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Generalise interpretive rules for multi-guideline support (#268) (#283)

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* Generalise interpretive rules for multi-guideline support (#268)

- Rename data-raw/eucast_rules.tsv → interpretive_rules.tsv; add rule.provider
  column (value: "EUCAST") to distinguish future CLSI rows
- Rename EUCAST_RULES_DF → INTERPRETIVE_RULES_DF in _pre_commit_checks.R;
  filter by rule.provider == guideline when applying rules in interpretive_rules()
- Rename custom_eucast_rules() → custom_interpretive_rules() with new S3 class
  "custom_interpretive_rules"; old function becomes a deprecated wrapper in
  zz_deprecated.R; backward-compat S3 dispatch shims added for old class
- Remove stop_if(guideline == "CLSI", ...) so clsi_rules() no longer errors
- Add .onLoad shim in zzz.R to create INTERPRETIVE_RULES_DF from EUCAST_RULES_DF
  for transitional compatibility until sysdata.rda is regenerated

https://claude.ai/code/session_01D46BTsfJSPo3HnLWp3PRkP

* Fix namespace load failure: remove assignInNamespace from .onLoad (#268)

assignInNamespace cannot add NEW bindings to a locked package namespace
(R locks namespace bindings before .onLoad runs). Replace the .onLoad
shim with a runtime fallback inside interpretive_rules(): if
INTERPRETIVE_RULES_DF is absent (pre-regeneration sysdata.rda), derive
it from EUCAST_RULES_DF by adding the rule.provider column. This also
fixes the screening_abx line to reuse the already-resolved
interpretive_rules_df_total instead of a bare INTERPRETIVE_RULES_DF
reference.

https://claude.ai/code/session_01D46BTsfJSPo3HnLWp3PRkP

* fixes

* fixes

---------

Co-authored-by: Claude <noreply@anthropic.com>
This commit is contained in:
Matthijs Berends
2026-05-01 18:38:51 +01:00
committed by GitHub
parent f7e9294bea
commit 24f24ecaf8
26 changed files with 1770 additions and 183 deletions
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7
tests/testthat/test-_deprecated.R
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@@ -32,4 +32,11 @@ test_that("test-_deprecated.R", {
expect_warning(example_isolates[, ab_class("mycobact")])
expect_warning(example_isolates[, ab_selector(name %like% "trim")])
# deprecated custom_interpretive_rules() still works and emits a warning
expect_warning(
x_old <- custom_eucast_rules(AMC == "R" ~ aminopenicillins == "R"),
regexp = "custom_eucast_rules"
)
expect_inherits(x_old, "custom_interpretive_rules")
})