From 022a2af54ef0587bedd1a73d4e415abe47fc0632 Mon Sep 17 00:00:00 2001 From: luciorq Date: Fri, 8 Nov 2024 14:11:48 -0500 Subject: [PATCH] chore: add contributor --- .Rbuildignore | 2 ++ .gitignore | 1 + DESCRIPTION | 9 +++++++-- README.Rmd | 4 ++-- README.md | 10 ++++++---- justfile | 2 +- man/condathis-package.Rd | 5 +++++ 7 files changed, 24 insertions(+), 9 deletions(-) diff --git a/.Rbuildignore b/.Rbuildignore index da58cb2..74f0a33 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -17,3 +17,5 @@ ^justfile$ ^data-raw$ ^vignettes/*_files$ +^README\.Rmd$ +^README\.html$ diff --git a/.gitignore b/.gitignore index a90b932..7cc7023 100644 --- a/.gitignore +++ b/.gitignore @@ -6,3 +6,4 @@ renv renv.lock .Rprofile +README.html diff --git a/DESCRIPTION b/DESCRIPTION index f92aa89..8334744 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -4,8 +4,13 @@ Version: 0.0.6.9007 Authors@R: c( person("Lucio", "Queiroz", , "luciorqueiroz@gmail.com", role = c("aut", "cre", "cph"), - comment = c(ORCID = "0000-0002-6090-1834")) - ) + comment = c(ORCID = "0000-0002-6090-1834")), + person(given = "Claudio", + family = "Zanettini", + role = c("aut", "ctb"), + email = "claudio.zanettini@gmail.com", + comment = c(ORCID = "0000-0001-5043-8033") + )) Description: Simplifies the execution of command line tools within isolated and reproducible environments. It enables users to effortlessly manage Conda environments, diff --git a/README.Rmd b/README.Rmd index bf284ef..5a70157 100644 --- a/README.Rmd +++ b/README.Rmd @@ -123,7 +123,7 @@ rm(temp_out_dir_2) ```{r} -condathis::create_env(packages = "fastqc==0.12.1", env_name = "fastqc_env") +condathis::create_env(packages = "fastqc==0.12.1", env_name = "fastqc_env", verbose = "output") ``` Then we run the command inside the environment just created which contains a version 0.12.1 of `fastqc`. @@ -163,7 +163,7 @@ libcurlVersion() However, we can choose to use a different version of `curl` run in a different environment. Here, for example, we are installing a different version of `curl` in a separate environment, and checking the version of the newly installed `curl`. ```{r} -condathis::create_env(packages = "curl==8.10.1", env_name = "curl_env") +condathis::create_env(packages = "curl==8.10.1", env_name = "curl_env", verbose = "output") out <- condathis::run("curl", "--version", env_name = "curl_env" # environment diff --git a/README.md b/README.md index 061763c..b50e8f9 100644 --- a/README.md +++ b/README.md @@ -116,7 +116,8 @@ manages all the library dependencies of `fastqc`, making sure that they are compatible with the specific operating system. ``` r -condathis::create_env(packages = "fastqc==0.12.1", env_name = "fastqc_env") +condathis::create_env(packages = "fastqc==0.12.1", env_name = "fastqc_env", verbose = "output") +#> ! Environment fastqc_env already exists. ``` Then we run the command inside the environment just created which @@ -143,8 +144,8 @@ In the our temp dir, `fastqc`generated the output files as expected. ``` r fs::dir_ls(temp_out_dir_2) -#> /var/folders/2q/937_bkg10svdwx1x00prs9nm0000gn/T/Rtmpn2TjYr/sample1_L001_R1_001_fastqc.html -#> /var/folders/2q/937_bkg10svdwx1x00prs9nm0000gn/T/Rtmpn2TjYr/sample1_L001_R1_001_fastqc.zip +#> /var/folders/2q/937_bkg10svdwx1x00prs9nm0000gn/T/RtmpptzAZk/sample1_L001_R1_001_fastqc.html +#> /var/folders/2q/937_bkg10svdwx1x00prs9nm0000gn/T/RtmpptzAZk/sample1_L001_R1_001_fastqc.zip ``` The code that we created with `{condathis}` **uses a system CLI tool but @@ -180,7 +181,8 @@ version of `curl` in a separate environment, and checking the version of the newly installed `curl`. ``` r -condathis::create_env(packages = "curl==8.10.1", env_name = "curl_env") +condathis::create_env(packages = "curl==8.10.1", env_name = "curl_env", verbose = "output") +#> ! Environment curl_env already exists. out <- condathis::run("curl", "--version", env_name = "curl_env" # environment diff --git a/justfile b/justfile index 618d483..a07cab8 100644 --- a/justfile +++ b/justfile @@ -13,7 +13,7 @@ github_org := 'luciorq' \builtin set -euxo pipefail; R -q -e 'devtools::load_all();styler::style_pkg();'; R -q -e 'devtools::load_all();devtools::document();'; - R -q -e 'rmarkdown::render("README.Rmd", encoding = "UTF-8")'; + R -q -e 'devtools::load_all();rmarkdown::render("README.Rmd", encoding = "UTF-8")'; R -q -e 'devtools::load_all();devtools::test();'; @check: diff --git a/man/condathis-package.Rd b/man/condathis-package.Rd index 9907334..c8af482 100644 --- a/man/condathis-package.Rd +++ b/man/condathis-package.Rd @@ -19,5 +19,10 @@ Useful links: \author{ \strong{Maintainer}: Lucio Queiroz \email{luciorqueiroz@gmail.com} (\href{https://orcid.org/0000-0002-6090-1834}{ORCID}) [copyright holder] +Authors: +\itemize{ + \item Claudio Zanettini \email{claudio.zanettini@gmail.com} (\href{https://orcid.org/0000-0001-5043-8033}{ORCID}) [contributor] +} + } \keyword{internal}