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Release builds for Windows and Linux (zip + AppImage) via GitHub Actions - #2

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adrobi merged 25 commits into
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Oct 31, 2026
Merged

Release builds for Windows and Linux (zip + AppImage) via GitHub Actions#2
adrobi merged 25 commits into
masterfrom
release

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@adrobi

@adrobi adrobi commented Oct 31, 2026

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Releases for Windows and Linux built by GitHub Actions. Stacked on #1 (foundation): once #1 is merged, retarget this PR to master.

What changes

The app runs on Linux

  • Tool names without .exe. Tools are looked up in bin/ first, then on PATH.
  • Settings go to ~/.config/phymlGUI (or $XDG_CONFIG_HOME), and never into the AppImage's temporary folder.
  • mpirun (OpenMPI) replaces mpiexec. A config brought over from Windows loads without errors.
  • "Open folder" uses xdg-open, and the theme follows the desktop palette.
  • PhyML picks the serial or the MPI build according to the MPI setting. The AppImage ships both, so serial PhyML works without OpenMPI.
  • Child programs no longer inherit the PyInstaller bundle's LD_LIBRARY_PATH.

Pinned third-party tools (packaging/third_party.json, every download checked by SHA256)

  • Windows: IQ-TREE, MUSCLE, PhyML-MPI. RAxML-NG 2.0.3 is built natively with MSYS2 plus packaging/patches/raxml-ng-2.0.3-windows.patch.
  • Linux: IQ-TREE, MUSCLE, RAxML-NG. PhyML and PhyML-MPI are built from source.
  • The appimagetool and AppImage runtime are pinned. The MS-MPI installer is pinned for the CI smoke test.

Packages and release (.github/workflows/release.yml)

  • PyInstaller onedir produces two packages:
    • phymlGUI-<v>-windows-x64.zip (phymlgui.exe plus phymlgui-cli.exe);
    • phymlGUI-<v>-x86_64.AppImage.
  • Each package is smoke-tested:
    • --version;
    • PhyML and IQ-TREE runs;
    • a PhyML-MPI run on Linux;
    • the window opens and closes offscreen.
  • On Linux the AppImage also runs in a clean ubuntu:22.04 container.
  • raxml_parity.py compares our Windows RAxML-NG build with the official Linux build: best tree RF = 0, |ΔlnL| < 1e-3, identical bootstrap replicates, and the same fixed-tree lnL.
  • A vX.Y.Z[-suffix] tag creates a draft release that is never published automatically. It holds the zip, the AppImage, SHA256SUMS, and the RAxML-NG source plus patch (AGPL-3.0). Tags with a suffix are marked pre-release.
  • A malformed tag fails the run before anything is built. An already published release is never modified.
  • tests.yml now runs Windows on Python 3.11/3.13 and Linux (ubuntu-22.04) on Python 3.12/3.13.

Verification

  • Local:
    • Windows: 596 passed, 1 skipped.
    • WSL Ubuntu: 597 passed, with real PhyML/MPI, IQ-TREE, MUSCLE and RAxML-NG.
  • A full trial run on GitHub, then the tag v2.0.0-rc1 (run 41192896314):
    • every job green;
    • a draft pre-release with all four files;
    • SHA256SUMS checked against the downloaded files.
  • A whole-branch review was done before merge. Its 2 Critical and 3 Important findings are fixed, each with a test.

Known limitation

On Linux with Python 3.11, the interpreter aborts at exit (bool_dealloc, an over-decref of True/False in a C extension) after every test has passed. It appears only in test files that create the main window; a bare PySide6/QApplication, matplotlib or psutil does not trigger it. Python 3.12+ makes these objects immortal, so the bug does not show there. The root cause was not isolated. Linux CI therefore uses 3.12/3.13, and the README says that running from source on Linux needs Python 3.12+. The packages bundle Python 3.13 and are not affected.

🤖 Generated with Claude Code

adrobi and others added 24 commits October 31, 2026 09:18
@adrobi @claude
Add the Release design spec (Windows zip and Linux AppImage via GitHu…
6da9717 
…b Actions)

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
@adrobi @claude
Add the Release implementation plan (8 tasks)
ac28dc4 
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
@adrobi @claude
Add a Linux build recipe for PhyML and PhyML-MPI
b898ed7 
Built and verified in Ubuntu: both binaries build from the v3.3.20260528
sources, a serial aLRT run and a 2-process MPI bootstrap run finish with
exit 0. Single-threaded make: parallel builds crashed GCC with an internal
compiler error in evolve.c. *.sh files are kept LF for Linux runners.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
@adrobi @claude
Make the app portable to Linux: tool names, data dir, mpirun, open fo…
2d964fc 
…lder, theme

