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Export incremental generate_pkg_*() helpers#103

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Export incremental generate_pkg_*() helpers#103
Copilot wants to merge 8 commits into
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copilot/export-prepare-functions-again

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Copilot AI commented May 17, 2026 •
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This exposes the package-generation substeps so maintainers can generate auth, request-prep, paths, and shared params independently instead of always going through generate_pkg(). It also adds the missing reader plumbing needed for those entry points to derive their inputs from package config and saved security metadata.

  • Public generation entry points

    • Exported:
      • generate_pkg_auth()
      • generate_pkg_req_prepare()
      • generate_pkg_paths()
      • generate_pkg_shared_params()
    • Renamed the corresponding source/test files to match the public API names.

  • Config + security-data plumbing

    • Added read_security_schemes() to load api_definition@components@security_schemes from the configured rapid file.
    • Added exported readers for saved security metadata and its configured filename:
      • read_security_data()
      • read_security_data_filename()
    • generate_pkg_auth() can now persist generated security_data to _beekeeper_security.yml and record that filename in _beekeeper.yml.

  • Setup refactor

    • Split .setup_r() into narrower helpers for:
      • creating R/
      • enabling testthat
      • enabling httptest2
      • adding nectar
      • adding beekeeper
    • Each exported generate_pkg_*() wrapper now performs only the setup it needs.

  • generate_pkg() delegation

    • Reworked generate_pkg() to compose the new exported helpers instead of calling the old internal monolith.
    • Preserved the existing explicit-argument workflow by only saving security metadata when a config file is present.

  • Docs, examples, and package surface

    • Expanded the roxygen descriptions for the new exported generation helpers.
    • Added package examples for saved security-data readers via:
      • inst/example_config.yml
      • inst/example_security_data.yml
    • Updated roxygen/NAMESPACE/man pages for the new exports and helper layout.
    • Added focused tests bringing R/read_config.R to 100% coverage.
    • Added a changelog entry for the new incremental generation workflow.

Example:

generate_pkg_auth()
generate_pkg_shared_params()
generate_pkg_req_prepare()
generate_pkg_paths()

Or, explicitly:

generate_pkg_auth(
  api_abbr = read_api_abbr(),
  security_schemes = read_security_schemes(),
  save_security_data = TRUE
)

[!WARNING]

Copilot AI linked an issue May 17, 2026 that may be closed by this pull request
Export prepare_*() functions #101
Open
Copilot AI and others added 2 commits May 17, 2026 18:06
@jonthegeek
feat: export generate_pkg_*() helpers
91e6f9e 
Agent-Logs-Url: https://github.com/api2r/beekeeper/sessions/56ddfe74-e2c3-46b4-95bc-8da9d5f754f1

Co-authored-by: jonthegeek <33983824+jonthegeek@users.noreply.github.com>
@jonthegeek
docs: regenerate exports and add changelog entry
f6176b2 
Agent-Logs-Url: https://github.com/api2r/beekeeper/sessions/56ddfe74-e2c3-46b4-95bc-8da9d5f754f1

Co-authored-by: jonthegeek <33983824+jonthegeek@users.noreply.github.com>
Copilot AI changed the title [WIP] Export prepare_*() functions for API helper Export incremental generate_pkg_*() helpers May 17, 2026
Copilot AI requested a review from jonthegeek May 17, 2026 18:10
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github-actions Bot commented May 17, 2026 •
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{qcthat} Report: User Acceptance

No issues are awaiting UAT.

This report was generated by this GitHub Actions run.

