3 Commits

Include renames

Author	SHA1	Message	Date
dr. M.S. (Matthijs) Berends	c8f6cea0a7	(v3.0.1.9128) Revamp console output of interpretive_rules() with cli styling and guideline-dependent SIR colours, make it 11 to 18 times faster with identical results, and fix counts of values that were not actually written (#259)	2026-10-13 12:27:38 +02:00
Matthijs Berends	2c33297cf6	new eucast breakpoints parsing	2026-08-20 13:29:16 +01:00
Matthijs BerendsandClaude	24f24ecaf8	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>	2026-05-01 18:38:51 +01:00