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Changelog

v2.2.14 - 2026-06-13

v2.2.14 is a maintenance-only release based on v2.2.13.

Added

  • Added the local scripts/release_gate.py release gate.
  • Added architecture audit documentation covering release tooling, CLI/config, workflow paths, acquisition, selection/evidence, taxonomy sources, reports, diagnostics, and tests.
  • Added CLI compatibility and workflow dispatch characterization tests.

Changed

  • Reorganized the release process and checklist into clearer three-phase preparation, verification, and publication steps.
  • Clarified the maintenance-release gate and local release readiness checks.
  • Continued the gradual cli.py parser, configuration, and dispatch refactoring without changing operator-facing workflow behavior.

Fixed

  • Fixed Python 3.10 compatibility for the local release gate.

Notes

  • No changes to download strategy, selection policy, or evidence thresholds.
  • No provider or ATCC automatic download support is introduced.
  • No new real-genus coverage is claimed.
  • No live downloads are required for this maintenance release.

v2.2.13 - 2026-06-10

v2.2.13 is a maintenance-only release based on v2.2.12.

Changed

  • Switched the default omitted---outdir behavior to workspace-based run directories.
  • Reorganized the maintained documentation system around current entry points, contracts, workspace policy, and archived historical notes.
  • Added documentation and workspace hygiene checks, including CI coverage for documentation hygiene.
  • Improved release consistency checking for version anchors and release readiness metadata.

Notes

  • No changes to download strategy, selection policy, or evidence thresholds.
  • No provider or ATCC automatic download support is introduced.
  • No new real-genus coverage is claimed.

v2.2.12 - 2026-06-06

v2.2.12 is a maintenance-only release based on v2.2.11.

Added

  • Added release consistency checker.

Changed

  • Reduced duplicated current-version wording in docs.
  • Documented handoff_index.md as a package navigation/operator handoff artifact.
  • Hardened maintenance release checklist/process.

Notes

  • No changes to download strategy, selection safety, or evidence thresholds.

v2.2.11 - 2026-06-06

v2.2.11 is a maintenance/refactor-only release based on v2.2.10.

Notes

  • No behavior changes.
  • No selection policy changes.
  • No evidence threshold changes.
  • No download strategy changes.
  • No real download validation.

v2.2.10 - 2026-06-06

v2.2.10 is a small UX/reporting polish release based on v2.2.9 real-world validation.

Changed

  • next-step avoids repeated Entrez fallback suggestions after fallback completion.
  • Plan-only next-step now prioritizes selection review and guarded downloads.
  • Taxonomy enrichment summaries clarify offline scaffold and cache-only runs.
  • package-results now writes handoff_index.md.

Notes

  • No changes to download strategy, selection safety, or evidence thresholds.

v2.2.9 - 2026-06-05

v2.2.9 improves handoff robustness and safe rerun behavior.

Changed

  • Prevent accidental cross-genus reuse of an existing outdir; use --allow-genus-change only when intentionally rebuilding an outdir for a different genus.
  • Improve zero accepted checklist guidance by pointing users to excluded_lpsn_taxa.tsv instead of guarded downloads.
  • Improve NCBI BioSample transient backend/network failure guidance with retry/cache-based next steps.
  • Expand package-results --failed-handoff to include available early acquisition, cache, and diagnostic artifacts.
  • Clarify plan-only run reviews when downloads were not executed.

Notes

  • Normal delivery packaging still requires manifest.tsv.
  • --failed-handoff only expands optional artifacts in failed-handoff mode.

v2.2.8 - 2026-06-04

Added

  • Added package-results --failed-handoff to create review artifacts for failed runs that stop before manifest.tsv.

Changed

  • Improved next-step guidance for duplicate selected assembly accession failures.

