adds the _freeze dir to the repo / remove renv

[tomjemmett]

previously we were recomputing all code chunks on github actions, but caching the _freeze dir.

this PR adds the _freeze dir to version control, with the expectation that all users run their code locally and add _freeze changes. this eliminates the need to run the r/python code on the action runner

[github-actions]

PR Preview Action v1.4.8
Preview removed because the pull request was closed.
2026-04-24 08:39 UTC

[Copilot]

Pull request overview

This PR shifts the Quarto site build strategy from “execute on GitHub Actions + cache _freeze/” to “commit _freeze/ and avoid executing code in CI”, while removing the renv-based dependency management scaffolding previously used across posts/presentations.

Changes:

• Remove renv configuration/lockfiles and all per-page renv::use(lockfile=...) chunks.
• Commit _freeze/ artifacts and set site-wide execute.freeze: true to rely on frozen results.
• Simplify presentations/index.qmd to use Quarto listing: metadata instead of an R-generated table; trim CI workflows accordingly.

Reviewed changes

Copilot reviewed 54 out of 163 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
renv/settings.json	Removed renv project settings as part of decommissioning renv.
renv/.gitignore	Removed renv ignore rules since renv/ is being removed.
renv.lock	Removed root renv lockfile.
presentations/index.qmd	Replaced custom R-generated listing with Quarto listing:.
presentations/2026-03-12_managing-your-environment/renv.lock	Removed per-presentation lockfile.
presentations/2025-12-04_whose_application/renv.lock	Removed per-presentation lockfile.
presentations/2025-12-04_multidisciplinary_pipelines/renv.lock	Removed per-presentation lockfile.
presentations/2025-11-13_nhsrpysoc-2025-word/renv.lock	Removed per-presentation lockfile.
presentations/2025-11-05_case-example/renv.lock	Removed per-presentation lockfile.
presentations/2025-09-11_efficient-coding/index.qmd	Updated YAML metadata (author/date) and removed renv::use() chunk.
presentations/2025-09-04_demand-presentation/renv.lock	Removed per-presentation lockfile.
presentations/2025-03-13_sconn-r-pkg-databricks/renv.lock	Removed per-presentation lockfile.
presentations/2025-02-27_word-not-quarto/renv.lock	Removed per-presentation lockfile.
presentations/2025-02-27_nhp-deployment/renv.lock	Removed per-presentation lockfile.
presentations/2025-01-16_c-and-c-databricks/renv.lock	Removed per-presentation lockfile.
presentations/2024-12-04_what-the-heck/renv.lock	Removed per-presentation lockfile.
presentations/2024-12-02_dhsc/renv.lock	Removed per-presentation lockfile.
presentations/2024-11-27_text-mining/renv.lock	Removed per-presentation lockfile.
presentations/2024-11-26_text-mining-yh/renv.lock	Removed per-presentation lockfile.
presentations/2024-11-22_github-team-sport-rpysoc/index.qmd	Removed renv::use() chunk.
presentations/2024-11-21_agile_project_management/renv.lock	Removed per-presentation lockfile.
presentations/2024-10-10_what-is-ai-yiwen/renv.lock	Removed per-presentation lockfile.
presentations/2024-10-10_what-is-ai-tom/index.qmd	Removed renv::use() chunk; minor R formatting tweaks.
presentations/2024-10-10_what-is-ai-matt/renv.lock	Removed per-presentation lockfile.
presentations/2024-10-09-rap-cautionary-tales/renv.lock	Removed per-presentation lockfile.
presentations/2024-09-05_earl-nhp/renv.lock	Removed per-presentation lockfile.
presentations/2024-08-22_agile-and-scrum/renv.lock	Removed per-presentation lockfile.
presentations/2024-05-30_open-source-licensing/index.qmd	Removed renv::use() chunk.
presentations/2024-05-23_github-team-sport/index.qmd	Removed renv::use() chunk.
presentations/2024-05-16_store-data-safely/index.qmd	Removed renv::use() chunk.
presentations/2024-01-25_coffee-and-coding/index.qmd	Removed renv::use() chunk.
presentations/2023-10-17_conference-check-in-app/index.qmd	Removed renv::use() chunk.
presentations/2023-10-09_nhs-r_conf_sd_in_health_social_care/index.qmd	Removed renv::use() chunk; whitespace/formatting cleanup.
presentations/2023-09-07_coffee_and_coding_functions/index.qmd	Removed renv::use() chunk; formatting cleanup and function example refactor.
presentations/2023-08-24_coffee-and-coding_geospatial/index.qmd	Removed renv::use() chunk; updated leaflet tile provider; formatting cleanup.
presentations/2023-08-23_nhs-r_unit-testing/index.qmd	Removed renv::use() chunk; formatting cleanup in examples.
presentations/2023-08-02_mlcsu-ksn-meeting/index.qmd	Removed renv::use() chunk.
presentations/2023-07-11_haca-nhp-demand-model/index.qmd	Removed renv::use() chunk.
presentations/2023-05-23_data-science-for-good/index.qmd	Removed renv::use() chunk.
presentations/2023-05-15_text-mining/index.qmd	Removed renv::use() chunk.
presentations/2023-03-23_collaborative-working/index.qmd	Removed renv::use() chunk.
presentations/2023-03-23_coffee-and-coding/index.qmd	Removed renv::use() chunk; formatting cleanup.
presentations/2023-03-09_midlands-analyst-rap/index.qmd	Removed renv::use() chunk.
presentations/2023-03-09_coffee-and-coding/index.qmd	Removed renv::use() chunk.
presentations/2023-02-23_coffee-and-coding/index.qmd	Removed renv::use() chunk.
