the vector.} @@ -80,7 +78,7 @@ The same code on a different locale might result in a different sorting. Add \code{strict = FALSE} to enforce the new order of factor levels. } \examples{ -meta(c(NA, "'NA'", '"NA"', "abc\\tdef", "abc\\ndef")) +meta(c(NA, "'NA'", '"NA"', "abc\tdef", "abc\ndef")) meta(1:3) meta(seq(1, 3, length = 4)) meta(factor(c("b", NA, "NA"), levels = c("NA", "b", "c"))) @@ -99,7 +97,9 @@ meta(as.Date("2019-02-01")) meta(as.Date("2019-02-01"), optimize = FALSE) } \seealso{ -Other internal: \code{\link{is_git2rdata}}, - \code{\link{is_git2rmeta}}, \code{\link{upgrade_data}} +Other internal: +\code{\link{is_git2rdata}()}, +\code{\link{is_git2rmeta}()}, +\code{\link{upgrade_data}()} } \concept{internal} diff --git a/man/prune_meta.Rd b/man/prune_meta.Rd index 677ad4f..9a0b6fd 100644 --- a/man/prune_meta.Rd +++ b/man/prune_meta.Rd @@ -7,8 +7,7 @@ \usage{ prune_meta(root = ".", path = NULL, recursive = TRUE, ...) -\method{prune_meta}{git_repository}(root, path = NULL, - recursive = TRUE, ..., stage = FALSE) +\method{prune_meta}{git_repository}(root, path = NULL, recursive = TRUE, ..., stage = FALSE) } \arguments{ \item{root}{The root of a project. Can be a file path or a \code{git-repository}. @@ -49,7 +48,7 @@ dir.create(root) # screen output junk <- write_vc(iris[1:6, ], "iris", root, sorting = "Sepal.Length") # write a standard tab separate file (non git2rdata object) -write.table(iris, file = file.path(root, "standard.tsv"), sep = "\\t") +write.table(iris, file = file.path(root, "standard.tsv"), sep = "\t") # write a YAML file yml <- list( authors = list( @@ -114,8 +113,11 @@ junk <- file.remove( repo_path) } \seealso{ -Other storage: \code{\link{list_data}}, - \code{\link{read_vc}}, \code{\link{relabel}}, - \code{\link{rm_data}}, \code{\link{write_vc}} +Other storage: +\code{\link{list_data}()}, +\code{\link{read_vc}()}, +\code{\link{relabel}()}, +\code{\link{rm_data}()}, +\code{\link{write_vc}()} } \concept{storage} diff --git a/man/pull.Rd b/man/pull.Rd index 78ba631..77b7f3a 100644 --- a/man/pull.Rd +++ b/man/pull.Rd @@ -7,8 +7,11 @@ See \code{\link[git2r]{pull}} in \code{git2r}. } \seealso{ -Other version_control: \code{\link{commit}}, - \code{\link{push}}, \code{\link{recent_commit}}, - \code{\link{repository}}, \code{\link{status}} +Other version_control: +\code{\link{commit}()}, +\code{\link{push}()}, +\code{\link{recent_commit}()}, +\code{\link{repository}()}, +\code{\link{status}()} } \concept{version_control} diff --git a/man/push.Rd b/man/push.Rd index 5d4c426..e352621 100644 --- a/man/push.Rd +++ b/man/push.Rd @@ -7,8 +7,11 @@ See \code{\link[git2r]{push}} in \code{git2r}. } \seealso{ -Other version_control: \code{\link{commit}}, - \code{\link{pull}}, \code{\link{recent_commit}}, - \code{\link{repository}}, \code{\link{status}} +Other version_control: +\code{\link{commit}()}, +\code{\link{pull}()}, +\code{\link{recent_commit}()}, +\code{\link{repository}()}, +\code{\link{status}()} } \concept{version_control} diff --git a/man/read_vc.Rd b/man/read_vc.Rd index 5241730..f2431e5 100644 --- a/man/read_vc.Rd +++ b/man/read_vc.Rd @@ -96,8 +96,11 @@ junk <- file.remove( repo_path) } \seealso{ -Other storage: \code{\link{list_data}}, - \code{\link{prune_meta}}, \code{\link{relabel}}, - \code{\link{rm_data}}, \code{\link{write_vc}} +Other storage: +\code{\link{list_data}()}, +\code{\link{prune_meta}()}, +\code{\link{relabel}()}, +\code{\link{rm_data}()}, +\code{\link{write_vc}()} } \concept{storage} diff --git a/man/recent_commit.Rd b/man/recent_commit.Rd index a3705b6..2204c9c 100644 --- a/man/recent_commit.Rd +++ b/man/recent_commit.Rd @@ -90,8 +90,11 @@ junk <- file.remove( repo_path) } \seealso{ -Other version_control: \code{\link{commit}}, - \code{\link{pull}}, \code{\link{push}}, - \code{\link{repository}}, \code{\link{status}} +Other version_control: +\code{\link{commit}()}, +\code{\link{pull}()}, +\code{\link{push}()}, +\code{\link{repository}()}, +\code{\link{status}()} } \concept{version_control} diff --git a/man/relabel.Rd b/man/relabel.Rd index 80db7c4..0a08c79 100644 --- a/man/relabel.Rd +++ b/man/relabel.Rd @@ -87,8 +87,11 @@ junk <- file.remove( repo_path) } \seealso{ -Other storage: \code{\link{list_data}}, - \code{\link{prune_meta}}, \code{\link{read_vc}}, - \code{\link{rm_data}}, \code{\link{write_vc}} +Other storage: +\code{\link{list_data}()}, +\code{\link{prune_meta}()}, +\code{\link{read_vc}()}, +\code{\link{rm_data}()}, +\code{\link{write_vc}()} } \concept{storage} diff --git a/man/repository.Rd b/man/repository.Rd index a6e8cad..b8e39e4 100644 --- a/man/repository.Rd +++ b/man/repository.Rd @@ -7,8 +7,11 @@ See \code{\link[git2r]{repository}} in \code{git2r}. } \seealso{ -Other version_control: \code{\link{commit}}, - \code{\link{pull}}, \code{\link{push}}, - \code{\link{recent_commit}}, \code{\link{status}} +Other version_control: +\code{\link{commit}()}, +\code{\link{pull}()}, +\code{\link{push}()}, +\code{\link{recent_commit}()}, +\code{\link{status}()} } \concept{version_control} diff --git a/man/rm_data.Rd b/man/rm_data.Rd index ab9069e..6478e66 100644 --- a/man/rm_data.Rd +++ b/man/rm_data.Rd @@ -7,9 +7,14 @@ \usage{ rm_data(root = ".", path = NULL, recursive = TRUE, ...) -\method{rm_data}{git_repository}(root, path = NULL, recursive = TRUE, - ..., stage = FALSE, type = c("unmodified", "modified", "ignored", - "all")) +\method{rm_data}{git_repository}( + root, + path = NULL, + recursive = TRUE, + ..., + stage = FALSE, + type = c("unmodified", "modified", "ignored", "all") +) } \arguments{ \item{root}{The root of a project. Can be a file path or a \code{git-repository}. @@ -59,7 +64,7 @@ dir.create(root) # screen output junk <- write_vc(iris[1:6, ], "iris", root, sorting = "Sepal.Length") # write a standard tab separate file (non git2rdata object) -write.table(iris, file = file.path(root, "standard.tsv"), sep = "\\t") +write.table(iris, file = file.path(root, "standard.tsv"), sep = "\t") # write a YAML file yml <- list( authors = list( @@ -124,8 +129,11 @@ junk <- file.remove( repo_path) } \seealso{ -Other storage: \code{\link{list_data}}, - \code{\link{prune_meta}}, \code{\link{read_vc}}, - \code{\link{relabel}}, \code{\link{write_vc}} +Other storage: +\code{\link{list_data}()}, +\code{\link{prune_meta}()}, +\code{\link{read_vc}()}, +\code{\link{relabel}()}, +\code{\link{write_vc}()} } \concept{storage} diff --git a/man/status.Rd b/man/status.Rd index 372a51d..8751eac 100644 --- a/man/status.Rd +++ b/man/status.Rd @@ -7,8 +7,11 @@ See \code{\link[git2r]{status}} in \code{git2r}. } \seealso{ -Other version_control: \code{\link{commit}}, - \code{\link{pull}}, \code{\link{push}}, - \code{\link{recent_commit}}, \code{\link{repository}} +Other version_control: +\code{\link{commit}()}, +\code{\link{pull}()}, +\code{\link{push}()}, +\code{\link{recent_commit}()}, +\code{\link{repository}()} } \concept{version_control} diff --git a/man/upgrade_data.Rd b/man/upgrade_data.Rd index 1d34204..d8e54d4 100644 --- a/man/upgrade_data.Rd +++ b/man/upgrade_data.Rd @@ -7,8 +7,15 @@ \usage{ upgrade_data(file, root = ".", verbose, ..., path) -\method{upgrade_data}{git_repository}(file, root = ".", verbose = TRUE, - ..., path, stage = FALSE, force = FALSE) +\method{upgrade_data}{git_repository}( + file, + root = ".", + verbose = TRUE, + ..., + path, + stage = FALSE, + force = FALSE +) } \arguments{ \item{file}{the name of the git2rdata object. Git2rdata objects cannot @@ -59,7 +66,9 @@ upgrade_data(path = ".", root = root) junk <- file.remove(list.files(root, full.names = TRUE), root) } \seealso{ -Other internal: \code{\link{is_git2rdata}}, - \code{\link{is_git2rmeta}}, \code{\link{meta}} +Other internal: +\code{\link{is_git2rdata}()}, +\code{\link{is_git2rmeta}()}, +\code{\link{meta}()} } \concept{internal} diff --git a/man/write_vc.Rd b/man/write_vc.Rd index 2b85132..1385b35 100644 --- a/man/write_vc.Rd +++ b/man/write_vc.Rd @@ -5,11 +5,29 @@ \alias{write_vc.git_repository} \title{Store a Data.Frame as a Git2rdata Object on Disk} \usage{ -write_vc(x, file, root = ".", sorting, strict = TRUE, - optimize = TRUE, na = "NA", ...) +write_vc( + x, + file, + root = ".", + sorting, + strict = TRUE, + optimize = TRUE, + na = "NA", + ... +) -\method{write_vc}{git_repository}(x, file, root, sorting, strict = TRUE, - optimize = TRUE, na = "NA", ..., stage = FALSE, force = FALSE) +\method{write_vc}{git_repository}( + x, + file, + root, + sorting, + strict = TRUE, + optimize = TRUE, + na = "NA", + ..., + stage = FALSE, + force = FALSE +) } \arguments{ \item{x}{the \code{data.frame}.} @@ -130,8 +148,11 @@ junk <- file.remove( repo_path) } \seealso{ -Other storage: \code{\link{list_data}}, - \code{\link{prune_meta}}, \code{\link{read_vc}}, - \code{\link{relabel}}, \code{\link{rm_data}} +Other storage: +\code{\link{list_data}()}, +\code{\link{prune_meta}()}, +\code{\link{read_vc}()}, +\code{\link{relabel}()}, +\code{\link{rm_data}()} } \concept{storage} From a97393d75d4a1936d1a65a6386da9ba31dc70f72 Mon Sep 17 00:00:00 2001 From: Thierry Onkelinx Date: Wed, 12 Aug 2020 16:45:26 +0200 Subject: [PATCH 02/13] Bump package version --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 33be424..c65e9f5 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: git2rdata Title: Store and Retrieve Data.frames in a Git Repository -Version: 0.2.1 +Version: 0.2.2 Authors@R: c( person( "Thierry", "Onkelinx", role = c("aut", "cre"), From 85a9726fc15ed2a26f4180fbb151a47d7308778c Mon Sep 17 00:00:00 2001 From: Thierry Onkelinx Date: Wed, 12 Aug 2020 17:59:26 +0200 Subject: [PATCH 03/13] Setup machinery for checklist::check_package() --- .github/workflows/check_on_branch.yml | 17 + .github/workflows/check_on_master.yml | 19 + DESCRIPTION | 82 ++-- LICENSE.md | 675 ++++++++++++++++++++++++++ checklist.yml | 5 + codecov.yml | 17 + 6 files changed, 778 insertions(+), 37 deletions(-) create mode 100644 .github/workflows/check_on_branch.yml create mode 100644 .github/workflows/check_on_master.yml create mode 100644 LICENSE.md create mode 100644 checklist.yml create mode 100644 codecov.yml diff --git a/.github/workflows/check_on_branch.yml b/.github/workflows/check_on_branch.yml new file mode 100644 index 0000000..7b4f0f0 --- /dev/null +++ b/.github/workflows/check_on_branch.yml @@ -0,0 +1,17 @@ +on: + push: + branches-ignore: + - master + - ghpages + +name: "check package" + +jobs: + check-package: + runs-on: ubuntu-latest + name: "check package" + steps: + - uses: inbo/actions/check_pkg@master + with: + CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} + ORCID_TOKEN: ${{ secrets.ORCID_TOKEN }} diff --git a/.github/workflows/check_on_master.yml b/.github/workflows/check_on_master.yml new file mode 100644 index 0000000..9d1cb83 --- /dev/null +++ b/.github/workflows/check_on_master.yml @@ -0,0 +1,19 @@ +on: + push: + branches: + - master + schedule: + - cron: '6 0 * * 1' + +name: "check package on master" + +jobs: + check-package: + runs-on: ubuntu-latest + name: "check package" + steps: + - uses: inbo/actions/check_pkg@master + with: + CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} + ORCID_TOKEN: ${{ secrets.ORCID_TOKEN }} + token: ${{ secrets.pat }} diff --git a/DESCRIPTION b/DESCRIPTION index c65e9f5..fc422c4 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,47 +1,57 @@ Package: git2rdata Title: Store and Retrieve Data.frames in a Git Repository Version: 0.2.2 -Authors@R: c( - person( - "Thierry", "Onkelinx", role = c("aut", "cre"), - email = "thierry.onkelinx@inbo.be", - comment = c(ORCID = "0000-0001-8804-4216")), - person( - "Floris", "Vanderhaeghe", role = "ctb", - email = "floris.vanderhaeghe@inbo.be", - comment = c(ORCID = "0000-0002-6378-6229")), - person( - "Peter", "Desmet", role = "ctb", - email = "peter.desmet@inbo.be", - comment = c(ORCID = "0000-0002-8442-8025")), - person( - "Els", "Lommelen", role = "ctb", - email = "els.lommelen@inbo.be", - comment = c(ORCID = "0000-0002-3481-5684")), - person( - "Research Institute for Nature and Forest", - role = c("cph", "fnd"), email = "info@inbo.be")) -Description: Make versioning of data.frame easy and efficient using git repositories. -Depends: R (>= 3.5.0) +Authors@R: + c(person(given = "Thierry", + family = "Onkelinx", + role = c("aut", "cre"), + email = "thierry.onkelinx@inbo.be", + comment = c(ORCID = "0000-0001-8804-4216")), + person(given = "Floris", + family = "Vanderhaeghe", + role = "ctb", + email = "floris.vanderhaeghe@inbo.be", + comment = c(ORCID = "0000-0002-6378-6229")), + person(given = "Peter", + family = "Desmet", + role = "ctb", + email = "peter.desmet@inbo.be", + comment = c(ORCID = "0000-0002-8442-8025")), + person(given = "Els", + family = "Lommelen", + role = "ctb", + email = "els.lommelen@inbo.be", + comment = c(ORCID = "0000-0002-3481-5684")), + person(given = "Research Institute for Nature and Forest", + role = c("cph", "fnd"), + email = "info@inbo.be")) +Description: Make versioning of data.frame easy and efficient using git + repositories. +License: GPL-3 +URL: https://github.com/ropensci/git2rdata, + https://doi.org/10.5281/zenodo.1485309 +BugReports: https://github.com/ropensci/git2rdata/issues +Depends: + R (>= 3.5.0) Imports: - assertthat, - git2r (>= 0.23.0), - methods, - yaml + assertthat, + git2r (>= 0.23.0), + methods, + yaml Suggests: - spelling, - ggplot2, - knitr, - microbenchmark, - rmarkdown, - testthat -License: GPL-3 + ggplot2, + knitr, + microbenchmark, + rmarkdown, + spelling, + testthat +VignetteBuilder: + knitr Encoding: UTF-8 +Language: en-GB LazyData: true Roxygen: list(markdown = TRUE) RoxygenNote: 7.1.1 -URL: https://github.com/ropensci/git2rdata, https://doi.org/10.5281/zenodo.1485309 -BugReports: https://github.com/ropensci/git2rdata/issues Collate: 'clean_data_path.R' 'datahash.R' @@ -58,5 +68,3 @@ Collate: 'relabel.R' 'upgrade_data.R' 'utils.R' -VignetteBuilder: knitr -Language: en-GB diff --git a/LICENSE.md b/LICENSE.md new file mode 100644 index 0000000..2fb2e74 --- /dev/null +++ b/LICENSE.md @@ -0,0 +1,675 @@ +### GNU GENERAL PUBLIC LICENSE + +Version 3, 29 June 2007 + +Copyright (C) 2007 Free Software Foundation, Inc. + + +Everyone is permitted to copy and distribute verbatim copies of this +license document, but changing it is not allowed. + +### Preamble + +The GNU General Public License is a free, copyleft license for +software and other kinds of works. + +The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. By contrast, +the GNU General Public License is intended to guarantee your freedom +to share and change all versions of a program--to make sure it remains +free software for all its users. We, the Free Software Foundation, use +the GNU General Public License for most of our software; it applies +also to any other work released this way by its authors. You can apply +it to your programs, too. + +When we speak of free software, we are referring to freedom, not +price. Our General Public Licenses are designed to make sure that you +have the freedom to distribute copies of free software (and charge for +them if you wish), that you receive source code or can get it if you +want it, that you can change the software or use pieces of it in new +free programs, and that you know you can do these things. + +To protect your rights, we need to prevent others from denying you +these rights or asking you to surrender the rights. Therefore, you +have certain responsibilities if you distribute copies of the +software, or if you modify it: responsibilities to respect the freedom +of others. + +For example, if you distribute copies of such a program, whether +gratis or for a fee, you must pass on to the recipients the same +freedoms that you received. You must make sure that they, too, receive +or can get the source code. And you must show them these terms so they +know their rights. + +Developers that use the GNU GPL protect your rights with two steps: +(1) assert copyright on the software, and (2) offer you this License +giving you legal permission to copy, distribute and/or modify it. + +For the developers' and authors' protection, the GPL clearly explains +that there is no warranty for this free software. For both users' and +authors' sake, the GPL requires that modified versions be marked as +changed, so that their problems will not be attributed erroneously to +authors of previous versions. + +Some devices are designed to deny users access to install or run +modified versions of the software inside them, although the +manufacturer can do so. This is fundamentally incompatible with the +aim of protecting users' freedom to change the software. The +systematic pattern of such abuse occurs in the area of products for +individuals to use, which is precisely where it is most unacceptable. +Therefore, we have designed this version of the GPL to prohibit the +practice for those products. If such problems arise substantially in +other domains, we stand ready to extend this provision to those +domains in future versions of the GPL, as needed to protect the +freedom of users. + +Finally, every program is threatened constantly by software patents. +States should not allow patents to restrict development and use of +software on general-purpose computers, but in those that do, we wish +to avoid the special danger that patents applied to a free program +could make it effectively proprietary. To prevent this, the GPL +assures that patents cannot be used to render the program non-free. + +The precise terms and conditions for copying, distribution and +modification follow. + +### TERMS AND CONDITIONS + +#### 0. Definitions. + +"This License" refers to version 3 of the GNU General Public License. + +"Copyright" also means copyright-like laws that apply to other kinds +of works, such as semiconductor masks. + +"The Program" refers to any copyrightable work licensed under this +License. Each licensee is addressed as "you". "Licensees" and +"recipients" may be individuals or organizations. + +To "modify" a work means to copy from or adapt all or part of the work +in a fashion requiring copyright permission, other than the making of +an exact copy. The resulting work is called a "modified version" of +the earlier work or a work "based on" the earlier work. + +A "covered work" means either the unmodified Program or a work based +on the Program. + +To "propagate" a work means to do anything with it that, without +permission, would make you directly or secondarily liable for +infringement under applicable copyright law, except executing it on a +computer or modifying a private copy. Propagation includes copying, +distribution (with or without modification), making available to the +public, and in some countries other activities as well. + +To "convey" a work means any kind of propagation that enables other +parties to make or receive copies. Mere interaction with a user +through a computer network, with no transfer of a copy, is not +conveying. + +An interactive user interface displays "Appropriate Legal Notices" to +the extent that it includes a convenient and prominently visible +feature that (1) displays an appropriate copyright notice, and (2) +tells the user that there is no warranty for the work (except to the +extent that warranties are provided), that licensees may convey the +work under this License, and how to view a copy of this License. If +the interface presents a list of user commands or options, such as a +menu, a prominent item in the list meets this criterion. + +#### 1. Source Code. + +The "source code" for a work means the preferred form of the work for +making modifications to it. "Object code" means any non-source form of +a work. + +A "Standard Interface" means an interface that either is an official +standard defined by a recognized standards body, or, in the case of +interfaces specified for a particular programming language, one that +is widely used among developers working in that language. + +The "System Libraries" of an executable work include anything, other +than the work as a whole, that (a) is included in the normal form of +packaging a Major Component, but which is not part of that Major +Component, and (b) serves only to enable use of