├── .Rbuildignore ├── .github └── workflows │ ├── build-packages-file.yml │ ├── build-registry.yml │ └── rebuild-roweb3.yml ├── .gitignore ├── .nojekyll ├── DESCRIPTION ├── Makefile ├── README.md ├── example.json ├── info ├── exclude_list.txt ├── final_categories.csv ├── not_transferred.json └── staff.csv ├── old-registry.json ├── packages.json ├── raw_cm.json ├── registry.json ├── roregistry.Rproj ├── scripts └── update_categories.R └── spec.json /.Rbuildignore: -------------------------------------------------------------------------------- 1 | ^.*\.Rproj$ 2 | ^\.Rproj\.user$ 3 | -------------------------------------------------------------------------------- /.github/workflows/build-packages-file.yml: -------------------------------------------------------------------------------- 1 | name: build-packages-file 2 | 3 | on: 4 | workflow_dispatch: 5 | schedule: 6 | - cron: "25,55 * * * *" 7 | 8 | jobs: 9 | build: 10 | runs-on: ubuntu-latest 11 | container: ghcr.io/ropensci-org/makeregistry 12 | env: 13 | GITHUB_PAT: ${{ secrets.ANONYMOUS_PAT }} 14 | steps: 15 | 16 | - uses: actions/checkout@v4 17 | 18 | - name: Build packages.json 19 | run: | 20 | makeregistry::build_ropensci_packages_json() 21 | shell: Rscript {0} 22 | 23 | - name: push 24 | if: success() && github.ref == 'refs/heads/gh-pages' 25 | run: | 26 | echo "pushing changes to github" 27 | git config --global user.email "accounts+ropenscibot@ropensci.org" 28 | git config --global user.name "ropenscibot" 29 | git config --global --add safe.directory /__w/roregistry/roregistry 30 | git add packages.json 31 | git commit -m 'packages.json updated' || exit 0 32 | git pull --rebase 33 | git push 34 | -------------------------------------------------------------------------------- /.github/workflows/build-registry.yml: -------------------------------------------------------------------------------- 1 | name: build-registry 2 | 3 | on: 4 | workflow_dispatch: 5 | push: 6 | paths: 7 | - 'packages.json' 8 | schedule: 9 | - cron: "45 7 * * *" 10 | 11 | jobs: 12 | build: 13 | runs-on: ubuntu-latest 14 | env: 15 | GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} 16 | GITHUB_GRAPHQL_TOKEN: ${{ secrets.GITHUB_TOKEN }} 17 | REPO_PAT: ${{ secrets.GITHUB_TOKEN }} 18 | R_REMOTES_NO_ERRORS_FROM_WARNINGS: false 19 | steps: 20 | - uses: actions/checkout@v4 21 | 22 | - uses: r-lib/actions/setup-r@v2 23 | 24 | - uses: r-lib/actions/setup-r-dependencies@v2 25 | with: 26 | extra-packages: ropensci-org/makeregistry 27 | 28 | - name: Build registry 29 | run: | 30 | makeregistry::make_registry() 31 | shell: Rscript {0} 32 | 33 | - name: push 34 | if: success() && github.ref == 'refs/heads/gh-pages' 35 | run: | 36 | echo "pushing changes to github" 37 | git config --global user.email "accounts+ropenscibot@ropensci.org" 38 | git config --global user.name "ropenscibot" 39 | git add registry.json raw_cm.json 40 | git commit -m 'registry.json updated' || exit 0 41 | git pull --rebase 42 | git push 43 | -------------------------------------------------------------------------------- /.github/workflows/rebuild-roweb3.yml: -------------------------------------------------------------------------------- 1 | on: 2 | push: 3 | branches: 4 | gh-pages 5 | 6 | name: Rebuild website 7 | 8 | jobs: 9 | ping: 10 | name: Ping 11 | runs-on: ubuntu-latest 12 | steps: 13 | - name: Ping 14 | run: curl -X POST -d '{}' ${{ secrets.NETLIFY_HOOK }} 15 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | .Rproj.user 