Notes

  • Normal delivery packaging still requires manifest.tsv.
  • Failed handoff packages are review artifacts, not completed genome delivery packages.

v2.2.7 - 2026-06-03

  • Cleaned up the v2.2.x handoff path around completion/manual_supplement_hints.tsv, making the manual supplement task queue the explicit place for curator follow-up after expanded discovery, rejected candidate review, or missing external candidate checks.
  • Aligned report/summary.md, report/run_review.md, status, and next-step vocabulary around reason, recommended_action, and handoff_path so ordinary users can follow the same review path from reports and CLI navigation.
  • Recorded the Clostridium limited smoke as a small cache-based/synthetic verification of guarded planning, handoff visibility, status/report output, and packaging, not as genus completion.
  • Tightened release documentation and install reproducibility checks so package metadata, typetreeflow.__version__, CLI --version, README, docs, and release notes agree on 2.2.7.
  • Non-goals: no full Clostridium completion, no expanded discovery auto-selection, no provider/ATCC auto-download, and no evidence model rewrite.

v2.2.6 - 2026-06-03

  • Strengthened the representative species identity guard so top-ranked exploratory fallbacks cannot cover a different checklist species.
  • Rejected explicit organism/checklist species mismatches before auto-selection, keeping mismatched candidates out of balanced and representative selected outputs.
  • Made duplicate selected accessions fail at the selection stage and surface a clear next-step explanation instead of allowing ambiguous downstream plans.
  • Updated report/summary.md and report/run_review.md explanations for rejected_species_mismatch and species_identity_mismatch rows.
  • Verified the Clostridium cache-based plan-only regression with no duplicate selected accession and no erroneous GCF_055383455.1 coverage for Clostridium nitritogenes.

v2.2.5 - 2026-06-01

  • Unified the package metadata, Python package version, CLI --version, doctor diagnostics, README, and release notes on version 2.2.5.
  • Improved Entrez fallback provenance reporting so fallback-derived sequence records are easier to distinguish and audit in reports.
  • Clarified 16S provenance by separating same-genome barrnap 16S evidence from Entrez fallback 16S evidence.
  • Improved resume behavior, report handoff clarity, and release credibility checks for the v2.2.x workflow.
  • Added v2.2.x integration release notes and an end-to-end acceptance checklist for the v2.2.2 shared acquisition/gap reporting, v2.2.3 expanded discovery audit, and v2.2.4 NCBI Taxonomy enrichment work.
  • Clarified that expanded discovery and taxonomy-derived rows are audit-only: they do not automatically modify manifest.tsv, selection/user_selection.tsv, completion metrics, or evidence levels, and they do not promise automatic 100% coverage.
  • Completed release verification with 932 passing tests, CLI smoke coverage for help/doctor commands, and targeted smoke checks for report/run_review, resume, Entrez fallback provenance, and expanded discovery history.
  • Fixed resume dry-run handling so --dry-run takes priority over real execution enable flags, and protected combined 16S assembly from primary FASTA header collisions while preserving Entrez fallback provenance fields.

v2.2.1 - 2026-05-29

  • Raised TSV CSV field-size handling for release verification, status, delivery, and CLI summary readers so long NCBI Datasets CLI stderr fields do not break post-download reporting.
  • Hardened manifest path normalization and resolution for repo-relative, outdir-relative, and manifest-relative genome and 16S paths.
  • Fixed barrnap execution to resolve genome FASTA inputs relative to the manifest while keeping rrna plan outputs portable and relative.
  • Added regression coverage from the Spirosoma post-release validation path.

v2.2.0 - 2026-05-29

  • Added high-level verify-genus orchestration for LPSN-first genus planning, guarded download execution with --auto-accept-selection --enable-downloads, and optional barrnap 16S extraction.
  • Added verify-release-genus to run balanced and representative release verification directories and update verification_matrix.tsv plus a Markdown release summary.
  • Added package-results delivery bundles with manifest, selection, evidence, download, report, genome, and 16S handoff files while excluding credentials, NCBI ZIP cache files, and local environment files.
  • Added doctor, status, and next-step commands for dependency checks, run-state inspection, and actionable workflow guidance.
  • Added run_state.json as a stable machine-readable workflow status file.
  • Structured selection evidence in manifest.tsv, preserving strict-confirmed, likely type-material, and representative-only layers across resume and report generation.
  • Standardized manifest genome and 16S paths as relative POSIX paths while retaining compatibility with older Windows-style manifest paths.
  • Hardened dry-run, BioSample Entrez, and high-level download argument validation so conflicting combinations fail before workflow execution.
  • Improved missing external-tool messages, including explicit guidance that the required datasets executable is the NCBI Datasets CLI, not the Python package named datasets.
  • Updated README, cookbook, release checklist, and output-layout documentation so high-level workflow commands are the recommended user entry point.