the work with that +Major Component, or to implement a Standard Interface for which an +implementation is available to the public in source code form. A +"Major Component", in this context, means a major essential component +(kernel, window system, and so on) of the specific operating system +(if any) on which the executable work runs, or a compiler used to +produce the work, or an object code interpreter used to run it. + +The "Corresponding Source" for a work in object code form means all +the source code needed to generate, install, and (for an executable +work) run the object code and to modify the work, including scripts to +control those activities. However, it does not include the work's +System Libraries, or general-purpose tools or generally available free +programs which are used unmodified in performing those activities but +which are not part of the work. For example, Corresponding Source +includes interface definition files associated with source files for +the work, and the source code for shared libraries and dynamically +linked subprograms that the work is specifically designed to require, +such as by intimate data communication or control flow between those +subprograms and other parts of the work. + +The Corresponding Source need not include anything that users can +regenerate automatically from other parts of the Corresponding Source. + +The Corresponding Source for a work in source code form is that same +work. + +#### 2. Basic Permissions. + +All rights granted under this License are granted for the term of +copyright on the Program, and are irrevocable provided the stated +conditions are met. This License explicitly affirms your unlimited +permission to run the unmodified Program. The output from running a +covered work is covered by this License only if the output, given its +content, constitutes a covered work. This License acknowledges your +rights of fair use or other equivalent, as provided by copyright law. + +You may make, run and propagate covered works that you do not convey, +without conditions so long as your license otherwise remains in force. +You may convey covered works to others for the sole purpose of having +them make modifications exclusively for you, or provide you with +facilities for running those works, provided that you comply with the +terms of this License in conveying all material for which you do not +control copyright. Those thus making or running the covered works for +you must do so exclusively on your behalf, under your direction and +control, on terms that prohibit them from making any copies of your +copyrighted material outside their relationship with you. + +Conveying under any other circumstances is permitted solely under the +conditions stated below. Sublicensing is not allowed; section 10 makes +it unnecessary. + +#### 3. Protecting Users' Legal Rights From Anti-Circumvention Law. + +No covered work shall be deemed part of an effective technological +measure under any applicable law fulfilling obligations under article +11 of the WIPO copyright treaty adopted on 20 December 1996, or +similar laws prohibiting or restricting circumvention of such +measures. + +When you convey a covered work, you waive any legal power to forbid +circumvention of technological measures to the extent such +circumvention is effected by exercising rights under this License with +respect to the covered work, and you disclaim any intention to limit +operation or modification of the work as a means of enforcing, against +the work's users, your or third parties' legal rights to forbid +circumvention of technological measures. + +#### 4. Conveying Verbatim Copies. + +You may convey verbatim copies of the Program's source code as you +receive it, in any medium, provided that you conspicuously and +appropriately publish on each copy an appropriate copyright notice; +keep intact all notices stating that this License and any +non-permissive terms added in accord with section 7 apply to the code; +keep intact all notices of the absence of any warranty; and give all +recipients a copy of this License along with the Program. + +You may charge any price or no price for each copy that you convey, +and you may offer support or warranty protection for a fee. + +#### 5. Conveying Modified Source Versions. + +You may convey a work based on the Program, or the modifications to +produce it from the Program, in the form of source code under the +terms of section 4, provided that you also meet all of these +conditions: + +- a) The work must carry prominent notices stating that you modified + it, and giving a relevant date. +- b) The work must carry prominent notices stating that it is + released under this License and any conditions added under + section 7. This requirement modifies the requirement in section 4 + to "keep intact all notices". +- c) You must license the entire work, as a whole, under this + License to anyone who comes into possession of a copy. This + License will therefore apply, along with any applicable section 7 + additional terms, to the whole of the work, and all its parts, + regardless of how they are packaged. This License gives no + permission to license the work in any other way, but it does not + invalidate such permission if you have separately received it. +- d) If the work has interactive user interfaces, each must display + Appropriate Legal Notices; however, if the Program has interactive + interfaces that do not display Appropriate Legal Notices, your + work need not make them do so. + +A compilation of a covered work with other separate and independent +works, which are not by their nature extensions of the covered work, +and which are not combined with it such as to form a larger program, +in or on a volume of a storage or distribution medium, is called an +"aggregate" if the compilation and its resulting copyright are not +used to limit the access or legal rights of the compilation's users +beyond what the individual works permit. Inclusion of a covered work +in an aggregate does not cause this License to apply to the other +parts of the aggregate. + +#### 6. Conveying Non-Source Forms. + +You may convey a covered work in object code form under the terms of +sections 4 and 5, provided that you also convey the machine-readable +Corresponding Source under the terms of this License, in one of these +ways: + +- a) Convey the object code in, or embodied in, a physical product + (including a physical distribution medium), accompanied by the + Corresponding Source fixed on a durable physical medium + customarily used for software interchange. +- b) Convey the object code in, or embodied in, a physical product + (including a physical distribution medium), accompanied by a + written offer, valid for at least three years and valid for as + long as you offer spare parts or customer support for that product + model, to give anyone who possesses the object code either (1) a + copy of the Corresponding Source for all the software in the + product that is covered by this License, on a durable physical + medium customarily used for software interchange, for a price no + more than your reasonable cost of physically performing this + conveying of source, or (2) access to copy the Corresponding + Source from a network server at no charge. +- c) Convey individual copies of the object code with a copy of the + written offer to provide the Corresponding Source. This + alternative is allowed only occasionally and noncommercially, and + only if you received the object code with such an offer, in accord + with subsection 6b. +- d) Convey the object code by offering access from a designated + place (gratis or for a charge), and offer equivalent access to the + Corresponding Source in the same way through the same place at no + further charge. You need not require recipients to copy the + Corresponding Source along with the object code. If the place to + copy the object code is a network server, the Corresponding Source + may be on a different server (operated by you or a third party) + that supports equivalent copying facilities, provided you maintain + clear directions next to the object code saying where to find the + Corresponding Source. Regardless of what server hosts the + Corresponding Source, you remain obligated to ensure that it is + available for as long as needed to satisfy these requirements. +- e) Convey the object code using peer-to-peer transmission, + provided you inform other peers where the object code and + Corresponding Source of the work are being offered to the general + public at no charge under subsection 6d. + +A separable portion of the object code, whose source code is excluded +from the Corresponding Source as a System Library, need not be +included in conveying the object code work. + +A "User Product" is either (1) a "consumer product", which means any +tangible personal property which is normally used for personal, +family, or household purposes, or (2) anything designed or sold for +incorporation into a dwelling. In determining whether a product is a +consumer product, doubtful cases shall be resolved in favor of +coverage. For a particular product received by a particular user, +"normally used" refers to a typical or common use of that class of +product, regardless of the status of the particular user or of the way +in which the particular user actually uses, or expects or is expected +to use, the product. A product is a consumer product regardless of +whether the product has substantial commercial, industrial or +non-consumer uses, unless such uses represent the only significant +mode of use of the product. + +"Installation Information" for a User Product means any methods, +procedures, authorization keys, or other information required to +install and execute modified versions of a covered work in that User +Product from a modified version of its Corresponding Source. The +information must suffice to ensure that the continued functioning of +the modified object code is in no case prevented or interfered with +solely because