Last updated: 2026-05-17 21:42:52 UTC

Session Info ─ Session info ───────────────────────────────────────────────────────────────

setting value

version R version 4.6.0 (2026-04-24)

os Ubuntu 24.04.4 LTS

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language (EN)

collate en_US.UTF-8

ctype en_US.UTF-8

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date 2026-05-17

pandoc 3.1.3 @ /usr/bin/pandoc

quarto NA

─ Packages ───────────────────────────────────────────────────────────────────

package * version date (UTC) lib source

askpass 1.2.1 2024-10-04 [1] RSPM

astgrepr 0.1.1 2025-06-07 [1] RSPM

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grid 4.6.0 2026-04-24 [2] local

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knitr 1.51 2025-12-20 [1] RSPM

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ps 1.9.3 2026-04-20 [1] RSPM

purrr 1.2.2 2026-04-10 [1] RSPM

qcthat 1.1.2 2026-05-17 [1] Github (Gilead-BioStats/qcthat@d0958dc)

R6 2.6.1 2025-02-15 [1] RSPM

ragg 1.5.2 2026-03-23 [1] RSPM

rapid 0.0.0.9003 2026-05-17 [1] Github (api2r/rapid@4fd4d2a)

rappdirs 0.3.4 2026-01-17 [1] RSPM

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Rcpp 1.1.1-1.1 2026-04-24 [1] RSPM

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rmarkdown 2.31 2026-03-26 [1] RSPM

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rrapply 1.2.8 2025-11-25 [1] RSPM

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rvest 1.0.5 2025-08-29 [1] RSPM

S7 0.2.2 2026-04-22 [1] RSPM

sass 0.4.10 2025-04-11 [1] RSPM

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sessioninfo 1.2.3 2025-02-05 [1] RSPM

shiny 1.13.0 2026-02-20 [1] RSPM

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[1] /usr/local/lib/R/site-library

[2] /usr/local/lib/R/library

[3] /__w/_temp/Library

  • ── Packages attached to the search path.

──────────────────────────────────────────────────────────────────────────────

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github-actions Bot commented May 17, 2026 •
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{qcthat} Reports

PR-Associated Issues

✅ A qcthat issue test matrix with 1 milestone, 1 issue, and 5 tests 
└─█─Milestone: v0.5.0 Parameter docs and type checks (1 issue, 5 tests)
  └─📥─Feature 101: Export `prepare_*()` functions
    ├─✅─generate_pkg_auth() writes auth files and saved security data (#101)
    ├─✅─generate_pkg_paths() reads saved inputs from config (#101)
    ├─✅─generate_pkg_req_prepare() reads saved inputs from config (#101)
    ├─✅─generate_pkg_shared_params() reads saved security data (#101)
    └─✅─read_security_schemes() reads security schemes (#101)
# Issue state: 📥 = open, ☑️ = closed (completed), ⛔ = closed (won't fix)
# Test disposition: ✅ = passed, ❌ = failed, 🚫 = skipped
✅ All tests passed