presentations/2023-02-01_what-is-data-science/index.qmd	Removed renv::use() chunk.
index.qmd	Removed a setup chunk that loaded packages for rendering.
blogs/posts/2025-04-30_using-github-apps-for-authentication/index.qmd	Removed execute.enabled: false; replaced Quarto code-fold options with HTML <details> wrappers and plain code fences.
blogs/posts/2024-12-04-gha-branch-preview/renv.lock	Removed per-post lockfile.
blogs/posts/2024-12-04-gha-branch-preview/index.qmd	Removed renv::use() chunk.
blogs/posts/2024-11-29-mapping-my-r-learning/renv.lock	Removed per-post lockfile.
blogs/posts/2024-11-29-mapping-my-r-learning/index.qmd	Removed renv::use() chunk.
blogs/posts/2024-11-12_coffee-coding-github-planner/renv.lock	Removed per-post lockfile.
blogs/posts/2024-11-12_coffee-coding-github-planner/index.qmd	Removed renv::use() chunk.
blogs/posts/2024-08-08_map-and-nest/index.qmd	Removed lockfile chunk; formatting/indentation improvements in examples.
blogs/posts/2024-05-22_storing-data-safely/index.qmd	Removed renv::use() chunk; formatting cleanup in examples.
blogs/posts/2024-05-13_one-year-coffee-code/index.qmd	Removed renv::use() chunk.
blogs/posts/2024-03-21_rstudio-tips/index.qmd	Removed renv::use() chunk; minor whitespace cleanup.
blogs/posts/2024-02-28_sankey_plot/index.qmd	Removed renv::use() chunk; made file loading more robust; formatting cleanup.
blogs/posts/2024-01-17_nearest_neighbour/index.qmd	Removed renv::use() chunk; formatting cleanup.
blogs/posts/2024-01-10_advent-of-code-and-test-driven-development/index.qmd	Removed renv::use() chunk.
blogs/posts/2023-04-26_reinstalling-r-packages/index.qmd	Removed renv::use() chunk.
blogs/posts/2023-04-26_alternative_remotes/index.qmd	Removed renv::use() chunk.
blogs/posts/2023-03-24_hotfix-with-git/index.qmd	Removed renv::use() chunk.
_quarto.yml	Changed execute.freeze from auto to true to rely on committed freeze outputs.
_freeze/presentations/2025-11-13_error_messages_with_cli/index/execute-results/html.json	Added frozen execution output for a presentation.
_freeze/presentations/2025-07-17_deploy-to-connect/index/execute-results/html.json	Added frozen execution output for a presentation.
_freeze/presentations/2024-10-10_what-is-ai-tom/index/execute-results/html.json	Added frozen execution output for a presentation.
_freeze/presentations/2024-10-10_what-is-ai-matt/index/execute-results/html.json	Added frozen execution output for a presentation.
_freeze/presentations/2024-10-10_what-is-ai-chris/index/execute-results/html.json	Added frozen execution output for a presentation.
_freeze/presentations/2024-08-22_agile-and-scrum/index/execute-results/html.json	Added frozen execution output for a presentation.
_freeze/presentations/2024-05-30_open-source-licensing/index/execute-results/html.json	Added frozen execution output for a presentation.
_freeze/presentations/2024-01-25_coffee-and-coding/index/execute-results/html.json	Added frozen execution output for a presentation.
_freeze/presentations/2023-09-07_coffee_and_coding_functions/index/execute-results/html.json	Added frozen execution output for a presentation.
_freeze/presentations/2023-03-23_coffee-and-coding/index/execute-results/html.json	Added frozen execution output for a presentation.
_freeze/presentations/2023-03-09_coffee-and-coding/index/execute-results/html.json	Added frozen execution output for a presentation.
_freeze/blogs/posts/2024-08-08_map-and-nest/index/execute-results/html.json	Added frozen execution output for a blog post.
_freeze/blogs/posts/2024-05-22_storing-data-safely/index/execute-results/html.json	Added frozen execution output for a blog post.
_freeze/blogs/posts/2024-03-21_rstudio-tips/index/execute-results/html.json	Added frozen execution output for a blog post.
_freeze/blogs/posts/2024-01-10_advent-of-code-and-test-driven-development/index/execute-results/html.json	Added frozen execution output for a blog post.
_freeze/blogs/posts/2023-04-26_reinstalling-r-packages/index/execute-results/html.json	Added frozen execution output for a blog post.
_freeze/blogs/posts/2023-04-26_alternative_remotes/index/execute-results/html.json	Added frozen execution output for a blog post.
_freeze/blogs/posts/2023-03-24_hotfix-with-git/index/execute-results/html.json	Added frozen execution output for a blog post.
README.md	Removed the standalone {renv} section; adjusted contributor instructions (but still contains stale renv guidance elsewhere).
.renvignore	Removed renv ignore configuration.
.gitignore	Stopped ignoring _freeze/ so frozen outputs can be committed.
.github/workflows/renew_cache.yaml	Removed workflow that refreshed cached _freeze/.
.github/workflows/rebuild_system_dependencies.r	Removed script that computed apt sysreqs from renv.lock.
.github/workflows/publish.yaml	Removed R/Python/renv setup and caching steps; updated checkout action version (currently invalid).
.github/workflows/preview.yml	Removed R/Python/renv setup and caching steps; updated checkout action version (currently invalid).
.github/workflows/install_system_deps.sh	Removed system dependency installation script for CI.
.Rprofile	Removed renv activation hook.

