Validator 2 - #374
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R scripts: parse args with docopt::docopt() (matching leapfrogr/scripts/create_model_output.R's existing convention) instead of raw commandArgs(); call leapfrog::/leapfrog::: qualified rather than library(leapfrog). Ruff: the ignore list was copied wholesale from codegen/pyproject.toml. Cleared it and re-ran against the real codebase -- only docstring rules and subprocess S603/S607 actually fired. Added real docstrings to every flagged public class/function in src/ (16 sites), exempted test functions from docstring rules per-file (matching leapfrog-py/tests' existing undocumented-test-function convention), and kept S603/S607 ignored with a one-line justification -- shelling out to git/R/uv with argument lists is this tool's whole job, not untrusted input reaching a shell. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
…ssue 17) Extends leapfrog-validate's diff command from the walking skeleton's single total_population check to all five blessed indicators (adding hiv_population, treatment_population, aids_deaths_single_age, aids_deaths_on_treatment), through one common registry shape. The two indicators with no p_-level array are reconstructed by summing the adult/ child ART arrays over CD4/duration and concatenating their age domains. Adds a reviewable, per-PJNZ exclusion mechanism (leapfrog_validate.exclusions) that requires both a reason and a link, so a known discrepancy can be carved out of the tolerance rollup without loosening tolerance for any other PJNZ. diff now checks all five indicators by default with a strict AND rollup (--indicator still selects one), and a new --pjnz option matches exclusion entries. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Range read as Python's half-open range() semantics, but Exclusion's year/sex/age bounds are inclusive on both ends -- caught in code review.
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