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Adopt the Python distribution policy and guarded noarch publication route #78
Description
TopoMT actual recovery and retained debt — 2026-10-09
CI/distribution stay partial; early maturity and the approved coverage deferral stay unchanged. No component changes, new science run, package/version/tag/pin operation or stability deadline.
At 74191c225850e5e54cc40bc278d077388f2d4057, actual daily 37946142584 observes 78 skipped commits / no successful executed full watermark. Detector and independent reporting/distribution/environment governance pass. All eight Linux/macOS arm64 × Python 3.11–3.14 cells execute installation, installed-source Git-context/dependency checks, import and interpreter/architecture assertions successfully, then fail in Run tests. Representative 3.14 results: Linux 6 failed / 2004 passed / 85 skipped / 5 xfailed; macOS arm64 7 failed / 2003 passed / 85 skipped / 5 xfailed. The full daily remains failed and clears no debt. Scientific interpretation/repair stays with #16.
Exact probe 37841619267 retains the same 78/no-watermark facts and deliberately omits science. Exact policy, Conda controls and Ruff pass. Source/workflow/event/attempt/complete job inventories and mandatory executed steps are qualified. Historical manual 36716726423, previously recorded running, has completed: all six then-configured actual science steps failed. This corrects that stale observation, without claiming recovery.
Twenty protected controls retain accepted be72f8c1d77bfbf853e3e65ee29de71132b13443 bytes; later guide/developer memory-tool changes are separate. Ten strict required checks, explicit zero-approval PR integration and administrator direct pushes remain. Publication still retains SDK 2d32048, source/environment SDK 8f00e6d, 609 mandatory paths, eight installed cells/four steps and the twelve-job candidate example. Current accepted PR/platform review remains #58; source-free ordinary environments, a real owner-selected plan/candidate/access/archive/installed/public/admission outcome remain #78/#16. No new requirement or mandatory checker rollout follows. Keep both owner issues open. #81 retains its owner-selected early-maturity coverage deferral; no badge or coverage execution is requested.
Immutable receiving receipt. Local six tests and offline guard pass. Exact central governance 38028953243, attempt 1: 447 tests, publisher controls, XML retention and coverage upload pass. Global private-OpenCASTp access audits remain a separate uibcdf/molsyssuite#102 limitation. Upload execution is not downstream processing or a scientific/public-package certificate.
Previous issue context (retained)
What — Adopt the Python distribution policy and guarded noarch publication route under uibcdf/molsyssuite#45. Status remains partial; Python/platform qualification is also owned by #16.
Delivered (2026-10-07) — Source be72f8c1d77bfbf853e3e65ee29de71132b13443 adopts publication SDK 2d32048457c6d37093ae509f5626d00a5cda121b and separately qualified dependency/environment SDK 8f00e6d9de943b6e4710ea62936e2ebea00fad24 (uibcdf/molsyssuite#108). The current inventory covers 609 tracked core/addon paths, bounded package discovery and reference assets. The installed descriptor requires all four installation/resource/science/provenance steps in eight Linux/macOS arm64 × Python 3.11–3.14 cells. The candidate example requires twelve executed jobs and the promotion wrapper separates qualification SHA from the original producer commit and artifact identity.
Dependency/environment controls — Nineteen routes, twelve original source records and seven contexts bind both original Git input manifests, distinct older/Python 3.14 MolSysMT/Viewer revisions and actual bootstrap overlays. Existing science commands, source pins, matrix, triggers and recovery are preserved. Five ordinary environment documents use shared optional tooling; specialized scientific inputs remain component-owned. By explicit maintainer decision, unused nglview leaves recipe/production runtime and remains development/test/docs tooling. Routine Ruff uses Python 3.14. Public installation claims now state managed-source prerequisites rather than infer public package availability.
Measured — Eighteen distribution and eight environment-helper guards plus eight existing reporting/CI tests pass locally. Scoped type, Ruff/format, actionlint, declared preflight, environment drift and conformance checks pass. Exact-head native policy 37591125458, publication controls 37591125843, Ruff 37591124818, and the Reporting/CI governance job in 37591124705 pass executed job/step verification. The latter verifies that administrative job only, not the full scientific matrix.
Remaining — Actual source-free environment closure, successful exact-candidate science/platform execution, a real reviewed release plan, confirmed credential access, the original staged archive, complete installed qualification and same-byte authorized promotion/public receiving evidence. Scientific defects and release choices remain with the component team. Missing/skipped/failed required evidence blocks publication. Ordinary internal push policy is unchanged.
Record — Owner analysis. Central immutable receipt.
Historical scope — Earlier isolated illustrative 0.0.0 wheel evidence covered 297 paths at the earlier source; it does not qualify the current 609-path candidate. No actual Conda build, installed-science dispatch, environment create/update, tag, upload or promotion was performed in this control adoption.
Activity
LMMV commentedon Oct 3, 2026
Shared noarch publisher correction available for review/adoption — 2026-10-03
At the MolSysSuite maintainer's request, this is the component adoption handoff for uibcdf/molsyssuite#78. The existing proposed change uibcdf/molsyssuite#81 has been integrated directly into published main at 2a2a459cc3795bb92766fffa0fe28f4d80f01ad4.