🟢 All issues have at least one test

Completed Issues

✅ A qcthat issue test matrix with 3 milestones, 12 issues, and 25 tests 
├─█─Milestone: v0.1.0 (4 issues, 3 tests)
│ ├─☑️─Feature 35: Create testthat/setup.R
│ │ └─✅─generate_pkg() returns a vector of created files (#15, #16, #35, #82)
│ ├─☑️─Feature 17: Auto-generate auth for api_key (query or header)
│ │ └─✅─generate_pkg() generates call function with API keys (#17, #82)
│ ├─☑️─Feature 16: Generate tests for basic call function
│ │ ├─✅─.setup_r() sets up dependencies (#16)
│ │ └─✅─generate_pkg() returns a vector of created files (#15, #16, #35, #82)
│ └─☑️─Feature 15: Auto-generate apis.guru caller from rapid
│   └─✅─generate_pkg() returns a vector of created files (#15, #16, #35, #82)
├─█─Milestone: v0.4.0 (2 issues, 2 tests)
│ ├─☑️─Infrastructure 52: Eliminate dplyr dependency
│ │ └─✅─%|% works (#52)
│ └─☑️─Infrastructure 10: Config 
│   └─✅─use_beekeeper writes a yml config (#10)
└─█─Milestone: v0.5.0 Parameter docs and type checks (6 issues, 22 tests)
  ├─☑️─Feature 99: Better read helpers
  │ ├─✅─read_api_abbr() reads api abbrs (#99)
  │ └─✅─read_api_title() reads api titles (#99)
  ├─☑️─Feature 85: Parameter type documentation
  │ └─✅─.compile_param_class_descriptions() uses class names (#85)
  ├─☑️─Feature 84: Header and cookie parameters
  │ └─✅─.generate_paths_file() renders header and cookie params correctly (#84, #69)
  ├─☑️─Feature 82: Separate Config Loader Function
  │ ├─✅─generate_pkg() returns a vector of created files (#15, #16, #35, #82)
  │ ├─✅─generate_pkg() generates call function with API keys (#17, #82)
  │ ├─✅─generate_pkg() falls back to config file when arguments are NULL (#82)
  │ ├─✅─read_config() reads configs (#82)
  │ └─✅─read_api_definition() reads api definitions (#82)
  ├─☑️─Feature 69: Param validation 
  │ ├─✅─.params_to_validations() only includes supported checks (#69)
  │ ├─✅─.paths_need_stbl() flags actionable validations (#69)
  │ ├─✅─.paths_need_stbl() returns FALSE for empty paths (#69)
  │ ├─✅─.generate_paths_file() renders header and cookie params correctly (#84, #69)
  │ └─✅─.maybe_use_stbl() can add stbl to imports (#69)
  └─☑️─Feature 65: Path file per endpoint
    ├─✅─.generate_paths() returns empty character for empty paths (#65)
    ├─✅─.generate_paths() calls correct templates for guru (#65)
    ├─✅─.generate_paths() writes correct templates for guru (#65)
    ├─✅─.generate_paths() calls correct templates for fec (#65)
    ├─✅─.generate_paths() writes correct paths.R for fec (#65)
    ├─✅─.generate_paths() writes correct paths.R for trello (#65)
    ├─✅─.generate_shared_params() returns file path for no-security API (#65)
    ├─✅─.generate_shared_params() writes correct content for no-security API (#65)
    └─✅─.generate_shared_params() writes security params for API with security (#65)
# Issue state: 📥 = open, ☑️ = closed (completed), ⛔ = closed (won't fix)
# Test disposition: ✅ = passed, ❌ = failed, 🚫 = skipped
✅ All tests passed

🟢 All issues have at least one test

🙈 6 issues with label "qcthat-nocov" were ignored

This report was generated by this GitHub Actions run.

Last updated: 2026-05-17 21:42:53 UTC

Session Info ─ Session info ───────────────────────────────────────────────────────────────

setting value

version R version 4.6.0 (2026-04-24)

os Ubuntu 24.04.4 LTS

system x86_64, linux-gnu

ui X11

language (EN)

collate en_US.UTF-8

ctype en_US.UTF-8

tz UTC

date 2026-05-17

pandoc 3.1.3 @ /usr/bin/pandoc

quarto NA

─ Packages ───────────────────────────────────────────────────────────────────

package * version date (UTC) lib source

askpass 1.2.1 2024-10-04 [1] RSPM

astgrepr 0.1.1 2025-06-07 [1] RSPM

backports 1.5.1 2026-04-03 [1] RSPM

base * 4.6.0 2026-04-24 [2] local

base64enc 0.1-6 2026-02-02 [1] RSPM

beekeeper 0.4.0.9000 2026-05-17 [1] local

boot 1.3-32 2025-08-29 [2] CRAN (R 4.6.0)

brew 1.0-10 2023-12-16 [1] RSPM

brio 1.1.5 2024-04-24 [1] RSPM

bslib 0.11.0 2026-05-16 [1] RSPM

cachem 1.1.0 2024-05-16 [1] RSPM

callr 3.7.6 2024-03-25 [1] RSPM

checkmate 2.3.4 2026-02-03 [1] RSPM

class 7.3-23 2025-01-01 [2] CRAN (R 4.6.0)

cli 3.6.6 2026-04-09 [1] RSPM

clipr 0.8.0 2022-02-22 [1] RSPM

cluster 2.1.8.2 2026-02-05 [2] CRAN (R 4.6.0)

