various enhancements

[pawelru]

these are various enhancements that I have collected over a time of running verdepcheck on our codebase. That includes:

• docs
• edge-cases fixes
• get_ref_release will not return early but rather collects candidates and return ref for which ver is the maximum ver over candidates
• get_release_date.remote_ref_github will use pkgdepends to resolve ref and get commit sha and reach GH with that sha
• use binaries. This hardcodes the repos but it's fine for the time being. We are anyway relaying on PPM when using snapshots.

[github-actions]

Code Coverage Summary

Filename                          Stmts    Miss  Cover    Missing
------------------------------  -------  ------  -------  ------------------------
R/check.R                            37      37  0.00%    26-170
R/deps_installation_proposal.R      139     139  0.00%    58-269
R/desc_utils.R                       71      43  39.44%   15-32, 108, 117-168, 186
R/get_ref.R                         233     232  0.43%    13-455, 473-516
R/solve.R                            84      84  0.00%    9-170
R/utils.R                            66      42  36.36%   3-23, 41, 47, 57-104
TOTAL                               630     577  8.41%

Diff against main

Filename          Stmts    Miss  Cover
--------------  -------  ------  --------
R/desc_utils.R       +1      +1  -0.56%
R/get_ref.R         +15     +15  -0.03%
R/solve.R            +3      +3  +100.00%
R/utils.R            -4     -13  +14.94%
TOTAL               +15      +6  +1.26%

Results for commit: 8a41033

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

[github-actions]

Unit Tests Summary

 1 files   4 suites   2s ⏱️
41 tests 13 ✅ 28 💤 0 ❌
94 runs  65 ✅ 29 💤 0 ❌

Results for commit 8a41033.

♻️ This comment has been updated with latest results.

[pawelru]

@averissimo please have a look if you can but this is not urgent

[github-actions]

CLA Assistant Lite bot ✅ All contributors have signed the CLA

[pawelru]

I have read the CLA Document and I hereby sign the CLA

[averissimo]

I have read the CLA Document and I hereby sign the CLA

[pawelru]

I'm testing my changes here: https://github.com/insightsengineering/teal.data/actions/workflows/scheduled.yaml?query=branch%3Aenhancements

[averissimo]

This works for most cases, jsonlite on {teal.data} (and I suppose in others) is still trying to install the source version as the binary is not available in snapshots for versions prior to 2.8.7 (in snapshots from 2023-06-30).

We could bump rmarkdown to 2.23 (from 2023-07-01) which will solve this particular problem.

[pawelru]

I just did that (insightsengineering/teal.data@63e5b4b) and it all passed -> https://github.com/insightsengineering/teal.data/actions/runs/9093304868

One great outcome of this PR is that it's a little bit faster when binaries were used. The aforementioned successful run took 6m 24s whereas the latest finished one - 9m 16s.

This is ready for review.

[averissimo]

The enhancements are very nice!

I suggested some extra cleanup. I can take care of it

The binary preference on cohort and isolate is quite interesting and will speed up the actions as well as avoid weird problems 👍

[averissimo]

I have all 19 local branches that have rmarkdown (>=2.19) updated to 2.23 and ready to push to create PRs. (bash was a timesaver here)

Also detected that rmarkdown is missing from:

teal.widgets, teal.modules.general, citril.metadata, osprey and teal.goshawk.

These packages have knitr, but not rmarkdown

[pawelru]

I have all 19 local branches that have rmarkdown (>=2.19) updated to 2.23 and ready to push to create PRs. (bash was a timesaver here)

Also detected that rmarkdown is missing from:

teal.widgets, teal.modules.general, citril.metadata, osprey and teal.goshawk.

These packages have knitr, but not rmarkdown

Thanks. Would you able to open PRs for these?

I just pushed changes with regards to the review comments. Unfortunately this is still WIP as the tests are failing. I will continue on this tomorrow

[github-actions]

Unit Test Performance Difference

Additional test case details

Test Suite	$Status$	Time on main	$±Time$	Test Case
get_ref	💀	$0.01$	$-0.01$	get_cran_data_returns_date_for_Bioconductor
get_ref	👶		$+0.02$	get_release_data_returns_date_for_Bioconductor
get_ref	👶		$+0.03$	get_release_date.remote_ref_cran_will_retrieve_missing_date_NA_for_package.does.not.exist_1.1.0
get_ref	💀	$0.03$	$-0.03$	get_release_date.remote_ref_cran_will_retrieve_missing_date_NA_for_rlang_0.0.0
get_ref	👶		$+0.05$	get_release_date.remote_ref_github_will_retrieve_missing_date_NA_for_r_lib_rlang_v0.0.0
get_ref	💀	$0.03$	$-0.03$	get_release_date.remote_ref_github_will_retrieve_missing_date_NA_for_rlang_0.0.0

Results for commit 62e964c

♻️ This comment has been updated with latest results.

[averissimo]

This is a step ahead. Great work!