{"id":30019620,"url":"https://github.com/veupathdb/study-wrangler","last_synced_at":"2026-01-29T14:12:19.627Z","repository":{"id":146804573,"uuid":"543735275","full_name":"VEuPathDB/study-wrangler","owner":"VEuPathDB","description":"Code to keep study data tidy","archived":false,"fork":false,"pushed_at":"2025-08-04T12:29:21.000Z","size":539,"stargazers_count":0,"open_issues_count":25,"forks_count":0,"subscribers_count":19,"default_branch":"main","last_synced_at":"2025-08-04T15:47:28.132Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/VEuPathDB.png","metadata":{"files":{"readme":"README.org","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2022-09-30T18:24:51.000Z","updated_at":"2025-07-28T20:51:42.000Z","dependencies_parsed_at":null,"dependency_job_id":"cb2ada39-4e1c-468f-8532-f68c6413713e","html_url":"https://github.com/VEuPathDB/study-wrangler","commit_stats":null,"previous_names":[],"tags_count":15,"template":false,"template_full_name":null,"purl":"pkg:github/VEuPathDB/study-wrangler","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/VEuPathDB%2Fstudy-wrangler","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/VEuPathDB%2Fstudy-wrangler/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/VEuPathDB%2Fstudy-wrangler/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/VEuPathDB%2Fstudy-wrangler/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/VEuPathDB","download_url":"https://codeload.github.com/VEuPathDB/study-wrangler/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/VEuPathDB%2Fstudy-wrangler/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":270831844,"owners_count":24653426,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-08-17T02:00:09.016Z","response_time":129,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2025-08-06T01:20:05.493Z","updated_at":"2026-01-07T18:11:33.044Z","avatar_url":"https://github.com/VEuPathDB.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"#+TITLE: README\n\nstudy.wranger R package for tidying data in a way compatible with VEuPathDB workflows for EDA loading.\n\n\n* Install in existing R environment or RStudio\n\n#+BEGIN_SRC R\n# Install the remotes package\ninstall.packages(\"remotes\") # if you don't already have 'remotes'\n\n# Install (or upgrade) the study.wrangler package from GitHub\nremotes::install_github(\"VEuPathDB/study-wrangler\", build_vignettes = TRUE, upgrade = FALSE)\n# And load all its functions into your namespace\nlibrary(study.wrangler)\n\n# Browse the vignettes (tutorials) in your web browser\nbrowseVignettes(\"study.wrangler\")\n\n# If your web browser doesn't open with the vignette index page, use one of these:\noptions(browser = \"xdg-open\")   # Linux\n# or\noptions(browser = \"open\")       # macOS\n# or\noptions(browser = \"C:/Program Files/Google/Chrome/Application/chrome.exe\")  # Windows\n# and then try again with \nbrowseVignettes(\"study.wrangler\")\n\n#+END_SRC\n\n** Tip: GitHub rate limiting\n\nIf you see errors like HTTP error 403 or API rate limit exceeded when installing packages from GitHub, you may be hitting the unauthenticated GitHub API limit (60 requests/hour).\n\nTo avoid this, set a GitHub Personal Access Token (PAT):\n1. Generate a token via https://github.com/settings/personal-access-tokens\n   Only the default read-only permissions to public repositories are needed.\n\n2. If you're using R from the command line (not RStudio), set your token in your shell config:\n\n   - zsh (default on most Macs): Add \n     #+BEGIN_SRC sh\n     export GITHUB_PAT=github_pat_...\n     #+END_SRC\n     to your =~/.zshrc=\n      \n   - bash: Add it to =~/.bash_profile= or =~/.bashrc=\n\n3. For RStudio, we recommend setting it in your R environment file via:\n   #+BEGIN_SRC sh\n   usethis::edit_r_environ()\n   #+END_SRC\n   Add the line\n   #+BEGIN_SRC sh\n   GITHUB_PAT=github_pat_...\n   #+END_SRC\n   Save and restart your R-session\n\n** Tip: Edit and run the vignette as a notebook\n\nTo experiment with the vignette code interactively:\n\n1. Clone the source repo:\n   #+BEGIN_SRC sh\n   git clone https://github.com/VEuPathDB/study-wrangler.git\n   #+END_SRC\n\n2. Open the =.Rmd= file in RStudio (File -\u003e Open):\n   #+BEGIN_SRC\n   study-wrangler/vignettes/cleaning-and-preparing-basics.Rmd\n   #+END_SRC\n\nYou can now run code chunks interactively and modify them/play around.\n\n\n* To build a docker image\n\n#+begin_example\ndocker build -t veupathdb/study-wrangler .\n#+end_example\n\nBuild notes:\n- add `--progress=plain` if you want to see the errors more easily\n- each `remotes::install_github()` command in the Dockerfile eats into a rate limit for anonymous users at GitHub (60 per hour!) - so if you are playing around with things you almost certainly will hit the limit\n- setting up credentials for a higher limit seems not worth the cost\n\nTo run in docker:\n#+begin_example\ndocker run --rm -ti -e PASSWORD=password -p 8989:8787 veupathdb/study-wrangler\n# Then in your web browser navigate to localhost:8989 and login with \"rstudio\" and \"password\"\n#+end_example\n\nTo add R functions to the repo (using docker):\n#+begin_example\ndocker run --rm -ti --name study-wrangler-dev -v $PWD:/study.wrangler -e PASSWORD=password -p 8888:8787 veupathdb/study-wrangler\n# Then in your web browser navigate to localhost:8888 and login with \"rstudio\" and \"password\"\n\n# at the RStudio prompt\n\u003e library(devtools)\n# then in the file browser:\n# 1. navigate into ./study.wrangler directory\n# 2. Set As Working Directory (gear icon in file browser)\n# 3. (or do `setwd(\"~/study.wrangler\")` in console)\n\u003e devtools::test()\n# actually just `test()` will work\n\n# If running commands in console, you will need to do\n\u003e load_all()\n# after making changes in the code.\n\n# To update the documentation and/or NAMESPACE file\n\u003e document()\n\u003e build(path='dist')\n\u003e install()\n# Note that we are not committing the man/*.Rd files to the repo at the moment\n#+end_example\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fveupathdb%2Fstudy-wrangler","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fveupathdb%2Fstudy-wrangler","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fveupathdb%2Fstudy-wrangler/lists"}