2 | .Rhistory 3 | .RData 4 | .Ruserdata 5 | -------------------------------------------------------------------------------- /.nojekyll: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- 1 | Package: roregistry 2 | Type: Package 3 | Title: What the Package Does (Title Case) 4 | Version: 0.1.1 5 | Author: Who wrote it 6 | Maintainer: The package maintainer 7 | Description: More about what it does (maybe more than one line) 8 | Use four spaces when indenting paragraphs within the Description. 9 | License: What license is it under? 10 | Encoding: UTF-8 11 | -------------------------------------------------------------------------------- /Makefile: -------------------------------------------------------------------------------- 1 | RSCRIPT = Rscript --no-init-file 2 | 3 | all: 4 | ${RSCRIPT} -e 'library(methods)' 5 | 6 | make_urls: 7 | cat registry.json | jq --raw-output '.packages[] | select(.on_cran == false) | .name' | sort | awk '{print "http://crandb.r-pkg.org/"$$1}' 8 | 9 | now_on_cran: 10 | cat registry.json | jq --raw-output '.packages[] | select(.on_cran == false) | .name' | sort | awk '{print "http://crandb.r-pkg.org/"$$1}' | xargs curl --silent --output /dev/null -w "\n%{http_code}\t%{url_effective}\n" > output.txt 11 | 12 | # No real targets! 13 | .PHONY: all make_urls now_on_cran 14 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | rOpenSci Package Registry 2 | ========================= 3 | 4 | ## What is this 5 | 6 | This repository contains 2 files that define the official rOpenSci package suite: 7 | 8 | - [packages.json](packages.json): the official list of rOpenSci packages, identified by the package name and git url (updated hourly). 9 | - [registry.json](registry.json): lots of metadata about these packages collected using [codemetar](https://docs.ropensci.org/codemetar) (updated daily). 10 | 11 | The rOpenSci package suite consists of all R packages in the [ropensci](https://github.com/ropensci) and [ropenscilabs](https://github.com/ropenscilabs) GitHub organizations, except for packages listed in [exclude list](info/exclude_list.txt), plus some extra packages listed in [not_transferred.json](info/not_transferred.json). 12 | 13 | The CI automatically updates the [packages.json](packages.json) and [registry.json](registry.json) files using the [makeregistry](https://github.com/ropensci-org/makeregistry) package. 14 | 15 | 16 | ## Generating packages.json 17 | 18 | The code to re-generate packages.json and registry.json is in the [makeregistry](https://github.com/ropensci-org/makeregistry) package. The `build_ropensci_packages_json()` function works as follows: 19 | 20 | 1. It queries the GitHub API for all repositories in `ropensci` and `ropenscilabs`. 21 | 2. It removes entries from the [exclude list](info/exclude_list.txt) 22 | 3. It adds packages listed in [not_transferred.json](info/not_transferred.json) 23 | 4. Saves the final list in `packages.json` 24 | 25 | This function should take less then a minute to complete, be very reliable, and we run it frequently. 