codetools 0.2-20 2024-03-31 [2] CRAN (R 4.6.0)

commonmark 2.0.0 2025-07-07 [1] RSPM

compiler 4.6.0 2026-04-24 [2] local

covr 3.6.5 2025-11-09 [1] RSPM

crayon 1.5.3 2024-06-20 [1] RSPM

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digest 0.6.39 2025-11-19 [1] RSPM

docopt 0.7.2 2025-03-25 [1] RSPM (R 4.6.0)

downlit 0.4.5 2025-11-14 [1] RSPM

dplyr 1.2.1 2026-04-03 [1] RSPM

ellipsis 0.3.3 2026-04-04 [1] RSPM

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evaluate 1.0.5 2025-08-27 [1] RSPM

fansi 1.0.7 2025-11-19 [1] RSPM

fastmap 1.2.0 2024-05-15 [1] RSPM

fontawesome 0.5.3 2024-11-16 [1] RSPM

foreign 0.8-91 2026-01-29 [2] CRAN (R 4.6.0)

fs 2.1.0 2026-04-18 [1] RSPM

generics 0.1.4 2025-05-09 [1] RSPM

gert 2.3.1 2026-01-11 [1] RSPM

gh 1.5.0 2025-05-26 [1] RSPM

git2r 0.36.2 2025-03-29 [1] RSPM

gitcreds 0.1.2 2022-09-08 [1] RSPM

glue 1.8.1 2026-04-17 [1] RSPM

graphics * 4.6.0 2026-04-24 [2] local

grDevices * 4.6.0 2026-04-24 [2] local

grid 4.6.0 2026-04-24 [2] local

highr 0.12 2026-03-06 [1] RSPM

hms 1.1.4 2025-10-17 [1] RSPM

htmltools 0.5.9 2025-12-04 [1] RSPM

htmlwidgets 1.6.4 2023-12-06 [1] RSPM

httptest2 1.2.2 2025-11-16 [1] RSPM

httpuv 1.6.17 2026-03-18 [1] RSPM

httr 1.4.8 2026-02-13 [1] RSPM

httr2 1.2.2 2025-12-08 [1] RSPM

ini 0.3.1 2018-05-20 [1] RSPM

janitor 2.2.1 2024-12-22 [1] RSPM

jquerylib 0.1.4 2021-04-26 [1] RSPM

jsonlite 2.0.0 2025-03-27 [1] RSPM

KernSmooth 2.23-26 2025-01-01 [2] CRAN (R 4.6.0)

knitr 1.51 2025-12-20 [1] RSPM

later 1.4.8 2026-03-05 [1] RSPM

lattice 0.22-9 2026-02-09 [2] CRAN (R 4.6.0)

lifecycle 1.0.5 2026-01-08 [1] RSPM

littler 0.3.23 2026-04-12 [1] RSPM (R 4.6.0)

lubridate 1.9.5 2026-02-04 [1] RSPM

magick 2.9.1 2026-02-28 [1] RSPM

magrittr 2.0.5 2026-04-04 [1] RSPM

MASS 7.3-65 2025-02-28 [2] CRAN (R 4.6.0)

Matrix 1.7-5 2026-03-21 [2] CRAN (R 4.6.0)

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──────────────────────────────────────────────────────────────────────────────

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🌐 PR pkgdown deployed

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Last updated: 2026-05-17 21:43:08 UTC

Session Info ─ Session info ───────────────────────────────────────────────────────────────

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──────────────────────────────────────────────────────────────────────────────

jonthegeek
jonthegeek requested changes May 17, 2026
View reviewed changes
Comment thread R/read_config.R Outdated
Comment on lines +145 to +146
#' @keywords internal
.read_security_data_filename <- function(
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Suggested change
#' @keywords internal
.read_security_data_filename <- function(
#' @export
#' @family config readers
read_security_data_filename <- function(

This needs to be exported, since it's called in the signature of an exported function (ie, users can use it). Also add an example (by adding this field to inst/example_config.yml).

