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Foundation: Qt-free core, pytest suite, CI, and bug fixes - #1

Merged

adrobi merged 36 commits into

masterfrom

foundation

Oct 31, 2026

Merged

Foundation: Qt-free core, pytest suite, CI, and bug fixes#1
adrobi merged 36 commits into
masterfrom
foundation

Commits on Oct 24, 2026
- UI polish: settings button in the far bottom-right corner, margin from the right splitter, scrollbars without the dotted page background
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  fc85020
- Tree viewer stage 2: custom renderer, layouts, supports, collapse, outgroup, consensus, RF
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  61a9072
- Stage 3: run history, parameter presets, batch queue with retry, open folder
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- Stage 4: IQ-TREE engine with ModelFinder, alignment info, XLSX export
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- Stage 5: tests in the repository, CI workflow, headless CLI
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  bbe1087
- Fix crash on Run click and margin from the left splitter in the tree pane
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  a631dd7
- Rework tree rendering: real distance grid, non-overlapping supports, theme-aware canvas
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  bb7d1bb
- Fix tree direction: internal nodes sit at their own cumulative depth
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  55e6b20
- Fix empty-input worker crash, IQ-TREE UFBoot/model errors, circular polytomy angles
  
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  40ebc15
- Add Foundation design spec and RAxML-NG Windows build spike
  
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- Keep .patch files LF so they apply to upstream sources on Windows checkouts
  
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- Add the Foundation implementation plan (15 tasks)
  
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  4f10619
- Move binary-free test checks to pytest with fixtures in tests/data
  
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- Move end-to-end and GUI suites to pytest with binary markers
  
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- Share window and warned fixtures, bound the IQ-TREE probe, restore locale key check
  
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- Add AppPaths and settings with atomic save, type coercion and legacy migration
  
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- Make legacy migration copy-once without overwrites and let load raise on unreadable files
  
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- Add HistoryStore with full run params and engine-aware presets
  
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- Drop non-dict history entries on load and derive the folder label from the record
  
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- Store settings and history in the data dir via AppPaths, migrate legacy files once
  
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Commits on Oct 30, 2026
- Block auto-save after a failed migration while the data dir has no config
  
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- Add launchers, the Engine interface and the PhyML engine with argv tests
  
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- Add the IQ-TREE engine and an engine registry; the model list comes from engines
  
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  42fcd73
- Add alignment helpers with BOM-tolerant reading and ID collision detection
  
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  79cbba3
- Read FASTA with a locale-encoding fallback and write PHYLIP in the locale encoding
  
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  6b5bb5c
- Add a Qt-free PipelineRunner that never raises and cancels whole process trees
  
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  78d79be
- Keep the error of a failure that coincides with a cancel and kill outside the runner lock
  
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  b09caf4
- Move the CSV/XLSX run summary into phyml_core.report
  
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  b9a790a
- Drive the window through PipelineRunner and RunWorker; log levels come from the core
  
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  c9156bc
- Allow one run at a time and kill the run's process tree synchronously when the window closes
  
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  a25dccc
- Run the CLI on PipelineRunner without importing PySide6
  
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  fb16519
- Split LogConsole, SettingsDialog and the status bar out of main_window
  
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Commits on Oct 31, 2026
- Split parameter and navigation panels; main_window only composes the window
  
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- Run the full pytest suite in CI with pinned IQ-TREE and MUSCLE
  
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  d32e2ac
- Fix findings of the final foundation review
  
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  af62efe
- Make the fake tool write bytes so Cyrillic paths survive a cp1252 pipe
  
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  eab0e34

Commits

Commits on Oct 24, 2026

Commits on Oct 30, 2026

Commits on Oct 31, 2026