26 | 27 | On a daily basis we also try to collect metadata from all ropensci packages, using `make_registry()` function. This function uses the following steps: 28 | 29 | - load the package list from packages.json 30 | - pull down the latest commit from every rOpenSci repository 31 | - run [codemetar][] against each repository to generate its [codemeta.json](https://github.com/ropensci/codemetar#why-create-a-codemetajson-for-your-package) data 32 | - combine all package codemeta data into one big codemeta (`raw_cm.json`) 33 | - extract a smaller subset of metadata from the big codemeta file to make the `registry.json` file 34 | - push the `raw_cm.json` and `registry.json` files up to this repo 35 | 36 | This second function can run up to 10 minutes and requires many API calls (multiple per package). It is not very robust and sometimes fails for a number of random reasons. 37 | 38 | ## Why the CI runs in a container 39 | 40 | To speed up the CI builds, the roregistry workflow runs in a docker container which has R and makeregistry preinstalled. This container is automatically built and published on GHCR using [this workflow](https://github.com/ropensci-org/makeregistry/blob/master/.github/workflows/docker-build.yml). 41 | 42 | When a change is committed to makeregistry, it takes a few minutes before the container is updated. This is exactly the time we save for each CI run in roregistry because it does not have to install R and makeregistry + dependencies for each build. 43 | 44 | ## Getting the registry 45 | 46 | To get just the raw JSON of the registry, go to 47 | 48 | To read in from R with `jsonlite`: 49 | 50 | ```r 51 | url <- "https://ropensci.github.io/roregistry/registry.json" 52 | z <- jsonlite::fromJSON(url) 53 | tibble::as_tibble(z$packages) 54 | ``` 55 | 56 | ```r 57 | #> # A tibble: 388 x 13 58 | #> name description details maintainer keywords github status onboarding on_cran on_bioc url ropensci_catego… 59 | #> 60 | #> 1 auk eBird Data… "Extra… Matthew S… "datase… https… active "https://… TRUE FALSE http… data-access 61 | #> 2 tree… Base Class… "'tree… Guangchua… "export… https… active "https://… FALSE TRUE http… data-tools 62 | #> 3 apip… Package Ge… "Packa… Scott Cha… "yaml" https… wip "" FALSE FALSE http… http-tools 63 | #> 4 arre… Arrested D… "Here … Lucy D'Ag… "unconf… https… conce… "" FALSE FALSE http… data-access 64 | #> 5 aspa… Client for… "Clien… Scott Cha… "archiv… https… conce… "" FALSE FALSE http… literature 65 | #> 6 astr Decompose … "Decom… Scott Cha… "" https… conce… "" FALSE FALSE http… NA 66 | #> 7 bind… Create req… "Compu… Saras Win… "ozunco… https… conce… "" FALSE FALSE http… NA 67 | #> 8 blog… Helps Edit… "More … Maëlle Sa… "" https… wip "" FALSE FALSE http… scalereprod 68 | #> 9 cche… Client for… "Clien… Scott Cha… "cran, … https… conce… "" FALSE FALSE http… scalereprod 69 | #> 10 chan… A simple i… "This … Nick Gold… "ozunco… https… conce… "" FALSE FALSE http… scalereprod 70 | #> # … with 378 more rows, and 1 more variable: date_last_commit 71 | ``` 72 | -------------------------------------------------------------------------------- /example.json: -------------------------------------------------------------------------------- 1 | { 2 | "name": "rgbif", 3 | "type": "package", 4 | "maintainer": "Scott Chamberlain", 5 | "email": "myrmecocystus@gmail.com", 6 | "status": "good", 7 | "installable": true, 8 | "on_cran": true, 9 | "cran_archived": false, 10 | "url": "https://github.com/ropensci/rgbif", 11 | "root": "", 12 | "fork": false, 13 | "description": "Access more than 400 million species occurrence records from across the globe in one place, from the Global Biodiversity Information Facility", 14 | "system_dependencies": null, 15 | "category": "biology", 16 | "keywords": ["biology","occurrence","records","coordinates","gbif","global","biodiversity","information", 