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Exported and documented with an example backed by inst/example_config.yml in 57bebb2.

Comment thread R/read_config.R Outdated
Comment on lines +202 to +206
#' @keywords internal
.read_security_data <- function(
pkg_dir = ".",
config_filename = "_beekeeper.yml",
security_data_filename = .read_security_data_filename(
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Suggested change
#' @keywords internal
.read_security_data <- function(
pkg_dir = ".",
config_filename = "_beekeeper.yml",
security_data_filename = .read_security_data_filename(
#' @export
#' @family config readers
read_security_data <- function(
pkg_dir = ".",
config_filename = "_beekeeper.yml",
security_data_filename = read_security_data_filename(

This needs to be exported, since it's called in the signature of an exported function (ie, users can use it). Also add an example (by adding a new inst/example_security_data.yml).

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Exported and documented with an example backed by inst/example_security_data.yml in 57bebb2.

Comment thread R/generate_pkg_auth.R
@@ -1,3 +1,38 @@
#' Generate authentication helpers
#'
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Since this is now an exported function, add a full description.

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Added a fuller roxygen description for generate_pkg_auth() in 57bebb2.

Comment thread R/generate_pkg_paths.R
@@ -1,3 +1,36 @@
#' Generate files for API paths
#'
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Since this is now an exported function, add a full description.

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Added a fuller roxygen description for generate_pkg_paths() in 57bebb2.

Comment thread R/generate_pkg_req_prepare.R
@@ -1,3 +1,33 @@
#' Generate request-prepare helpers
#'
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Since this is now an exported function, add a full description.

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Added a fuller roxygen description for generate_pkg_req_prepare() in 57bebb2.

Comment thread R/generate_pkg_shared.R
@@ -0,0 +1,32 @@
#' Generate shared parameter docs
#'
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Since this is now an exported function, add a full description.

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Added a fuller roxygen description for generate_pkg_shared_params() in 57bebb2.

Comment thread tests/testthat/test-read_config.R
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Add tests to reach 100% code coverage for this file. Tag the new tests with (#101).

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Added focused read_config tests and verified R/read_config.R is now at 100% coverage in 57bebb2.

Comment thread NEWS.md Outdated
@@ -0,0 +1,3 @@
# beekeeper 0.4.0.9000

* `generate_pkg_auth()`, `generate_pkg_req_prepare()`, `generate_pkg_paths()`, and `generate_pkg_shared_params()` can now be run one step at a time, with `read_security_schemes()` supporting auth generation (@jonthegeek, #101).
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Suggested change
* `generate_pkg_auth()`, `generate_pkg_req_prepare()`, `generate_pkg_paths()`, and `generate_pkg_shared_params()` can now be run one step at a time, with `read_security_schemes()` supporting auth generation (@jonthegeek, #101).
* `generate_pkg_auth()`, `generate_pkg_req_prepare()`, `generate_pkg_paths()`, and `generate_pkg_shared_params()` can now be run one step at a time, with `read_security_schemes()` supporting auth generation (#101).

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Updated the NEWS entry wording in 57bebb2.

Copilot AI and others added 2 commits May 17, 2026 21:52
@jonthegeek
docs: address exported reader feedback
57bebb2 
Agent-Logs-Url: https://github.com/api2r/beekeeper/sessions/cd29a1e1-233e-4675-adc6-25d20ae9a66b

Co-authored-by: jonthegeek <33983824+jonthegeek@users.noreply.github.com>
@jonthegeek
docs: refine example security data text
5c1c500 
Agent-Logs-Url: https://github.com/api2r/beekeeper/sessions/cd29a1e1-233e-4675-adc6-25d20ae9a66b

Co-authored-by: jonthegeek <33983824+jonthegeek@users.noreply.github.com>
Copilot AI requested a review from jonthegeek May 17, 2026 21:55
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Export prepare_*() functions

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