The current
.github/workflows/build_and_upload_conda_packages.yamlselects shared source42e4de425871c125ef058842075c39e50fc6ac64. Review and update only its shared build caller to:The shared builder now selects qualified provider
8da628d9b393e184c3bf3722708b19dcfbf7ef0a. Its compilation/conversion usescommand condato find the activated environment's executable rather than the base-backed shell function. This repairs the pre-archive failure reproduced by Ackredit run 37109889925 and Pytest Receptor run 37111808160. Provider issues uibcdf/action-build-and-upload-conda-packages#46 and uibcdf/action-build-and-upload-conda-packages#47 are resolved; 37115921728 qualifies real recipe tests on Linux named/base, macOS ARM named and Windows named environments, and 37115921702 qualifies the variant/installed-import fixture.Central offline governance and 273 local unittest tests pass, including a regression protecting this build source and the separate exact-upload pins. Hosted governance 37125099269 passes the published integration on the configured Python 3.14 lane. Recipe tests, version freeze, resource/archive checks, exact-file uploads, promotion controls and independent public checks retain their existing requirements.
Please record the reviewed caller commit here. Before claiming a usable component producer, verify an actual exact-candidate staged build with recipe tests and inspected archive/producer evidence, then apply the committed installed matrix before promotion. A notification or configuration update alone does not qualify a package. Keep scientific failures and release decisions in this component's owning work. This notice does not request scientific suites on each internal push or authorize any new public release.
Coordination record: MolSysSuite #78 handoff.
LMMV commentedon Oct 3, 2026
Installed noarch test-tool capability qualified — MolSysSuite #77
The shared installed workflow now supports component-owned bounded test dependencies committed in
devtools/conda-build/resources.toml:Review the reusable installed caller at immutable source baac208f3f592e00eaf99fa78a879878f98dc141:
Local equivalents may call
installed_noarch.py tools --root COMPONENT --python MINOR --output RECEIPTfrom that same source. The running prefix and declared minor are bound explicitly, using only ordinaryuibcdf, thenconda-forge, strict channels. Missing extra declarations preserve standard tools. Python and the candidate cannot be tool dependencies; when testing Pytest Receptor, the candidate supplies the receptor plugin. URLs, channel qualifiers, markers, extras and unbounded specs are rejected by the initial adapter.Qualification run 37127638411 passes Linux/macOS ARM × Python 3.11–3.14. Every cell actually executes both optional plugins and rejects source shadow and collection-only success. Central governance 37127589232 passes all 278 tests.
Please review this extension for your next installed candidate. Keep your scientific selection, matrix and release decisions local; a caller pin or this dummy-consumer receipt does not qualify your actual staged artifact. The current build correction remains uibcdf/molsyssuite#78, and no policy-caller bump or public package upload follows from this capability.
Contract; archived provider record.
LMMV commentedon Oct 3, 2026
Qualified exact-upload adoption — MolSysSuite #86 / #78
The maintainer approved direct adoption. Existing central PR #85 is integrated at 2fb344525ca0eea817dc24a518f4a6bf26e311cf, using the more completely qualified upload provider 1aa2011f902a1a9d533564572245bb29f6862e86 from uibcdf/molsyssuite#86, rather than its earlier implementation-only pin.
The reviewed shared caller is:
This component's thin caller changes from
uibcdf/molsyssuite/.github/workflows/publish-noarch-conda.yaml@42e4de425871c125ef058842075c39e50fc6ac64. Prepared adoption commit: 8a3e438, based on fetched main73f5ff2d733846145729777e82958e557283ffec; it will be pushed directly after this notice. The only component change is this immutable publisher reference. Its administrative publication-contract check passes. Existing installed/promotion callers, candidate plans, tests, secrets and release decisions retain their contracts.Central governance 37130795870 passes at the exact published source on Python 3.14. The central regression rejects the earlier pin and protects both qualified uploads plus the separately qualified upload-free build. Provider qualification 37129463375 passes the actual composite in named Linux/macOS Conda environments for success and client failure, plus the offline contract. Client and registry are simulated: this qualifies the shell/client boundary, not actual package delivery.
For the next component candidate, obtain fresh native gates at its exact full SHA, inspect current all-label registry state, and keep recipe/archive/resource checks plus the committed installed matrix. An old absent-coordinate observation or failed upload receipt does not authorize repeating a mutation. Record actual producer/artifact/upload evidence here and cross-link uibcdf/molsyssuite#78. Scientific failures and public-release decisions remain component-owned; this adoption adds no full suite to each internal push and performs no registry mutation.
Contract: https://github.com/uibcdf/molsyssuite/blob/2fb344525ca0eea817dc24a518f4a6bf26e311cf/devguide/noarch_conda_workflow.md . Central record: devguide/pending_proposals/adopt_qualified_exact_upload_environment.md.
dprada commentedon Oct 3, 2026
Shared installed-gate correction proposed in uibcdf/molsyssuite#88 / uibcdf/molsyssuite#91, exact source
3350615eee8c95903aca916e42789ecbdcc1f8ef: public dependency solving followed by digest-checked exact staging URL installation; optional separately reviewed qualification-workflow SHA with a native attempt-qualified original-source/file binding; three/four-step profile compatibility; helper launch underPYTHONSAFEPATH.The eight-cell Pytest Receptor installed run https://github.com/uibcdf/pytest-receptor/actions/runs/37148738757 now passes on Linux/macOS ARM × Python 3.11–3.14 with unchanged producer source and archive. All 284 provider tests and hosted governance 37148069479 pass. This proves that receiving candidate, not other consumers' compatibility or publication. Existing same-source callers retain their default contract.
For a blocked staged candidate, review this source and qualify your own immutable archive, committed dependencies and complete installed selection; supply a qualification SHA to promotion only when using a corrected workflow revision. Avoid rebuilding or overwriting occupied coordinates. Existing provider pins remain reviewable until receiving adoption. This is an installed-gate correction, separate from deferred action v2.3.0 rollout. Pipeline effort follow-up: uibcdf/molsyssuite#92. Pytest Receptor public delivery remains uibcdf/pytest-receptor#32.