v2.2.0rc1 - Manual review and evidence explanation

  • Added manual_review_report.md as a stable human-readable companion to the manual deposit-evidence and species-gap review outputs.
  • Added stable ranking_reasons and blocking_reasons explanation fields to user_selection.tsv so candidate ranking and policy blocks are auditable.
  • Hardened BioSample field-level deposit ID extraction and stable BioSample evidence markers for candidate rows, including deposit ID fields and type-material evidence markers.
  • Added selection/download_preflight_summary.tsv as a single-row preflight summary for selected records before download planning/execution.
  • Added representative-only download risk summaries so exploratory representative rows are visible before guarded downloads and report-only summaries.
  • Updated the documented strict, likely type-material, and representative-only routes so strict completion remains deposit-equivalence based while balanced and representative routes remain review/exploration surfaces.
  • Strengthened provider planning and external FASTA boundary documentation: provider planning remains review-only, and external FASTA registration remains curator-reviewed local evidence.
  • Non-goals: this release does not add ATCC, DSMZ, JCM, NCTC, or other provider auto-downloaders; does not loosen strict completion; and does not count likely_type_material or representative_only rows toward strict type-strain completion.

2.1.0 - 2026-05-27

  • Added the representative selection policy for exploratory top-ranked fallback selection while marking unconfirmed rows as representative-only.
  • Added selection, report, and manifest risk layering with evidence_level and type_confirmation_status values for strict-confirmed, likely type-material, and representative-only records.
  • Tightened balanced selection to strong-evidence automatic selection only.
  • Hardened completion audit counting so likely type-material and representative-only rows cannot inflate strict completion metrics.
  • Added BioSample enrichment UX guidance for strict and balanced acquisition when guarded Entrez lookup is appropriate.

2.0.0 - 2026-05-26

  • Stable provider automation framework release for guarded, review-only provider planning on top of the stable LPSN-first type-strain acquisition and audit workflow.
  • Stabilized the provider capability registry with explicit unavailable, planning-only, metadata-only, and download-enabled capability states.
  • Kept provider network behavior disabled by default.
  • Stabilized ATCC planning-only behavior behind the downloader gate, so ATCC remains planning-only unless a future review explicitly enables downloader behavior.
  • Added the credential-like redaction helper as a stable safety boundary for provider planning outputs.
  • Documented the private provider cache policy: provider data stays out of cache/ncbi/, and this release does not write provider cache artifacts.
  • Stabilized review-only provider planning as a supported planning and audit surface that does not create acquisition evidence or alter completion metrics.
  • This stable release does not include an ATCC or provider downloader, provider login, scraping, browser automation, credential storage, terms acceptance, provider manifest/name-map writes, provider download-plan writes, provider external_genomes.tsv writes, or completion metric changes from provider planning rows.

2.0.0rc1 - 2026-05-26

  • Added the provider automation framework skeleton with provider adapter interface, registry, policy boundaries, and offline provider planning notes.
  • Added the provider capability registry with fail-closed statuses for unavailable, planning-only, metadata-only, and download-enabled modes.
  • Kept provider network behavior disabled by default, with provider planning continuing to emit review-only rows and no network, download, credential, manifest, name-map, external registration, or NCBI download-plan actions.
  • Added ATCC planning-only behavior gated by an unavailable/not-passed downloader review, including deterministic gate-failure and user-assisted handoff notes.
  • Added a credential-like redaction helper for provider planning outputs.
  • Added private provider cache policy boundaries that keep provider data out of cache/ncbi/ and do not write provider cache artifacts in this skeleton.
  • Documented that provider planning remains review-only and does not change completion metrics until curator-reviewed external registration occurs.
  • This release candidate does not include an ATCC or provider downloader, provider login, scraping, browser automation, credential storage, terms acceptance, provider manifest/name-map writes, provider download-plan writes, provider external_genomes.tsv writes, or completion metric changes from provider planning rows.

