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v0.1.1

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@mbhall88 mbhall88 released this 22 Oct 19:43
0.1.1
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0.1.1 (2026-10-22)

Bug Fixes

  • build: upstream Conda portability and automate licence bundles (#81) (79ee21f)
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Pterobacter 0.1.0

Pterobacter 0.1.0

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@mbhall88 mbhall88 released this 22 Oct 00:13
0.1.0
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Posted by: Codex Astra (gpt-6-astra)

Pterobacter 0.1.0 classifies whole Enterobacter isolate assemblies by species and subspecies, reports MLST and supported genomovar matches, and explains uncertain calls.

Install from crates.io:

cargo install pterobacter --version 0.1.0 --locked
ptero database install 2026-10-15
ptero --report-dir isolate-report isolate.fasta

Cargo installation needs Rust and GNU C++. Precompiled downloads below support Linux x86_64 and Apple Silicon macOS. Mac binaries require brew install gcc xz. The container is ghcr.io/mbhall88/pterobacter:0.1.0 for Linux amd64.

Installation guide · Real-genome examples · Container usage

Check downloads against SHA256SUMS. The combined executable is distributed under GPL-3.0-or-later terms, with complete corresponding source and notices supplied alongside it. Pterobacter-authored source remains MIT. Reference data are downloaded separately from the versioned Figshare deposit.

Changelog

0.1.0 (2026-10-21)

⚠ BREAKING CHANGES

  • the public binaries are now ptero and pterobacter.

Features

  • add tero and terobacter commands and a saved-evidence v1 tracer (c29e5cc)
  • anim: compare MUMmer4 with persistent resource limits (a5bb4d9)
  • anim: measure reciprocal pairs with maintained MUMmer4 (98acf42)
  • anim: probe MUMmer4 maintenance and shared-process concurrency (96202ea)
  • authenticate versioned reference package (1720a35)
  • bind the release candidate to the P4a evaluation interface (#35) (834f4c2), closes #17
  • cli: accept assembly lists, sample sheets and sample names (1416522), closes #40
  • cli: run batches concurrently and reuse verified ANIm pairs (4dccd3d), closes #16
  • database: manage pinned references and optional typing (7ff49bf)
  • database: pin published reference version 2026-10-15 (1fad912)
  • decision: reproduce frozen v1 species and subspecies decisions (ffa2818)
  • default to boundary ANIm and simplify public options (#45) (0060527)
  • enable MLST by default and simplify the user guide (2ec46e3)
  • genomovar: add development-only masking diagnostics (5a22848), closes #14
  • genomovar: report authenticated all-member assignments (46282f5)
  • make ANIm execution limits opt-in (0e32774)
  • mlst: add candidate runner and comparison harness, calibrate X-drop (1ff5896)
  • mlst: add fixture generator, comparator runner and probe crate (0fcfe78)
  • mlst: measure all candidate routes and record results (3188d96)
  • mlst: report optional historical sequence typing (fdfc825)
  • reference: authenticate the versioned reference package (9d19630)
  • reference: verify component indexes and expose roles and scope (f931d69)
  • report: add TSV and Markdown reports and usage guide (aa53a8e), closes #15
  • rescue: decide v2 rescue from saved evidence with a dry rescue plan (585e4a3), closes #9
  • skani: embed pinned engine with portable AVX2 compatibility (56b5955)
  • thresholds: support custom v2 ANI settings (bde093b)
  • workflow: classify whole assemblies under v1 (4f5e2de), closes #7
  • workflow: run native v2 ANIm rescue (aa83775)

Bug Fixes

  • anim: charge failed cleanup overruns before further admission (1220beb)
  • anim: contain timed workers and retain failed comparisons (96f168e)
  • anim: make filter tie handling portable (bf5d877)
  • anim: monitor native peak RSS on macOS (8b7c56d)
  • anim: normalize native FASTA formatting without changing bases (62cb48f)
  • anim: preserve exact JSON worker time limits (e82d690)
  • anim: stop candidate admission after native failure (1c25b24)
  • anim: validate saved context and delta record headers (a65f09b)
  • anim: write portable LF endings in synthetic result tables (cb79e25)
  • build: discover Homebrew GNU C++ and preserve vendored measurements (#38) (eae4bc6)
  • cli: support real-genome examples and command-name option values (49a0a2d)
  • evidence: reject unmapped assignable references (6ab918b)
  • match frozen reference validation and flag unapplied v1 checks (adde942)
  • mlst: act on code review, show state and candidate ST per fixture (e355f62)
  • mlst: enforce stop rules, retain diagnostics, check real importer (24d0ff2)
  • mlst: share CPU budget across drivers, safe launch, stop crashed perf runs (f8eacda)
  • reference: authenticate the frozen package model (8434f55)
  • reference: require the expected manifest digest and refuse symlinks (7dfce0e)
  • reject percentages with more than two decimals instead of rounding (cea638b)
  • skani: make orientation ties independent of filenames (22a377a)

Code Refactoring

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