LMMV commentedon Oct 3, 2026
MolSysSuite #88/#89's corrected installed-file route is accepted at immutable
c3e2b9b3dabf3d1c65349c389a23048957bea21a, directly integrating existing PR #90/#91. All 286 central tests and exact-source hosted governance 37151428556 pass on Python 3.14. Existing publisher/build/upload/promotion-provider references and internal-push CI policy remain unchanged.For the next applicable installed qualification, review adoption of
.github/workflows/test-installed-noarch-conda.yamland.github/workflows/promote-noarch-conda.yamlat that SHA. The fix installs the digest-checked exact staging URL after solving dependencies on ordinary strict public channels, accepts both the legacy three-step and actual four-step profiles, and usespython -Pfor scientific execution without breaking administrative subprocess helper imports.An already registered archive can be tested by a reviewed corrected wrapper: preserve original
candidate_sha, file and SHA-256; retain the corrected native component head in the new attempt-qualifiedinstalled-source-binding-RUN-ATTEMPTartifact. When it differs from producer source, pass that reviewed componentqualification_shaexplicitly to promotion. Do not put the central workflow SHA in that field. Native complete matrix/job/step/attempt and binding identity/digest checks still apply.Exact caller/receipt handoff: https://github.com/uibcdf/molsyssuite/blob/c3e2b9b3dabf3d1c65349c389a23048957bea21a/devguide/noarch_conda_workflow.md and uibcdf/molsyssuite#78 / uibcdf/ackredit#22. Review under this component's existing owner-controlled publication plan and declared supported matrix; the notice is not an adoption or scientific/public-delivery claim. No archive rebuild/replacement is needed for an administrative wrapper correction. General action v2.3.0 adoption and withdrawal remain deferred/outside scope.
LMMV commentedon Oct 3, 2026
Shared release operator implementation notice — uibcdf/molsyssuite#92
Reviewed central source prepared for direct publication:
fb45a15f546a244c2ee3f7c2e87781c7125e8754. The new read-onlydevtools/scripts/noarch_release.pyderives original producer source/version/archive/digest from native staging receipts, verifies an existing installed matrix when supplied, checks current registry state, and prepares argv for the existing qualification/promoter wrappers. It never dispatches, builds, installs or mutates the registry. Already-public bytes produce no next publication command.The bounded JSON-artifact reader is shared with installed-source verification; existing immutable consumer pins retain their execution contracts. Usage and normal/recovery paths:
devguide/noarch_release_operations.md; source/measurement record:devguide/pending_proposals/qualify_and_simplify_shared_release_pipeline.md; native read-only examples/baseline:devguide/rollouts/release_pipeline_92.json.298 central tests pass on Python 3.14.7; Ruff, governance and administrative publication checks pass. Real read-only checks bind Ackredit 0.9.0 and Pytest Receptor 1.2.1 to their original producers, full existing installed matrices and public hashes. Those are retained evidence checks, not fresh tests or dependency solves. Missing/expired evidence, uncertain upload, changed file/source/attempt, dropped caller inputs or moved ref stop the handoff.
This is an optional administrative tool available to shared-noarch publishers; there is no required consumer commit or pin change now. For later use, choose a reviewed immutable central clone and follow the documented entry point. Component release/scientific decisions remain in their owner issues. Independent provider execution qualification and a later ordinary-release effort comparison remain open under #92 / uibcdf/moli#43; v2.3.0 rollout is separate.
LMMV commentedon Oct 4, 2026
Shared-provider advance notice: uibcdf/molsyssuite#101, discovered while reviewing ArgDigest 0.14.0 under uibcdf/molsyssuite#98 / #92.
The read-only
noarch_release.pyoperator currently accepts a caller with an additional required input it never generates. Reproduced against ArgDigest's immutable promotion caller at be39e899f3b9fef2d4ce705799ae19770f41f769: standard/recovery fields pass, but mandatorycore_run_idis absent. No incomplete dispatch was attempted; the real release and its original file are already independently public-verified.Prepared central correction: reject such a caller before emitting any command, name the missing fields and point to a reviewed component adapter or the existing local route. Preserve extra component gates. Required defaults are not silently chosen; optional extra inputs continue to work. Read-only post-publication verification still emits no mutation. The regression fails on the old code and all 14 operator tests pass after the correction; the actual ArgDigest caller now yields the expected
core_run_idrejection.No member workflow, provider pin, dependency, scientific selection, package bytes or publication is changed. This is a fix to the existing bounded administrative operator contract, not a new policy gate or provider v2.3.0 rollout. Known post-publication operator users are Ackredit, Pytest Receptor and ArgDigest; TopoMT, PharmacophoreMT, ElastNetMT and LinDelINT are candidate users from the registered publisher inventory, not proven operator adopters. Standard callers with all generated required fields remain supported. The exact central commit and hosted CI will be delivered after publication through #101/#92.
Verified delivery
Published operator correction: c9b5a87633386816cfe55781b023439479863dd8. Contract; reproducer/guard rationale. All 14 operator tests, Ruff, offline governance and 331 hosted central tests pass. #101 is resolved; #92 retains independent operator/effort qualification.
Use the immutable corrected operator for a future standard administrative handoff; extra required inputs explicitly require a reviewed adapter or the maintained local route. No caller/policy-pin migration is requested. No scientific gate, component workflow, artifact or release is changed/reexecuted by this delivery. Existing public-file read-only verification remains supported.
LMMV commentedon Oct 4, 2026
Preparación de la entrega compartida de uibcdf/molsyssuite#92, antes de publicar la implementación.
