This outlines how to propose a change to hubUtils. For more general info about contributing to this, and other hubverse packages, please see the hubverse contributing guide.
You can fix typos, spelling mistakes, or grammatical errors in the documentation directly using the GitHub web interface, as long as the changes are made in the source file. This generally means you’ll need to edit roxygen2 comments in an .R, not a .Rd file. You can find the .R file that generates the .Rd by reading the comment in the first line.
Bigger changes
If you want to make a bigger change, it’s a good idea to first file an issue and make sure someone from the team agrees that it’s needed. If you’ve found a bug, please file an issue that illustrates the bug with a minimal reprex (this will also help you write a unit test, if needed).
Our procedures for contributing bigger changes, code in particular, generally follow those advised by the tidyverse dev team, including following the tidyverse style guide for code and recording user facing changes in NEWS.md.
Pull request process
Fork the package and clone onto your computer. If you haven’t done this before, we recommend using
usethis::create_from_github("hubverse-org/hubUtils", fork = TRUE).Install all development dependencies with
devtools::install_dev_deps(), and then make sure the package passes R CMD check by runningdevtools::check(). If R CMD check doesn’t pass cleanly, it’s a good idea to ask for help before continuing.Follow the pull request checklist to create a Git branch for your pull request (PR). We recommend using
usethis::pr_init("name/brief-description/issue").Make your changes, commit to git, and then create a PR by running
usethis::pr_push(), and following the prompts in your browser. The title of your PR should briefly describe the change. The body of your PR should containFixes #issue-number.For user-facing changes, add a bullet to the top of
NEWS.md(i.e. just below the first heading—usually labelled “development version”). Follow the style described in https://style.tidyverse.org/news.html.
Code style
New code should follow the tidyverse style guide. You can use the styler package to apply these styles, but please don’t restyle code that has nothing to do with your PR.
We use roxygen2, with Markdown syntax, for documentation.
We use testthat for unit tests. Contributions with test cases included are easier to accept.
Synchronizing with hubverse-org/schemas
The official home for the hubverse schemas are at https://github.com/hubverse-org/schemas. These schemas are copied over here under the inst/schemas folder, which allows offline validation for hubs.
If you are developing against an in-development version of the hubverse schemas, you must ensure that the schemas in this repository are synchronized.
Synchronization script
The script that synchronizes the schemas is in data-raw/schemas.R and it can be run from within R, as a standalone script, or as a git hook. It takes one environment variable HUBUTILS_SCHEMA_BRANCH. If the environment variable is unset, the branch information from the inst/schemas/update.json is used.
Usage: within R
source("data-raw/schemas.R")Usage: commit hook
See Installing the Git Hook. A Git hook is a way to run a local script before or after you do something in Git. For example, a pre-push hook (the one we use here) will run every time before you push to the remote repository.
Details
By default, this script will make a single call to the GitHub API to determine the status of the most recent commit on the branch listed in inst/schemas/update.json. If the sha and branch match and the timestamp is ahead of the the most recent commit, then you are good to go!
If an update is needed, then your system git is used to clone the branch and copy it over to inst/schemas.
When running this as a script (not interactive), then when a schema update happens, the tests are re-run.
Synchronizing a development branch
In order to synchronize a development branch, you should set a temporary environment variable called HUBUTILS_SCHEMA_BRANCH to the name of the branch. This can only be done interactively in R or as a BASH script.
Via R
Sys.setenv("HUBUTILS_SCHEMA_BRANCH" = "br-v4.0.1")
source("data-raw/schemas.R")
#> ✔ removing /path/to/hubUtils/inst/schemas
#> ✔ Creating inst/schemas/.
#> ℹ Fetching the latest version of the schemas from GitHub
#> Cloning into '/path/to/temp/folder'...
#> ✔ Copying v4.0.1, v4.0.0, v3.0.1, v3.0.0, v2.0.1, v2.0.0, v1.0.0, v0.0.1, v0.0.0.9,
#> and NEWS.md to inst/schemas
#> [ ... snip ... ]
#> ✔ Done
#> ✔ Schemas up-to-date!
#> ℹ branch: "br-v4.0.1"
#> ℹ sha: "43b2c8aceb3a316b7a1929dbe8d8ead2711d4e84"
#> ℹ timestamp: "2024-12-19T16:40:16Z"
Sys.unsetenv("HUBUTILS_DEV_BRANCH")Via BASH
When run via script (both manually and via git hook), if any synchronization happens, tests are automatically run:
HUBUTILS_SCHEMA_BRANCH=br-v4.0.1 Rscript data-raw/schemas.R \
&& unsetenv HUBUTILS_SCHEMA_BRANCH
#> ✔ removing /path/to/hubUtils/inst/schemas
#> ✔ Creating inst/schemas/.