1.5.0 - 2026-05-26

  • Hardened provider handoff planning so proposal outputs remain explicit review-only rows with local FASTA path, SHA-256, terms, and manual-review prompts before any external registration handoff.
  • Added provider proposal review-only guarantees: provider planning proposals always stay external_genome_manual_review_required and must be copied into external_genomes.tsv before --register-external-genomes can validate and install them.
  • Expanded report-only provider proposal summaries with risk/count reporting for proposed rows, unexpected registered statuses, manual-review rows, missing local FASTA paths, and missing SHA-256 checksums.
  • Polished the real external F. mortiferum pilot workflow and templates to clarify reviewed proposal handoff, installed local FASTA evidence, checksum verification, and downstream mixed-provenance readiness.
  • Added a local artifact normalization design for a future offline, curator-supplied FASTA preparation layer before external registration.
  • Kept tests and documentation consistent around provider proposal boundaries, local artifact non-scope, report-only behavior, and completion metric separation.
  • This release does not include an ATCC or provider downloader, provider login, scraping, credential handling, provider download, provider manifest/name-map writes, provider download-plan writes, or completion metric changes from provider proposals or normalization outputs.

1.0.0 - 2026-05-26

  • Stable v1.0.0 release of the LPSN-first type-strain acquisition and audit workflow, covering the guarded CLI, stable I/O contracts, completion boundaries, provider-planning review boundary, documentation, and packaging readiness.
  • This stable release does not include an ATCC or provider downloader, provider login, scraping, browser automation, credential handling, provider downloads, provider-backed manifest/name-map writes, provider-backed NCBI download-plan writes, FASTA installation from provider planning rows, or completion metric changes from provider planning rows.

1.0.0rc1 - 2026-05-26

  • Release candidate for the v1.0.0 LPSN-first type-strain acquisition and audit workflow, scoped as release hardening for the existing guarded CLI, stable I/O contracts, completion boundaries, provider-planning review boundary, documentation, and packaging readiness.
  • Prepared v1.0.0rc1 release-candidate readiness documentation by tightening release checklist gates for v1.0 scope, provider/ATCC automation non-scope, stable contract review, and clean validation artifact cleanup.
  • Note: v1.0.0rc1 does not include an ATCC or provider downloader, provider login, scraping, browser automation, credential handling, provider downloads, provider-backed manifest/name-map writes, provider-backed NCBI download-plan writes, FASTA installation from provider planning rows, or completion metric changes from provider planning rows.

0.9.0 - 2026-05-26

  • Added a v0.9.0 provider adapter spike with a dry-run-only --plan-provider-registration CLI, provider_request.tsv parsing, provider/provider_registration_plan.tsv, and provider/proposed_external_genomes.tsv review outputs.
  • Added provider planning documentation, schema/status/output contracts, a synthetic examples/provider_request_minimal.tsv fixture, report-only provider planning counts, overwrite protection, and manual handoff compatibility with the existing external_genomes.tsv workflow.
  • Note: v0.9.0 provider planning does not automate ATCC/provider login, scraping, browser automation, credential handling, downloads, FASTA installation, manifest/name-map writes, NCBI download-plan writes, or completion metric changes.

0.8.0 - 2026-05-26

  • Clarified v0.8.0 planning, external workflow, and provider-automation boundaries so ATCC/provider automation remains out of scope.
  • Added real F. mortiferum external pilot template documentation for local curator-provided FASTA evidence packages without committing restricted data.
  • Tightened completion audit and report wording so external-inclusive 17/17 readiness is not confused with NCBI Assembly strict 17/17 completion.
  • Note: v0.8.0 does not automate ATCC Genome Portal or any other provider portal, and does not include provider download automation.

0.7.0 - 2026-05-25

  • Added an explicit --write-completion-audit workflow for local species-checklist completion auditing.
  • Added source_audit/completion_audit.tsv and source_audit/completion_summary.tsv outputs for mixed NCBI and external registered genome evidence.
  • Added report consumption of an existing completion summary, with optional completion audit detail when present.
  • Added a minimal mixed-provenance acceptance fixture covering NCBI, external, missing, and conflicting completion states.
  • Documented the implemented --write-completion-audit workflow and report consumption boundary for completion audit outputs.
  • Added a Fusobacterium mortiferum external registered genome pilot procedure for curator-run external-inclusive 17/17 evaluation without claiming 17/17 NCBI Assembly strict completion.
  • Note: v0.7.0 does not automate ATCC Genome Portal or any other provider portal.

0.6.1 - 2026-05-25

  • Fixed example fixture line-ending attributes so the external genome FASTA checksum remains reproducible on Windows clones with core.autocrlf=true.