La ruta existente
devtools/scripts/noarch_release.pyincorpora perfiles optativos de gates adicionales. Conserva los workflows, guards y selección científica locales. Sin perfil, los callers con inputs obligatorios desconocidos siguen rechazándose; las rutas actuales siguen disponibles.Primer perfil:
argdigest-core, con hashes de las fuentes revisadas y--gate-run core_run_id=ID. Comprueba workflow/evento, commit productor, título con archivo/SHA-256, matriz completa, pasos ejecutados y estabilidad del intento. Rechaza evidencia incompleta, omitida, de otro archivo/commit o fuentes distintas.--qualification-shaconserva la identidad de validación instalada;--promotion-shapermite revisar por separado el caller de promoción. El perfil de ArgDigest exigemainpara preparar esa llamada.Evidencia: 30 pruebas específicas pasan. Verificación real de solo lectura: ArgDigest 0.14.0, productor
0fa776af2d271065c60727c28480b20c3ce09aee, validación instaladabe39e899f3b9fef2d4ce705799ae19770f41f769, caller42b2f93346fdcd1573ade66a3f82a1717a496184, core https://github.com/uibcdf/argdigest/actions/runs/37211211381 (12 jobs). Conserva SHA-256983dca0f6bd0944d81fb1efc01e1dfa5c951e95abac6e7a0a08a13b7370d3b9e, devuelvepublic-verifiedsin comando ni mutación. No se ha reconstruido, promovido ni ejecutado una suite científica.Adopción: optativa; ArgDigest puede usar el perfil revisado. Los demás publicadores son candidatos para perfiles futuros si tienen un gate adicional: antes de adoptarlo se revisan y registran su caller, fuentes y evidencia en el issue propietario. No exige cambios de pins, dependencias o workflow. La guía
devguide/noarch_release_operations.mddescribe el contrato. Falta medir la ruta en una publicación ordinaria y recibir resultados de los propietarios; #92 permanece parcial.Commit inmutable publicado:
23a350ff2ed8a14ac4118e7bed6b9aaed357dda0. Contrato: https://github.com/uibcdf/molsyssuite/blob/23a350ff2ed8a14ac4118e7bed6b9aaed357dda0/devguide/noarch_release_operations.md . Recibo: https://github.com/uibcdf/molsyssuite/blob/23a350ff2ed8a14ac4118e7bed6b9aaed357dda0/devguide/rollouts/release_gate_profiles_92_20261004.json . Validación hospedada del commit exacto: https://github.com/uibcdf/molsyssuite/actions/runs/37233058629 . GH Run Receptor 1.2.0 y los jobs/logs nativos corroboran éxito: guard de gobernanza, 337 pruebas centrales (OK), controles Conda y subida de cobertura. Las auditorías entre repositorios de la entrega anterior bloqueadas por OpenCASTp temporalmente privado quedan pendientes en uibcdf/molsyssuite#102; este CI central no las certifica.LMMV commentedon Oct 6, 2026
Accepted scope for uibcdf/gh-run-receptor#60: prepare an additive noarch Python Conda route, preserving the existing GitHub modes. The first release plan, staging archive, twelve native installed cells and credential evidence remain pending; public 1.2.0 bytes/tags will not be rebuilt or replaced.
Provider need under uibcdf/molsyssuite#45:
noarch_conda.inspect_recipecurrently checks Python requirements but cannot bind an externally distributed executable floor in the exact archive. We are adding optional top-levelexternal_run_requirementsandexternal_run_reasontoresources.toml. For GHR,gh>=2.48.0will be checked against recipe and archive metadata; GHR separately ties that value to its actual adapter floor and checks the installed command. Native executables still cannot be bundled in a noarch Python payload.Compatibility: absent fields preserve current behavior and existing pins; no forced migration or release action. Components needing this capability can explicitly adopt the accepted immutable provider commit after its native checks. Notice applies to seven shared publishers from
devguide/rollouts/conda_publishers.json(ArgDigest, Pytest Receptor, TopoMT, PharmacophoreMT, ElastNetMT, Ackredit, LinDelINT), existing route-audit consumers SMonitor, DepDigest and PyUnitWizard, and new GHR. Delivery will record the exact commit and regression evidence separately from consumer adoption and tested artifacts.Prepublication impact notice: uibcdf/molsyssuite#45 (comment) . No action is required for the currently pinned provider. If this component later needs an external command dependency, adopt the accepted full provider SHA announced in central #45, declare the constraint/reason explicitly and add owner-installed executable checks. This notice is neither consumer adoption nor release evidence.
LMMV commentedon Oct 7, 2026
Prospective shared environment-tool delivery (#108)
We are implementing optional independently reusable operations in MolSysSuite, replacing PharmacophoreMT's import-time broadcaster and unchecked create/update helpers. The previous accepted dependency SDK is
2d32048457c6d37093ae509f5626d00a5cda121b; a new immutable commit and executed qualification will be handed off before first adoption.Known current need: uibcdf/pharmacophoremt#10. Candidate consumers from registered distribution review work: uibcdf/elastnetmt#18, uibcdf/lindelint#13 and later #78. These candidates retain their present pins and local controls; this notice does not establish adoption or require migration.
The new API/CLI will select explicitly registered environment documents, derive runtime bounds from package metadata, preserve reviewed source/context and Python restrictions, validate all proposed outputs before writing, and provide a non-mutating drift check. Conda/Mamba invocation will require explicit manager and target identity, checked argument-vector execution, strict priority and temporary-file cleanup. Imports will not invoke tools or rewrite files.
Compatibility: additive opt-in tooling; existing dependency/publication contracts remain unchanged. Recipes, release plans, Git source inputs and unselected specialized environments will not be generation targets. Owner tooling/native/scientific choices stay local. No actual environment installation, artifact build, upload, promotion or release choice is authorized by administrative tests.