modification has been made. + +If you convey an object code work under this section in, or with, or +specifically for use in, a User Product, and the conveying occurs as +part of a transaction in which the right of possession and use of the +User Product is transferred to the recipient in perpetuity or for a +fixed term (regardless of how the transaction is characterized), the +Corresponding Source conveyed under this section must be accompanied +by the Installation Information. But this requirement does not apply +if neither you nor any third party retains the ability to install +modified object code on the User Product (for example, the work has +been installed in ROM). + +The requirement to provide Installation Information does not include a +requirement to continue to provide support service, warranty, or +updates for a work that has been modified or installed by the +recipient, or for the User Product in which it has been modified or +installed. Access to a network may be denied when the modification +itself materially and adversely affects the operation of the network +or violates the rules and protocols for communication across the +network. + +Corresponding Source conveyed, and Installation Information provided, +in accord with this section must be in a format that is publicly +documented (and with an implementation available to the public in +source code form), and must require no special password or key for +unpacking, reading or copying. + +#### 7. Additional Terms. + +"Additional permissions" are terms that supplement the terms of this +License by making exceptions from one or more of its conditions. +Additional permissions that are applicable to the entire Program shall +be treated as though they were included in this License, to the extent +that they are valid under applicable law. If additional permissions +apply only to part of the Program, that part may be used separately +under those permissions, but the entire Program remains governed by +this License without regard to the additional permissions. + +When you convey a copy of a covered work, you may at your option +remove any additional permissions from that copy, or from any part of +it. (Additional permissions may be written to require their own +removal in certain cases when you modify the work.) You may place +additional permissions on material, added by you to a covered work, +for which you have or can give appropriate copyright permission. + +Notwithstanding any other provision of this License, for material you +add to a covered work, you may (if authorized by the copyright holders +of that material) supplement the terms of this License with terms: + +- a) Disclaiming warranty or limiting liability differently from the + terms of sections 15 and 16 of this License; or +- b) Requiring preservation of specified reasonable legal notices or + author attributions in that material or in the Appropriate Legal + Notices displayed by works containing it; or +- c) Prohibiting misrepresentation of the origin of that material, + or requiring that modified versions of such material be marked in + reasonable ways as different from the original version; or +- d) Limiting the use for publicity purposes of names of licensors + or authors of the material; or +- e) Declining to grant rights under trademark law for use of some + trade names, trademarks, or service marks; or +- f) Requiring indemnification of licensors and authors of that + material by anyone who conveys the material (or modified versions + of it) with contractual assumptions of liability to the recipient, + for any liability that these contractual assumptions directly + impose on those licensors and authors. + +All other non-permissive additional terms are considered "further +restrictions" within the meaning of section 10. If the Program as you +received it, or any part of it, contains a notice stating that it is +governed by this License along with a term that is a further +restriction, you may remove that term. If a license document contains +a further restriction but permits relicensing or conveying under this +License, you may add to a covered work material governed by the terms +of that license document, provided that the further restriction does +not survive such relicensing or conveying. + +If you add terms to a covered work in accord with this section, you +must place, in the relevant source files, a statement of the +additional terms that apply to those files, or a notice indicating +where to find the applicable terms. + +Additional terms, permissive or non-permissive, may be stated in the +form of a separately written license, or stated as exceptions; the +above requirements apply either way. + +#### 8. Termination. + +You may not propagate or modify a covered work except as expressly +provided under this License. Any attempt otherwise to propagate or +modify it is void, and will automatically terminate your rights under +this License (including any patent licenses granted under the third +paragraph of section 11). + +However, if you cease all violation of this License, then your license +from a particular copyright holder is reinstated (a) provisionally, +unless and until the copyright holder explicitly and finally +terminates your license, and (b) permanently, if the copyright holder +fails to notify you of the violation by some reasonable means prior to +60 days after the cessation. + +Moreover, your license from a particular copyright holder is +reinstated permanently if the copyright holder notifies you of the +violation by some reasonable means, this is the first time you have +received notice of violation of this License (for any work) from that +copyright holder, and you cure the violation prior to 30 days after +your receipt of the notice. + +Termination of your rights under this section does not terminate the +licenses of parties who have received copies or rights from you under +this License. If your rights have been terminated and not permanently +reinstated, you do not qualify to receive new licenses for the same +material under section 10. + +#### 9. Acceptance Not Required for Having Copies. + +You are not required to accept this License in order to receive or run +a copy of the Program. Ancillary propagation of a covered work +occurring solely as a consequence of using peer-to-peer transmission +to receive a copy likewise does not require acceptance. However, +nothing other than this License grants you permission to propagate or +modify any covered work. These actions infringe copyright if you do +not accept this License. Therefore, by modifying or propagating a +covered work, you indicate your acceptance of this License to do so. + +#### 10. Automatic Licensing of Downstream Recipients. + +Each time you convey a covered work, the recipient automatically +receives a license from the original licensors, to run, modify and +propagate that work, subject to this License. You are not responsible +for enforcing compliance by third parties with this License. + +An "entity transaction" is a transaction transferring control of an +organization, or substantially all assets of one, or subdividing an +organization, or merging organizations. If propagation of a covered +work results from an entity transaction, each party to that +transaction who receives a copy of the work also receives whatever +licenses to the work the party's predecessor in interest had or could +give under the previous paragraph, plus a right to possession of the +Corresponding Source of the work from the predecessor in interest, if +the predecessor has it or can get it with reasonable efforts. + +You may not impose any further restrictions on the exercise of the +rights granted or affirmed under this License. For example, you may +not impose a license fee, royalty, or other charge for exercise of +rights granted under this License, and you may not initiate litigation +(including a cross-claim or counterclaim in a lawsuit) alleging that +any patent claim is infringed by making, using, selling, offering for +sale, or importing the Program or any portion of it. + +#### 11. Patents. + +A "contributor" is a copyright holder who authorizes use under this +License of the Program or a work on which the Program is based. The +work thus licensed is called the contributor's "contributor version". + +A contributor's "essential patent claims" are all patent claims owned +or controlled by the contributor, whether already acquired or +hereafter acquired, that would be infringed by some manner, permitted +by this License, of making, using, or selling its contributor version, +but do not include claims that would be infringed only as a +consequence of further modification of the contributor version. For +purposes of this definition, "control" includes the right to grant +patent sublicenses in a manner consistent with the requirements of +this License. + +Each contributor grants you a non-exclusive, worldwide, royalty-free +patent license under the contributor's essential patent claims, to +make, use, sell, offer for sale, import and otherwise run, modify and +propagate the contents of its contributor version. + +In the following three paragraphs, a "patent license" is any express +agreement or commitment, however denominated, not to enforce a patent +(such as an express permission to practice a patent or covenant not to +sue for patent infringement). To "grant" such a patent license to a +party means to make such an agreement or commitment not to enforce a +patent against the party. + +If you convey a covered work, knowingly relying on a patent license, +and the Corresponding Source of the work is not available for anyone +to copy, free of charge and under the terms of this License, through a +publicly available network server or other readily accessible means, +then you must either (1) cause the Corresponding Source to be so +available, or (2) arrange to deprive yourself of the benefit of the +patent license for this particular work, or (3) arrange, in a manner +consistent with the requirements of