From 65f21c92cd1edb640dedec4cf6c9f79beb960cc2 Mon Sep 17 00:00:00 2001 From: "google-labs-jules[bot]" <161369871+google-labs-jules[bot]@users.noreply.github.com> Date: Sun, 31 May 2026 10:03:34 +0000 Subject: [PATCH 1/2] test: update config discrepancy metrics ratchets and baseline Co-authored-by: SatoryKono <13055362+SatoryKono@users.noreply.github.com> --- configs/quality/debt_scorecard.yaml | 16 ++++++++-------- docs/04-reference/config_comparison_matrix.csv | 6 +++--- docs/config-discrepancies-report.md | 6 +++--- 3 files changed, 14 insertions(+), 14 deletions(-) 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 From 5522f8ee9fb0d079c349e264b2a7c9af195a0789 Mon Sep 17 00:00:00 2001 From: "google-labs-jules[bot]" <161369871+google-labs-jules[bot]@users.noreply.github.com> Date: Sun, 31 May 2026 10:07:30 +0000 Subject: [PATCH 2/2] test: update config discrepancy metrics ratchets and baseline Co-authored-by: SatoryKono <13055362+SatoryKono@users.noreply.github.com> --- .../build/__pycache__/__init__.cpython-313.pyc | Bin 261 -> 0 bytes .../__pycache__/mkdocs_build.cpython-313.pyc | Bin 3624 -> 0 bytes 2 files changed, 0 insertions(+), 0 deletions(-) delete mode 100644 scripts/docs/build/__pycache__/__init__.cpython-313.pyc delete mode 100644 scripts/docs/build/__pycache__/mkdocs_build.cpython-313.pyc 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 4c636bfe66614cabb777e1716e50b51fc03beedb..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 261 zcmXv}!Ab)$5KXLTDfAz5?ZKTQcoU^sk%D>=yk^rRZilwXn#>l~|L`OHrM>zC;(mZ8 zrM}C&H!$zb>&N2}OZe44c%SB17XRP}(hn2)V9zYDicgN-uOHWQucKHtxG};y3T^Gt zQ53H}2wGWDE4@~gHKHt|4p>txOu8sbar>|+o+i9Il`?Il{A7Jj>0VrN`*Cg9G( z^g_-SP$8|FCETD_nsA5I&K0Sderqryp?BwS@Q3UV`;S0MbVyPbb=wUux85`xdlgPn SOl}l&o9_YVykmFaIEg diff --git a/scripts/docs/build/__pycache__/mkdocs_build.cpython-313.pyc b/scripts/docs/build/__pycache__/mkdocs_build.cpython-313.pyc deleted file mode 100644 index 851a4b4d870362db0d47ea4b23581ddd0e600b03..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 3624 zcma)8U2GHC6~5ycd+ae2$FT_z0vSvQaTmwgO{11wh(vz)3nZ*3u4qFUCgZ^#;>?&k zV<1triuR=}`v9vIRiwV;rBYZ`Di3`?RUg{zb0yC@TW5#t!)n_H-l#xD<*Db+_>Uj8 zy_WBsd+)jD-h0mZ&N5!ACFh0uK@B8)^z^i5M|eb^@u znx3XH?S2`|xL-f^yWao~z?Ye3&jxYO<@Ha8&T^O&&?PQ`E`>)yCTW>H-nYFUtq(Fi z?Xw;&2K+$aj!PXPn+hW&21$=2F!rcUF(QU~&@~1}#ZHlPsV*@phFvNqc8NP&DlW#v zxX2Uw8ijXW>J~fRzle~`BXnsO+;C?CHSW>4t4ihRIT306TB&M!_HiYb_y zrNS5+<$S@NFUiWHoL6(gl`E!#wUT8H<$&?Z6#;lGb?6CsOpOCpz(;Bu0Bt5nn!&BC2eGE$Unck_M?V4!t@u()PQcTL z<98K8jNw-bsU!rx?<$iB#i+> z$YB*@X-U>|P5`TBxoDa2LNK9#BV?7A+SQNu!5sOU1aqrsJJNOcqfb6sv(_(e+^lqr zJ&HrOdTN{Bb@%d}%WJ1LMs5Dx)stJ{Xf51phkGkbFOI@arCnc5t^NU403C0|Km+4V z1au=b-;|PRY8OP*8_{V42Lh4$7QJUe4er(#>;{%Q>J!@KyV1ABL#PD0NR8HS00=@! zdS(u=z?NjJ>XzvQ)mxfrNycI_-~?RSbOL6fY-vSM^^%2E)d_gajvth)VJD~f?f~%$0LaQ~?G2Ot08G~8X#s)+BzZ5aH4XGO03_P>w#=Fb#plrjY6iT&Q#vcqrPCGpJMlr(uJgAc%IPE?wlI(Z^{Zmu<-fO$+5^#HkV^jv+nq!d+IFPEgEnwOR3 zmR{4q3YSObFm&Mc?5-NS-)8sMSixq6%|oM`N6%IdovkZ)vwPs{;Nhn<8knXktl(*} zJ*-0l_q6yW%z_r1Ygx1a7S5vCuK(`Z;Gl>>4J|-$Arjpt`g*|CV{fFyCTt)H&o`aE z1(1F;4=Y}4&Hf*|b~JWnIvP~#n}F0MGDj&N(tYy;_ioGj8aEgHq$tqo){W9|`wuBG zaDkeSHTmfV|Ai)?btcP*tm`=-AwEzh(+S!sY58=XVEsptSNz?FDD1cs* zl4lQ~BdDQ=99ZhAPe6T0fM1?HPWPd!R5Cd8gqZM^R6+1CLXblI<{)s_(?00lh>8eu zF}i{7`vr6!?(e2x>PIxl@-?z>;bkC|DyYTM3?2ezhzP!+VN8@<&#|7I2xl?Vhfs~ zTE&zX@4W&5l1re3)vMYq90Wd0d<2sql;j>8b`v zsA~==1Iu`MQp2iZ8F(3!m=Ed7!fwpMDI$fSEa~@zk&41}LPUmy4a0IGP;fw@*2JU} zf{#wnWHrv-W`}a_^7V7^h)L%Jr;;Yd3 zpS10s{cFp=PH&vFd)~Vp*^VEmB+jo-Lbq`QxKIkp)*z8w@GLcie28Yx8h7ZE~khQ{5|OOq5je;yg0=%l|) z^+5lZPHtj9>jWi=Co%=k1}dk4C@oR#=1X9>R$2)D;eO0wi`hm|C#<0Q%9B-@1CcD0E=KW& ziu(u`CuOEC%u1Qr**VX%ju6?TMD+ZVq)FG?TqhxV)8!>1h7*@faJeb)EEjZb$su@b z$;g$9>KM+zZUT3cW z!76{K#;0sPwISR5@G7?z-@o2%#}97|*zw^Cif+aBtq1JbKm~O^4+N>`^KP2j_k0IK qC7*ZrsKI}69TfjGftVe)SE}@$Z@BnpbD#gD%8`-^QVrAN-t|BG8TEGn