find . -type d \( -name __pycache__ -o -name .pytest_cache \) -prune -exec rm -rf {} +
find . -maxdepth 2 -type d -name '*.egg-info' -prune -exec rm -rf {} +
find . -type f \( -name '*.pyc' -o -name '.DS_Store' -o -name '._*' \) -delete
/private/tmp/pk-audit-20261002-py312/bin/python tools/validate_library.py .
Library validation: OK
Warnings (1-compartment attainability and basis assumptions):
- abciximab: t_half_h 0.4166666666666667 h conflicts with CL/V implied 6.36332 h (rel_error=14.3; threshold=0.25). This target may be unattainable by the 1-compartment fixture without choosing a different independent parameter pair.
- aciclovir: t_half_h 2.5 h conflicts with CL/V implied 1.64867 h (rel_error=0.341; threshold=0.25). This target may be unattainable by the 1-compartment fixture without choosing a different independent parameter pair.
- alfentanil: t_half_h 1.675 h conflicts with CL/V implied 2.31049 h (rel_error=0.379; threshold=0.25). This target may be unattainable by the 1-compartment fixture without choosing a different independent parameter pair.
- amikacin: t_half_h 2.0 h conflicts with CL/V implied 2.77259 h (rel_error=0.386; threshold=0.25). This target may be unattainable by the 1-compartment fixture without choosing a different independent parameter pair.
- cimetidine: t_half_h 2.0 h conflicts with CL/V implied 1.30694 h (rel_error=0.347; threshold=0.25). This target may be unattainable by the 1-compartment fixture without choosing a different independent parameter pair.
- clarithromycin: t_half_h 5.0 h conflicts with CL/V implied 2.052 h (rel_error=0.59; threshold=0.25). This target may be unattainable by the 1-compartment fixture without choosing a different independent parameter pair.
- dapagliflozin: t_half_h 12.9 h conflicts with CL/V implied 6.58546 h (rel_error=0.489; threshold=0.25). This target may be unattainable by the 1-compartment fixture without choosing a different independent parameter pair.
- felodipine: t_half_h 24.5 h conflicts with CL/V implied 5.39114 h (rel_error=0.78; threshold=0.25). This target may be unattainable by the 1-compartment fixture without choosing a different independent parameter pair.
- itraconazole: t_half_h 22.0 h conflicts with CL/V implied 29.0889 h (rel_error=0.322; threshold=0.25). This target may be unattainable by the 1-compartment fixture without choosing a different independent parameter pair.
- montelukast: t_half_h 6.7 h conflicts with CL/V implied 3.63827 h (rel_error=0.457; threshold=0.25). This target may be unattainable by the 1-compartment fixture without choosing a different independent parameter pair.
- omeprazole: t_half_h 0.75 h conflicts with CL/V implied 0.256191 h (rel_error=0.658; threshold=0.25). This target may be unattainable by the 1-compartment fixture without choosing a different independent parameter pair.
/private/tmp/pk-audit-20261002-py312/bin/python tools/check_value_provenance.py .
Value provenance check: OK
/private/tmp/pk-audit-20261002-py312/bin/python tools/validate_pharmacology_data.py .
Pharmacology data validation: OK
/private/tmp/pk-audit-20261002-py312/bin/python tools/codex_harness_check.py .
Codex harness check: OK
PYTHONDONTWRITEBYTECODE=1 /private/tmp/pk-audit-20261002-py312/bin/python -m pytest -q -p no:cacheprovider
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/private/tmp/pk-audit-20261002-py312/bin/python tools/regen_check.py .
Regeneration check: OK
/private/tmp/pk-audit-20261002-py312/bin/python tools/check_derived_drift.py . --strict
# derived-block drift report

- Drugs scanned: 37
- Drugs with drift vs current derive_quantities: 0
- pk_parsed.clearance_basis persisted: 37/37

## ke convention used by committed pk.yml

| Convention | Drugs |
| --- | ---: |
| CL/V | 19 |
| both_coincide | 18 |

`ln2/t_half` is what validate_library.py enforces; `CL/V` is what the current
derive_quantities produces. Where committed uses `ln2/t_half`, regenerating with
the current generator would change ke and FAIL validate_library's ke check.