First adoption will be delivered in uibcdf/pharmacophoremt#10 with an immutable SDK pin, thin local selection, regression evidence and protected-file hashes. Follow-up owner: MolSysSuite/LMMV for the shared operation; each consumer owns its configuration and subsequent actual environment/scientific evidence. Interim fallback remains reviewed files plus the accepted preflight. Current unknowns include actual solver/native compatibility and other consumers not yet inspected.
LMMV commentedon Oct 7, 2026
Shared environment tooling qualified and first adoption delivered
Provider: uibcdf/molsyssuite@8f00e6d. Its 406 central tests, including 12 new regression guards, pass locally and in hosted governance 37588128776. The exact source/attempt/native jobs and steps, including the dependent coverage upload, are verified. Contract and API/CLI.
First consumer: uibcdf/pharmacophoremt@448e47e, integrated over the concurrent owner scientific commit 9b308b54e50e065c126f6f8483ebcdfb74cf42d1. Thin wrappers replace duplicated import-time/unchecked helpers. The owner profile generates only production, development, docs, setup and build documents; metadata owns runtime and local groups own tooling. Eight protected recipe/plan/source/scientific/fixture files keep their original bytes. Scientific source pins, test commands, eight-cell source matrix, triggers and recovery are unchanged. Publication wrappers retain the separately qualified 2d32048457c6d37093ae509f5626d00a5cda121b; source/helper preflight uses the additive new SDK.
Executed adoption evidence:
Compatibility/migration: the provider API is additive and opt-in. Existing candidate consumers keep their local tools/pins. PharmacophoreMT usage documents explicit manager/new-name or active-prefix commands, whole-minor/routine/source restrictions and the retired unsafe startup flags. Startup is now explicit creation at Python 3.14; activation, editable installation and optional kernel registration are separate actions. There is no implicit update fallback or pruning, and imports are inert.
This completes shared capability and first source adoption under uibcdf/molsyssuite#108. It does not create/update a real environment, run an installed scientific dispatch, select a release, build/upload/promote a package or establish public receiving evidence. PharmacophoreMT #10/#23 and central #45 remain partial for those owner-controlled prerequisites. The existing #82 workspace closure and #102 private OpenCASTp acquisition debt remain separate. Candidate consumers uibcdf/elastnetmt#18, uibcdf/lindelint#13 and #78 may adopt the qualified SDK through reviewed owner profiles; this notice is not their adoption. Next ordered control review: #78.
Durable resolution/guard: archived #108 record; native qualification/adoption and protected-file receipt. The final central record update passes 150 affected governance/distribution/operator tests locally; the previously qualified SDK code is unchanged.
LMMV commentedon Oct 7, 2026
Current distribution/source-control adoption — TopoMT #78 / MolSysSuite #45
Current owner base:
bfbd28f8c3d25a438c7b3d1e526097dd56f63d3c; isolated review leaves the main clone's modified generated version file intact. This authorized direct-push chunk updates stale package discovery/resources (297 declared paths versus 609 tracked files across TopoMT and its MolSysViewer addon), adopts the accepted four-step/eight-cell installed controls, source/context preflight and optional shared environment tools. No actual release plan, build/upload/promotion or installed-science manual dispatch is being selected.Reviewed provider identities: publication SDK
2d32048457c6d37093ae509f5626d00a5cda121b, source/helper SDK8f00e6d9de943b6e4710ea62936e2ebea00fad24(406 hosted central tests, shared capability uibcdf/molsyssuite#108). Existing exact scientific Git manifests, older/Python3.14 MolSysMT/Viewer distinctions, optional-engine scientific workflow, source test commands/matrix/triggers and recovery are preserved. Missing Python bounds are qualified; the source-free ordinary declarations remain separate from actual solver/native proof.The maintainer explicitly chose to remove unused
nglviewfrom package/production runtime while retaining it as development/test/documentation tooling. No other scientific API floor or dependency selection is invented. Existing required core and optional extras remain owner-defined. Candidate plans will require exact executed source/admin steps, not a successful configuration-only check.Remaining whole-policy criteria continue to belong to this issue and admission #16: actual source-free closure, complete successful exact-candidate science, real plan/access/original archive/full installed qualification/same-byte public promotion/receiving evidence. Shared/provider notices do not prove this consumer adoption; the delivery will record immutable owner source and executed administrative evidence after push.
LMMV commentedon Oct 7, 2026
Control adoption is delivered at
be72f8c1d77bfbf853e3e65ee29de71132b13443and registered centrally at2e3cabaecdfdb3406e4148e55dbe625368fb50db. This issue remains partial/open.Immutable evidence and remaining work records the accepted source, separate publication/dependency SDK pins, 26 new guards, eight existing governance tests and exact native gates.
nglviewwas removed from package/production runtime with maintainer approval and retained as tooling.Owner handoff: use
devtools/README.md,devtools/conda-envs/README.mdand the publication README at the accepted source. Ordinary environment management now uses explicit shared-operator targets/profiles; retired implicit environment discovery/legacy local flags are documented there. Specialized scientific environments and original source pins are preserved. Actual environment closure, candidate science, a real release plan/access, staged bytes and installed/public qualification remain your work under this issue and #16. Existing SDK pins stay immutable; the central receipt commit is a record, not a replacement SDK pin.This completes the ordered early-scientific component control review for uibcdf/molsyssuite#45. It does not declare a release or clear scientific debt.
