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ab1kit 1.1.0: clone verification, refreshed UI, CLI, Linux release - #1

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adrobi merged 44 commits into

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feature/clone-verification

Oct 31, 2026

Merged

ab1kit 1.1.0: clone verification, refreshed UI, CLI, Linux release#1
adrobi merged 44 commits into
mainfrom
feature/clone-verification

adrobi commented Oct 30, 2026

Owner

Summary

ab1kit 1.1.0: clone verification of plasmid constructs becomes the main screen, plus analysis accuracy fixes, a refreshed UI, a CLI, an app icon and Windows + Linux release builds.

Clone verification (chrom_core/clones.py, ui/construct/*): load a construct (FASTA / GenBank / SnapGene, circular or linear), drop a folder of reads, reads are grouped into clones by file name (editable), set a region → per-clone verdict ok / errors / incomplete / mixed / no_data in a matrix on a shared axis; clicking a difference shows the chromatograms of all reads of the clone at that position. CDS effects (synonymous / missense / stop / frameshift / in-frame) when the construct is annotated. Projects (.ab1proj), CSV/XLSX reports.
Analysis accuracy: dye-normalised secondary-peak detection at any read position (peaks.py), circular alignment with origin-spanning reads, ambiguity = distinct placements.
UI: tabs, QSS light/dark theme, Lucide icons, one status palette, coloured quality bars, background tasks with cancel; main_window.py split into ui/read_view/*.
CLI: ab1kit verify-clones | qc | export (no Qt import on the CLI path).
Release: release.yml builds ab1kit.exe and ab1kit-linux-x86_64.tar.gz, smoke-tests the frozen CLI, one release job; CI gains an ubuntu-22.04 test leg. App icon (SVG → PNG/ICO).
Fixed (pre-existing): reverse-strand reads were indexed in the wrong orientation in expected-SNP verification and the reference overlay; reverse-complement misplaced peak positions (sessions saved after a flip with ≤1.0.0 hold wrong peaks — see CHANGELOG).

Design spec: docs/superpowers/specs/2026-10-25-clone-verification-design.md · plan: docs/superpowers/plans/2026-10-25-clone-verification.md.

Test plan

pytest -q on Windows: 380 passed, 1 skipped (timing tests behind -m perf: 2 passed)
Real-data corpus: sangeranalyseR reads (MIT) + NCBI references (COI, pUC19)
Frozen Windows exe built with PyInstaller 6.22.3; verify-clones smoke test passes; exe carries the icon
CI ubuntu-22.04 leg (first run on this PR)
Release workflow Linux leg — run once via workflow_dispatch before tagging
Manual look at the real window (renders were checked offscreen only)

🤖 Generated with Claude Code

adrobi and others added 30 commits

October 25, 2026 01:22


          Design spec: clone verification, peak analysis accuracy, UI refresh

bf49808

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>


          Implementation plan: clone verification, peak accuracy, UI refresh, CLI

ab05234

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>


          Test corpus: real sangeranalyseR reads, COI and pUC19 references

2cd6d19

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>


          Test corpus: per-sample COI references for divergent lineages

2954b65

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>


          peaks: normalised secondary-peak analysis at any read position

236340f

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>


          Fix untranslated verify notes, Q=0 mean for reads without quality, re…

ac89e13

…verse-strand indexing

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>


          reference: load constructs from FASTA, GenBank and SnapGene

faabf63

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>


          tests: well-formed LOCUS line in reference test

474b04e

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>


          align: circular constructs with origin-spanning reads

20706df

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>


          align: count circular alternatives distinct modulo construct length

1437a42

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>


          clones: group reads into clones by file name

6f4d061

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>


          clones: keep a lone well-shaped token as the clone name

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Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>


          clones: per-clone coverage, merged differences and verdicts

ced2057

verify_clone/verify_all with VerifyParams, ReadResult, CloneDifference and
CloneReport; reads are quality-trimmed before alignment and mapped back to
full displayed indices. load_read (session-aware) replaces batch._edited_read.

Also fixes EditableRead.reverse_complement mapping peaks against the last
peak instead of the trace length, which misplaced every peak of a flipped
read relative to its flipped traces.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>


          align: count distinct placements; clones: ambiguity by placements

a46c619

ReadAlignment.placements clusters co-optimal paths whose reference spans
overlap (mod L for circular constructs), so alternative gap positions in a
homopolymer are one placement. verify_clone marks a read ambiguous only for
placements > 1; alternatives is unchanged.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>


          effects: amino-acid consequences of clone differences in CDS

58510f6

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>


          clone_report: CSV and Excel reports for clone verification

514cd4c

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>


          project: .ab1proj files for clone verification sessions

0c040b3

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>


          ui: background tasks with progress and cancel

e438777

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>


          ui: tasks cancel on close, last-start-wins per key, safe on destroyed…

2fdde1b

… parent

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>


          ui: split main window into read_view modules (no behaviour change)

df1f57c

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>


          ui: ReadView owns undo/redo actions; broaden read_edited tests

b118e60

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>


          ui: QSS theme, icons, unified status palette, coloured quality bars

cf0423e

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>


          ui: checkbox ticks in channel colours, theme-aware status cells, weak…

6f89ae5

… icon bindings, tooltip/stretch tweaks

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>


          ui: construct summary bar and clone matrix

a7ca545

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>


          ui: matrix review fixes: cached name width, out-of-region marks, holl…

90d35cd

…ow disputed, 1-based ruler

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>


          ui: difference detail pane with stacked chromatograms

f2c0b60

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>


          ui: detail pane review fixes: disputed colour, dimmed out-of-region r…

03e0282

…ows, shared zoom, failed/ambiguous reads

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>


          ui: detail pane survives corrupt ab1 (AssertionError/IndexError)

94be6c3

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>


          ui: construct verification workspace with grouping and project files

eb9377e

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>


          ui: construct workspace review fixes: inactive viewer actions, clear …

f836f42

…resets results, drop/project edge cases

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

adrobi and others added 14 commits

October 30, 2026 16:38


          CLI subcommands verify-clones/qc/export; docs and v1.1.0

faa2c07

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>


          CLI review fixes: console code page, early -o check, README exit-code…

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… and verdict notes

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>


          CLI: console code page fallback to utf-8, all-or-nothing console attach

77ec9d3

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>


          App icon: SVG source, PNG/ICO, window and exe icon

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>


          App icon tests: compare decoded pixels, not bytes

e6165d1

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>


          Release workflow: Windows and Linux builds with smoke test, single re…

12c770f

…lease job

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>


          Clone verification: merge deletion runs into one difference (in-frame…

8a549c3

… deletions)

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>


          verify-clones: report unusable reads (stderr, read_issues column); di…

c05bd45

…fferences count = what the verdict uses

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>


          Tests: timing tests behind a perf marker, bounds scaled by AB1KIT_PER…

0048eaa

…F_FACTOR

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>


          Project files: a malformed grouping is a ValueError

87d96b2

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>


          Grouping: natural sort uses isdecimal (no crash on superscript digits)

a1a4494

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>


          Theme: no tick/arrow image instead of a crash when TEMP is not writable

39be495

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>


          Detail pane: an index past an edited read counts as not covered

d358584

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>


          CI: Linux test leg (ubuntu-22.04, Python 3.13); release trigger note;…

5d3d95a

… README Linux runtime libraries; changelog

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

adrobi merged commit 234fed6 into main

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