Add manual progress fallback when progress package unavailable

[jennajiali]

#29

Summary

Fixes the issue where calling sample_chain() with show_progress_bar = TRUE would silently produce no output if the progress package was not installed, making it appear to the user as though the program had halted — particularly problematic for long chains.

When progress is unavailable, the function now emits a one-time informational message and then prints percentage-based progress updates with elapsed time at 10% intervals to the console.

Example output when progress is not installed:

progress package is not installed, so will print progress updates below.
Warm-up: 10% done (1000/10000 iterations) | elapsed: 0.6s
Warm-up: 20% done (2000/10000 iterations) | elapsed: 1.2s
...
Warm-up: 100% done (10000/10000 iterations) | elapsed: 6.1s
Main: 10% done (1000/10000 iterations) | elapsed: 0.6s
...
Main: 100% done (10000/10000 iterations) | elapsed: 6.0s

Changes

R/chains.R

• Add is_package_available() helper — a thin wrapper around requireNamespace() that lives in the package namespace, making it mockable in tests via with_mocked_bindings()
• Split use_progress_bar into two booleans — progress_available (is the package installed?) and show_progress_bar (did the user ask for progress?) are now kept separate and passed independently through sample_chain() and chain_loop(), so the fallback path can distinguish between the two cases
• Upfront warning in sample_chain() — prints a one-time message when show_progress_bar = TRUE but progress is unavailable
• Updated get_progress_bar() signature — now accepts show_progress_bar and progress_available separately instead of the collapsed use_progress_bar
• Fallback branch in chain_loop() — added else if branch alongside the existing progress bar tick, printing a formatted stage: X% done (n/total) | elapsed: Xs message at every 10% interval using proc.time() (base R, no dependencies)
• Post-loop 100% guard — prints a final "100% done" message after the loop when n_iteration is not an exact multiple of tick_amount, ensuring completion is always reported
• Updated @param show_progress_bar roxygen doc — reflects that the parameter now controls both the progress bar (when progress is installed) and the fallback text output (when it is not)

tests/testthat/test-chains.R

• Add make_fallback_test_inputs() helper — extracts shared setup (target distribution, adapters, initial position) used by both new tests into a single function to avoid duplication
• New test: fallback messages are emitted — mocks is_package_available() to return FALSE, captures all messages with capture_messages(), and asserts the correct total count, that the upfront warning is present, and that both 10% and 100% interval messages appear
• New test: silent when show_progress_bar = FALSE — same mock, asserts expect_no_message() confirming the fallback is correctly gated on the user's flag

Testing

All existing tests continue to pass. The two new tests covering the fallback path and the silent-when-disabled case also pass.

Notes

This PR is a draft / work in progress

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 100.00%. Comparing base (504f5ea) to head (b6dc6b0).

Additional details and impacted files

@@            Coverage Diff            @@
##              main      #124   +/-   ##
=========================================
  Coverage   100.00%   100.00%           
=========================================
  Files           11        11           
  Lines          595       620   +25     
=========================================
+ Hits           595       620   +25     

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[matt-graham]

Hi @jennajiali. This is looking really good. I have suggested some minor changes to resolve linter warnings and improve code readability and maintainability a bit.

As well as the linter warnings, currently the checks are also failing as your changes to the roxygen comment for sample_chains needs a corresponding change to the man/sample_chain.Rd manual page which is generated from this comment. If you have devtools loaded, running document() in an R session should regenerate this file and then you can commit updated version.

Some of the failing checks are run as part of our pre-commit (https://pre-commit.com/) hooks for the project. If you install pre-commit locally and install the hooks in your local repository by running

pre-commit install

from the root of the repository, this will run the checks each time you try to make a commit and give an error and/or changes to fix when you try to commit.

[matt-graham]

Hi @jennajiali - apologies for all the back and forth. Some of my suggested changes introduced a new styler error causing the pre-commit check to fail and also didn't fix the missing lines in coverage as I'd expected. I've opened a PR off the top of your PR in jennajiali#1 which should resolve the remaining failing checks 🤞 (or at least I get no styler warnings and 100% coverage locally with those changes).