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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>
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@@ -49,6 +49,7 @@ S3method(as.data.frame,mo)
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S3method(as.double,mic)
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S3method(as.double,sir)
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S3method(as.list,custom_eucast_rules)
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S3method(as.list,custom_interpretive_rules)
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S3method(as.list,custom_mdro_guideline)
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S3method(as.list,mic)
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S3method(as.matrix,mic)
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@@ -66,6 +67,7 @@ S3method(c,ab)
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S3method(c,amr_selector)
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S3method(c,av)
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S3method(c,custom_eucast_rules)
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S3method(c,custom_interpretive_rules)
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S3method(c,custom_mdro_guideline)
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S3method(c,disk)
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S3method(c,mic)
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@@ -96,6 +98,7 @@ S3method(print,amr_selector)
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S3method(print,av)
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S3method(print,bug_drug_combinations)
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S3method(print,custom_eucast_rules)
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S3method(print,custom_interpretive_rules)
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S3method(print,custom_mdro_guideline)
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S3method(print,deprecated_amr_dataset)
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S3method(print,disk)
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@@ -228,6 +231,7 @@ export(count_df)
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export(count_resistant)
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export(count_susceptible)
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export(custom_eucast_rules)
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export(custom_interpretive_rules)
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export(custom_mdro_guideline)
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export(eucast_dosage)
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export(eucast_exceptional_phenotypes)
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