LMMV commentedon Oct 7, 2026
Advance shared-provider notice — uibcdf/molsyssuite#110 is preparing reusable installed import-origin checks for every Python root in a distribution, including addons and namespace paths. The installed runner will clear inherited pytest pythonpath and enforce importlib collection after component arguments, retaining administrative helper subprocess behavior and exact source/archive bindings. Optional integrations are checked when loaded, not imported eagerly.
Known shared consumers come from the maintained Conda publisher inventory. Existing immutable calls remain pinned; there is no automatic migration, release dispatch or rewriting of historical evidence. DockingMT #47 is the initial reproduced consumer, TopoMT #78 a candidate addon consumer; actual affected public qualifications are unknown.
The provider will deliver an exact accepted commit after regressions and native central CI. When adopting, review declared runtime roots/source-dependent helpers and qualify the real installed candidate with that exact provider before removing a receiving workaround. Keep actual producer commit, file and SHA-256 unchanged when using the authorized separate qualification route. No new scientific dependency/API floor or full-suite-per-push rule follows.
LMMV commentedon Oct 7, 2026
Accepted shared provider for uibcdf/molsyssuite#110:
948d0267de8fa43c542ab7eba28b9f8b7fbf095e.Exact reusable workflow:
uibcdf/molsyssuite/.github/workflows/test-installed-noarch-conda.yaml@948d0267de8fa43c542ab7eba28b9f8b7fbf095e. No workflow input, producer/file/digest binding or mandatory installed step name changes. Twelve new regression guards and 58 focused checks pass; native central 37602443801 independently verifies 428 tests, publisher controls and dependent coverage upload. Three actual-runner cases failed on the original provider and pass after correction. The existing administrative-helper subprocess regression also passes.The runner clears inherited pytest pythonpath and enforces importlib collection. It checks the primary and all loaded addon/namespace roots inferred from reviewed Python payload, before and after tests. Optional integrations are not eagerly imported. Optional top-level import_roots can add roots but cannot omit the primary/payload roots. TopoMT, ElastNetMT and DockingMT declare addon roots in the nine reviewed inventories; these observations do not certify actual scientific artifacts.
Adoption: retain current pins until reviewing this provider against the component's real installed candidate and source-dependent helper needs. Existing explicit pythonpath overrides remain compatible. Preserve the original producer commit/file/SHA and use the authorized separate qualification route when applicable; do not rebuild existing bytes to change validator. No automatic rollout, science dispatch, release or rewriting of past receipts.
Archived resolution; qualified provider receipt. Provider work is complete; optional source adoption and actual installed evidence remain in this component's existing owner issue.
LMMV commentedon Oct 9, 2026
Advance provider notice — uibcdf/molsyssuite#112 corrects native Windows route discovery in the existing shared dependency preflight. SMonitor's original schedule 37935661439 fails before tests because devtools\conda-build\meta.yaml is compared with the portable inventory identity devtools/conda-build/meta.yaml. The new audit-level regression reproduces exactly that failure on the original provider; source correction uses POSIX relative identities for discovery only. Inventory meaning, missing/unclassified-route refusal, exact workflow hashes, dependency bounds, input schemas and publication gates remain unchanged.
This is an optional compatibility correction for registered preflight clients/candidates under #45, not evidence that every listed member executes Windows preflight. SMonitor receiving is uibcdf/smonitor#46; CI reconciliation stays #39. Existing accepted immutable provider pins remain until deliberate receiving review. No automatic migration, scientific test dispatch, new policy gate/cohort, release or package mutation. The exact accepted commit and executed central controls will be delivered after verification. Actual Windows receiving and installed/public artifact qualification remain separate; failed schedules cannot clear debt.
LMMV commentedon Oct 9, 2026
Accepted optional shared SDK for uibcdf/molsyssuite#112: 6d6172d6cd00c5ac2d4ebadb71df554ec5b7fa26.
devtools/scripts/dependency_routes.py::_filesnow compares slash-separated relative identities on Windows as on Linux/macOS, preserving filesystem access, new/missing-route refusal, exact workflow-byte hashes and existing @1/@2/@3/directory inputs. The audit-level Windows-semantics regression fails on original source with the exact SMonitor error, then passes after correction and still rejects an unreviewed environment/changed workflow. Forty-six focused route/context/constraint tests and six CI-policy checks pass; exact central governance 37991982473 independently verifies both jobs and all executed mandatory steps, 447 tests, publisher controls and coverage retention/upload. Upload success is not service processing or installed-artifact proof.The first source checkpoint 738e6f3 failed only the old live-registry assertion expecting Pytest Receptor partial; it was not handed off as accepted. That failure and the explicit Linux/macOS adopted-review correction are retained in the immutable receipt. Provider resolution.
Receiving: keep your accepted pins unless deliberately adopting this correction. Review your wrapper/provider interface and every SDK checkout identity paired with its inventory; refresh changed workflow hashes only after checking actual routes/selections. Missing/changed constraints or unrelated inputs remain errors. SMonitor #46 owns the demonstrated Windows recovery; native Windows preflight execution is still pending, so the original failed schedule cannot clear debt. Other registered recipients are clients/candidates, not proven Windows users. No mandatory SDK migration, pilot enforcement/cohort, scientific dispatch, release/version/package mutation or historical artifact repair follows. Existing public receipts retain their original source/file/digest scope.
LMMV commentedon Oct 10, 2026
TopoMT actual recovery and retained debt — 2026-10-09
CI/distribution stay partial; early maturity and the approved coverage deferral stay unchanged. No component changes, new science run, package/version/tag/pin operation or stability deadline.