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
@adrobi @claude
Make the test suite pass on Linux and document Linux use
baa19e4 
The full suite (558 tests, incl. real PhyML/OpenMPI, IQ-TREE, MUSCLE runs)
passes on Ubuntu as on Windows: conftest finds tools by platform name and
on PATH, Windows-only test fakes got POSIX variants, and tests that check
Windows semantics pin the platform.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
@adrobi @claude
Describe third-party tools per platform and add build steps
ea60daa 
third_party.json gains windows/linux sections (PhyML-MPI from the v1.2
release, RAxML-NG built from source on Windows; IQ-TREE, MUSCLE, RAxML-NG
official Linux builds and PhyML built from source on Linux). The fetch
script handles tar.gz, build commands and POSIX modes. The RAxML-NG
Windows recipe was verified in MSYS2 UCRT64. Upstream license texts are
bundled. CI now also runs the suite on ubuntu-22.04 with PhyML/OpenMPI.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
@adrobi @claude
Package the Windows zip with PyInstaller and smoke-test it
377331b 
packaging/package.py stamps the version into a build copy and runs
PyInstaller (one bundle, two executables on Windows: the windowed GUI and
a console phymlgui-cli.exe, since a windowed exe has no stdout). The CLI
gains --version and the entry point a --smoke-gui check. A local 0.0.0-dev
zip with all bundled tools (incl. RAxML-NG built in MSYS2) passed the smoke
test: --version, PhyML+MUSCLE and IQ-TREE runs, window open/close.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
@adrobi @claude
Build and smoke-test the Linux AppImage
d39660c 
package.py builds an AppDir (AppRun, .desktop, icon, PyInstaller bundle in
usr/bin, tools in usr/bin/bin, licenses) and packs it with the pinned
appimagetool 1.9.1 and type2 runtime 20251108 (--runtime-file, so nothing
unpinned is downloaded at build time). Inside an AppImage the app folder is
never used for settings: with --appimage-extract-and-run it is a throwaway
temp copy. A local 0.0.0-dev AppImage passed the smoke test in Ubuntu incl.
a PhyML-MPI run over OpenMPI.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
@adrobi @claude
Add the RAxML-NG Windows vs Linux parity check
d7007e1 
Two steps because the binaries run on different CI runners: 'run' executes
an ML search, 50 bootstraps and a fixed-tree evaluation (seed 42) on a
synthetic alignment; 'compare' requires RF 0 and |dlnL| < 1e-3 for the best
tree, identical replicates and the same fixed-tree lnL to 6 decimals. The
locally built raxml-ng.exe matches the official Linux binary.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
@adrobi @claude
Add the release workflow: tools, packages, smoke tests, draft release
865c856 
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
@adrobi @claude
Fix the release review findings: serial PhyML on Linux, pytest-free r…
f191b49 
…elease scripts, child env, MS-MPI

- pick phyml or phyml-mpi by the MPI mode (the AppImage bundles both)
- move the synthetic dataset to tests/e2e/dataset_gen.py so release jobs need no pytest
- start child programs without the PyInstaller LD_LIBRARY_PATH (runner, Open folder)
- install pinned MS-MPI before the Windows smoke test; the bundled PhyML needs msmpi.dll
- pin the RAxML-NG SIMD kernel in the parity runs; a manual run never creates a release
- conftest uses its Windows .exe fallbacks only on Windows

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
@adrobi @claude
Temporarily run the release workflow on pushes to the release branch
983cbd3 
A trial build before release.yml reaches master; the release job still runs only for tags.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
@adrobi @claude
Make the fake tool write bytes so Cyrillic paths survive a cp1252 pipe
02bc59a 
English Windows runners pipe child output as cp1252; the fake crashed printing
a Cyrillic path. The Cyrillic-path test now forces cp1252 everywhere.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
@adrobi @claude
TEMPORARY: find which test file crashes Python 3.11 on Linux at exit
4aef719 
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
@adrobi @claude
TEMPORARY: narrow down the Python 3.11 exit crash on Linux
fbee051 
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
@adrobi @claude
TEMPORARY: per-file and per-test runs for the Python 3.11 exit crash
cfe01fa 
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
@adrobi @claude
TEMPORARY: measure psutil True/False refcounts on Python 3.11
a8a5621 
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
@adrobi @claude
TEMPORARY: measure psutil wait refcounts on Python 3.11
caef407 
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
@adrobi @claude
TEMPORARY: fix the refcount probe indentation
7acd77a 
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
@adrobi @claude
TEMPORARY: per-test True/False refcount probe on Python 3.11
312ca14 
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
@adrobi @claude
Remove the temporary Python 3.11 crash diagnostics
6cfe48c 
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
@adrobi @claude
Test Linux on Python 3.12 and 3.13; document Python 3.12+ for Linux s…
0c2035b 
…ource runs

On Python 3.11 a C extension's True/False over-decref aborts the interpreter at
exit on Linux (bool_dealloc) after all tests pass; 3.12+ makes those objects
immortal. The packages bundle Python 3.13.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
@adrobi @claude
Mark suffixed versions as pre-releases; drop the temporary branch tri…
4f24bc6 
…gger

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
@adrobi @claude
README in the style of the other projects, CHANGELOG and bilingual re…
fde5d99 
…lease notes

- README.md and README.ru.md with screenshots of real runs (scripts/make_screenshots.py)
- CHANGELOG.md in Keep a Changelog format
- release notes in English and Russian, with per-version highlights from
  packaging/release_notes/<version>[.ru].md
- version 2.0.0 in the sources; drop the stale 'v1.4' panel labels; 'Наклонная'
  for the slanted tree layout

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
@adrobi
adrobi changed the base branch from foundation to master October 31, 2026 11:03
@adrobi @claude
Build Linux PhyML for x86-64-v2 instead of -march=native
bfcb8ae 
PhyML's configure.ac compiles with -march=native, so the binary built on one
CI runner died with SIGILL (illegal instruction) on another, and the AppImage
would do the same on CPUs older than the build runner. x86-64-v2 keeps the SSE
likelihood code; the script fails if -march=native is left in a Makefile.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
@adrobi
adrobi merged commit 6bcea14 into master Oct 31, 2026
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@adrobi