0.6.0 - 2026-05-25

  • Added manual external genome registration for curator-provided local FASTA files. --register-external-genomes validates external_genomes.tsv, writes reviewable registration results and install plans, and in non-dry-run mode copies valid FASTA files into genomes/references/.
  • Added external registered genome manifest and name-map integration. Installed external records use external_registered_genome provenance, keep assembly_accession empty, preserve external IDs in notes, and can be appended to an existing manifest with --merge-manifest.
  • Added explicit separation from NCBI downloads: external records do not create NCBI Datasets download work, and download plans can mark them as external_genome_download_not_applicable instead of missing an accession.
  • Added report-only and downstream planning compatibility for external registered genome records, including provenance counts, an external registered genomes report section, barrnap/ANI/16S phylogeny dry-run planning, and a minimal synthetic external genome smoke workflow.
  • Note: v0.6.0 manual external registration does not automate ATCC Genome Portal or any other provider portal, and performs no external login, scraping, purchasing, or provider download.

0.5.0 - 2026-05-24

  • Added LPSN-first strict type-strain acquisition workflow for correct-valid species.
  • Added official LPSN API/cache support and checklist-compatible acquisition inputs.
  • Added validly published and correct-name filtering for acquisition candidates.
  • Added culture collection audit and synonym-aware discovery support.
  • Added NCBI Assembly and BioSample enrichment for candidate evidence.
  • Added strict, balanced, and review-only selection policies.
  • Added source audit policy for genome and same-genome 16S provenance.
  • Added manual curator evidence workflow and review templates.
  • Added Fusobacterium strict NCBI type-strain delivery case study support.
  • Documented Fusobacterium strict NCBI Assembly completion as 16/17 correct-valid LPSN species, with F. mortiferum remaining outside the current high-confidence NCBI Assembly workflow.
  • Note: External ATCC Genome Portal ingestion is not implemented in v0.5.0.
  • Note: External registered type genomes are not represented as NCBI assembly_accession values in v0.5.0 and need separate provenance/status fields in a future design.
  • Note: v0.5.0 does not claim Fusobacterium 17/17 NCBI Assembly strict completion.
  • Note: External type-genome ingestion should be designed separately for a later release.

0.4.0 - 2026-05-22

  • Added the documented minimal offline checklist-guided workflow covering LPSN Child taxa TSV conversion, local discovery-cache candidate generation, selection preparation, selection dry-run planning, guarded selection-driven downloads, and resume dry-run downstream planning.
  • Added Phase 19-24 acquisition workflow polish: LPSN Child taxa to checklist conversion, taxonomy/source audit reporting, selection-driven planning and downloads, local-cache and guarded NCBI assembly candidate discovery, and an offline end-to-end smoke workflow.

0.3.0 - 2026-05-22

  • Added LPSN-first acquisition design documentation.
  • Added LPSN/checklist-compatible schema fields.
  • Added offline LPSN adapter/cache interfaces.
  • Added assembly candidate tables and ranking helpers.
  • Added culture collection ID parsing.
  • Added sequence source audit data model.
  • Added offline user selection TSV support via --prepare-selection, --selection-tsv, and --strains-per-species.
  • Added candidate/selection examples and docs.
  • Note: real LPSN API, NCBI candidate discovery, and selection-driven downloads are not yet implemented.

0.2.1 - 2026-05-21

  • Added Apache-2.0 license, NOTICE, citation metadata, contribution guidance, security policy, and GitHub Actions CI.

0.2.0 - 2026-05-21

  • Added user-provided species checklist audit via --species-checklist.
  • Added taxonomy/checklist_comparison.tsv.
  • Added Taxonomic Audit report section.
  • Added species checklist docs and example TSV.
  • Clarified GTDB/LPSN taxonomic scope.

0.1.0 - 2026-05-21

  • Initial MVP release.
  • GTDB metadata parsing and type-material selection.
  • Guarded NCBI Datasets downloads with ZIP extraction and genome registration.
  • barrnap 16S extraction.
  • Entrez fallback guarded by email/API key.
  • FastANI query-vs-reference execution, parsing, summary, and PNG.
  • Reference-only and query-inclusive all_16S assembly.
  • MAFFT/trimAl/IQ-TREE phylogeny workflow.
  • report/summary.md and report-only refresh.
  • Real smoke validations: Aalborgiella and Actinocorallia.