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

* 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>

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 3.0.1.9055
+# AMR 3.0.1.9056
 
 This will become release v3.1.0, intended for launch end of May.
 
@@ -45,6 +45,7 @@ This will become release v3.1.0, intended for launch end of May.
 * Fixed `as.sir()` ignoring `info = FALSE` for columns with no breakpoints (e.g. cefoxitin against *E. coli*)
 
 ### Updates
+* Renamed `custom_eucast_rules()` to `custom_interpretive_rules()`; old function is now a deprecated wrapper. Renamed `data-raw/eucast_rules.tsv` to `interpretive_rules.tsv` and added `rule.provider` column for multi-guideline (EUCAST/CLSI) support. `clsi_rules()` no longer throws an error (#268)
 * `as.sir()` with `reference_data`: custom guideline names now correctly classify values as R using EUCAST convention (`> breakpoint_R` for MIC, `< breakpoint_R` for disk); custom breakpoints with `host = NA` now serve as a host-agnostic fallback when no host-specific row matches (#239)
 * Extensive `cli` integration for better message handling and clickable links in messages and warnings (#191, #265)
 * `mdro()` now infers resistance for a _missing_ base drug column from an _available_ corresponding drug+inhibitor combination showing resistance (e.g., piperacillin is absent but required, while piperacillin/tazobactam available and resistant). Can be set with the new argument `infer_from_combinations`, which defaults to `TRUE` (#209). Note that this can yield a higher MDRO detection (which is a good thing as it has become more reliable).