#> ℹ Fetching the latest version of the schemas from GitHub
#> Cloning into '/path/to/temp/folder'...
#> ✔ Copying v4.0.1, v4.0.0, v3.0.1, v3.0.0, v2.0.1, v2.0.0, v1.0.0, v0.0.1, v0.0.0.9,
#> and NEWS.md to inst/schemas
#> [ ... snip ... ]
#> ✔ Done
#> ✔ Schemas up-to-date!
#> ℹ branch: "br-v4.0.1"
#> ℹ sha: "43b2c8aceb3a316b7a1929dbe8d8ead2711d4e84"
#> ℹ timestamp: "2024-12-19T16:40:16Z"
#>
#> ── ⚠ schema updated ──
#>
#> ! Re-running tests.
#> ℹ Testing hubUtils
#> ✔ | F W S OK | Context
#> ✔ | 7 | as_config
#> ✔ | 9 | as_model_out_tbl
#> ✔ | 5 | check_deprecated_schema
#> ✔ | 17 | model_id_merge
#> ✔ | 7 | read_config [6.4s]
#> ✔ | 7 | utils-get_hub
#> ✔ | 16 | utils-model_out_tbl
#> ✔ | 14 | utils-round_ids
#> ✔ | 8 | utils-round-config
#> ✔ | 39 | utils-schema-versions
#> ✔ | 14 | utils-schema [1.2s]
#> ✔ | 3 | utils-task_ids
#> ✔ | 7 | v3-schema-utils
#>
#> ══ Results ════════════════════════════
#> Duration: 9.0 s
#>
#> [ FAIL 0 | WARN 0 | SKIP 0 | PASS 153 ]
#> ✔ OKInstalling the Git Hook
It is optional, but recommended to use this script as a pre-push hook so that the schemas are checked for updates before each commit.
usethis::use_git_hook("pre-push", readLines(usethis::proj_path("data-raw/schemas.R")))This will create or overwrite .git/hooks/pre-push.
If you want to uninstall the git hook, remove the .git/hooks/pre-push file
In addition to checking that the schemas in inst/schemas are synchronized, as demonstrated above, this hook will also check:
- the local hook is up-to-date
- the
inst/schemasfolder contents are all committed
When you install this as a git hook, you will get a message before every successful push:
$ git push
#>
#> ── pre-push: schema synchronization ───────────────────────────────────────
#>
#> ── pre-push: checking that the hook is up-to-date ──
#>
#> ✔ Setting active project to "/path/to/hubUtils".
#> ✔ OK
#>
#> ── pre-push: checking that schemas are up-to-date ──
#>
#> → branch: "main"
#> → sha: "0163a89cc38ba3846cd829545f6d65c1e40501a6"
#> → timestamp: "2024-12-19T16:56:13Z"
#> ✔ OK
#>
#> ── pre-push: checking for changes in inst/schemas ──
#>
#> ✔ OKWhen the schema updates
If the schemas are updated but not committed, this hook will prevent you from pushing the changes until they are updated:
$ git push
#> [ ... snip ... ]
#>
#> ── ⚠ schema updated ──
#>
#> [ ... snip ... ]
#> ✔ OK
#>
#> ── pre-push: checking for changes in inst/schemas ──
#>
#> Error in `check_status()`:
#> ! New schemas must be committed before pushing.
#> Backtrace:
#> ▆
#> 1. └─global check_status(usethis::proj_path())
#> 2. └─cli::cli_abort(c("New schemas must be committed before pushing."))
#> 3. └─rlang::abort(...)
#> Execution halted
#> error: failed to push some refs to 'https://github.com/hubverse-org/hubUtils.git'When the script changes
If the git hook script changes, you will be given instructions to update:
$ git push
#>
#> ── pre-push: schema synchronization ───────────────────────────────────────
#>
#> ── pre-push: checking that the hook is up-to-date ──
#>
#> ✔ Setting active project to "/path/to/hubUtils".
#> Error in `check_hook()`:
#> ! git hook outdated
#> ℹ Use `usethis::use_git_hook("pre-push", readLines(usethis::proj_path("data-raw/schemas.R")))`
#> to update your hook.
#> Backtrace:
#> ▆
#> 1. └─global check_hook(usethis::proj_path())
#> 2. └─cli::cli_abort(c("git hook outdated", i = "Use {.code {cmd}} to update your hook."))
#> 3. └─rlang::abort(...)
#> Execution halted
#> error: failed to push some refs to 'https://github.com/hubverse-org/hubUtils.git'Code of Conduct
Please note that the hubUtils project is released with a Contributor Code of Conduct. By contributing to this project you agree to abide by its terms.