At
74191c225850e5e54cc40bc278d077388f2d4057, actual daily 37946142584 observes 78 skipped commits / no successful executed full watermark. Detector and independent reporting/distribution/environment governance pass. All eight Linux/macOS arm64 × Python 3.11–3.14 cells execute installation, installed-source Git-context/dependency checks, import and interpreter/architecture assertions successfully, then fail in Run tests. Representative 3.14 results: Linux 6 failed / 2004 passed / 85 skipped / 5 xfailed; macOS arm64 7 failed / 2003 passed / 85 skipped / 5 xfailed. The full daily remains failed and clears no debt. Scientific interpretation/repair stays with #16.Exact probe 37841619267 retains the same 78/no-watermark facts and deliberately omits science. Exact policy, Conda controls and Ruff pass. Source/workflow/event/attempt/complete job inventories and mandatory executed steps are qualified. Historical manual 36716726423, previously recorded running, has completed: all six then-configured actual science steps failed. This corrects that stale observation, without claiming recovery.
Twenty protected controls retain accepted
be72f8c1d77bfbf853e3e65ee29de71132b13443bytes; later guide/developer memory-tool changes are separate. Ten strict required checks, explicit zero-approval PR integration and administrator direct pushes remain. Publication still retains SDK2d32048, source/environment SDK8f00e6d, 609 mandatory paths, eight installed cells/four steps and the twelve-job candidate example. Current accepted PR/platform review remains #58; source-free ordinary environments, a real owner-selected plan/candidate/access/archive/installed/public/admission outcome remain #78/#16. No new requirement or mandatory checker rollout follows. Keep both owner issues open. #81 retains its owner-selected early-maturity coverage deferral; no badge or coverage execution is requested.Immutable receiving receipt. Local six tests and offline guard pass. Exact central governance 38028953243, attempt 1: 447 tests, publisher controls, XML retention and coverage upload pass. Global private-OpenCASTp access audits remain a separate uibcdf/molsyssuite#102 limitation. Upload execution is not downstream processing or a scientific/public-package certificate.
dprada commentedon Oct 21, 2026
Advance shared-provider handoff for uibcdf/molsyssuite#92: reviewed local implementation
d8d8f59a6e48d29dab2901eeeeac02f6bb77a34bvalidatesinstalled_tests.conda_dependenciesduring the first noarch candidate check, before version freezing, building or staging. It reuses the installed parser and retains the existinginstalled_noarch.test_dependenciesimport and valid tool selection. Unbounded specs such aspackaging>=24, candidate/interpreter replacement and unsupported source specs now fail earlier. Provider-bound support also checks the extracted parser against the SDK commit.All 516 central administrative tests pass locally (one existing opt-in native Mamba skip), including a real CLI before-freeze regression and clean-commit support execution; publication/native CI remains a separate final delivery check. Your recorded shared-workflow pin is unchanged. Before a future qualifying release, review this immutable SDK and adopt explicitly if appropriate; a pin update still needs your existing source/installed/artifact gates. Suspended historical noarch callers remain suspended. This notice does not reopen a completed adoption review, select a package/version, change a workflow or authorize publication.
Provider contract:
devguide/noarch_conda_workflow.md; implementation/delivery receipt:devguide/rollouts/early_installed_test_dependencies_92_20261021.json. Central advance notice: uibcdf/molsyssuite#92 (comment) . Final published source/native evidence will be linked centrally under #92.dprada commentedon Oct 21, 2026
Advance consumer handoff for uibcdf/molsyssuite#92: provider implementation 2c32a6f, prepared before provider publication; central scope and notice.
The shared publisher's evidence readers now allow up to three GET requests for selected transient failures, with at most ten seconds of total backoff and server-requested delays respected. Installed/source gate checks allow three observations of delayed required-step metadata within the same completed successful run, source, attempt and job identities. Explicit failures, changed identities and invalid evidence still refuse verification. Exhaustion stays unverified, classified as
acquisition_unavailable,metadata_pendingorinvalid_evidence; no dispatch/publication command is emitted.The registered caller and immutable pin were rechecked at this repository's current default-branch source (recorded in the central receipt). Existing pins and successful receipt schemas remain compatible and unchanged. The component owner may evaluate this commit in the next deliberately chosen pin update, retaining exact-candidate native and installed evidence; keeping the current pin is the fallback. No adoption, workflow execution, package build/upload or issue reopening is requested by this notice. Provider checks: 533 unit tests passed, with one existing optional native-Mamba skip. Real ordinary-release operator effort remains separate #92 acceptance work.
LMMV commentedon Oct 30, 2026
Accepted common policy delivery under MolSysSuite #137: canonical source 3feec0e6534200820a53fd4b131609ce38b653f9; guide-only delivery
0f82d5adfae73ae24846f713ab5bf62782a4f1ad. Byte-identical committed guide and mandatory AGENTS routing checks pass locally.The general runtime requirement is
provider>=X, with X grounded in the consumed API. Add a component-specific ceiling/exclusion only for a justified incompatibility, recording provider/version, concrete incompatible contract/evidence, owning issue and reassessment/removal condition. Do not cap the next minor solely because it is untested or 0.x. Preserve Python support, actual ABI/scientific/optional-engine restrictions, optionality and exact CI/build/release reproducibility pins. Components are expected to preserve compatibility with newer published siblings.Inspected required-runtime summary: 8 declarations, 7 without an inclusive floor and 0 carrying a restriction needing owner classification. This is source inspection only; exact tooling/profile pins and optional scientific conditions must be distinguished from public runtime bounds.
Use this existing review for applicable adoption: establish missing floors and justify/retire public runtime restrictions with relevant evidence; if declarations already follow the default, retain their prior API-floor evidence and no metadata rewrite is needed. No component code or constraint has been changed centrally, and no full scientific suite per internal push, release/stability deadline or automatic migration is added. Central #137 keeps guide/owner/runtime states separate. This does not reopen earlier completed distribution acceptance.