this License, to extend the patent +license to downstream recipients. "Knowingly relying" means you have +actual knowledge that, but for the patent license, your conveying the +covered work in a country, or your recipient's use of the covered work +in a country, would infringe one or more identifiable patents in that +country that you have reason to believe are valid. + +If, pursuant to or in connection with a single transaction or +arrangement, you convey, or propagate by procuring conveyance of, a +covered work, and grant a patent license to some of the parties +receiving the covered work authorizing them to use, propagate, modify +or convey a specific copy of the covered work, then the patent license +you grant is automatically extended to all recipients of the covered +work and works based on it. + +A patent license is "discriminatory" if it does not include within the +scope of its coverage, prohibits the exercise of, or is conditioned on +the non-exercise of one or more of the rights that are specifically +granted under this License. You may not convey a covered work if you +are a party to an arrangement with a third party that is in the +business of distributing software, under which you make payment to the +third party based on the extent of your activity of conveying the +work, and under which the third party grants, to any of the parties +who would receive the covered work from you, a discriminatory patent +license (a) in connection with copies of the covered work conveyed by +you (or copies made from those copies), or (b) primarily for and in +connection with specific products or compilations that contain the +covered work, unless you entered into that arrangement, or that patent +license was granted, prior to 28 March 2007. + +Nothing in this License shall be construed as excluding or limiting +any implied license or other defenses to infringement that may +otherwise be available to you under applicable patent law. + +#### 12. No Surrender of Others' Freedom. + +If conditions are imposed on you (whether by court order, agreement or +otherwise) that contradict the conditions of this License, they do not +excuse you from the conditions of this License. If you cannot convey a +covered work so as to satisfy simultaneously your obligations under +this License and any other pertinent obligations, then as a +consequence you may not convey it at all. For example, if you agree to +terms that obligate you to collect a royalty for further conveying +from those to whom you convey the Program, the only way you could +satisfy both those terms and this License would be to refrain entirely +from conveying the Program. + +#### 13. Use with the GNU Affero General Public License. + +Notwithstanding any other provision of this License, you have +permission to link or combine any covered work with a work licensed +under version 3 of the GNU Affero General Public License into a single +combined work, and to convey the resulting work. The terms of this +License will continue to apply to the part which is the covered work, +but the special requirements of the GNU Affero General Public License, +section 13, concerning interaction through a network will apply to the +combination as such. + +#### 14. Revised Versions of this License. + +The Free Software Foundation may publish revised and/or new versions +of the GNU General Public License from time to time. Such new versions +will be similar in spirit to the present version, but may differ in +detail to address new problems or concerns. + +Each version is given a distinguishing version number. If the Program +specifies that a certain numbered version of the GNU General Public +License "or any later version" applies to it, you have the option of +following the terms and conditions either of that numbered version or +of any later version published by the Free Software Foundation. If the +Program does not specify a version number of the GNU General Public +License, you may choose any version ever published by the Free +Software Foundation. + +If the Program specifies that a proxy can decide which future versions +of the GNU General Public License can be used, that proxy's public +statement of acceptance of a version permanently authorizes you to +choose that version for the Program. + +Later license versions may give you additional or different +permissions. However, no additional obligations are imposed on any +author or copyright holder as a result of your choosing to follow a +later version. + +#### 15. Disclaimer of Warranty. + +THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY +APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT +HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT +WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT +LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR +A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND +PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE +DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR +CORRECTION. + +#### 16. Limitation of Liability. + +IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING +WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR +CONVEYS THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, +INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES +ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT +NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR +LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM +TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER +PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. + +#### 17. Interpretation of Sections 15 and 16. + +If the disclaimer of warranty and limitation of liability provided +above cannot be given local legal effect according to their terms, +reviewing courts shall apply local law that most closely approximates +an absolute waiver of all civil liability in connection with the +Program, unless a warranty or assumption of liability accompanies a +copy of the Program in return for a fee. + +END OF TERMS AND CONDITIONS + +### How to Apply These Terms to Your New Programs + +If you develop a new program, and you want it to be of the greatest +possible use to the public, the best way to achieve this is to make it +free software which everyone can redistribute and change under these +terms. + +To do so, attach the following notices to the program. It is safest to +attach them to the start of each source file to most effectively state +the exclusion of warranty; and each file should have at least the +"copyright" line and a pointer to where the full notice is found. + + + Copyright (C) + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see . + +Also add information on how to contact you by electronic and paper +mail. + +If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + Copyright (C) + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands \`show w' and \`show c' should show the +appropriate parts of the General Public License. Of course, your +program's commands might be different; for a GUI interface, you would +use an "about box". + +You should also get your employer (if you work as a programmer) or +school, if any, to sign a "copyright disclaimer" for the program, if +necessary. For more information on this, and how to apply and follow +the GNU GPL, see . + +The GNU General Public License does not permit incorporating your +program into proprietary programs. If your program is a subroutine +library, you may consider it more useful to permit linking proprietary +applications with the library. If this is what you want to do, use the +GNU Lesser General Public License instead of this License. But first, +please read . diff --git a/checklist.yml b/checklist.yml new file mode 100644 index 0000000..2b728d9 --- /dev/null +++ b/checklist.yml @@ -0,0 +1,5 @@ +description: Configuration file for checklist::check_pkg() +package: yes +allowed: + warnings: [] + notes: [] diff --git a/codecov.yml b/codecov.yml new file mode 100644 index 0000000..2938b0e --- /dev/null +++ b/codecov.yml @@ -0,0 +1,17 @@ +comment: true + +coverage: + precision: 2 + round: down + range: "70...100" + status: + project: + default: + target: auto + threshold: 1% + informational: true + patch: + default: + target: auto + threshold: 1% + informational: true From 4837f4758669cfbb8f5b328ca22e8ff79eec5809 Mon Sep 17 00:00:00 2001 From: Thierry Onkelinx Date: Wed, 12 Aug 2020 18:03:39 +0200 Subject: [PATCH 04/13] Remove Travis and AppVeyor settings --- .travis.yml | 71 ---------------------------------------------------- README.md | 2 -- appveyor.yml | 55 ---------------------------------------- tic.R | 15 ----------- 4 files changed, 143 deletions(-) delete mode 100644 .travis.yml delete mode 100644 appveyor.yml delete mode 100644 tic.R diff --git a/.travis.yml b/.travis.yml deleted file mode 100644 index 7284610..0000000 --- a/.travis.yml +++ /dev/null @@ -1,71 +0,0 @@ -# R for travis: see documentation at https://docs.travis-ci.com/user/languages/r -# Default configuration for use with tic package -# Usually you shouldn't need to change the first part of the file - -# DO NOT CHANGE THE CODE BELOW -before_install: R -q -e 'install.packages(c("remotes", "curl")); remotes::install_github("ropenscilabs/tic"); tic::prepare_all_stages(); tic::before_install()' -install: R -q -e 'tic::install()' -after_install: R -q -e 'tic::after_install()' -before_script: R -q -e 'tic::before_script()' -script: R -q -e 'tic::script()' -after_success: R -q -e 'tic::after_success()' -after_failure: R -q -e 'tic::after_failure()' -before_deploy: R -q -e 'tic::before_deploy()' -deploy: - provider: script - script: R -q -e 'tic::deploy()' - on: - branch: master - dist: xenial - condition: - - $TRAVIS_PULL_REQUEST = false - - $TRAVIS_EVENT_TYPE != cron - - $TRAVIS_R_VERSION_STRING = release -after_deploy: R -q -e 'tic::after_deploy()' -after_script: R -q -e 'tic::after_script()' -# DO NOT CHANGE THE CODE ABOVE - -# Custom parts: - -# Header -language: r -latex: false -matrix: - include: - - dist: trusty - r: oldrel - addons: - apt: - packages: - - libgit2-dev - - dist: xenial - r: release - addons: - apt: - packages: - - libgit2-dev - - dist: xenial - r: devel - addons: - apt: - packages: - - libgit2-dev - - os: osx - r: release - brew_packages: openssl -sudo: false -cache: packages - -#env -env: - global: - - _R_CHECK_FORCE_SUGGESTS_=false - - MAKEFLAGS="-j 2" - -notifications: - email: - on_success: change - on_failure: change - -#services -services: diff --git a/README.md b/README.md index 019b1a9..d3a83d7 100644 --- a/README.md +++ b/README.md @@ -9,8 +9,6 @@ [![Licence](https://img.shields.io/badge/licence-GPL--3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0.en.html) [![minimal R version](https://img.shields.io/badge/R%3E%3D-3.5.0-6666ff.svg)](https://cran.r-project.org/) [![DOI](https://zenodo.org/badge/147685405.svg)](https://zenodo.org/badge/latestdoi/147685405) -[![Travis-CI Build Status](https://travis-ci.org/ropensci/git2rdata.svg?branch=master)](https://travis-ci.org/ropensci/git2rdata) -[![AppVeyor Build status](https://ci.appveyor.com/api/projects/status/cfbjb835fqb3dc7m/branch/master?svg=true)](https://ci.appveyor.com/project/ThierryO/git2rdata-n60yg/branch/master) [![codecov](https://codecov.io/gh/ropensci/git2rdata/branch/master/graph/badge.svg)](https://codecov.io/gh/ropensci/git2rdata) ![GitHub forks](https://img.shields.io/github/forks/ropensci/git2rdata.svg?style=social) ![GitHub stars](https://img.shields.io/github/stars/ropensci/git2rdata.svg?style=social) diff --git a/appveyor.yml b/appveyor.yml deleted file mode 100644 index 45d9160..0000000 --- a/appveyor.yml +++ /dev/null @@ -1,55 +0,0 @@ -# DO NOT CHANGE the "init" and "install" sections below - -# branches to build -branches: - # blacklist - except: - - gh-pages - -# Download script file from GitHub -init: - ps: | - $ErrorActionPreference = "Stop" - Invoke-WebRequest http://raw.github.com/krlmlr/r-appveyor/master/scripts/appveyor-tool.ps1 -OutFile "..\appveyor-tool.ps1" - Import-Module '..\appveyor-tool.ps1' -install: - ps: Bootstrap - -cache: - - C:\RLibrary - -# Adapt as necessary starting from here - -build_script: - - travis-tool.sh install_deps - -test_script: - - travis-tool.sh run_tests - -on_failure: - - 7z a failure.zip *.Rcheck\* - - appveyor PushArtifact failure.zip - -environment: - GITHUB_PAT: - secure: VXO22OHLkl4YhVIomSMwCZyOTx03Xf2WICaVng9xH7gISlAg8a+qrt1DtFtk8sK5 - PKGTYPE: 'win.binary' - -artifacts: - - path: '*.Rcheck\**\*.log' - name: Logs - - - path: '*.Rcheck\**\*.out' - name: Logs - - - path: '*.Rcheck\**\*.fail' - name: Logs - - - path: '*.Rcheck\**\*.Rout' - name: Logs - - - path: '\*_*.tar.gz' - name: Bits - - - path: '\*_*.zip' - name: Bits diff --git a/tic.R b/tic.R deleted file mode 100644 index 9c703ec..0000000 --- a/tic.R +++ /dev/null @@ -1,15 +0,0 @@ -add_package_checks() - -if (Sys.getenv("id_rsa") != "" && inherits(ci(), "TravisCI")) { - # pkgdown documentation can be built optionally. Other example criteria: - # - `inherits(ci(), "TravisCI")`: Only for Travis CI - # - `ci()$is_tag()`: Only for tags, not for branches - # - `Sys.getenv("BUILD_PKGDOWN") != ""`: If the env var "BUILD_PKGDOWN" is set - # - `Sys.getenv("TRAVIS_EVENT_TYPE") == "cron"`: Only for Travis cron jobs - get_stage("before_deploy") %>% - add_step(step_setup_ssh()) - - get_stage("deploy") %>% - add_step(step_build_pkgdown()) %>% - add_step(step_push_deploy(path = "docs", branch = "gh-pages")) -} From 1b626611bba69a18ec8a71f1f5380f61a81d7925 Mon Sep 17 00:00:00 2001 From: Thierry Onkelinx Date: Wed, 12 Aug 2020 18:12:26 +0200 Subject: [PATCH 05/13] Fix linter --- R/utils.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/utils.R b/R/utils.R index bc4b7e1..b93e3a5 100644 --- a/R/utils.R +++ b/R/utils.R @@ -2,6 +2,6 @@ # gramr is avaible from https://github.com/ropenscilabs/gramr release_questions <- function() { # nocov start c( - 'Did you ran `gramr::check_project(exclude_chunks = TRUE)`' + "Did you ran `gramr::check_project(exclude_chunks = TRUE)`" ) } # nocov end From 160a8fe310f55cf6a250c3ea2b724bfb7d537c68 Mon Sep 17 00:00:00 2001 From: Thierry Onkelinx Date: Thu, 13 Aug 2020 09:09:26 +0200 Subject: [PATCH 06/13] Update NEWS.md to requirements of checklist::check_package() --- NEWS.md | 263 +++++++++++++++++++++++++++++--------------------------- 1 file changed, 138 insertions(+), 125 deletions(-) diff --git a/NEWS.md b/NEWS.md index 453c8e6..8fee349 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,132 +1,145 @@ -git2rdata 0.2.1 (2020-02-03) -================================= +# git2rdata 0.2.2 -### Bugfixes +* Use the [checklist](https://inbo.github.io/checklist) package for CI. - * Explicitly use the `stringsAsFactors` of `data.frame()` in the examples and - unit tests if the dataframe contains characters. The upcoming change in - default value of `stringsAsFactors` requires this change. See - https://developer.r-project.org/Blog/public/2020/02/16/stringsasfactors/index.html +# git2rdata 0.2.1 -git2rdata 0.2.0 (2019-11-08) -================================= +## Bugfixes -### BREAKING FEATURES +* Explicitly use the `stringsAsFactors` of `data.frame()` in the examples and + unit tests if the dataframe contains characters. + The upcoming change in default value of `stringsAsFactors` requires this + change. + See https://developer.r-project.org/Blog/public/2020/02/16/stringsasfactors/index.html - * Calculation of data hash has changed (#53). - You must use `upgrade_data()` to read data stored by an older version. - * `is_git2rdata()` and `upgrade_data()` do not test equality in data hashes any more (but `read_vc()` still does). - * `write_vc()` and `read_vc()` fail when `file` is a location outside of `root` (#50). - * Reordering factor levels requires `strict = TRUE`. - -### Bugfixes +# git2rdata 0.2.0 - * Linux and Windows machines now generated the same data hash (#49). - -### NEW FEATURES +## BREAKING FEATURES - * Internal sorting uses the "C" locale, regardless of the current locale. - * `read_vc()` reads older stored in an older version (#44). - When the version is too old, it prompts to `upgrade_data()`. - * Improve `warnings()` and `error()` messages. - * Use vector version of logo. - -git2rdata 0.1 (2019-06-04) -============================ - - * Transfer to rOpenSci. - * Use new logo (@peterdesmet, #37). - * Add estimate of upper bound of the number of commits. - -git2rdata 0.0.5 (2019-05-21) -============================ - - * `upgrade_data()` uses the same order of the metadata as `write_vc()`. - -git2rdata 0.0.4 (2019-05-16) -============================ - -### BREAKING FEATURES - - * `write_vc()` stores the `git2rdata` version number to the metadata. Use `upgrade_data()` to update existing data. - -### NEW FEATURES - - * `read_vc()` checks the meta data hash. A mismatch results in an error. - * The meta data gains a data hash. A mismatch throws a warning when reading the object. This tolerates updating the data by other software, while informing the user that such change occurred. - * `is_git2rmeta()` validates metadata. - * `list_data()` lists files with valid metadata. - * `rm_data()` and `prune_meta()` remove files with valid metadata. - They don't touch `tsv` file without metadata or `yml` files not associated with `git2rdata`. - * Files with invalid metadata yield a warning with `list_data()`, `rm_data()` and `prune_meta()`. - -### Bugfixes - - * `write_vc()` and `relabel()` handle empty strings (`''`) in characters and factors (#24). - * `read_vc()` no longer treats `#` as a comment character. - * `read_vc()` handles non ASCII characters on Windows. - -### Other changes - - * Use a faster algorithm to detect duplicates (suggestion by @brodieG). - * Improve documentation. - * Fix typo's in documentation, vignettes and README. - * Add a rOpenSci review badge to the README. - * The README mentions on upper bound on the size of dataframes. - * Set lifecycle to "maturing" and repo status to "active". - * The functions handle `root` containing regex expressions. - * Rework `vignette("workflow", package = "git2rdata")`. - * Update timings in `vignette("efficiency", package = "git2rdata")` - * Minor tweaks in `vignette("plain_text", package = "git2rdata")` - -git2rdata 0.0.3 (2019-03-12) -============================ - - * Fix typo's in documentation, vignettes and README. - -git2rdata 0.0.2 (2019-02-26) -============================ - -### BREAKING CHANGES - - * `meta()` appends the metadata as a list to the objects rather than in YAML format. - * `yaml::write_yaml()` writes the metadata list in YAML format. - * `write_vc()` now uses the 'strict' argument instead of 'override'. - * `rm_data()` removes the data files. Use `prune_meta()` to remove left-over metadata files (#9). - -### NEW FEATURES - - * Vignette on [efficiency](https://ropensci.github.io/git2rdata/articles/efficiency.html) added (#2). - * Three separate vignettes instead of one large vignette. - * Focus on the [plain text format](https://ropensci.github.io/git2rdata/articles/plain_text.html). - * Focus on [version control](https://ropensci.github.io/git2rdata/articles/version_control.html). - * Focus on [workflows](https://ropensci.github.io/git2rdata/articles/workflow.html). - * S3 methods replace the old S4 methods (#8). - * Optimized factors use stable indices. Adding or removing levels result in smaller diffs (#13). - * Use `relabel()` to alter factor levels without changing their index (#13). - * `write.table()` stores the raw data instead of `readr::write_tsv()` (#7). This avoids the `readr` dependency. - * `write_vc()` and `read_vc()` use the current working directory as default root (#6, @florisvdh). - * The user can specify a string to code missing values (default = `NA`). This allows the storage of the character string `"NA"`. - * `write_vc()` returns a list of issues which potentially result in large diffs. - * `list_data()` returns a vector with dataframes in the repository. - -### Other changes - - * `write_vc()` allows to use a custom `NA` string. - * Each helpfile contains a working example (#11). - * README