Comments suppressed due to low confidence (1)

README.md:37

• This README section still instructs contributors to use renv::snapshot() and add renv::use(lockfile = "renv.lock"), but this PR removes renv from the repo. Update the blogpost/presentation contribution instructions to reflect the new workflow (e.g., how to render locally and commit _freeze outputs) so new contributors don’t follow broken steps.

### How to create a new blogpost 

1. Navigate to the `blogs/posts` folder
2. Create a folder for your blogpost, following the naming convention `YYYY-MM-DD_title-of-post`
3. Copy a previous blogpost index.qmd file into your folder and use that as your template
4. Write your blogpost. To preview changes, run `quarto preview path/to/index.qmd` in terminal.
5. If your blogpost requires any specific packages, capture them with `renv::snapshot("PATH_TO_THE_FOLDER")` and ensure that you include in the top of your .qmd file (after the yaml) the following code chunk, without the hashes (#)

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[tomjemmett]

closing #434 because this removes the need for that PR

[yiwen-h]

Should we add to README about the need to commit _freeze as well? From Slack:

add _freeze to version control: you will need to have run your code before pushing to github, and include _freeze in the commits
remove renv entirely - don't bother capturing the package versions used (maybe add a session info to end of all posts though in a <details> box?
avoid certain quarto features: turns out if you add any of the code folding stuff to a specific chunk it's going to force partial recomputation and installation of rmarkdown and knitr...
change the presentations index page: from memory early quarto didn't like us using a blog style listen page for the presentations folder, because the subitems weren't posts. but it does work now, eliminating the need to do any computation
remove setup-r from the actions - this will ensure you have _freeze'd your stuff

[tomjemmett]

@yiwen-h should have addressed this in 65fac6e