LMMV commentedon Nov 3, 2026
Completing MolSysSuite #162 owner routing: reuse this existing open packaging review for its applicable license metadata/build-tool scope. The central starter repair and migration reference are published; this notice neither changes your source nor establishes completed adoption.
Please post an explicit Review completed outcome before closing this scope: exact reviewed commit; license/notice and affected metadata/build/host/no-build-isolation routes; disposition (already compatible, corrected, or owned justified deferral/non-applicability); relevant actual commands/results; and precisely pending wheel/sdist/rebuilt-wheel/minimum qualification. Keep inspected source, modern-tool success, deliberate minimum tests and original public-file evidence distinct. For a deferral, record the owner, reason, interim compatible route and dated review or concrete revisit/removal trigger. Link the disposition back to MolSysSuite #162.
Preserve actual license choices/copyright/third-party notices, justified native/optional/versioning profiles and original qualified bytes. Existing compatible >=77.0 declarations are not rejected solely because the seed qualifies >=77.0.3. No immediate publication, scientific/full-suite campaign, blanket environment/tool upgrade, new universal CI gate or stability deadline is requested. Early-development/scientific deferrals retain their authority. A delivered notice or green unrelated CI is not the requested completed review.
LMMV commentedon Nov 3, 2026
What — Advance owner handoff for resumed MolSysSuite #87: review adoption of Conda provider v2.3.0 at immutable
87c70b1443d5f22d738ee3ddf812bdbe0152f6c2. Central build, separate exact-upload and promotion pins are reviewed and being published; the exact central delivery commit will follow here. This notice does not authorize a release or registry mutation.Observed source —
0f82d5adfae73ae24846f713ab5bf62782a4f1ad, committed active workflow declarations:.github/workflows/build_and_upload_conda_packages.yaml, jobpublish:uibcdf/molsyssuite/.github/workflows/publish-noarch-conda.yaml@2d32048457c6d37093ae509f5626d00a5cda121b.How — Review the delivered full MolSysSuite commit for your reusable publish and promotion callers; do not put the external action SHA in a MolSysSuite workflow reference. Compare with your existing SDK, preserving your local gate profiles, installed descriptor, helper/operator pins and input compatibility. A workflow reference being present does not mean its route is currently enabled or qualified.
Why / verified scope — The final-source original build/variant, active Conda environment and offline label-contract jobs pass independent source/attempt/job/step verification. Exact-upload's successful preceding hosted source has all eight relevant execution/fixture/workflow/test files byte-identical at v2.3.0. Twenty-nine adopted-operation provider tests pass locally on Python 3.14.7 in an isolated tool venv. Provider registry transports are simulated; these are no real publication or consumer installed/scientific claims.
Acceptance — Please respond Review completed, naming your reviewed source, affected build/upload/promotion scopes, adopted commit and relevant executed governance/publication-contract checks, or an explicit owner deferral with reason, interim route and reassessment trigger. Keep candidate source/file/digest identities, inspection before upload, installed qualification before promotion, and independent public receiving. A pin update must not rewrite an old producer receipt, rebuild or substitute existing staged/public bytes, weaken required tests, or silently activate a suspended publisher.
Ownership / limits — Your team owns component edits and release/scientific evidence. No active local clone is being edited centrally. Early maturity, scientific deferrals and routine internal direct-push cadence remain unchanged. Withdrawal, new packages/releases, public upload/promotion, credential changes and environment replacement are outside this task. Platform-direct coordination is MolI #42.
LMMV commentedon Nov 3, 2026
Immutable central delivery for MolSysSuite #87 is now published:
95f693be10c9205ab9b912cb53453710a207bf45.Candidate shared caller references (review your existing SDK/profile before adopting):
These lines illustrate separate jobs, not a complete runnable workflow. Preserve your existing inputs, explicit secret mapping, original candidate/qualification identities and component gates. Do not replace every helper/installed pin blindly: review each operation and your existing special profile.
Reviewed operation compatibility, limitations and owner acceptance; provider/native/local proof and advance owner routes.
Executed central checks: 84 passing test nodes plus 59 passing subtests, Ruff/format, offline governance, publisher contract and diff checks. Two controlled gate-order regressions fail as intended. Provider adopted-operation tests: 29/29. Hosted central publication CI is a separate receipt, not implied by these local results. Neither this delivery nor provider fixture tests claim real package/registry/installed/scientific validation.
Please confirm Review completed with exact source, scopes, adopted commit/checks or an owned justified deferral/trigger. The component team owns its changes. No release is requested; existing bytes, suspended routes, maturity/CI deferrals and all applicable candidate gates remain. Withdrawal stays excluded.
dprada commentedon Nov 12, 2026
Central #167 source-hint handoff (2026-11-12), reusing this distribution owner issue.
At immutable source
1128000801f69635dddfb547736b75de89ac12b4, the reviewed literal dependency hints contain:molsysmt,UNREVIEWED_SUITE_PYPI_HINT.Please inspect current source and use
pypi=None, the actual Conda package name and explicitchannel="uibcdf"for these current suite routes. Preserve optional features, third-party routes and local pip source/editable installs. The central current-state inventory and reusablepackage_channels.py MEMBERgenerate the reviewed dictionaries; configuration does not qualify artifacts or engines. Pytest Receptor retains its separate PyPI exception.This is a bounded static finding, not exhaustive docs/runtime qualification. No README defect, new dependency floor or scientific execution is selected. Component source repair/guards and receiving remain with this owner; central #167 stays partial until actual repairs, independently of synchronized common-guide bytes.