17 | "facilty","species","specimen","taxonomy"], 18 | "data": [ 19 | { 20 | "taxonomy": ["plantae", "animalia"] 21 | }, 22 | { 23 | "spatial": [180,90,-180,-90] 24 | }, 25 | { 26 | "temporal": [1900, 2016] 27 | } 28 | ] 29 | } 30 | -------------------------------------------------------------------------------- /info/exclude_list.txt: -------------------------------------------------------------------------------- 1 | acme 2 | agent 3 | antweb-guide 4 | archeology 5 | atomize 6 | auunconf 7 | available 8 | betty 9 | bienapi 10 | bienapidocs 11 | monthly 12 | bmc 13 | buffy 14 | buffy-api 15 | cchecksapi 16 | champions-program 17 | ChampionsProgram 18 | champions-program-playbook 19 | cheatsheets 20 | citation_tracking 21 | cityquant 22 | colorpile 23 | containerit 24 | craft 25 | creating-a-pipeline-in-blue-ocean 26 | dashboard 27 | dashboard 28 | db-gbif 29 | db-itis 30 | dbgrowth 31 | deck 32 | dev_guide 33 | devroadmap 34 | discussions 35 | dotgithubfiles 36 | drake-manual 37 | drat 38 | elastic_data 39 | etseed 40 | exploRingJSON 41 | fishbaseapi 42 | fishbaseapidocs 43 | fishbasestatus 44 | FTCFOSS-Guide 45 | fulltext-book 46 | gbif-backbone-sql 47 | geofilter 48 | geoflowr 49 | geojsonpolys 50 | geolocart 51 | geoparser 52 | greta 53 | heythere 54 | hirsutosa 55 | http-testing-book 56 | Hydrology 57 | icon 58 | jumpin 59 | knowtifier 60 | launchboat 61 | leafier 62 | learngganimate 63 | logos 64 | lumier 65 | madewithr 66 | miner 67 | miner_book 68 | neurobio 69 | nneo 70 | notary-repos 71 | occurrence-manual 72 | onboarding-guide 73 | open-science-with-R 74 | ozdata 75 | ozunconf-projects 76 | ozunconf17 77 | ozunconf18 78 | ozunconf19 79 | ozwomensport 80 | PackageDevelopment 81 | phylodiv 82 | proj 83 | proxy-bias-vignette 84 | pubpatterns 85 | pubpatternsapi 86 | r-docker-tutorial 87 | r-security-practices 88 | rbot 89 | rcheatsheet 90 | realtime 91 | redland-bindings 92 | remake-tutorial 93 | reproducibility-guide 94 | robridgems 95 | rocites 96 | rOpenInterviews 97 | ropensci_citations 98 | ropensci_intro 99 | ropenscibin 100 | rOpenSciEd 101 | roregistry 102 | rostats 103 | rotwmentions 104 | roweb2 105 | roweb3 106 | rrocksdb 107 | rubfuns 108 | runconf17-projects 109 | runconf18-projects 110 | scatrr 111 | screencasts 112 | siftgeojson 113 | software-review 114 | software-review-meta 115 | spsqlite 116 | staging 117 | t-437 118 | tabulizerjars 119 | talks 120 | taxize-book 121 | taxizedbs 122 | taxizesoap 123 | taxonomy 124 | textmine 125 | textworkshop17 126 | textworkshop18 127 | tic.blogdown 128 | tic.bookdown 129 | tic.covrpage 130 | tic.drat 131 | tic.drat.repo 132 | tic.figshare 133 | tic.package 134 | tic.packagedocs 135 | tic.website 136 | timeraster 137 | travis-goodpractice 138 | twitpic 139 | umapr 140 | uncertVis 141 | unconf14 142 | unconf15 143 | unconf16 144 | unconf17 145 | unconf18 146 | UntweetdAus 147 | vitae 148 | webrockets 149 | webservices 150 | wishlist 151 | rtd 152 | stellar 153 | col-sql 154 | annual-report-help 155 | ropensci-tweets 156 | community-calls 157 | ropenscilabs.github.io 158 | crandata 159 | makeregistry 160 | ocrstuff 161 | docs 162 | sheetseeR 163 | maptools 164 | status 165 | testing 166 | ronfhir 167 | rokit 168 | rivis 169 | rglobalnames 170 | opendata 171 | rrrpkg 172 | roapi 173 | gpapi 174 | geoplyr 175 | doidata 176 | data-packages 177 | ausElectR 178 | apispecs 179 | ImpactReport 180 | binomen 181 | gghdr 182 | actions_sandbox 183 | quizlite 184 | aRt_class 185 | learningtower 186 | bnf 187 | smoky 188 | OZdatasets 189 | ozroaddeaths 190 | goodtables 191 | corporateR 192 | gramr 193 | Rcademy 194 | hideandseek 195 | syn 196 | expanding-peer-review 197 | weatherdata 198 | outsider-testsuites 199 | statistical-software-peer-review 200 | statistical-software 201 | crevents 202 | seaaroundus 203 | motifator 204 | emldown 205 | .github 206 | taxdictionaries 207 | bbox 208 | lq 209 | taxadc 210 | identifires 211 | gbifloc 212 | cranchecksdocs 213 | rthings 214 | mdb 215 | actions 216 | canpaginate 217 | elasticdsl 218 | dappr 219 | rwdpa 220 | zissou 221 | feetures 222 | scitations 223 | rflybase 224 | reuropeana 225 | geojsonrewind 226 | pegax 227 | rdpla 228 | tpl-sqlite 229 | statistical-software-review 230 | statistical-software-review-book 231 | review-robot-test 232 | commcalls 233 | legacy 234 | testprivate 235 | ropensci.github.io 236 | censo2017-cartografias 237 | climatrends 238 | starchart 239 | 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"package": "weathercan", 3577 | "url": "https://github.com/ropensci/weathercan", 3578 | "branch": "main", 3579 | "metadata": { 3580 | "review": { 3581 | "id": 160, 3582 | "status": "reviewed", 3583 | "version": "0.2.2.9000", 3584 | "organization": "rOpenSci Software Review", 3585 | "url": "https://github.com/ropensci/software-review/issues/160" 3586 | } 3587 | } 3588 | }, 3589 | { 3590 | "package": "webchem", 3591 | "url": "https://github.com/ropensci/webchem", 3592 | "branch": "master" 3593 | }, 3594 | { 3595 | "package": "webmockr", 3596 | "url": "https://github.com/ropensci/webmockr", 3597 | "branch": "main" 3598 | }, 3599 | { 3600 | "package": "wikitaxa", 3601 | "url": "https://github.com/ropensci/wikitaxa", 3602 | "branch": "master" 3603 | }, 3604 | { 3605 | "package": "wmm", 3606 | "url": "https://github.com/wfrierson/wmm", 3607 | "branch": "main", 3608 | "metadata": { 3609 | "review": { 3610 | "id": 522, 3611 | "status": "reviewed", 3612 | "version": "1.1.1", 3613 | "organization": "rOpenSci Software Review", 3614 | "url": "https://github.com/ropensci/software-review/issues/522" 3615 | } 3616 | } 3617 | }, 3618 | { 3619 | "package": "workloopR", 3620 | "url": "https://github.com/ropensci/workloopR", 3621 | "branch": "master", 3622 | "metadata": { 3623 | "review": { 3624 | "id": 326, 3625 | "status": "reviewed", 3626 | "version": "1.0.0", 3627 | "organization": "rOpenSci Software Review", 3628 | "url": "https://github.com/ropensci/software-review/issues/326" 3629 | } 3630 | } 3631 | }, 3632 | { 3633 | "package": "worrms", 3634 | "url": "https://github.com/ropensci/worrms", 3635 | "branch": "master" 3636 | }, 3637 | { 3638 | "package": "writexl", 3639 | "url": "https://github.com/ropensci/writexl", 3640 | "branch": "master" 3641 | }, 3642 | { 3643 | "package": "xslt", 3644 | "url": "https://github.com/ropensci/xslt", 3645 | "branch": "master" 3646 | }, 3647 | { 3648 | "package": "yfR", 3649 | "url": "https://github.com/ropensci/yfR", 3650 | "branch": "main", 3651 | "metadata": { 3652 | "review": { 3653 | "id": 523, 3654 | "status": "reviewed", 3655 | "version": "0.0.1", 3656 | "organization": "rOpenSci Software Review", 3657 | "url": "https://github.com/ropensci/software-review/issues/523" 3658 | } 3659 | } 3660 | } 3661 | ] 3662 | -------------------------------------------------------------------------------- /roregistry.Rproj: -------------------------------------------------------------------------------- 1 | Version: 1.0 2 | 3 | RestoreWorkspace: Default 4 | SaveWorkspace: Default 5 | AlwaysSaveHistory: Default 6 | 7 | EnableCodeIndexing: Yes 8 | UseSpacesForTab: Yes 9 | NumSpacesForTab: 2 10 | Encoding: UTF-8 11 | 12 | RnwWeave: Sweave 13 | LaTeX: pdfLaTeX 14 | 15 | AutoAppendNewline: Yes 16 | StripTrailingWhitespace: Yes 17 | 18 | BuildType: Makefile 19 | -------------------------------------------------------------------------------- /scripts/update_categories.R: -------------------------------------------------------------------------------- 1 | # current categories information 2 | categories <- readr::read_csv( 3 | here::here( 4 | file.path( 5 | "info", 6 | "final_categories.csv" 7 | ) 8 | ) 9 | ) 10 | 11 | library("magrittr") 12 | 13 | # current packages 14 | pkgs <- jsonlite::read_json("registry.json") %>% 15 | .[[1]] 16 | 17 | purrr::map_chr(pkgs, "name") -> packages 18 | grepl("ropenscilabs", purrr::map_chr(pkgs, "github")) -> ropenscilabs 19 | 20 | categories <- dplyr::left_join( 21 | tibble::tibble(name = packages, 22 | ropenscilabs = ropenscilabs), 23 | categories 24 | ) 25 | categories <- dplyr::select(categories, name, ropensci_category, ropenscilabs) 26 | # update csv by hand and save it 27 | 28 | # only keep categories information 29 | # for current packages 30 | categories <- dplyr::filter(categories, 31 | name %in% packages) 32 | readr::write_csv(categories, here::here( 33 | file.path( 34 | "info", 35 | "final_categories.csv" 36 | ) 37 | ) 38 | ) 39 | 40 | 41 | -------------------------------------------------------------------------------- /spec.json: -------------------------------------------------------------------------------- 1 | { 2 | "name": "[str] Package name, also the name in the DESCRIPTION file, note that this may be different from the GitHub repo name", 3 | "type": "[str] Type - only 'package' allowed now, may include others later", 4 | "maintainer": "[str] Package maintainer name", 5 | "email": "[str] Package maintainer email", 6 | "status": { 7 | "description": "Current state of the package, different from installable", 8 | "levels": { 9 | "good": "Everything is good, everything should work fine", 10 | "hiatus": "Taking a break for a reason, e.g., waiting for next version of an API", 11 | "deprecated": "Not maintaining any longer, though may still be installable" 12 | } 13 | }, 14 | "installable": "[bool] Should the package install", 15 | "ropensci_category": "[str] ropensci category - a single string category to group packages by", 16 | "category": "[array] Category - what the package does/data it deals with", 17 | "on_cran": "[bool] Is the package on CRAN", 18 | "cran_archived": "[bool] If the package is on CRAN, is it archived?", 19 | "url": "[str] Code repository URL, usually a GitHub repository", 20 | "root": "[str] Path to root of the R package (if an R package exists). If in root of repo, then zero length string", 21 | "fork": "[bool] Is the repo a fork", 22 | "description": "[str] Brief description of the package", 23 | "system_dependencies": "[str] System dependencies, e.g., libcurl, libgdal", 24 | "category": "[array[str]] Category - what the package does/data it deals with", 25 | "data": "[hash] Data available via this package, broken out by different categories: taxonomy, spatial, historical, geopolitical, etc.", 26 | } 27 | --------------------------------------------------------------------------------