## Per-drug drift

| Drug | ke conv | basis saved | drifted fields | keys+gen | keys+committed |
| --- | --- | :-: | --- | --- | --- |
| abciximab | CL/V | Y | - | - | - |
| aciclovir | CL/V | Y | - | - | - |
| albuterol | both_coincide | Y | - | - | - |
| alfentanil | CL/V | Y | - | - | - |
| alprazolam | CL/V | Y | - | - | - |
| amikacin | CL/V | Y | - | - | - |
| apixaban | both_coincide | Y | - | - | - |
| atazanavir | CL/V | Y | - | - | - |
| buprenorphine | both_coincide | Y | - | - | - |
| carbamazepine | both_coincide | Y | - | - | - |
| cda1 | CL/V | Y | - | - | - |
| cimetidine | CL/V | Y | - | - | - |
| clarithromycin | CL/V | Y | - | - | - |
| dapagliflozin | CL/V | Y | - | - | - |
| efavirenz | both_coincide | Y | - | - | - |
| erythromycin | both_coincide | Y | - | - | - |
| ethinylestradiol | both_coincide | Y | - | - | - |
| felodipine | CL/V | Y | - | - | - |
| fluconazole | both_coincide | Y | - | - | - |
| fluvoxamine | both_coincide | Y | - | - | - |
| inulin | both_coincide | Y | - | - | - |
| itraconazole | CL/V | Y | - | - | - |
| mefenamic_acid | CL/V | Y | - | - | - |
| metoprolol | both_coincide | Y | - | - | - |
| mexiletine | both_coincide | Y | - | - | - |
| moclobemide | CL/V | Y | - | - | - |
| montelukast | CL/V | Y | - | - | - |
| motavizumab_medi_524 | CL/V | Y | - | - | - |
| motavizumab_yte | both_coincide | Y | - | - | - |
| omeprazole | CL/V | Y | - | - | - |
| raltegravir | both_coincide | Y | - | - | - |
| sildenafil | both_coincide | Y | - | - | - |
| sufentanil | both_coincide | Y | - | - | - |
| tefibazumab | CL/V | Y | - | - | - |
| tizanidine | both_coincide | Y | - | - | - |
| triazolam | both_coincide | Y | - | - | - |
| verapamil | CL/V | Y | - | - | - |

/private/tmp/pk-audit-20261002-py312/bin/python tools/make_calibrated_oral_spec.py . --check

calibrated profiles: 11 eligible drug(s); would change 0.
/private/tmp/pk-audit-20261002-py312/bin/python -m tools.pk_fixture_cli --help
pk_fixture_cli: CLI entrypoint for pkdummy-harness

Usage:
  python -m tools.pk_fixture_cli <command> [args...]
  (run from the repository root)

Commands:
  doctor                        Check local Python/R/Quarto/simPop readiness.
  run                           Run a harness YAML config.
  workflow                      Run post-simulation validate/sample/SDTM-like/analysis workflow.
  validate-simulation           Recalculate AUC/Cmax/Tmax/t1/2 from sim_full.csv.
  validate-config               Validate a run_harness YAML config.
  sample-timepoints             Sample dense simulation output at nominal clinical times.
  make-sdtm                     Generate limited SDTM-like DM/VS/LB/EX/PC CSVs.
  make-background               Generate Japan/US population-referenced subject backgrounds.
  prepare-background-reference  Normalize pinned public Japan/US population tables without API keys.
  prepare-body-reference        Normalize e-Stat NHNS / CDC NHANES height and weight statistics.
  make-analysis                 Generate ADPC/NCA/PopPK smoke-test input CSVs.
  downstream-smoke              Run downstream NCA/PopPK parser smoke checks.
  site-adapter                  Generate site-specific adapter CSVs from a YAML mapping.
  external-validation           Probe or run optional Phoenix/NONMEM/nlmixr2 profiles.
  manifest-viewer               Render a MANIFEST.yml to a static HTML viewer.
  examples-check                Regenerate versioned examples in a temp dir and compare.
  audit-library                 Read-only internal-first library priority audit.
  cdisc-reference               Fetch optional CDISC DM/EX reference fixtures.
  parameter-provenance          Export PK/source/model parameter provenance inventory.

Examples:
  python -m tools.pk_fixture_cli doctor
  python -m tools.pk_fixture_cli run harness_examples/demo_set.yml
  python -m tools.pk_fixture_cli workflow --sim-full outputs/<run>/raw/sim_full.csv --drug aciclovir --times 0,1,2 --out-dir outputs/<run>/workflow
  python -m tools.pk_fixture_cli parameter-provenance --out-dir outputs/parameter_provenance

