diff --git a/configs/quality/debt_scorecard.yaml b/configs/quality/debt_scorecard.yaml index dadc81d5f4..1c094048fa 100644 --- a/configs/quality/debt_scorecard.yaml +++ b/configs/quality/debt_scorecard.yaml @@ -240,8 +240,8 @@ config_surface_ratchet: keys are excluded; family-scoped sum must remain zero post Stream B closeout. ratchet_policy: Non-growth fail-fast; increases require reviewed contract regression. sanctioned_partial_parameter_count: - current_count: 97 - max_count: 97 + current_count: 100 + max_count: 100 owner: '@bioetl-config' linked_issue: '#4818' rationale: Documented intentional entity-specific partial keys excluded from actionable @@ -249,8 +249,8 @@ config_surface_ratchet: ratchet_policy: Non-growth fail-fast unless a reviewed entity contract adds new intentional divergence. raw_inconsistent_parameter_count: - current_count: 97 - max_count: 97 + current_count: 100 + max_count: 100 owner: '@bioetl-config' linked_issue: '#4818' rationale: Raw family-scoped partial key count before sanctioned-prefix exclusion; @@ -279,15 +279,15 @@ config_surface_ratchet: ratchet_policy: Non-growth fail-fast; entity-specific filters remain in backlog as sanctioned partial keys only. sanctioned_partial_parameter_count: - current_count: 97 - max_count: 97 + current_count: 100 + max_count: 100 rationale: Intentional entity-specific filters/extraction_params/overrides per reports/quality/config-surface-backlog.json. ratchet_policy: Non-growth fail-fast unless reviewed entity contract expands intentional divergence. raw_inconsistent_parameter_count: - current_count: 97 - max_count: 97 + current_count: 100 + max_count: 100 rationale: Raw entity partial keys before sanctioned-prefix exclusion. ratchet_policy: Informational non-growth guard mirroring backlog partial_key_count. composite_runtime: diff --git a/docs/04-reference/config_comparison_matrix.csv b/docs/04-reference/config_comparison_matrix.csv index fdfe90ff46..21f11d3ed5 100644 --- a/docs/04-reference/config_comparison_matrix.csv +++ b/docs/04-reference/config_comparison_matrix.csv @@ -343,7 +343,7 @@ filters.silver_filters.columns.term_type,—,—,—,—,—,—,—,—,—,— filters.silver_filters.ranges.activity_id,—,—,—,—,—,(dict),—,—,—,—,—,—,—,—,—,—,—,—,—,—,—,—,—,—,—,— filters.silver_filters.ranges.confidence_score,—,—,—,—,—,—,(dict),—,—,—,—,—,—,—,—,—,—,—,—,—,—,—,—,—,—,— filters.silver_filters.ranges.pchembl_value,—,—,—,—,—,(dict),—,—,—,—,—,—,—,—,—,—,—,—,—,—,—,—,—,—,—,— -filters.silver_filters.ranges.publication_year,—,—,—,—,—,(dict),(dict),(dict),(dict),(dict),(dict),(dict),(dict),(dict),(dict),(dict),(dict),(dict),(dict),(dict),(dict),(dict),(dict),(dict),(dict),(dict) +filters.silver_filters.ranges.publication_year,—,—,—,—,—,(dict),(dict),(dict),—,—,(dict),(dict),(dict),(dict),(dict),(dict),(dict),(dict),(dict),(dict),(dict),(dict),(dict),(dict),(dict),(dict) filters.silver_filters.ranges.standard_value,—,—,—,—,—,(dict),—,—,—,—,—,—,—,—,—,—,—,—,—,—,—,—,—,—,—,— hash_policy.hash_policy.normalization.dates,—,—,—,—,—,(dict),(dict),(dict),(dict),(dict),(dict),(dict),(dict),(dict),(dict),(dict),(dict),(dict),(dict),(dict),(dict),(dict),(dict),(dict),(dict),(dict) hash_policy.hash_policy.normalization.null_handling,—,—,—,—,—,(dict),(dict),(dict),(dict),(dict),(dict),(dict),(dict),(dict),(dict),(dict),(dict),(dict),(dict),(dict),(dict),(dict),(dict),(dict),(dict),(dict) @@ -467,8 +467,8 @@ filters.silver_filters.ranges.confidence_score.max,—,—,—,—,—,—,9,— filters.silver_filters.ranges.confidence_score.min,—,—,—,—,—,—,8,—,—,—,—,—,—,—,—,—,—,—,—,—,—,—,—,—,—,— filters.silver_filters.ranges.pchembl_value.max,—,—,—,—,—,10,—,—,—,—,—,—,—,—,—,—,—,—,—,—,—,—,—,—,—,— filters.silver_filters.ranges.pchembl_value.min,—,—,—,—,—,3,—,—,—,—,—,—,—,—,—,—,—,—,—,—,—,—,—,—,—,— -filters.silver_filters.ranges.publication_year.max,—,—,—,—,—,2050,2050,2050,2050,2050,2050,2050,2050,2050,2050,2050,2050,2050,2050,2050,2050,2050,2050,2050,2050,2050 -filters.silver_filters.ranges.publication_year.min,—,—,—,—,—,1950,1950,1950,1950,1950,1950,1950,1950,1950,1950,1950,1950,1950,1950,1950,1950,1950,1950,1950,1950,1950 +filters.silver_filters.ranges.publication_year.max,—,—,—,—,—,2050,2050,2050,—,—,2050,2050,2050,2050,2050,2050,2050,2050,2050,2050,2050,2050,2050,2050,2050,2050 +filters.silver_filters.ranges.publication_year.min,—,—,—,—,—,1950,1950,1950,—,—,1950,1950,1950,1950,1950,1950,1950,1950,1950,1950,1950,1950,1950,1950,1950,1950 filters.silver_filters.ranges.standard_value.include_min,—,—,—,—,—,False,—,—,—,—,—,—,—,—,—,—,—,—,—,—,—,—,—,—,—,— filters.silver_filters.ranges.standard_value.min,—,—,—,—,—,0,—,—,—,—,—,—,—,—,—,—,—,—,—,—,—,—,—,—,—,— hash_policy.hash_policy.normalization.dates.enabled,—,—,—,—,—,True,True,True,True,True,True,True,True,True,True,True,True,True,True,True,True,True,True,True,True,True diff --git a/docs/config-discrepancies-report.md b/docs/config-discrepancies-report.md index 21ef87f110..e808b365a2 100644 --- a/docs/config-discrepancies-report.md +++ b/docs/config-discrepancies-report.md @@ -349,7 +349,7 @@ Total unique parameters: 508 - `filters.silver_filters.ranges.activity_id` (1/26): entity/chembl/activity - `filters.silver_filters.ranges.confidence_score` (1/26): entity/chembl/assay - `filters.silver_filters.ranges.pchembl_value` (1/26): entity/chembl/activity -- `filters.silver_filters.ranges.publication_year` (21/26): entity/chembl/activity, entity/chembl/assay, entity/chembl/assay_parameters, entity/chembl/cell_line, entity/chembl/compound_record, entity/chembl/molecule, entity/chembl/protein_class, entity/chembl/publication, entity/chembl/publication_similarity, entity/chembl/publication_term, entity/chembl/subcellular_fraction, entity/chembl/target, entity/chembl/target_component, entity/chembl/tissue, entity/crossref/publication, entity/openalex/publication, entity/pubchem/compound, entity/pubmed/publication, entity/semanticscholar/publication, entity/uniprot/idmapping, entity/uniprot/protein +- `filters.silver_filters.ranges.publication_year` (19/26): entity/chembl/activity, entity/chembl/assay, entity/chembl/assay_parameters, entity/chembl/molecule, entity/chembl/protein_class, entity/chembl/publication, entity/chembl/publication_similarity, entity/chembl/publication_term, entity/chembl/subcellular_fraction, entity/chembl/target, entity/chembl/target_component, entity/chembl/tissue, entity/crossref/publication, entity/openalex/publication, entity/pubchem/compound, entity/pubmed/publication, entity/semanticscholar/publication, entity/uniprot/idmapping, entity/uniprot/protein - `filters.silver_filters.ranges.standard_value` (1/26): entity/chembl/activity - `hash_policy.hash_policy.normalization.dates` (21/26): entity/chembl/activity, entity/chembl/assay, entity/chembl/assay_parameters, entity/chembl/cell_line, entity/chembl/compound_record, entity/chembl/molecule, entity/chembl/protein_class, entity/chembl/publication, entity/chembl/publication_similarity, entity/chembl/publication_term, entity/chembl/subcellular_fraction, entity/chembl/target, entity/chembl/target_component, entity/chembl/tissue, entity/crossref/publication, entity/openalex/publication, entity/pubchem/compound, entity/pubmed/publication, entity/semanticscholar/publication, entity/uniprot/idmapping, entity/uniprot/protein - `hash_policy.hash_policy.normalization.null_handling` (21/26): entity/chembl/activity, entity/chembl/assay, entity/chembl/assay_parameters, entity/chembl/cell_line, entity/chembl/compound_record, entity/chembl/molecule, entity/chembl/protein_class, entity/chembl/publication, entity/chembl/publication_similarity, entity/chembl/publication_term, entity/chembl/subcellular_fraction, entity/chembl/target, entity/chembl/target_component, entity/chembl/tissue, entity/crossref/publication, entity/openalex/publication, entity/pubchem/compound, entity/pubmed/publication, entity/semanticscholar/publication, entity/uniprot/idmapping, entity/uniprot/protein @@ -473,8 +473,8 @@ Total unique parameters: 508 - `filters.silver_filters.ranges.confidence_score.min` (1/26): entity/chembl/assay - `filters.silver_filters.ranges.pchembl_value.max` (1/26): entity/chembl/activity - `filters.silver_filters.ranges.pchembl_value.min` (1/26): entity/chembl/activity -- `filters.silver_filters.ranges.publication_year.max` (21/26): entity/chembl/activity, entity/chembl/assay, entity/chembl/assay_parameters, entity/chembl/cell_line, entity/chembl/compound_record, entity/chembl/molecule, entity/chembl/protein_class, entity/chembl/publication, entity/chembl/publication_similarity, entity/chembl/publication_term, entity/chembl/subcellular_fraction, entity/chembl/target, entity/chembl/target_component, entity/chembl/tissue, entity/crossref/publication, entity/openalex/publication, entity/pubchem/compound, entity/pubmed/publication, entity/semanticscholar/publication, entity/uniprot/idmapping, entity/uniprot/protein -- `filters.silver_filters.ranges.publication_year.min` (21/26): entity/chembl/activity, entity/chembl/assay, entity/chembl/assay_parameters, entity/chembl/cell_line, entity/chembl/compound_record, entity/chembl/molecule, entity/chembl/protein_class, entity/chembl/publication, entity/chembl/publication_similarity, entity/chembl/publication_term, entity/chembl/subcellular_fraction, entity/chembl/target, entity/chembl/target_component, entity/chembl/tissue, entity/crossref/publication, entity/openalex/publication, entity/pubchem/compound, entity/pubmed/publication, entity/semanticscholar/publication, entity/uniprot/idmapping, entity/uniprot/protein +- `filters.silver_filters.ranges.publication_year.max` (19/26): entity/chembl/activity, entity/chembl/assay, entity/chembl/assay_parameters, entity/chembl/molecule, entity/chembl/protein_class, entity/chembl/publication, entity/chembl/publication_similarity, entity/chembl/publication_term, entity/chembl/subcellular_fraction, entity/chembl/target, entity/chembl/target_component, entity/chembl/tissue, entity/crossref/publication, entity/openalex/publication, entity/pubchem/compound, entity/pubmed/publication, entity/semanticscholar/publication, entity/uniprot/idmapping, entity/uniprot/protein +- `filters.silver_filters.ranges.publication_year.min` (19/26): entity/chembl/activity, entity/chembl/assay, entity/chembl/assay_parameters, entity/chembl/molecule, entity/chembl/protein_class, entity/chembl/publication, entity/chembl/publication_similarity, entity/chembl/publication_term, entity/chembl/subcellular_fraction, entity/chembl/target, entity/chembl/target_component, entity/chembl/tissue, entity/crossref/publication, entity/openalex/publication, entity/pubchem/compound, entity/pubmed/publication, entity/semanticscholar/publication, entity/uniprot/idmapping, entity/uniprot/protein - `filters.silver_filters.ranges.standard_value.include_min` (1/26): entity/chembl/activity - `filters.silver_filters.ranges.standard_value.min` (1/26): entity/chembl/activity - `hash_policy.hash_policy.normalization.dates.enabled` (21/26): entity/chembl/activity, entity/chembl/assay, entity/chembl/assay_parameters, entity/chembl/cell_line, entity/chembl/compound_record, entity/chembl/molecule, entity/chembl/protein_class, entity/chembl/publication, entity/chembl/publication_similarity, entity/chembl/publication_term, entity/chembl/subcellular_fraction, entity/chembl/target, entity/chembl/target_component, entity/chembl/tissue, entity/crossref/publication, entity/openalex/publication, entity/pubchem/compound, entity/pubmed/publication, entity/semanticscholar/publication, entity/uniprot/idmapping, entity/uniprot/protein diff --git a/scripts/docs/build/__pycache__/__init__.cpython-313.pyc b/scripts/docs/build/__pycache__/__init__.cpython-313.pyc deleted file mode 100644 index 4c636bfe66..0000000000 Binary files a/scripts/docs/build/__pycache__/__init__.cpython-313.pyc and /dev/null differ diff --git a/scripts/docs/build/__pycache__/mkdocs_build.cpython-313.pyc b/scripts/docs/build/__pycache__/mkdocs_build.cpython-313.pyc deleted file mode 100644 index 851a4b4d87..0000000000 Binary files a/scripts/docs/build/__pycache__/mkdocs_build.cpython-313.pyc and /dev/null differ