updated (#12). - * Updated the rationale with links to the vignettes. - * `git2rdata` has a hexagon sticker logo. - * Add the [![DOI](https://zenodo.org/badge/147685405.svg)](https://zenodo.org/badge/latestdoi/147685405). - * The installation instructions use `remotes` and build the vignettes. - * We removed `auto_commit()` because of limited extra functionality over `git2r::commit()`. - -git2rdata 0.0.1 (2018-11-12) -============================ - -### NEW FEATURES - - * Use `readr` to write and read plain text files. - * Allow storage of strings with "NA" or special characters. - * Handle ordered factors. - * Stop handling complex numbers. +* Calculation of data hash has changed (#53). + You must use `upgrade_data()` to read data stored by an older version. +* `is_git2rdata()` and `upgrade_data()` do not test equality in data hashes + anymore (but `read_vc()` still does). +* `write_vc()` and `read_vc()` fail when `file` is a location outside of `root` + (#50). +* Reordering factor levels requires `strict = TRUE`. + +## Bugfixes + +* Linux and Windows machines now generated the same data hash (#49). + +## NEW FEATURES + +* Internal sorting uses the "C" locale, regardless of the current locale. +* `read_vc()` reads older stored in an older version (#44). + When the version is too old, it prompts to `upgrade_data()`. +* Improve `warnings()` and `error()` messages. +* Use vector version of logo. + +# git2rdata 0.1 + +* Transfer to rOpenSci. +* Use new logo (@peterdesmet, #37). +* Add estimate of upper bound of the number of commits. + +# git2rdata 0.0.5 + +* `upgrade_data()` uses the same order of the metadata as `write_vc()`. + +# git2rdata 0.0.4 + +## BREAKING FEATURES + +* `write_vc()` stores the `git2rdata` version number to the metadata. + Use `upgrade_data()` to update existing data. + +## NEW FEATURES + +* `read_vc()` checks the meta data hash. A mismatch results in an error. +* The meta data gains a data hash. + A mismatch throws a warning when reading the object. + This tolerates updating the data by other software, while informing the user + that such change occurred. +* `is_git2rmeta()` validates metadata. +* `list_data()` lists files with valid metadata. +* `rm_data()` and `prune_meta()` remove files with valid metadata. + They don't touch `tsv` file without metadata or `yml` files not associated + with `git2rdata`. +* Files with invalid metadata yield a warning with `list_data()`, `rm_data()` + and `prune_meta()`. + +## Bugfixes + +* `write_vc()` and `relabel()` handle empty strings (`''`) in characters and + factors (#24). +* `read_vc()` no longer treats `#` as a comment character. +* `read_vc()` handles non ASCII characters on Windows. + +## Other changes + +* Use a faster algorithm to detect duplicates (suggestion by @brodieG). +* Improve documentation. +* Fix typo's in documentation, vignettes and README. +* Add a rOpenSci review badge to the README. +* The README mentions on upper bound on the size of dataframes. +* Set lifecycle to "maturing" and repo status to "active". +* The functions handle `root` containing regex expressions. +* Rework `vignette("workflow", package = "git2rdata")`. +* Update timings in `vignette("efficiency", package = "git2rdata")` +* Minor tweaks in `vignette("plain_text", package = "git2rdata")` + +# git2rdata 0.0.3 + +* Fix typo's in documentation, vignettes and README. + +# git2rdata 0.0.2 + +## BREAKING CHANGES + +* `meta()` appends the metadata as a list to the objects rather than in YAML + format. +* `yaml::write_yaml()` writes the metadata list in YAML format. +* `write_vc()` now uses the 'strict' argument instead of 'override'. +* `rm_data()` removes the data files. Use `prune_meta()` to remove left-over + metadata files (#9). + +## NEW FEATURES + +* Vignette on [efficiency](https://ropensci.github.io/git2rdata/articles/efficiency.html) added (#2). +* Three separate vignettes instead of one large vignette. + * Focus on the [plain text format](https://ropensci.github.io/git2rdata/articles/plain_text.html). + * Focus on [version control](https://ropensci.github.io/git2rdata/articles/version_control.html). + * Focus on [workflows](https://ropensci.github.io/git2rdata/articles/workflow.html). +* S3 methods replace the old S4 methods (#8). +* Optimized factors use stable indices. Adding or removing levels result in + smaller diffs (#13). +* Use `relabel()` to alter factor levels without changing their index (#13). +* `write.table()` stores the raw data instead of `readr::write_tsv()` (#7). + This avoids the `readr` dependency. +* `write_vc()` and `read_vc()` use the current working directory as default root + (#6, @florisvdh). +* The user can specify a string to code missing values (default = `NA`). + This allows the storage of the character string `"NA"`. +* `write_vc()` returns a list of issues which potentially result in large diffs. +* `list_data()` returns a vector with dataframes in the repository. + +## Other changes + +* `write_vc()` allows to use a custom `NA` string. +* Each helpfile contains a working example (#11). +* README updated (#12). + * Updated the rationale with links to the vignettes. + * `git2rdata` has a hexagon sticker logo. + * Add the [![DOI](https://zenodo.org/badge/147685405.svg)](https://zenodo.org/badge/latestdoi/147685405). + * The installation instructions use `remotes` and build the vignettes. +* We removed `auto_commit()` because of limited extra functionality over + `git2r::commit()`. + +# git2rdata 0.0.1 + +## NEW FEATURES + +* Use `readr` to write and read plain text files. +* Allow storage of strings with "NA" or special characters. +* Handle ordered factors. +* Stop handling complex numbers. From e1909b40ea97e8620bef876056d48d25e59ec743 Mon Sep 17 00:00:00 2001 From: Thierry Onkelinx Date: Thu, 13 Aug 2020 10:29:19 +0200 Subject: [PATCH 07/13] fix filenames --- DESCRIPTION | 2 +- R/{git2rdata-package.R => git2rdata_package.R} | 0 man/git2rdata-package.Rd | 5 +++-- 3 files changed, 4 insertions(+), 3 deletions(-) rename R/{git2rdata-package.R => git2rdata_package.R} (100%) diff --git a/DESCRIPTION b/DESCRIPTION index fc422c4..e453c04 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -55,7 +55,7 @@ RoxygenNote: 7.1.1 Collate: 'clean_data_path.R' 'datahash.R' - 'git2rdata-package.R' + 'git2rdata_package.R' 'write_vc.R' 'is_git2rdata.R' 'is_git2rmeta.R' diff --git a/R/git2rdata-package.R b/R/git2rdata_package.R similarity index 100% rename from R/git2rdata-package.R rename to R/git2rdata_package.R diff --git a/man/git2rdata-package.Rd b/man/git2rdata-package.Rd index f1dc2b7..2f1001c 100644 --- a/man/git2rdata-package.Rd +++ b/man/git2rdata-package.Rd @@ -1,12 +1,13 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/git2rdata-package.R +% Please edit documentation in R/git2rdata_package.R \docType{package} \name{git2rdata-package} \alias{git2rdata} \alias{git2rdata-package} \title{git2rdata: Store and Retrieve Data.frames in a Git Repository} \description{ -Make versioning of data.frame easy and efficient using git repositories. +Make versioning of data.frame easy and efficient using git + repositories. } \seealso{ Useful links: From fe8a49994502d285891d5bfe3db34cc7c0b3e8fa Mon Sep 17 00:00:00 2001 From: Thierry Onkelinx Date: Thu, 13 Aug 2020 10:31:36 +0200 Subject: [PATCH 08/13] Update .Rbuildignore --- .Rbuildignore | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.Rbuildignore b/.Rbuildignore index 423d7a1..c1ec89c 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -1,16 +1,16 @@ ^\.github$ ^\.Rproj\.user$ -^\.travis\.yml$ ^_pkgdown.yml$ -^appveyor\.yml$ ^codemeta\.json$ ^.zenodo\.json$ ^docs$ ^man-roxygen$ ^pkgdown$ ^sticker$ -^tic\.R$ ^.*\.Rproj$ ^cran-comments\.md$ ^CRAN-RELEASE$ ^\.httr-oauth$ +^checklist.yml$ +^codecov.yml$ +^LICENSE.md$ From 3b42f2091bfd7a57fadf8d001bce303206072659 Mon Sep 17 00:00:00 2001 From: Thierry Onkelinx Date: Thu, 13 Aug 2020 13:00:02 +0200 Subject: [PATCH 09/13] Update filenames to naming conventions --- R/is_git2rdata.R | 2 +- R/is_git2rmeta.R | 2 +- R/list_data.R | 2 +- R/prune.R | 4 ++-- R/read_vc.R | 2 +- R/write_vc.R | 2 +- _pkgdown.yml | 2 +- man-roxygen/{example-io.R => example_io.R} | 0 .../{example-isgit2r.R => example_isgit2r.R} | 0 man-roxygen/{example-prune.R => example_prune.R} | 1 - man/figures/{logo_en.png => logo-en.png} | Bin 11 files changed, 8 insertions(+), 9 deletions(-) rename man-roxygen/{example-io.R => example_io.R} (100%) rename man-roxygen/{example-isgit2r.R => example_isgit2r.R} (100%) rename man-roxygen/{example-prune.R => example_prune.R} (99%) rename man/figures/{logo_en.png => logo-en.png} (100%) diff --git a/R/is_git2rdata.R b/R/is_git2rdata.R index 8ec1779..d505796 100644 --- a/R/is_git2rdata.R +++ b/R/is_git2rdata.R @@ -8,7 +8,7 @@ #' @rdname is_git2rdata #' @export #' @family internal -#' @template example-isgit2r +#' @template example_isgit2r is_git2rdata <- function(file, root = ".", message = c("none", "warning", "error")) { UseMethod("is_git2rdata", root) diff --git a/R/is_git2rmeta.R b/R/is_git2rmeta.R index 7066b3f..d350e82 100644 --- a/R/is_git2rmeta.R +++ b/R/is_git2rmeta.R @@ -14,7 +14,7 @@ #' @rdname is_git2rmeta #' @export #' @family internal -#' @template example-isgit2r +#' @template example_isgit2r is_git2rmeta <- function(file, root = ".", message = c("none", "warning", "error")) { UseMethod("is_git2rmeta", root) diff --git a/R/list_data.R b/R/list_data.R index 2a45602..5dab7ae 100644 --- a/R/list_data.R +++ b/R/list_data.R @@ -8,7 +8,7 @@ #' @param path relative `path` from the `root`. Defaults to the `root` #' @inheritParams base::list.files #' @export -#' @template example-prune +#' @template example_prune #' @return A character vector of git2rdata object names, including their #' relative path. #' @family storage diff --git a/R/prune.R b/R/prune.R index e60c239..f99d272 100644 --- a/R/prune.R +++ b/R/prune.R @@ -19,7 +19,7 @@ #' @inheritParams write_vc #' @export #' @family storage -#' @template example-prune +#' @template example_prune rm_data <- function( root = ".", path = NULL, recursive = TRUE, ... ) { @@ -113,7 +113,7 @@ rm_data.git_repository <- function( #' @inheritParams write_vc #' @export #' @family storage -#' @template example-prune +#' @template example_prune prune_meta <- function( root = ".", path = NULL, recursive = TRUE, ... ) { diff --git a/R/read_vc.R b/R/read_vc.R index 618b830..aac44b6 100644 --- a/R/read_vc.R +++ b/R/read_vc.R @@ -15,7 +15,7 @@ #' @rdname read_vc #' @export #' @family storage -#' @template example-io +#' @template example_io read_vc <- function(file, root = ".") { UseMethod("read_vc", root) } diff --git a/R/write_vc.R b/R/write_vc.R index 40be4a7..47f987e 100644 --- a/R/write_vc.R +++ b/R/write_vc.R @@ -29,7 +29,7 @@ #' contain the hashes of the files. #' @export #' @family storage -#' @template example-io +#' @template example_io #' @note `..generic` is a reserved name for the metadata and is a forbidden #' column name in a `data.frame`. write_vc <- function( diff --git a/_pkgdown.yml b/_pkgdown.yml index 4629d14..f81a74f 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -43,4 +43,4 @@ authors: href: "https://www.muscardinus.be" Research Institute for Nature and Forest: href: "https://www.inbo.be/en" - html: "" + html: "" diff --git a/man-roxygen/example-io.R b/man-roxygen/example_io.R similarity index 100% rename from man-roxygen/example-io.R rename to man-roxygen/example_io.R diff --git a/man-roxygen/example-isgit2r.R b/man-roxygen/example_isgit2r.R similarity index 100% rename from man-roxygen/example-isgit2r.R rename to man-roxygen/example_isgit2r.R diff --git a/man-roxygen/example-prune.R b/man-roxygen/example_prune.R similarity index 99% rename from man-roxygen/example-prune.R rename to man-roxygen/example_prune.R index d8fcba8..8046fc7 100644 --- a/man-roxygen/example-prune.R +++ b/man-roxygen/example_prune.R @@ -72,4 +72,3 @@ #' rev(list.files(repo_path, full.names = TRUE, recursive = TRUE, #' include.dirs = TRUE, all.files = TRUE)), #' repo_path) - diff --git a/man/figures/logo_en.png b/man/figures/logo-en.png similarity index 100% rename from man/figures/logo_en.png rename to man/figures/logo-en.png From 5533905e8c219488e576a95f58f1a8ef7aec1fb5 Mon Sep 17 00:00:00 2001 From: Thierry Onkelinx Date: Sat, 15 Aug 2020 12:27:44 +0200 Subject: [PATCH 10/13] rerender documentation --- man/rm_data.Rd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/man/rm_data.Rd b/man/rm_data.Rd index 6478e66..7c31dd1 100644 --- a/man/rm_data.Rd +++ b/man/rm_data.Rd @@ -33,7 +33,7 @@ is relative to \code{root}.} the git history and unchanged since the last commit. \code{modified} are files in the git history and changed since the last commit. \code{ignored} refers to file listed in a \code{.gitignore} file. Selecting \code{modified} will remove both -\code{unmodified} and \code{modified} data files. Selecting \code{ìgnored} will remove +\code{unmodified} and \code{modified} data files. Selecting \verb{ìgnored} will remove \code{unmodified}, \code{modified} and \code{ignored} data files. \code{all} refers to all visible data files, including \code{untracked} files.} } From 7a95f7694910da4d3f8fc58ae4edb17f3faf7614 Mon Sep 17 00:00:00 2001 From: Thierry Onkelinx Date: Sat, 15 Aug 2020 15:16:22 +0200 Subject: [PATCH 11/13] update codemeta.json --- codemeta.json | 49 +++++++++++++++++++++++-------------------------- 1 file changed, 23 insertions(+), 26 deletions(-) diff --git a/codemeta.json b/codemeta.json index 048c4fb..34c1dd6 100644 --- a/codemeta.json +++ b/codemeta.json @@ -5,7 +5,7 @@ ], "@type": "SoftwareSourceCode", "identifier": "git2rdata", - "description": "Make versioning of data.frame easy and efficient using git repositories.", + "description": "Make versioning of data.frame easy and efficient using git\n repositories.", "name": "git2rdata: Store and Retrieve Data.frames in a Git Repository", "codeRepository": "https://github.com/ropensci/git2rdata", "relatedLink": [ @@ -14,14 +14,13 @@ ], "issueTracker": "https://github.com/ropensci/git2rdata/issues", "license": "https://spdx.org/licenses/GPL-3.0", - "version": "0.2.1", + "version": "0.2.2", "programmingLanguage": { "@type": "ComputerLanguage", "name": "R", - "version": "3.6.2", "url": "https://r-project.org" }, - "runtimePlatform": "R version 3.6.2 (2019-12-12)", + "runtimePlatform": "R version 4.0.2 (2020-06-22)", "author": [ { "@type": "Person", @@ -78,18 +77,6 @@ } ], "softwareSuggestions": [ - { - "@type": "SoftwareApplication", - "identifier": "spelling", - "name": "spelling", - "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=spelling" - }, { "@type": "SoftwareApplication", "identifier": "ggplot2", @@ -138,6 +125,18 @@ }, "sameAs": "https://CRAN.R-project.org/package=rmarkdown" }, + { + "@type": "SoftwareApplication", + "identifier": "spelling", + "name": "spelling", + "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=spelling" + }, { "@type": "SoftwareApplication", "identifier": "testthat", @@ -203,16 +202,9 @@ ], "releaseNotes": "https://github.com/ropensci/git2rdata/blob/master/NEWS.md", "readme": "https://github.com/ropensci/git2rdata/blob/master/README.md", - "fileSize": "341.883KB", - "contIntegration": [ - "https://travis-ci.org/inbo/git2rdata", - "https://ci.appveyor.com/project/ThierryO/git2rdata/branch/master", - "https://codecov.io/gh/inbo/git2rdata" - ], - "developmentStatus": [ - "https://www.repostatus.org/#active", - "https://www.tidyverse.org/lifecycle/#maturing" - ], + "fileSize": "1762.61KB", + "contIntegration": "https://codecov.io/gh/ropensci/git2rdata", + "developmentStatus": ["https://www.repostatus.org/#active", "https://www.tidyverse.org/lifecycle/#maturing"], "keywords": [ "r", "rstats", @@ -225,5 +217,10 @@ "@type": "Organization", "name": "Comprehensive R Archive Network (CRAN)", "url": "https://cran.r-project.org" + }, + "review": { + "@type": "Review", + "url": "https://github.com/ropensci/software-review/issues/263", + "provider": "https://ropensci.org" } } From 267552d3258654c610df0d04e4ccd8f86bdcb77f Mon Sep 17 00:00:00 2001 From: Thierry Onkelinx Date: Sun, 16 Aug 2020 22:39:43 +0200 Subject: [PATCH 12/13] update codemeta.json --- .Rbuildignore | 13 ++++++------- codemeta.json | 2 +- 2 files changed, 7 insertions(+), 8 deletions(-) diff --git a/.Rbuildignore b/.Rbuildignore index c1ec89c..af21982 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -1,16 +1,15 @@ -^\.github$ +^.*\.Rproj$ ^\.Rproj\.user$ -^_pkgdown.yml$ +^\.github$ ^codemeta\.json$ ^.zenodo\.json$ -^docs$ ^man-roxygen$ ^pkgdown$ -^sticker$ -^.*\.Rproj$ +^_pkgdown.yml$ +^docs$ ^cran-comments\.md$ -^CRAN-RELEASE$ -^\.httr-oauth$ +# checklist ^checklist.yml$ ^codecov.yml$ ^LICENSE.md$ +^\.httr-oauth$ diff --git a/codemeta.json b/codemeta.json index 34c1dd6..71ff4c5 100644 --- a/codemeta.json +++ b/codemeta.json @@ -202,7 +202,7 @@ ], "releaseNotes": "https://github.com/ropensci/git2rdata/blob/master/NEWS.md", "readme": "https://github.com/ropensci/git2rdata/blob/master/README.md", - "fileSize": "1762.61KB", + "fileSize": "578.382KB", "contIntegration": "https://codecov.io/gh/ropensci/git2rdata", "developmentStatus": ["https://www.repostatus.org/#active", "https://www.tidyverse.org/lifecycle/#maturing"], "keywords": [ From 24f2db9de4ab69dbfc404574774542877e3a1927 Mon Sep 17 00:00:00 2001 From: Thierry Onkelinx Date: Tue, 18 Aug 2020 21:40:26 +0200 Subject: [PATCH 13/13] Add GitHub Actions to test the package on different OSes. --- .github/workflows/check_on_different_r_os.yml | 93 +++++++++++++++++++ 1 file changed, 93 insertions(+) create mode 100644 .github/workflows/check_on_different_r_os.yml diff --git a/.github/workflows/check_on_different_r_os.yml b/.github/workflows/check_on_different_r_os.yml new file mode 100644 index 0000000..01cfc5a --- /dev/null +++ b/.github/workflows/check_on_different_r_os.yml @@ -0,0 +1,93 @@ +on: + push: + branches: + - master + pull_request: + branches: + - master + +name: R-CMD-check + +jobs: + R-CMD-check: + runs-on: ${{ matrix.config.os }} + + name: ${{ matrix.config.os }} (${{ matrix.config.r }}) + + strategy: + fail-fast: false + matrix: + config: + - {os: macOS-latest, r: 'devel'} + - {os: macOS-latest, r: 'release'} + - {os: windows-latest, r: 'release'} + - {os: ubuntu-16.04, r: 'oldrel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} + + env: + R_REMOTES_NO_ERRORS_FROM_WARNINGS: true + RSPM: ${{ matrix.config.rspm }} + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + ORCID_TOKEN: ${{ secrets.ORCID_TOKEN }} + + steps: + - uses: actions/checkout@v2 + + - uses: r-lib/actions/setup-r@master + with: + r-version: ${{ matrix.config.r }} + + - uses: r-lib/actions/setup-pandoc@master + + - name: Query dependencies + run: | + install.packages('remotes') + saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) + writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") + shell: Rscript {0} + + - name: Cache R packages + if: runner.os != 'Windows' + uses: actions/cache@v1 + with: + path: ${{ env.R_LIBS_USER }} + key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }} + restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1- + + - name: Install system dependencies + if: runner.os == 'Linux' + env: + RHUB_PLATFORM: linux-x86_64-ubuntu-gcc + run: | + Rscript -e "remotes::install_github('r-hub/sysreqs')" + sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))") + sudo -s eval "$sysreqs" + - name: Install dependencies + run: | + remotes::install_deps(dependencies = TRUE) + remotes::install_cran("rcmdcheck") + shell: Rscript {0} + + - name: Session info + run: | + options(width = 100) + pkgs <- installed.packages()[, "Package"] + sessioninfo::session_info(pkgs, include_base = TRUE) + shell: Rscript {0} + + - name: Check + env: + _R_CHECK_CRAN_INCOMING_: false + run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check") + shell: Rscript {0} + + - name: Show testthat output + if: always() + run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true + shell: bash + + - name: Upload check results + if: failure() + uses: actions/upload-artifact@master + with: + name: ${{ runner.os }}-r${{ matrix.config.r }}-results + path: check