Boundary:
  Generated data are workflow fixtures, not clinical inference or dose-selection evidence.
/private/tmp/pk-audit-20261002-py312/bin/python -m tools.pk_fixture_cli doctor --json
{
  "purpose": "pk_fixture_harness_preflight",
  "status": "WARN",
  "checks": [
    {
      "name": "python3",
      "status": "OK",
      "level": "required",
      "message": "Python CLI is available."
    },
    {
      "name": "python_package:yaml",
      "status": "OK",
      "level": "required",
      "message": "PyYAML is importable."
    },
    {
      "name": "Rscript",
      "status": "OK",
      "level": "recommended",
      "message": "Rscript is available for reporting tools."
    },
    {
      "name": "R_package:ggplot2",
      "status": "OK",
      "level": "recommended",
      "message": "ggplot2 is available for concentration plots."
    },
    {
      "name": "R_package:yaml",
      "status": "OK",
      "level": "recommended",
      "message": "yaml is available for the mrgsolve runner."
    },
    {
      "name": "R_package:mrgsolve",
      "status": "OK",
      "level": "recommended",
      "message": "mrgsolve is available for ODE PopPK simulation."
    },
    {
      "name": "quarto",
      "status": "OK",
      "level": "recommended",
      "message": "Quarto is available for DOCX report rendering."
    },
    {
      "name": "R_package:simpop",
      "status": "WARN",
      "level": "optional",
      "message": "simpop is missing; built-in fallback subject fixtures can still be used."
    }
  ]
}
/private/tmp/pk-audit-20261002-py312/bin/python tools/check_examples.py examples
Examples check: OK
checked: minimal_aciclovir
checked: minimal_albuterol_iv
checked: minimal_cda1_mab_iv
/private/tmp/pk-audit-20261002-py312/bin/python tools/run_downstream_smoke.py --analysis-dir examples/minimal_aciclovir/workflow/analysis_inputs --out-dir outputs/downstream_smoke_check/minimal_aciclovir
Downstream smoke: OK
Output directory: outputs/downstream_smoke_check/minimal_aciclovir
adapter_manifest: outputs/downstream_smoke_check/minimal_aciclovir/adapters/MANIFEST.yml
manifest: outputs/downstream_smoke_check/minimal_aciclovir/DOWNSTREAM_SMOKE_MANIFEST.yml
nca_summary_csv: outputs/downstream_smoke_check/minimal_aciclovir/nca_smoke/NCA_SUMMARY.csv
nlmixr2_model_template: outputs/downstream_smoke_check/minimal_aciclovir/poppk_smoke/nlmixr2_parser_template.R
nonmem_control_template: outputs/downstream_smoke_check/minimal_aciclovir/poppk_smoke/nonmem_parser_template.ctl
poppk_summary_yml: outputs/downstream_smoke_check/minimal_aciclovir/poppk_smoke/POPPK_PARSE_SUMMARY.yml
/private/tmp/pk-audit-20261002-py312/bin/python tools/run_downstream_smoke.py --analysis-dir examples/minimal_albuterol_iv/workflow/analysis_inputs --out-dir outputs/downstream_smoke_check/minimal_albuterol_iv
Downstream smoke: OK
Output directory: outputs/downstream_smoke_check/minimal_albuterol_iv
adapter_manifest: outputs/downstream_smoke_check/minimal_albuterol_iv/adapters/MANIFEST.yml
manifest: outputs/downstream_smoke_check/minimal_albuterol_iv/DOWNSTREAM_SMOKE_MANIFEST.yml
nca_summary_csv: outputs/downstream_smoke_check/minimal_albuterol_iv/nca_smoke/NCA_SUMMARY.csv
nlmixr2_model_template: outputs/downstream_smoke_check/minimal_albuterol_iv/poppk_smoke/nlmixr2_parser_template.R
nonmem_control_template: outputs/downstream_smoke_check/minimal_albuterol_iv/poppk_smoke/nonmem_parser_template.ctl
poppk_summary_yml: outputs/downstream_smoke_check/minimal_albuterol_iv/poppk_smoke/POPPK_PARSE_SUMMARY.yml
/private/tmp/pk-audit-20261002-py312/bin/python tools/make_site_adapters.py --analysis-dir examples/minimal_aciclovir/workflow/analysis_inputs --spec-yml external_validation/site_adapter_template.yml --out-dir outputs/site_adapter_check/minimal_aciclovir
Site adapters written: OK
Output directory: outputs/site_adapter_check/minimal_aciclovir
manifest: outputs/site_adapter_check/minimal_aciclovir/SITE_ADAPTER_MANIFEST.yml
site_nca_example: outputs/site_adapter_check/minimal_aciclovir/site_nca_example.csv
site_poppk_example: outputs/site_adapter_check/minimal_aciclovir/site_poppk_example.csv
/private/tmp/pk-audit-20261002-py312/bin/python tools/run_external_tool_validation.py --downstream-dir outputs/downstream_smoke_check/minimal_aciclovir --out-dir outputs/external_validation_probe/minimal_aciclovir
External tool validation: WARN
execute=false
manifest: outputs/external_validation_probe/minimal_aciclovir/EXTERNAL_TOOL_VALIDATION.yml
nlmixr2: OK - probe passed; execute=false
nonmem: SKIPPED - executable not found: nmfe75
phoenix: SKIPPED - executable not found: phoenix-placeholder
/Applications/Xcode.app/Contents/Developer/usr/bin/make clean
find . -type d \( -name __pycache__ -o -name .pytest_cache \) -prune -exec rm -rf {} +
find . -maxdepth 2 -type d -name '*.egg-info' -prune -exec rm -rf {} +
find . -type f \( -name '*.pyc' -o -name '.DS_Store' -o -name '._*' \) -delete
/private/tmp/pk-audit-20261002-py312/bin/python tools/codex_harness_check.py .
Codex harness check: OK